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+attention_probs_dropout_prob: + value: 0.1 +auto_find_batch_size: + value: false +bad_words_ids: + value: null +begin_suppress_tokens: + value: null +bf16: + value: false +bf16_full_eval: + value: false +bos_token_id: + value: null +cache_dir: + value: null +checkpointing: + value: false +chunk_size_feed_forward: + value: 0 +classifier_dropout: + value: null +cross_attention_hidden_size: + value: null +data_seed: + value: null +dataloader_drop_last: + value: false +dataloader_num_workers: + value: 0 +dataloader_pin_memory: + value: false +ddp_backend: + value: null +ddp_broadcast_buffers: + value: null +ddp_bucket_cap_mb: + value: null +ddp_find_unused_parameters: + value: null +ddp_timeout: + value: 1800 +debug: + value: [] +decoder_start_token_id: + value: null +deepspeed: + value: null +disable_tqdm: + value: false +dispatch_batches: + value: null +diversity_penalty: + value: 0 +do_eval: + value: true +do_predict: + value: false +do_sample: + value: false +do_train: + value: false +early_stopping: + value: false +encoder_no_repeat_ngram_size: + value: 0 +eos_token_id: + value: null +eval_accumulation_steps: + value: null +eval_and_save_results: + value: true +eval_delay: + value: 0 +eval_steps: + value: 100 +evaluation_strategy: + value: epoch +exponential_decay_length_penalty: + value: null +find_unused_parameters: + value: false +finetuning_task: + value: null +forced_bos_token_id: + value: null +forced_eos_token_id: + value: null +fp16: + value: true +fp16_backend: + value: auto +fp16_full_eval: + value: false +fp16_opt_level: + value: O1 +fsdp: + value: [] +fsdp_config: + value: + min_num_params: 0 + xla: false + xla_fsdp_grad_ckpt: false +fsdp_min_num_params: + value: 0 +fsdp_transformer_layer_cls_to_wrap: + value: null +full_determinism: + value: false +gradient_accumulation_steps: + value: 1 +gradient_checkpointing: + value: false +gradient_checkpointing_kwargs: + value: null +greater_is_better: + value: true +group_by_length: + value: false 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+output_dir: + value: /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42 +output_hidden_states: + value: false +output_scores: + value: false +overwrite_output_dir: + value: true +pad_token_id: + value: 0 +past_index: + value: -1 +per_device_eval_batch_size: + value: 128 +per_device_train_batch_size: + value: 128 +per_gpu_eval_batch_size: + value: null +per_gpu_train_batch_size: + value: null +position_embedding_type: + value: absolute +prediction_loss_only: + value: false +prefix: + value: null +problem_type: + value: null +project_name: + value: super_binary_tune +push_to_hub: + value: false +push_to_hub_model_id: + value: null +push_to_hub_organization: + value: null +push_to_hub_token: + value: +ray_scope: + value: last +remove_invalid_values: + value: false +remove_unused_columns: + value: true +repetition_penalty: + value: 1 +report_to: + value: + - wandb +resume_from_checkpoint: + value: null +return_dict: + value: true +return_dict_in_generate: + value: false +run_name: + value: hg38_len2_5120_binary_VASC_lr1e-5_wd0.01_wr0.03_ep6_seed42 +save_model: + value: false +save_on_each_node: + value: false +save_safetensors: + value: true +save_steps: + value: 100 +save_strategy: + value: epoch +save_total_limit: + value: 1 +seed: + value: 42 +sep_token_id: + value: null +skip_memory_metrics: + value: true +split_batches: + value: false +suppress_tokens: + value: null +task_specific_params: + value: null +temperature: + value: 1 +tf_legacy_loss: + value: false +tf32: + value: null +tie_encoder_decoder: + value: false +tie_word_embeddings: + value: true +tokenizer_class: + value: null +top_k: + value: 50 +top_p: + value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 5120 +warmup_ratio: + value: 0.03 +warmup_steps: + value: 0 +weight_decay: + value: 0.01 diff --git a/VASC/len2_5120/wandb/run-20260305_083334-98d6pn0n/files/output.log b/VASC/len2_5120/wandb/run-20260305_083334-98d6pn0n/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..97f8c43cd84091c464d1a8b93210ed39752cabf1 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260305_083334-98d6pn0n/files/output.log @@ -0,0 +1,234 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.weight', 'bert.pooler.dense.bias', 'classifier.bias', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612] due to args.save_total_limit + 33%|███▎ | 4806/14418 [47:49<1:33:01, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.3347, 'learning_rate': 8.5219878441187e-06, 'epoch': 1.04} +{'loss': 0.3418, 'learning_rate': 8.45048265999285e-06, 'epoch': 1.08} +{'loss': 0.3346, 'learning_rate': 8.378977475867e-06, 'epoch': 1.12} +{'loss': 0.3278, 'learning_rate': 8.307472291741152e-06, 'epoch': 1.17} +{'loss': 0.3293, 'learning_rate': 8.235967107615302e-06, 'epoch': 1.21} +{'loss': 0.3408, 'learning_rate': 8.164461923489454e-06, 'epoch': 1.25} +{'loss': 0.3313, 'learning_rate': 8.092956739363604e-06, 'epoch': 1.29} +{'loss': 0.3364, 'learning_rate': 8.021451555237756e-06, 'epoch': 1.33} +{'loss': 0.3324, 'learning_rate': 7.949946371111906e-06, 'epoch': 1.37} +{'loss': 0.3396, 'learning_rate': 7.878441186986056e-06, 'epoch': 1.41} +{'loss': 0.3348, 'learning_rate': 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38441 + Batch size = 128 + 33%|███▎ | 4806/14418 [48:31<1:33:01, 1.72Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-4806/config.json +{'eval_loss': 0.3397637903690338, 'eval_accuracy': 0.8738846544054525, 'eval_f1': 0.6710734591743993, 'eval_matthews_correlation': 0.39511652932683594, 'eval_precision': 0.7879446891565471, 'eval_recall': 0.6355443229432234, 'eval_runtime': 41.8927, 'eval_samples_per_second': 917.607, 'eval_steps_per_second': 7.185, 'epoch': 2.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-4806/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-4806/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-4806/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [1:13:50<1:08:19, 1.76it/s]***** Running Evaluation ***** +{'loss': 0.3191, 'learning_rate': 6.80586342509832e-06, 'epoch': 2.04} +{'loss': 0.3287, 'learning_rate': 6.7343582409724705e-06, 'epoch': 2.08} +{'loss': 0.3171, 'learning_rate': 6.662853056846622e-06, 'epoch': 2.12} +{'loss': 0.317, 'learning_rate': 6.5913478727207724e-06, 'epoch': 2.16} +{'loss': 0.317, 'learning_rate': 6.519842688594924e-06, 'epoch': 2.21} +{'loss': 0.3228, 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612/config.json +{'eval_loss': 0.34253770112991333, 'eval_accuracy': 0.8702947373897661, 'eval_f1': 0.6800236129689574, 'eval_matthews_correlation': 0.39316047953145655, 'eval_precision': 0.7614588418113875, 'eval_recall': 0.6478006649101133, 'eval_runtime': 41.9812, 'eval_samples_per_second': 915.672, 'eval_steps_per_second': 7.17, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612/special_tokens_map.json + 83%|████████▎ | 12015/14418 [2:05:40<23:45, 1.69it/s]***** Running Evaluation ***** +{'loss': 0.2979, 'learning_rate': 3.375044690740079e-06, 'epoch': 4.04} +{'loss': 0.2949, 'learning_rate': 3.30353950661423e-06, 'epoch': 4.08} +{'loss': 0.2999, 'learning_rate': 3.2320343224883805e-06, 'epoch': 4.12} +{'loss': 0.2894, 'learning_rate': 3.1605291383625315e-06, 'epoch': 4.16} +{'loss': 0.2788, 'learning_rate': 3.0890239542366825e-06, 'epoch': 4.2} +{'loss': 0.2974, 'learning_rate': 3.0175187701108334e-06, 'epoch': 4.24} +{'loss': 0.2962, 'learning_rate': 2.9460135859849844e-06, 'epoch': 4.29} +{'loss': 0.2909, 'learning_rate': 2.874508401859135e-06, 'epoch': 4.33} +{'loss': 0.2971, 'learning_rate': 2.803003217733286e-06, 'epoch': 4.37} +{'loss': 0.2994, 'learning_rate': 2.731498033607437e-06, 'epoch': 4.41} +{'loss': 0.2936, 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'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 83%|████████▎ | 12015/14418 [2:06:22<23:45, 1.6Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-12015/config.json +{'eval_loss': 0.35137659311294556, 'eval_accuracy': 0.8661325147628833, 'eval_f1': 0.6731144608921611, 'eval_matthews_correlation': 0.3754835961236889, 'eval_precision': 0.7458648317223928, 'eval_recall': 0.6433591884311942, 'eval_runtime': 41.8205, 'eval_samples_per_second': 919.191, 'eval_steps_per_second': 7.197, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:31:43<00:00, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.2699, 'learning_rate': 1.6589202717196998e-06, 'epoch': 5.04} +{'loss': 0.2822, 'learning_rate': 1.5874150875938508e-06, 'epoch': 5.08} +{'loss': 0.2699, 'learning_rate': 1.5159099034680016e-06, 'epoch': 5.12} +{'loss': 0.2819, 'learning_rate': 1.4444047193421524e-06, 'epoch': 5.16} +{'loss': 0.2818, 'learning_rate': 1.3728995352163033e-06, 'epoch': 5.2} +{'loss': 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'epoch': 5.78} +{'loss': 0.273, 'learning_rate': 3.0103682516982484e-07, 'epoch': 5.83} +{'loss': 0.2789, 'learning_rate': 2.2953164104397572e-07, 'epoch': 5.87} +{'loss': 0.2731, 'learning_rate': 1.5802645691812657e-07, 'epoch': 5.91} +{'loss': 0.2759, 'learning_rate': 8.652127279227745e-08, 'epoch': 5.95} +{'loss': 0.2773, 'learning_rate': 1.501608866642832e-08, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [2:32:25<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35999754071235657, 'eval_accuracy': 0.8636611950781717, 'eval_f1': 0.6807228327111764, 'eval_matthews_correlation': 0.3804371330425835, 'eval_precision': 0.7346337636144588, 'eval_recall': 0.6542109817957393, 'eval_runtime': 41.7895, 'eval_samples_per_second': 919.873, 'eval_steps_per_second': 7.203, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-7209 (score: 0.6940972306942819). +100%|██████████| 14418/14418 [2:32:27<00:00, 1.77it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 9147.2119, 'train_samples_per_second': 201.72, 'train_steps_per_second': 1.576, 'train_loss': 0.3143618143552351, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:32:27<00:00, 1.58it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:07<00:00, 4.44it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_083334-98d6pn0n/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_083334-98d6pn0n/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260305_083334-98d6pn0n/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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b/VASC/len2_5120/wandb/run-20260305_083504-xd6znn4g/files/output.log @@ -0,0 +1,370 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['classifier.weight', 'bert.pooler.dense.bias', 'classifier.bias', 'bert.pooler.dense.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 10 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 24,030 + Number of trainable parameters = 88,402,178 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 10%|█ | 2403/24030 [24:44<3:21:25, 1.79it/s]***** Running Evaluation ***** +{'loss': 0.7058, 'learning_rate': 4.161464835622139e-07, 'epoch': 0.04} +{'loss': 0.6913, 'learning_rate': 8.322929671244278e-07, 'epoch': 0.08} +{'loss': 0.6741, 'learning_rate': 1.2484394506866417e-06, 'epoch': 0.12} +{'loss': 0.6701, 'learning_rate': 1.6645859342488557e-06, 'epoch': 0.17} +{'loss': 0.666, 'learning_rate': 2.0807324178110696e-06, 'epoch': 0.21} 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 20%|██ | 4806/24030 [50:56<3:00:37, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.6264, 'learning_rate': 9.95514865677163e-06, 'epoch': 1.04} +{'loss': 0.6339, 'learning_rate': 9.90891015859805e-06, 'epoch': 1.08} +{'loss': 0.6221, 'learning_rate': 9.862671660424469e-06, 'epoch': 1.12} +{'loss': 0.6247, 'learning_rate': 9.81643316225089e-06, 'epoch': 1.17} +{'loss': 0.6229, 'learning_rate': 9.770194664077312e-06, 'epoch': 1.21} +{'loss': 0.6246, 'learning_rate': 9.723956165903732e-06, 'epoch': 1.25} +{'loss': 0.6247, 'learning_rate': 9.677717667730154e-06, 'epoch': 1.29} +{'loss': 0.6232, 'learning_rate': 9.631479169556574e-06, 'epoch': 1.33} +{'loss': 0.6242, 'learning_rate': 9.585240671382994e-06, 'epoch': 1.37} +{'loss': 0.622, 'learning_rate': 9.539002173209415e-06, 'epoch': 1.41} +{'loss': 0.6258, 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Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [51:50<3:00:37, 1.77Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 0.6227526664733887, 'eval_accuracy': 0.6493847714679639, 'eval_f1': 0.6432647116341302, 'eval_matthews_correlation': 0.29603072055051993, 'eval_precision': 0.6514141899637047, 'eval_recall': 0.644692824910708, 'eval_runtime': 54.4808, 'eval_samples_per_second': 705.589, 'eval_steps_per_second': 5.525, 'epoch': 2.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-2403] due to args.save_total_limit + 30%|███ | 7209/24030 [1:16:55<2:35:29, 1.80it/s]***** Running Evaluation ***** +{'loss': 0.6075, 'learning_rate': 8.845424700605725e-06, 'epoch': 2.04} +{'loss': 0.6073, 'learning_rate': 8.799186202432147e-06, 'epoch': 2.08} +{'loss': 0.605, 'learning_rate': 8.752947704258567e-06, 'epoch': 2.12} +{'loss': 0.6085, 'learning_rate': 8.706709206084987e-06, 'epoch': 2.16} +{'loss': 0.6092, 'learning_rate': 8.660470707911408e-06, 'epoch': 2.21} +{'loss': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612/config.json +{'eval_loss': 0.6262840032577515, 'eval_accuracy': 0.6546916053172394, 'eval_f1': 0.6426906155917809, 'eval_matthews_correlation': 0.3112123447470725, 'eval_precision': 0.6640711840436494, 'eval_recall': 0.6475779005428581, 'eval_runtime': 54.2041, 'eval_samples_per_second': 709.19, 'eval_steps_per_second': 5.553, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612/special_tokens_map.json + 50%|█████ | 12015/24030 [2:08:43<1:53:18, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.5614, 'learning_rate': 6.6269015582373886e-06, 'epoch': 4.04} +{'loss': 0.5676, 'learning_rate': 6.58066306006381e-06, 'epoch': 4.08} +{'loss': 0.5641, 'learning_rate': 6.53442456189023e-06, 'epoch': 4.12} +{'loss': 0.5643, 'learning_rate': 6.488186063716651e-06, 'epoch': 4.16} +{'loss': 0.57, 'learning_rate': 6.4419475655430715e-06, 'epoch': 4.2} +{'loss': 0.5721, 'learning_rate': 6.396171452351228e-06, 'epoch': 4.24} +{'loss': 0.5718, 'learning_rate': 6.349932954177649e-06, 'epoch': 4.29} +{'loss': 0.5703, 'learning_rate': 6.303694456004069e-06, 'epoch': 4.33} +{'loss': 0.5648, 'learning_rate': 6.25745595783049e-06, 'epoch': 4.37} +{'loss': 0.575, 'learning_rate': 6.211217459656911e-06, 'epoch': 4.41} +{'loss': 0.565, 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Num examples = 38441 + Batch size = 128 + 50%|█████ | 12015/24030 [2:09:39<1:53:18, 1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/config.json +{'eval_loss': 0.6427122354507446, 'eval_accuracy': 0.6518040633698395, 'eval_f1': 0.6379027279632234, 'eval_matthews_correlation': 0.3067621363552497, 'eval_precision': 0.6632660483808156, 'eval_recall': 0.6440945763594139, 'eval_runtime': 55.1523, 'eval_samples_per_second': 696.997, 'eval_steps_per_second': 5.458, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [2:32:54<29:17, 5.47it/s]***** Running Evaluation ***** +{'loss': 0.5457, 'learning_rate': 5.5176399870532206e-06, 'epoch': 5.04} +{'loss': 0.5478, 'learning_rate': 5.471401488879642e-06, 'epoch': 5.08} +{'loss': 0.5401, 'learning_rate': 5.425625375687799e-06, 'epoch': 5.12} +{'loss': 0.5374, 'learning_rate': 5.379386877514219e-06, 'epoch': 5.16} +{'loss': 0.5376, 'learning_rate': 5.3331483793406395e-06, 'epoch': 5.2} +{'loss': 0.541, 'learning_rate': 5.28690988116706e-06, 'epoch': 5.24} +{'loss': 0.5363, 'learning_rate': 5.240671382993481e-06, 'epoch': 5.29} +{'loss': 0.5439, 'learning_rate': 5.194432884819901e-06, 'epoch': 5.33} +{'loss': 0.5484, 'learning_rate': 5.148194386646322e-06, 'epoch': 5.37} +{'loss': 0.544, 'learning_rate': 5.101955888472742e-06, 'epoch': 5.41} +{'loss': 0.5479, 'learning_rate': 5.055717390299163e-06, 'epoch': 5.45} +{'loss': 0.5463, 'learning_rate': 5.009478892125585e-06, 'epoch': 5.49} +{'loss': 0.5468, 'learning_rate': 4.9632403939520045e-06, 'epoch': 5.53} +{'loss': 0.5448, 'learning_rate': 4.917001895778425e-06, 'epoch': 5.58} +{'loss': 0.5463, 'learning_rate': 4.870763397604846e-06, 'epoch': 5.62} +{'loss': 0.5394, 'learning_rate': 4.824524899431267e-06, 'epoch': 5.66} +{'loss': 0.5413, 'learning_rate': 4.7782864012576875e-06, 'epoch': 5.7} +{'loss': 0.5451, 'learning_rate': 4.732047903084108e-06, 'epoch': 5.74} +{'loss': 0.5501, 'learning_rate': 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0.6523859157632009, 'eval_recall': 0.6476671564499512, 'eval_runtime': 17.2842, 'eval_samples_per_second': 2224.051, 'eval_steps_per_second': 17.415, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:55:59<1:01:24, 1.96it/s]***** Running Evaluation ***** +{'loss': 0.5209, 'learning_rate': 4.408378415869053e-06, 'epoch': 6.03} +{'loss': 0.5182, 'learning_rate': 4.362602302677209e-06, 'epoch': 6.08} +{'loss': 0.5094, 'learning_rate': 4.31636380450363e-06, 'epoch': 6.12} +{'loss': 0.5218, 'learning_rate': 4.270125306330051e-06, 'epoch': 6.16} +{'loss': 0.5158, 'learning_rate': 4.2238868081564715e-06, 'epoch': 6.2} +{'loss': 0.4989, 'learning_rate': 4.177648309982892e-06, 'epoch': 6.24} +{'loss': 0.5156, 'learning_rate': 4.131409811809313e-06, 'epoch': 6.28} +{'loss': 0.5112, 'learning_rate': 4.085171313635734e-06, 'epoch': 6.33} +{'loss': 0.5207, 'learning_rate': 4.0389328154621544e-06, 'epoch': 6.37} +{'loss': 0.5169, 'learning_rate': 3.992694317288574e-06, 'epoch': 6.41} +{'loss': 0.5125, 'learning_rate': 3.946455819114995e-06, 'epoch': 6.45} +{'loss': 0.5184, 'learning_rate': 3.900217320941417e-06, 'epoch': 6.49} +{'loss': 0.5223, 'learning_rate': 3.853978822767837e-06, 'epoch': 6.53} +{'loss': 0.5194, 'learning_rate': 3.8077403245942573e-06, 'epoch': 6.58} +{'loss': 0.5233, 'learning_rate': 3.761501826420678e-06, 'epoch': 6.62} +{'loss': 0.5114, 'learning_rate': 3.715263328247099e-06, 'epoch': 6.66} +{'loss': 0.5224, 'learning_rate': 3.669024830073519e-06, 'epoch': 6.7} +{'loss': 0.5183, 'learning_rate': 3.6227863318999402e-06, 'epoch': 6.74} +{'loss': 0.5131, 'learning_rate': 3.576547833726361e-06, 'epoch': 6.78} +{'loss': 0.5236, 'learning_rate': 3.5303093355527817e-06, 'epoch': 6.82} +{'loss': 0.5207, 'learning_rate': 3.484070837379202e-06, 'epoch': 6.87} +{'loss': 0.5204, 'learning_rate': 3.4382947241873587e-06, 'epoch': 6.91} +{'loss': 0.5227, 'learning_rate': 3.3920562260137794e-06, 'epoch': 6.95} +{'loss': 0.5225, 'learning_rate': 3.3458177278401998e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [2:56:48<1:01:24, 1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.6830966472625732, 'eval_accuracy': 0.6493847714679639, 'eval_f1': 0.6417410075041053, 'eval_matthews_correlation': 0.29676800248850593, 'eval_precision': 0.6529113463807945, 'eval_recall': 0.6439907001434909, 'eval_runtime': 49.7534, 'eval_samples_per_second': 772.63, 'eval_steps_per_second': 6.05, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:20:35<43:47, 1.83it/s]***** Running Evaluation ***** +{'loss': 0.4916, 'learning_rate': 3.2995792296666205e-06, 'epoch': 7.03} +{'loss': 0.4913, 'learning_rate': 3.2533407314930417e-06, 'epoch': 7.07} +{'loss': 0.4889, 'learning_rate': 3.207102233319462e-06, 'epoch': 7.12} +{'loss': 0.4922, 'learning_rate': 3.1608637351458827e-06, 'epoch': 7.16} +{'loss': 0.4849, 'learning_rate': 3.1146252369723035e-06, 'epoch': 7.2} +{'loss': 0.49, 'learning_rate': 3.068386738798724e-06, 'epoch': 7.24} +{'loss': 0.4982, 'learning_rate': 3.0221482406251445e-06, 'epoch': 7.28} +{'loss': 0.4838, 'learning_rate': 2.9759097424515653e-06, 'epoch': 7.32} +{'loss': 0.4887, 'learning_rate': 2.929671244277986e-06, 'epoch': 7.37} +{'loss': 0.4901, 'learning_rate': 2.8834327461044063e-06, 'epoch': 7.41} +{'loss': 0.4871, 'learning_rate': 2.8371942479308275e-06, 'epoch': 7.45} +{'loss': 0.4909, 'learning_rate': 2.7909557497572482e-06, 'epoch': 7.49} +{'loss': 0.4863, 'learning_rate': 2.744717251583669e-06, 'epoch': 7.53} +{'loss': 0.4954, 'learning_rate': 2.6984787534100893e-06, 'epoch': 7.57} +{'loss': 0.4967, 'learning_rate': 2.65224025523651e-06, 'epoch': 7.62} +{'loss': 0.4933, 'learning_rate': 2.6060017570629308e-06, 'epoch': 7.66} +{'loss': 0.5, 'learning_rate': 2.559763258889352e-06, 'epoch': 7.7} +{'loss': 0.4886, 'learning_rate': 2.513524760715772e-06, 'epoch': 7.74} +{'loss': 0.4883, 'learning_rate': 2.467286262542193e-06, 'epoch': 7.78} +{'loss': 0.494, 'learning_rate': 2.4215101493503492e-06, 'epoch': 7.82} +{'loss': 0.487, 'learning_rate': 2.37527165117677e-06, 'epoch': 7.87} +{'loss': 0.4925, 'learning_rate': 2.3290331530031907e-06, 'epoch': 7.91} +{'loss': 0.4935, 'learning_rate': 2.282794654829611e-06, 'epoch': 7.95} +{'loss': 0.4859, 'learning_rate': 2.236556156656032e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:21:20<43:47, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.7020118832588196, 'eval_accuracy': 0.6436096875731641, 'eval_f1': 0.6394580991117012, 'eval_matthews_correlation': 0.2837533867500214, 'eval_precision': 0.6437714871465139, 'eval_recall': 0.6400068714773316, 'eval_runtime': 45.0446, 'eval_samples_per_second': 853.399, 'eval_steps_per_second': 6.682, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:46:29<20:06, 1.99it/s]***** Running Evaluation ***** +{'loss': 0.4757, 'learning_rate': 2.1903176584824525e-06, 'epoch': 8.03} +{'loss': 0.4689, 'learning_rate': 2.1440791603088733e-06, 'epoch': 8.07} +{'loss': 0.4609, 'learning_rate': 2.097840662135294e-06, 'epoch': 8.11} +{'loss': 0.459, 'learning_rate': 2.0516021639617147e-06, 'epoch': 8.16} +{'loss': 0.47, 'learning_rate': 2.0053636657881355e-06, 'epoch': 8.2} +{'loss': 0.4755, 'learning_rate': 1.9591251676145562e-06, 'epoch': 8.24} +{'loss': 0.4728, 'learning_rate': 1.9128866694409765e-06, 'epoch': 8.28} +{'loss': 0.4721, 'learning_rate': 1.8666481712673973e-06, 'epoch': 8.32} +{'loss': 0.4647, 'learning_rate': 1.820409673093818e-06, 'epoch': 8.36} +{'loss': 0.4634, 'learning_rate': 1.7741711749202388e-06, 'epoch': 8.41} +{'loss': 0.4673, 'learning_rate': 1.7279326767466595e-06, 'epoch': 8.45} +{'loss': 0.465, 'learning_rate': 1.68169417857308e-06, 'epoch': 8.49} +{'loss': 0.4661, 'learning_rate': 1.6354556803995008e-06, 'epoch': 8.53} +{'loss': 0.4579, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.7317508459091187, 'eval_accuracy': 0.6415545901511407, 'eval_f1': 0.6358098100100388, 'eval_matthews_correlation': 0.27982546443223566, 'eval_precision': 0.6427870136322184, 'eval_recall': 0.6370963096588084, 'eval_runtime': 55.8314, 'eval_samples_per_second': 688.52, 'eval_steps_per_second': 5.391, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [4:12:35<00:00, 1.39s/it]***** Running Evaluation ***** +{'loss': 0.4588, 'learning_rate': 1.0810560872982845e-06, 'epoch': 9.03} +{'loss': 0.4443, 'learning_rate': 1.0348175891247053e-06, 'epoch': 9.07} +{'loss': 0.4508, 'learning_rate': 9.88579090951126e-07, 'epoch': 9.11} +{'loss': 0.4435, 'learning_rate': 9.423405927775467e-07, 'epoch': 9.16} +{'loss': 0.446, 'learning_rate': 8.961020946039674e-07, 'epoch': 9.2} +{'loss': 0.4492, 'learning_rate': 8.498635964303881e-07, 'epoch': 9.24} +{'loss': 0.4541, 'learning_rate': 8.036250982568086e-07, 'epoch': 9.28} +{'loss': 0.4515, 'learning_rate': 7.573866000832293e-07, 'epoch': 9.32} +{'loss': 0.4538, 'learning_rate': 7.1114810190965e-07, 'epoch': 9.36} +{'loss': 0.4535, 'learning_rate': 6.649096037360707e-07, 'epoch': 9.4} +{'loss': 0.4554, 'learning_rate': 6.186711055624914e-07, 'epoch': 9.45} +{'loss': 0.4541, 'learning_rate': 5.72432607388912e-07, 'epoch': 9.49} +{'loss': 0.4542, 'learning_rate': 5.261941092153328e-07, 'epoch': 9.53} +{'loss': 0.448, 'learning_rate': 4.799556110417534e-07, 'epoch': 9.57} +{'loss': 0.4519, 'learning_rate': 4.3371711286817404e-07, 'epoch': 9.61} +{'loss': 0.4551, 'learning_rate': 3.874786146945948e-07, 'epoch': 9.65} +{'loss': 0.4547, 'learning_rate': 3.4124011652101547e-07, 'epoch': 9.7} +{'loss': 0.455, 'learning_rate': 2.950016183474361e-07, 'epoch': 9.74} +{'loss': 0.4534, 'learning_rate': 2.4876312017385674e-07, 'epoch': 9.78} +{'loss': 0.4496, 'learning_rate': 2.0252462200027746e-07, 'epoch': 9.82} +{'loss': 0.4452, 'learning_rate': 1.5628612382669814e-07, 'epoch': 9.86} +{'loss': 0.4525, 'learning_rate': 1.1004762565311879e-07, 'epoch': 9.9} +{'loss': 0.4432, 'learning_rate': 6.380912747953947e-08, 'epoch': 9.95} +{'loss': 0.4474, 'learning_rate': 1.7570629305960146e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [4:13:30<00:00, 1.3Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.7562589645385742, 'eval_accuracy': 0.6396295621862075, 'eval_f1': 0.6350890261835063, 'eval_matthews_correlation': 0.27568463737852483, 'eval_precision': 0.6398938999972619, 'eval_recall': 0.6358208243676393, 'eval_runtime': 55.0617, 'eval_samples_per_second': 698.145, 'eval_steps_per_second': 5.467, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209 (score: 0.6493712255886945). +100%|██████████| 24030/24030 [4:13:32<00:00, 1.39s/it]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 15212.752, 'train_samples_per_second': 202.152, 'train_steps_per_second': 1.58, 'train_loss': 0.5512123809176289, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:13:32<00:00, 1.58it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:05<00:00, 4.57it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_083504-xd6znn4g/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_083504-xd6znn4g/files/requirements.txt new 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b/VASC/len2_5120/wandb/run-20260305_110836-w934r0hw/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.bias', 'bert.pooler.dense.weight', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 8 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 19,224 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 12%|█▎ | 2403/19224 [18:52<1:58:08, 2.37it/s]***** Running Evaluation ***** +{'loss': 0.5035, 'learning_rate': 1.7331022530329292e-06, 'epoch': 0.04} +{'loss': 0.3753, 'learning_rate': 3.4662045060658585e-06, 'epoch': 0.08} +{'loss': 0.3572, 'learning_rate': 5.199306759098788e-06, 'epoch': 0.12} +{'loss': 0.3538, 'learning_rate': 6.932409012131717e-06, 'epoch': 0.17} +{'loss': 0.36, 'learning_rate': 8.665511265164645e-06, 'epoch': 0.21} +{'loss': 0.3582, 'learning_rate': 9.987665576232103e-06, 'epoch': 0.25} +{'loss': 0.3561, 'learning_rate': 9.934037646806459e-06, 'epoch': 0.29} +{'loss': 0.3469, 'learning_rate': 9.880409717380811e-06, 'epoch': 0.33} +{'loss': 0.3594, 'learning_rate': 9.826781787955167e-06, 'epoch': 0.37} +{'loss': 0.3547, 'learning_rate': 9.773153858529523e-06, 'epoch': 0.42} +{'loss': 0.3521, 'learning_rate': 9.719525929103878e-06, 'epoch': 0.46} +{'loss': 0.3567, 'learning_rate': 9.665897999678234e-06, 'epoch': 0.5} +{'loss': 0.3483, 'learning_rate': 9.612270070252588e-06, 'epoch': 0.54} +{'loss': 0.3469, 'learning_rate': 9.558642140826944e-06, 'epoch': 0.58} +{'loss': 0.3543, 'learning_rate': 9.505014211401298e-06, 'epoch': 0.62} +{'loss': 0.3433, 'learning_rate': 9.451386281975654e-06, 'epoch': 0.67} +{'loss': 0.3462, 'learning_rate': 9.397758352550009e-06, 'epoch': 0.71} +{'loss': 0.3394, 'learning_rate': 9.344130423124363e-06, 'epoch': 0.75} +{'loss': 0.352, 'learning_rate': 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+{'loss': 0.3323, 'learning_rate': 8.057060116908887e-06, 'epoch': 1.75} +{'loss': 0.3454, 'learning_rate': 8.003432187483243e-06, 'epoch': 1.79} +{'loss': 0.3381, 'learning_rate': 7.949804258057597e-06, 'epoch': 1.83} +{'loss': 0.3343, 'learning_rate': 7.896176328631953e-06, 'epoch': 1.87} +{'loss': 0.3335, 'learning_rate': 7.842548399206307e-06, 'epoch': 1.91} +{'loss': 0.3302, 'learning_rate': 7.788920469780662e-06, 'epoch': 1.96} +{'loss': 0.3244, 'learning_rate': 7.735292540355018e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 25%|██▌ | 4806/19224 [39:19<1:39:51, 2.41Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-4806/config.json +{'eval_loss': 0.34018510580062866, 'eval_accuracy': 0.8739106682968705, 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38%|███▊ | 7209/19224 [1:00:13<1:24:37, 2.37it/s]***** Running Evaluation ***** +{'loss': 0.3219, 'learning_rate': 7.681664610929372e-06, 'epoch': 2.04} +{'loss': 0.3304, 'learning_rate': 7.628036681503728e-06, 'epoch': 2.08} +{'loss': 0.3204, 'learning_rate': 7.574408752078083e-06, 'epoch': 2.12} +{'loss': 0.3173, 'learning_rate': 7.520780822652438e-06, 'epoch': 2.16} +{'loss': 0.3187, 'learning_rate': 7.4671528932267935e-06, 'epoch': 2.21} +{'loss': 0.3241, 'learning_rate': 7.413524963801149e-06, 'epoch': 2.25} +{'loss': 0.3222, 'learning_rate': 7.359897034375504e-06, 'epoch': 2.29} +{'loss': 0.3249, 'learning_rate': 7.306269104949858e-06, 'epoch': 2.33} +{'loss': 0.3231, 'learning_rate': 7.252641175524213e-06, 'epoch': 2.37} +{'loss': 0.3189, 'learning_rate': 7.199013246098568e-06, 'epoch': 2.41} +{'loss': 0.3254, 'learning_rate': 7.1453853166729235e-06, 'epoch': 2.46} +{'loss': 0.3234, 'learning_rate': 7.091757387247279e-06, 'epoch': 2.5} +{'loss': 0.3238, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3366709351539612, 'eval_accuracy': 0.8728961265315679, 'eval_f1': 0.69113659753568, 'eval_matthews_correlation': 0.41179398697944275, 'eval_precision': 0.7676939183531514, 'eval_recall': 0.6583658388240978, 'eval_runtime': 38.2102, 'eval_samples_per_second': 1006.039, 'eval_steps_per_second': 7.877, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:21:45<1:06:59, 2.39it/s]***** Running Evaluation ***** +{'loss': 0.3043, 'learning_rate': 6.394594304713896e-06, 'epoch': 3.04} +{'loss': 0.3081, 'learning_rate': 6.340966375288251e-06, 'epoch': 3.08} +{'loss': 0.3031, 'learning_rate': 6.287338445862605e-06, 'epoch': 3.12} +{'loss': 0.3095, 'learning_rate': 6.23371051643696e-06, 'epoch': 3.16} +{'loss': 0.3054, 'learning_rate': 6.1800825870113155e-06, 'epoch': 3.2} +{'loss': 0.2988, 'learning_rate': 6.126454657585671e-06, 'epoch': 3.25} +{'loss': 0.3145, 'learning_rate': 6.072826728160026e-06, 'epoch': 3.29} +{'loss': 0.2976, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [1:42:11<21:13, 5.66it/s]***** Running Evaluation ***** +{'loss': 0.2977, 'learning_rate': 5.108596557086931e-06, 'epoch': 4.04} +{'loss': 0.2935, 'learning_rate': 5.054968627661287e-06, 'epoch': 4.08} +{'loss': 0.2968, 'learning_rate': 5.001340698235642e-06, 'epoch': 4.12} +{'loss': 0.2908, 'learning_rate': 4.947712768809997e-06, 'epoch': 4.16} +{'loss': 0.281, 'learning_rate': 4.894084839384351e-06, 'epoch': 4.2} +{'loss': 0.294, 'learning_rate': 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'eval_runtime': 18.5923, 'eval_samples_per_second': 2067.574, 'eval_steps_per_second': 16.189, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [2:04:48<33:30, 2.39it/s]***** Running Evaluation ***** +{'loss': 0.2641, 'learning_rate': 3.821526250871454e-06, 'epoch': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3601226508617401, 'eval_accuracy': 0.8611898753934601, 'eval_f1': 0.6782232791096233, 'eval_matthews_correlation': 0.37308276119348727, 'eval_precision': 0.7269529589356034, 'eval_recall': 0.6533255474532624, 'eval_runtime': 31.7649, 'eval_samples_per_second': 1210.171, 'eval_steps_per_second': 9.476, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:27:09<17:20, 2.31it/s]***** Running Evaluation ***** +{'loss': 0.2635, 'learning_rate': 2.5349922239502335e-06, 'epoch': 6.03} +{'loss': 0.2565, 'learning_rate': 2.4813642945245886e-06, 'epoch': 6.08} +{'loss': 0.2489, 'learning_rate': 2.4277363650989438e-06, 'epoch': 6.12} +{'loss': 0.2607, 'learning_rate': 2.374108435673299e-06, 'epoch': 6.16} +{'loss': 0.2539, 'learning_rate': 2.320480506247654e-06, 'epoch': 6.2} +{'loss': 0.2508, 'learning_rate': 2.266852576822009e-06, 'epoch': 6.24} +{'loss': 0.254, 'learning_rate': 2.2132246473963644e-06, 'epoch': 6.28} +{'loss': 0.2552, 'learning_rate': 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+{'loss': 0.2549, 'learning_rate': 1.4093419853059476e-06, 'epoch': 6.91} +{'loss': 0.2515, 'learning_rate': 1.3557140558803025e-06, 'epoch': 6.95} +{'loss': 0.2509, 'learning_rate': 1.3020861264546577e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [2:27:38<17:20, 2.3Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3818974196910858, 'eval_accuracy': 0.8570276527665773, 'eval_f1': 0.6781782578085283, 'eval_matthews_correlation': 0.36749298729759916, 'eval_precision': 0.715156005923173, 'eval_recall': 0.656922293585819, 'eval_runtime': 28.9453, 'eval_samples_per_second': 1328.058, 'eval_steps_per_second': 10.399, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [2:48:53<00:00, 2.42it/s]***** Running Evaluation ***** +{'loss': 0.2393, 'learning_rate': 1.2484581970290129e-06, 'epoch': 7.03} +{'loss': 0.2379, 'learning_rate': 1.194830267603368e-06, 'epoch': 7.07} +{'loss': 0.2327, 'learning_rate': 1.141202338177723e-06, 'epoch': 7.12} +{'loss': 0.2441, 'learning_rate': 1.0875744087520781e-06, 'epoch': 7.16} +{'loss': 0.235, 'learning_rate': 1.0344827586206898e-06, 'epoch': 7.2} +{'loss': 0.2481, 'learning_rate': 9.808548291950447e-07, 'epoch': 7.24} +{'loss': 0.2329, 'learning_rate': 9.272268997693999e-07, 'epoch': 7.28} +{'loss': 0.2392, 'learning_rate': 8.735989703437551e-07, 'epoch': 7.32} +{'loss': 0.2445, 'learning_rate': 8.199710409181102e-07, 'epoch': 7.37} +{'loss': 0.2344, 'learning_rate': 7.663431114924654e-07, 'epoch': 7.41} +{'loss': 0.2344, 'learning_rate': 7.127151820668204e-07, 'epoch': 7.45} +{'loss': 0.2382, 'learning_rate': 6.590872526411756e-07, 'epoch': 7.49} +{'loss': 0.2452, 'learning_rate': 6.054593232155307e-07, 'epoch': 7.53} +{'loss': 0.2406, 'learning_rate': 5.518313937898858e-07, 'epoch': 7.57} +{'loss': 0.2491, 'learning_rate': 4.982034643642409e-07, 'epoch': 7.62} +{'loss': 0.2361, 'learning_rate': 4.4457553493859607e-07, 'epoch': 7.66} +{'loss': 0.2412, 'learning_rate': 3.9094760551295117e-07, 'epoch': 7.7} +{'loss': 0.2427, 'learning_rate': 3.3731967608730633e-07, 'epoch': 7.74} +{'loss': 0.237, 'learning_rate': 2.8369174666166143e-07, 'epoch': 7.78} +{'loss': 0.2392, 'learning_rate': 2.3006381723601653e-07, 'epoch': 7.82} +{'loss': 0.2424, 'learning_rate': 1.7643588781037166e-07, 'epoch': 7.87} +{'loss': 0.2497, 'learning_rate': 1.228079583847268e-07, 'epoch': 7.91} +{'loss': 0.2467, 'learning_rate': 6.918002895908189e-08, 'epoch': 7.95} +{'loss': 0.2357, 'learning_rate': 1.5552099533437016e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [2:49:29<00:00, 2.4Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.39618584513664246, 'eval_accuracy': 0.8551026248016441, 'eval_f1': 0.677219667070773, 'eval_matthews_correlation': 0.36389703905337517, 'eval_precision': 0.710291750811796, 'eval_recall': 0.6574254036601821, 'eval_runtime': 35.9304, 'eval_samples_per_second': 1069.875, 'eval_steps_per_second': 8.377, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209 (score: 0.69113659753568). +100%|██████████| 19224/19224 [2:49:31<00:00, 2.42it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 10171.5123, 'train_samples_per_second': 241.875, 'train_steps_per_second': 1.89, 'train_loss': 0.29728356272887546, 'epoch': 8.0} +100%|██████████| 19224/19224 [2:49:31<00:00, 1.89it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:56<00:00, 5.35it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_110836-w934r0hw/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_110836-w934r0hw/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260305_110836-w934r0hw/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 +nvidia-nccl-cu12==2.27.3 +debugpy==1.8.16 +ipython==8.18.1 +anyio==4.12.0 +prompt_toolkit==3.0.51 +mkl_fft==1.3.11 +httpcore==1.0.9 +Jinja2==3.1.6 +ply==3.11 +zipp==3.23.0 +setproctitle==1.3.6 +docker-pycreds==0.4.0 +nvidia-cuda-nvrtc-cu12==12.8.93 +urllib3==2.5.0 +kiwisolver==1.4.4 +nvidia-curand-cu12==10.3.9.90 +llvmlite==0.43.0 +six==1.17.0 +frozenlist==1.8.0 +wcwidth==0.2.13 +numexpr==2.10.1 +click==8.1.8 +multiprocess==0.70.18 +threadpoolctl==3.6.0 +typing_extensions==4.15.0 +decorator==5.2.1 +sip==6.7.12 +pure_eval==0.2.3 +async-timeout==5.0.1 +Pygments==2.19.2 +mkl-service==2.4.0 +transformers==4.35.2 +numba==0.60.0 +pyzmq==27.0.2 +mkl_random==1.2.8 +ptyprocess==0.7.0 +nvidia-cuda-cupti-cu12==12.8.90 +charset-normalizer==3.4.4 +nvidia-cublas-cu12==12.8.4.1 +PyQt5_sip==12.13.0 +Bottleneck==1.4.2 +networkx==3.2.1 +PySocks==1.7.1 +pysam==0.9.1 +tornado==6.5.2 +pandas==2.3.3 +smmap==5.0.2 +PyQt5==5.15.10 +nvidia-cufft-cu12==11.3.3.83 +safetensors==0.7.0 +requests==2.32.5 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.05" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.03" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune_3072 + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "557122830336" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 + host: sn4622116170 + memory: + total: "4316310355968" + os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 + program: /home/n5huang/dna_token/Finetune-screen/train.py + python: CPython 3.9.18 + root: /data/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120 + startedAt: "2026-03-05T12:51:09.423086Z" + writerId: lofhpyczq78w897gl73ld3inj48uawab + m: + - "1": train/global_step + "6": + - 3 + "7": [] + - "2": '*' + "5": 1 + "6": + - 1 + "7": [] + python_version: 3.9.18 + t: + "1": + - 1 + - 5 + - 11 + - 49 + - 51 + - 53 + - 71 + "2": + - 1 + - 5 + - 11 + - 49 + - 51 + - 53 + - 71 + "3": + - 7 + - 66 + "4": 3.9.18 + "5": 0.23.1 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [1:14:26<57:42, 2.08it/s] ***** Running Evaluation ***** +{'loss': 0.6055, 'learning_rate': 6.80586342509832e-06, 'epoch': 2.04} +{'loss': 0.604, 'learning_rate': 6.7343582409724705e-06, 'epoch': 2.08} +{'loss': 0.6019, 'learning_rate': 6.662853056846622e-06, 'epoch': 2.12} +{'loss': 0.6072, 'learning_rate': 6.5913478727207724e-06, 'epoch': 2.16} +{'loss': 0.6043, 'learning_rate': 6.519842688594924e-06, 'epoch': 2.21} +{'loss': 0.5988, 'learning_rate': 6.448337504469074e-06, 'epoch': 2.25} +{'loss': 0.6048, 'learning_rate': 6.376832320343226e-06, 'epoch': 2.29} +{'loss': 0.6096, 'learning_rate': 6.305327136217376e-06, 'epoch': 2.33} +{'loss': 0.6044, 'learning_rate': 6.2338219520915265e-06, 'epoch': 2.37} +{'loss': 0.6037, 'learning_rate': 6.162316767965678e-06, 'epoch': 2.41} +{'loss': 0.6103, 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:41:24<41:39, 1.92it/s]***** Running Evaluation ***** +{'loss': 0.5905, 'learning_rate': 5.0904540579192e-06, 'epoch': 3.04} +{'loss': 0.5952, 'learning_rate': 5.01894887379335e-06, 'epoch': 3.08} +{'loss': 0.5902, 'learning_rate': 4.947443689667502e-06, 'epoch': 3.12} +{'loss': 0.5948, 'learning_rate': 4.875938505541652e-06, 'epoch': 3.16} +{'loss': 0.5892, 'learning_rate': 4.804433321415803e-06, 'epoch': 3.2} +{'loss': 0.5894, 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+{'loss': 0.5902, 'learning_rate': 3.7325706113693244e-06, 'epoch': 3.83} +{'loss': 0.5884, 'learning_rate': 3.6610654272434754e-06, 'epoch': 3.87} +{'loss': 0.5846, 'learning_rate': 3.5895602431176264e-06, 'epoch': 3.91} +{'loss': 0.5909, 'learning_rate': 3.5180550589917774e-06, 'epoch': 3.95} +{'loss': 0.5912, 'learning_rate': 3.4465498748659284e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 67%|██████▋ | 9612/14418 [1:42:18<41:39, 1.92Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612/config.json +{'eval_loss': 0.6226817965507507, 'eval_accuracy': 0.6538851746832809, 'eval_f1': 0.647698706766702, 'eval_matthews_correlation': 0.30532540120249696, 'eval_precision': 0.6562774832975775, 'eval_recall': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:29:51<00:00, 2.06it/s]***** Running Evaluation ***** +{'loss': 0.5598, 'learning_rate': 1.6596353235609582e-06, 'epoch': 5.04} +{'loss': 0.5641, 'learning_rate': 1.5881301394351092e-06, 'epoch': 5.08} +{'loss': 0.5588, 'learning_rate': 1.5166249553092602e-06, 'epoch': 5.12} +{'loss': 0.5503, 'learning_rate': 1.4451197711834108e-06, 'epoch': 5.16} +{'loss': 0.5571, 'learning_rate': 1.3736145870575618e-06, 'epoch': 5.2} +{'loss': 0.5536, 'learning_rate': 1.3028244547729712e-06, 'epoch': 5.24} +{'loss': 0.5564, 'learning_rate': 1.2313192706471221e-06, 'epoch': 5.29} +{'loss': 0.5589, 'learning_rate': 1.159814086521273e-06, 'epoch': 5.33} +{'loss': 0.5605, 'learning_rate': 1.088308902395424e-06, 'epoch': 5.37} +{'loss': 0.5559, 'learning_rate': 1.0168037182695747e-06, 'epoch': 5.41} +{'loss': 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'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [2:30:40<00:00, 2.0Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.6417271494865417, 'eval_accuracy': 0.6490205769881117, 'eval_f1': 0.6453609290883082, 'eval_matthews_correlation': 0.2947197051744641, 'eval_precision': 0.6490429353634168, 'eval_recall': 0.6456957761975263, 'eval_runtime': 49.2396, 'eval_samples_per_second': 780.692, 'eval_steps_per_second': 6.113, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209 (score: 0.6481764606487644). +100%|██████████| 14418/14418 [2:30:42<00:00, 2.06it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 9042.3744, 'train_samples_per_second': 204.059, 'train_steps_per_second': 1.594, 'train_loss': 0.597083533251727, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:30:42<00:00, 1.59it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:58<00:00, 5.18it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_125109-mxo4ba7y/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_125109-mxo4ba7y/files/requirements.txt new file 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+{'loss': 0.3306, 'learning_rate': 8.50744347676863e-06, 'epoch': 1.75} +{'loss': 0.3443, 'learning_rate': 8.46454159337595e-06, 'epoch': 1.79} +{'loss': 0.3376, 'learning_rate': 8.42163970998327e-06, 'epoch': 1.83} +{'loss': 0.3341, 'learning_rate': 8.378737826590588e-06, 'epoch': 1.87} +{'loss': 0.3324, 'learning_rate': 8.335835943197907e-06, 'epoch': 1.91} +{'loss': 0.3298, 'learning_rate': 8.292934059805227e-06, 'epoch': 1.96} +{'loss': 0.3235, 'learning_rate': 8.250032176412546e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [44:15<2:14:43, 2.38Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 0.33843639492988586, 'eval_accuracy': 0.8739366821882886, 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30%|███ | 7209/24030 [1:03:00<1:58:51, 2.36it/s]***** Running Evaluation ***** +{'loss': 0.3191, 'learning_rate': 8.207130293019864e-06, 'epoch': 2.04} +{'loss': 0.3296, 'learning_rate': 8.164228409627184e-06, 'epoch': 2.08} +{'loss': 0.3199, 'learning_rate': 8.121326526234501e-06, 'epoch': 2.12} +{'loss': 0.3158, 'learning_rate': 8.078424642841821e-06, 'epoch': 2.16} +{'loss': 0.3163, 'learning_rate': 8.03552275944914e-06, 'epoch': 2.21} +{'loss': 0.3234, 'learning_rate': 7.99262087605646e-06, 'epoch': 2.25} +{'loss': 0.3198, 'learning_rate': 7.949718992663778e-06, 'epoch': 2.29} +{'loss': 0.3235, 'learning_rate': 7.906817109271098e-06, 'epoch': 2.33} +{'loss': 0.3231, 'learning_rate': 7.863915225878417e-06, 'epoch': 2.37} +{'loss': 0.3199, 'learning_rate': 7.821013342485737e-06, 'epoch': 2.41} +{'loss': 0.3243, 'learning_rate': 7.778111459093054e-06, 'epoch': 2.46} +{'loss': 0.3225, 'learning_rate': 7.735209575700374e-06, 'epoch': 2.5} +{'loss': 0.3251, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3374841511249542, 'eval_accuracy': 0.8726099737259697, 'eval_f1': 0.691666455223233, 'eval_matthews_correlation': 0.4117158618193067, 'eval_precision': 0.76608254231613, 'eval_recall': 0.6592644423400591, 'eval_runtime': 32.1206, 'eval_samples_per_second': 1196.772, 'eval_steps_per_second': 9.371, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:22:15<1:37:51, 2.46it/s]***** Running Evaluation ***** +{'loss': 0.304, 'learning_rate': 7.1774850915955215e-06, 'epoch': 3.04} +{'loss': 0.3083, 'learning_rate': 7.134583208202841e-06, 'epoch': 3.08} +{'loss': 0.3026, 'learning_rate': 7.09168132481016e-06, 'epoch': 3.12} +{'loss': 0.3081, 'learning_rate': 7.048779441417479e-06, 'epoch': 3.16} +{'loss': 0.3049, 'learning_rate': 7.005877558024799e-06, 'epoch': 3.2} +{'loss': 0.2964, 'learning_rate': 6.962975674632117e-06, 'epoch': 3.25} +{'loss': 0.3118, 'learning_rate': 6.920073791239435e-06, 'epoch': 3.29} +{'loss': 0.2985, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-9612/special_tokens_map.json + 50%|█████ | 12015/24030 [1:38:32<1:19:20, 2.52it/s]***** Running Evaluation ***** +{'loss': 0.2951, 'learning_rate': 6.148697927839033e-06, 'epoch': 4.04} +{'loss': 0.2893, 'learning_rate': 6.105796044446351e-06, 'epoch': 4.08} +{'loss': 0.2975, 'learning_rate': 6.062894161053671e-06, 'epoch': 4.12} +{'loss': 0.2893, 'learning_rate': 6.0199922776609896e-06, 'epoch': 4.16} +{'loss': 0.2762, 'learning_rate': 5.977090394268309e-06, 'epoch': 4.2} +{'loss': 0.2948, 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+{'loss': 0.2923, 'learning_rate': 5.333991162212021e-06, 'epoch': 4.83} +{'loss': 0.2921, 'learning_rate': 5.29108927881934e-06, 'epoch': 4.87} +{'loss': 0.2947, 'learning_rate': 5.248187395426659e-06, 'epoch': 4.91} +{'loss': 0.2856, 'learning_rate': 5.205285512033979e-06, 'epoch': 4.95} +{'loss': 0.2893, 'learning_rate': 5.162383628641297e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 12015/24030 [1:39:02<1:19:20, 2Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015/config.json +{'eval_loss': 0.3501196801662445, 'eval_accuracy': 0.8662365703285555, 'eval_f1': 0.6870135751850998, 'eval_matthews_correlation': 0.3932068135604753, 'eval_precision': 0.7422346391370918, 'eval_recall': 0.6595680109801313, 'eval_runtime': 30.1859, 'eval_samples_per_second': 1273.475, 'eval_steps_per_second': 9.972, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [1:56:33<1:04:38, 2.48it/s]***** Running Evaluation ***** +{'loss': 0.2638, 'learning_rate': 5.119481745248617e-06, 'epoch': 5.04} +{'loss': 0.2707, 'learning_rate': 5.076579861855936e-06, 'epoch': 5.08} +{'loss': 0.2621, 'learning_rate': 5.033677978463255e-06, 'epoch': 5.12} +{'loss': 0.2728, 'learning_rate': 4.990776095070574e-06, 'epoch': 5.16} +{'loss': 0.2738, 'learning_rate': 4.947874211677893e-06, 'epoch': 5.2} +{'loss': 0.2684, 'learning_rate': 4.904972328285212e-06, 'epoch': 5.24} +{'loss': 0.2621, 'learning_rate': 4.862070444892531e-06, 'epoch': 5.29} +{'loss': 0.2596, 'learning_rate': 4.81916856149985e-06, 'epoch': 5.33} +{'loss': 0.2744, 'learning_rate': 4.776266678107169e-06, 'epoch': 5.37} +{'loss': 0.2759, 'learning_rate': 4.733364794714489e-06, 'epoch': 5.41} +{'loss': 0.2724, 'learning_rate': 4.690462911321807e-06, 'epoch': 5.45} +{'loss': 0.2702, 'learning_rate': 4.647561027929127e-06, 'epoch': 5.49} +{'loss': 0.2679, 'learning_rate': 4.604659144536446e-06, 'epoch': 5.53} +{'loss': 0.2683, 'learning_rate': 4.561757261143764e-06, 'epoch': 5.58} +{'loss': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.36184051632881165, 'eval_accuracy': 0.8611118337192061, 'eval_f1': 0.6805085139013943, 'eval_matthews_correlation': 0.3762014750492938, 'eval_precision': 0.7265221646465267, 'eval_recall': 0.6561961387422165, 'eval_runtime': 30.3255, 'eval_samples_per_second': 1267.614, 'eval_steps_per_second': 9.926, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:14:33<47:30, 2.53it/s]***** Running Evaluation ***** +{'loss': 0.256, 'learning_rate': 4.089836543824274e-06, 'epoch': 6.03} +{'loss': 0.253, 'learning_rate': 4.046934660431593e-06, 'epoch': 6.08} +{'loss': 0.2384, 'learning_rate': 4.004032777038913e-06, 'epoch': 6.12} +{'loss': 0.2521, 'learning_rate': 3.961130893646231e-06, 'epoch': 6.16} +{'loss': 0.2511, 'learning_rate': 3.91822901025355e-06, 'epoch': 6.2} +{'loss': 0.2451, 'learning_rate': 3.8753271268608696e-06, 'epoch': 6.24} +{'loss': 0.2508, 'learning_rate': 3.832425243468188e-06, 'epoch': 6.28} +{'loss': 0.2475, 'learning_rate': 3.789523360075508e-06, 'epoch': 6.33} +{'loss': 0.2496, 'learning_rate': 3.746621476682827e-06, 'epoch': 6.37} +{'loss': 0.2496, 'learning_rate': 3.703719593290146e-06, 'epoch': 6.41} +{'loss': 0.2565, 'learning_rate': 3.661246728731392e-06, 'epoch': 6.45} +{'loss': 0.2501, 'learning_rate': 3.6183448453387104e-06, 'epoch': 6.49} +{'loss': 0.2435, 'learning_rate': 3.5754429619460295e-06, 'epoch': 6.53} +{'loss': 0.2436, 'learning_rate': 3.5325410785533486e-06, 'epoch': 6.58} +{'loss': 0.2445, 'learning_rate': 3.4896391951606677e-06, 'epoch': 6.62} +{'loss': 0.2494, 'learning_rate': 3.446737311767987e-06, 'epoch': 6.66} +{'loss': 0.252, 'learning_rate': 3.403835428375306e-06, 'epoch': 6.7} +{'loss': 0.2444, 'learning_rate': 3.360933544982625e-06, 'epoch': 6.74} +{'loss': 0.2495, 'learning_rate': 3.318031661589944e-06, 'epoch': 6.78} +{'loss': 0.2629, 'learning_rate': 3.275129778197263e-06, 'epoch': 6.82} +{'loss': 0.2449, 'learning_rate': 3.232227894804582e-06, 'epoch': 6.87} +{'loss': 0.248, 'learning_rate': 3.1893260114119012e-06, 'epoch': 6.91} +{'loss': 0.2466, 'learning_rate': 3.1464241280192204e-06, 'epoch': 6.95} +{'loss': 0.2446, 'learning_rate': 3.1035222446265395e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [2:15:03<47:30, 2.5Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3853612244129181, 'eval_accuracy': 0.8574959028121016, 'eval_f1': 0.676972983048542, 'eval_matthews_correlation': 0.3662341457454419, 'eval_precision': 0.7163447722445196, 'eval_recall': 0.6549927092279106, 'eval_runtime': 30.3046, 'eval_samples_per_second': 1268.487, 'eval_steps_per_second': 9.932, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [2:32:34<31:45, 2.52it/s]***** Running Evaluation ***** +{'loss': 0.2294, 'learning_rate': 3.0606203612338586e-06, 'epoch': 7.03} +{'loss': 0.2256, 'learning_rate': 3.0177184778411773e-06, 'epoch': 7.07} +{'loss': 0.2232, 'learning_rate': 2.9752456132824233e-06, 'epoch': 7.12} +{'loss': 0.2334, 'learning_rate': 2.9323437298897425e-06, 'epoch': 7.16} +{'loss': 0.2221, 'learning_rate': 2.8894418464970616e-06, 'epoch': 7.2} +{'loss': 0.2319, 'learning_rate': 2.8465399631043807e-06, 'epoch': 7.24} +{'loss': 0.2248, 'learning_rate': 2.8036380797117e-06, 'epoch': 7.28} +{'loss': 0.2285, 'learning_rate': 2.760736196319019e-06, 'epoch': 7.32} +{'loss': 0.2322, 'learning_rate': 2.717834312926338e-06, 'epoch': 7.37} +{'loss': 0.2183, 'learning_rate': 2.6749324295336564e-06, 'epoch': 7.41} +{'loss': 0.2301, 'learning_rate': 2.6320305461409755e-06, 'epoch': 7.45} +{'loss': 0.2271, 'learning_rate': 2.5891286627482946e-06, 'epoch': 7.49} +{'loss': 0.2354, 'learning_rate': 2.5462267793556138e-06, 'epoch': 7.53} +{'loss': 0.236, 'learning_rate': 2.503324895962933e-06, 'epoch': 7.57} +{'loss': 0.2364, 'learning_rate': 2.460423012570252e-06, 'epoch': 7.62} +{'loss': 0.2301, 'learning_rate': 2.417521129177571e-06, 'epoch': 7.66} +{'loss': 0.2262, 'learning_rate': 2.3746192457848903e-06, 'epoch': 7.7} +{'loss': 0.2308, 'learning_rate': 2.3317173623922094e-06, 'epoch': 7.74} +{'loss': 0.2245, 'learning_rate': 2.288815478999528e-06, 'epoch': 7.78} +{'loss': 0.2316, 'learning_rate': 2.2459135956068473e-06, 'epoch': 7.82} +{'loss': 0.231, 'learning_rate': 2.2030117122141664e-06, 'epoch': 7.87} +{'loss': 0.226, 'learning_rate': 2.1601098288214855e-06, 'epoch': 7.91} +{'loss': 0.2344, 'learning_rate': 2.1172079454288042e-06, 'epoch': 7.95} +{'loss': 0.2221, 'learning_rate': 2.0743060620361234e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [2:33:04<31:45, 2.5Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.4174255430698395, 'eval_accuracy': 0.853541791316563, 'eval_f1': 0.6648122631871216, 'eval_matthews_correlation': 0.3431148009300994, 'eval_precision': 0.7052179386915788, 'eval_recall': 0.6434179772098705, 'eval_runtime': 30.2701, 'eval_samples_per_second': 1269.932, 'eval_steps_per_second': 9.944, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [2:50:34<15:50, 2.53it/s]***** Running Evaluation ***** +{'loss': 0.2116, 'learning_rate': 2.0314041786434425e-06, 'epoch': 8.03} +{'loss': 0.2065, 'learning_rate': 1.9885022952507616e-06, 'epoch': 8.07} +{'loss': 0.211, 'learning_rate': 1.9456004118580808e-06, 'epoch': 8.11} +{'loss': 0.212, 'learning_rate': 1.9026985284653999e-06, 'epoch': 8.16} +{'loss': 0.2031, 'learning_rate': 1.859796645072719e-06, 'epoch': 8.2} +{'loss': 0.2127, 'learning_rate': 1.8168947616800377e-06, 'epoch': 8.24} +{'loss': 0.2122, 'learning_rate': 1.7739928782873569e-06, 'epoch': 8.28} +{'loss': 0.2118, 'learning_rate': 1.731090994894676e-06, 'epoch': 8.32} +{'loss': 0.209, 'learning_rate': 1.688189111501995e-06, 'epoch': 8.36} +{'loss': 0.212, 'learning_rate': 1.645287228109314e-06, 'epoch': 8.41} +{'loss': 0.2125, 'learning_rate': 1.6023853447166332e-06, 'epoch': 8.45} +{'loss': 0.2126, 'learning_rate': 1.5594834613239523e-06, 'epoch': 8.49} +{'loss': 0.2063, 'learning_rate': 1.5165815779312712e-06, 'epoch': 8.53} +{'loss': 0.2079, 'learning_rate': 1.4736796945385903e-06, 'epoch': 8.57} +{'loss': 0.2164, 'learning_rate': 1.4307778111459095e-06, 'epoch': 8.61} +{'loss': 0.2175, 'learning_rate': 1.3878759277532286e-06, 'epoch': 8.66} +{'loss': 0.2118, 'learning_rate': 1.3449740443605475e-06, 'epoch': 8.7} +{'loss': 0.2199, 'learning_rate': 1.3020721609678667e-06, 'epoch': 8.74} +{'loss': 0.2165, 'learning_rate': 1.2591702775751858e-06, 'epoch': 8.78} +{'loss': 0.211, 'learning_rate': 1.2166974130164316e-06, 'epoch': 8.82} +{'loss': 0.2071, 'learning_rate': 1.1737955296237507e-06, 'epoch': 8.86} +{'loss': 0.2084, 'learning_rate': 1.1308936462310696e-06, 'epoch': 8.91} +{'loss': 0.2212, 'learning_rate': 1.0879917628383887e-06, 'epoch': 8.95} +{'loss': 0.2203, 'learning_rate': 1.0450898794457077e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [2:51:04<15:50, 2.5Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.43451881408691406, 'eval_accuracy': 0.8514866938945397, 'eval_f1': 0.6698177797165067, 'eval_matthews_correlation': 0.34858611058539224, 'eval_precision': 0.7009511535580996, 'eval_recall': 0.651171409496188, 'eval_runtime': 30.2984, 'eval_samples_per_second': 1268.746, 'eval_steps_per_second': 9.935, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [3:08:37<00:00, 2.46it/s]***** Running Evaluation ***** +{'loss': 0.2002, 'learning_rate': 1.0021879960530268e-06, 'epoch': 9.03} +{'loss': 0.2066, 'learning_rate': 9.59286112660346e-07, 'epoch': 9.07} +{'loss': 0.197, 'learning_rate': 9.163842292676648e-07, 'epoch': 9.11} +{'loss': 0.204, 'learning_rate': 8.73482345874984e-07, 'epoch': 9.16} +{'loss': 0.196, 'learning_rate': 8.30580462482303e-07, 'epoch': 9.2} +{'loss': 0.2005, 'learning_rate': 7.876785790896221e-07, 'epoch': 9.24} +{'loss': 0.2032, 'learning_rate': 7.447766956969411e-07, 'epoch': 9.28} +{'loss': 0.1923, 'learning_rate': 7.018748123042603e-07, 'epoch': 9.32} +{'loss': 0.1969, 'learning_rate': 6.589729289115793e-07, 'epoch': 9.36} +{'loss': 0.1988, 'learning_rate': 6.160710455188983e-07, 'epoch': 9.4} +{'loss': 0.1945, 'learning_rate': 5.731691621262174e-07, 'epoch': 9.45} +{'loss': 0.2031, 'learning_rate': 5.302672787335365e-07, 'epoch': 9.49} +{'loss': 0.1998, 'learning_rate': 4.873653953408555e-07, 'epoch': 9.53} +{'loss': 0.1983, 'learning_rate': 4.444635119481746e-07, 'epoch': 9.57} +{'loss': 0.2107, 'learning_rate': 4.015616285554936e-07, 'epoch': 9.61} +{'loss': 0.1957, 'learning_rate': 3.5865974516281263e-07, 'epoch': 9.65} +{'loss': 0.193, 'learning_rate': 3.1618688060405857e-07, 'epoch': 9.7} +{'loss': 0.2033, 'learning_rate': 2.732849972113776e-07, 'epoch': 9.74} +{'loss': 0.2007, 'learning_rate': 2.3038311381869664e-07, 'epoch': 9.78} +{'loss': 0.2024, 'learning_rate': 1.8748123042601572e-07, 'epoch': 9.82} +{'loss': 0.1978, 'learning_rate': 1.4457934703333477e-07, 'epoch': 9.86} +{'loss': 0.202, 'learning_rate': 1.0167746364065382e-07, 'epoch': 9.9} +{'loss': 0.1968, 'learning_rate': 5.8775580247972894e-08, 'epoch': 9.95} +{'loss': 0.1962, 'learning_rate': 1.5873696855291948e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [3:09:08<00:00, 2.4Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.4502243101596832, 'eval_accuracy': 0.8482869852501236, 'eval_f1': 0.6720742251012075, 'eval_matthews_correlation': 0.3495522835317631, 'eval_precision': 0.6947777595556691, 'eval_recall': 0.6568284787762795, 'eval_runtime': 30.3629, 'eval_samples_per_second': 1266.052, 'eval_steps_per_second': 9.913, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209 (score: 0.691666455223233). +100%|██████████| 24030/24030 [3:09:09<00:00, 2.46it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 11349.5882, 'train_samples_per_second': 270.96, 'train_steps_per_second': 2.117, 'train_loss': 0.2770715732749085, 'epoch': 10.0} +100%|██████████| 24030/24030 [3:09:09<00:00, 2.12it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:45<00:00, 6.58it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_140038-cag5l4ho/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_140038-cag5l4ho/files/requirements.txt new file mode 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b/VASC/len2_5120/wandb/run-20260305_152412-l2w580i0/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.bias', 'bert.pooler.dense.weight', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 8 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 19,224 + Number of trainable parameters = 88,402,178 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 12%|█▎ | 2403/19224 [17:27<1:52:12, 2.50it/s]***** Running Evaluation ***** +{'loss': 0.697, 'learning_rate': 1.7331022530329292e-06, 'epoch': 0.04} +{'loss': 0.6723, 'learning_rate': 3.4662045060658585e-06, 'epoch': 0.08} +{'loss': 0.6617, 'learning_rate': 5.199306759098788e-06, 'epoch': 0.12} +{'loss': 0.6598, 'learning_rate': 6.932409012131717e-06, 'epoch': 0.17} +{'loss': 0.6525, 'learning_rate': 8.665511265164645e-06, 'epoch': 0.21} 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-2403] due to args.save_total_limit + 38%|███▊ | 7209/19224 [53:40<1:18:02, 2.57it/s]***** Running Evaluation ***** +{'loss': 0.6045, 'learning_rate': 7.681664610929372e-06, 'epoch': 2.04} +{'loss': 0.6034, 'learning_rate': 7.628036681503728e-06, 'epoch': 2.08} +{'loss': 0.6015, 'learning_rate': 7.574408752078083e-06, 'epoch': 2.12} +{'loss': 0.6051, 'learning_rate': 7.520780822652438e-06, 'epoch': 2.16} +{'loss': 0.6032, 'learning_rate': 7.4671528932267935e-06, 'epoch': 2.21} +{'loss': 0.5973, 'learning_rate': 7.413524963801149e-06, 'epoch': 2.25} +{'loss': 0.604, 'learning_rate': 7.359897034375504e-06, 'epoch': 2.29} +{'loss': 0.6079, 'learning_rate': 7.306269104949858e-06, 'epoch': 2.33} +{'loss': 0.6014, 'learning_rate': 7.252641175524213e-06, 'epoch': 2.37} +{'loss': 0.6029, 'learning_rate': 7.199013246098568e-06, 'epoch': 2.41} +{'loss': 0.6097, 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3.0} + Num examples = 38441 + Batch size = 128 + 38%|███▊ | 7209/19224 [54:18<1:18:02, 2.57Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.6167616248130798, 'eval_accuracy': 0.6542753830545511, 'eval_f1': 0.649378329259793, 'eval_matthews_correlation': 0.30561800580601933, 'eval_precision': 0.655474090011479, 'eval_recall': 0.6501895998650835, 'eval_runtime': 37.5517, 'eval_samples_per_second': 1023.681, 'eval_steps_per_second': 8.016, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:11:48<1:03:20, 2.53it/s]***** Running Evaluation ***** +{'loss': 0.5878, 'learning_rate': 6.395130584008153e-06, 'epoch': 3.04} +{'loss': 0.5935, 'learning_rate': 6.341502654582508e-06, 'epoch': 3.08} +{'loss': 0.5879, 'learning_rate': 6.287874725156862e-06, 'epoch': 3.12} +{'loss': 0.5902, 'learning_rate': 6.234246795731217e-06, 'epoch': 3.16} +{'loss': 0.5858, 'learning_rate': 6.1806188663055724e-06, 'epoch': 3.2} +{'loss': 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due to args.save_total_limit + 75%|███████▌ | 14418/19224 [1:47:01<13:54, 5.76it/s]***** Running Evaluation ***** +{'loss': 0.5468, 'learning_rate': 3.822062530165711e-06, 'epoch': 5.04} +{'loss': 0.5491, 'learning_rate': 3.7689708800343223e-06, 'epoch': 5.08} +{'loss': 0.5426, 'learning_rate': 3.7153429506086774e-06, 'epoch': 5.12} +{'loss': 0.5344, 'learning_rate': 3.6617150211830326e-06, 'epoch': 5.16} +{'loss': 0.5379, 'learning_rate': 3.6080870917573873e-06, 'epoch': 5.2} +{'loss': 0.543, 'learning_rate': 3.5544591623317425e-06, 'epoch': 5.24} +{'loss': 0.5361, 'learning_rate': 3.5008312329060976e-06, 'epoch': 5.29} +{'loss': 0.5476, 'learning_rate': 3.447203303480453e-06, 'epoch': 5.33} +{'loss': 0.5494, 'learning_rate': 3.393575374054808e-06, 'epoch': 5.37} +{'loss': 0.5442, 'learning_rate': 3.339947444629163e-06, 'epoch': 5.41} +{'loss': 0.5467, 'learning_rate': 3.2863195152035182e-06, 'epoch': 5.45} +{'loss': 0.5476, 'learning_rate': 3.2326915857778734e-06, 'epoch': 5.49} +{'loss': 0.5439, 'learning_rate': 3.1790636563522286e-06, 'epoch': 5.53} +{'loss': 0.5463, 'learning_rate': 3.1254357269265833e-06, 'epoch': 5.58} +{'loss': 0.5468, 'learning_rate': 3.0718077975009384e-06, 'epoch': 5.62} +{'loss': 0.5405, 'learning_rate': 3.018179868075294e-06, 'epoch': 5.66} +{'loss': 0.5405, 'learning_rate': 2.964551938649649e-06, 'epoch': 5.7} +{'loss': 0.5415, 'learning_rate': 2.9109240092240043e-06, 'epoch': 5.74} +{'loss': 0.5474, 'learning_rate': 2.857296079798359e-06, 'epoch': 5.78} +{'loss': 0.547, 'learning_rate': 2.8036681503727142e-06, 'epoch': 5.83} +{'loss': 0.5447, 'learning_rate': 2.7500402209470694e-06, 'epoch': 5.87} +{'loss': 0.5418, 'learning_rate': 2.6964122915214245e-06, 'epoch': 5.91} +{'loss': 0.5482, 'learning_rate': 2.64278436209578e-06, 'epoch': 5.95} +{'loss': 0.5434, 'learning_rate': 2.5891564326701344e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [1:47:17<13:54, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.6524204611778259, 'eval_accuracy': 0.6486563825082594, 'eval_f1': 0.6454793895962887, 'eval_matthews_correlation': 0.29400851164402825, 'eval_precision': 0.6483682475162411, 'eval_recall': 0.6456528036931798, 'eval_runtime': 16.3595, 'eval_samples_per_second': 2349.771, 'eval_steps_per_second': 18.399, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:05:39<17:05, 2.34it/s]***** Running Evaluation ***** +{'loss': 0.5324, 'learning_rate': 2.53552850324449e-06, 'epoch': 6.03} +{'loss': 0.5206, 'learning_rate': 2.481900573818845e-06, 'epoch': 6.08} +{'loss': 0.522, 'learning_rate': 2.4282726443932e-06, 'epoch': 6.12} +{'loss': 0.5271, 'learning_rate': 2.3746447149675555e-06, 'epoch': 6.16} +{'loss': 0.522, 'learning_rate': 2.3210167855419106e-06, 'epoch': 6.2} +{'loss': 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'eval_precision': 0.6445904068864807, 'eval_recall': 0.6422052388400994, 'eval_runtime': 40.8584, 'eval_samples_per_second': 940.834, 'eval_steps_per_second': 7.367, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [2:25:06<00:00, 2.13it/s]***** Running Evaluation ***** +{'loss': 0.5066, 'learning_rate': 1.2489944763232692e-06, 'epoch': 7.03} +{'loss': 0.5142, 'learning_rate': 1.1953665468976245e-06, 'epoch': 7.07} +{'loss': 0.5095, 'learning_rate': 1.142274896766236e-06, 'epoch': 7.12} +{'loss': 0.5088, 'learning_rate': 1.0886469673405912e-06, 'epoch': 7.16} +{'loss': 0.4981, 'learning_rate': 1.035019037914946e-06, 'epoch': 7.2} +{'loss': 0.5101, 'learning_rate': 9.813911084893013e-07, 'epoch': 7.24} +{'loss': 0.5159, 'learning_rate': 9.277631790636564e-07, 'epoch': 7.28} +{'loss': 0.4996, 'learning_rate': 8.741352496380115e-07, 'epoch': 7.32} +{'loss': 0.5084, 'learning_rate': 8.205073202123667e-07, 'epoch': 7.37} +{'loss': 0.5109, 'learning_rate': 7.668793907867219e-07, 'epoch': 7.41} +{'loss': 0.5038, 'learning_rate': 7.132514613610769e-07, 'epoch': 7.45} +{'loss': 0.501, 'learning_rate': 6.59623531935432e-07, 'epoch': 7.49} +{'loss': 0.5067, 'learning_rate': 6.059956025097871e-07, 'epoch': 7.53} +{'loss': 0.5053, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.6943593621253967, 'eval_accuracy': 0.6437917848130902, 'eval_f1': 0.6402728756398669, 'eval_matthews_correlation': 0.28413167476904966, 'eval_precision': 0.6435669980945109, 'eval_recall': 0.6405803730637307, 'eval_runtime': 40.8298, 'eval_samples_per_second': 941.494, 'eval_steps_per_second': 7.372, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209 (score: 0.649378329259793). +100%|██████████| 19224/19224 [2:25:48<00:00, 2.13it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 8748.7441, 'train_samples_per_second': 281.21, 'train_steps_per_second': 2.197, 'train_loss': 0.5738594784024255, 'epoch': 8.0} +100%|██████████| 19224/19224 [2:25:48<00:00, 2.20it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:53<00:00, 5.64it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_152412-l2w580i0/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_152412-l2w580i0/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260305_152412-l2w580i0/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 +nvidia-nccl-cu12==2.27.3 +debugpy==1.8.16 +ipython==8.18.1 +anyio==4.12.0 +prompt_toolkit==3.0.51 +mkl_fft==1.3.11 +httpcore==1.0.9 +Jinja2==3.1.6 +ply==3.11 +zipp==3.23.0 +setproctitle==1.3.6 +docker-pycreds==0.4.0 +nvidia-cuda-nvrtc-cu12==12.8.93 +urllib3==2.5.0 +kiwisolver==1.4.4 +nvidia-curand-cu12==10.3.9.90 +llvmlite==0.43.0 +six==1.17.0 +frozenlist==1.8.0 +wcwidth==0.2.13 +numexpr==2.10.1 +click==8.1.8 +multiprocess==0.70.18 +threadpoolctl==3.6.0 +typing_extensions==4.15.0 +decorator==5.2.1 +sip==6.7.12 +pure_eval==0.2.3 +async-timeout==5.0.1 +Pygments==2.19.2 +mkl-service==2.4.0 +transformers==4.35.2 +numba==0.60.0 +pyzmq==27.0.2 +mkl_random==1.2.8 +ptyprocess==0.7.0 +nvidia-cuda-cupti-cu12==12.8.90 +charset-normalizer==3.4.4 +nvidia-cublas-cu12==12.8.4.1 +PyQt5_sip==12.13.0 +Bottleneck==1.4.2 +networkx==3.2.1 +PySocks==1.7.1 +pysam==0.9.1 +tornado==6.5.2 +pandas==2.3.3 +smmap==5.0.2 +PyQt5==5.15.10 +nvidia-cufft-cu12==11.3.3.83 +safetensors==0.7.0 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.01" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.06" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "557709062144" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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50%|█████ | 7209/14418 [1:11:03<1:04:00, 1.88it/s]***** Running Evaluation ***** +{'loss': 0.3204, 'learning_rate': 7.02331759149941e-06, 'epoch': 2.04} +{'loss': 0.3292, 'learning_rate': 6.9495277449822905e-06, 'epoch': 2.08} +{'loss': 0.3186, 'learning_rate': 6.875737898465171e-06, 'epoch': 2.12} +{'loss': 0.3184, 'learning_rate': 6.801948051948053e-06, 'epoch': 2.16} +{'loss': 0.3169, 'learning_rate': 6.728158205430933e-06, 'epoch': 2.21} +{'loss': 0.3241, 'learning_rate': 6.654368358913814e-06, 'epoch': 2.25} +{'loss': 0.3221, 'learning_rate': 6.5805785123966945e-06, 'epoch': 2.29} +{'loss': 0.3239, 'learning_rate': 6.506788665879575e-06, 'epoch': 2.33} +{'loss': 0.3229, 'learning_rate': 6.432998819362456e-06, 'epoch': 2.37} +{'loss': 0.3178, 'learning_rate': 6.359208972845336e-06, 'epoch': 2.41} +{'loss': 0.3219, 'learning_rate': 6.285419126328219e-06, 'epoch': 2.46} +{'loss': 0.321, 'learning_rate': 6.211629279811099e-06, 'epoch': 2.5} +{'loss': 0.3229, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33755555748939514, 'eval_accuracy': 0.8707890013267084, 'eval_f1': 0.6942504227325976, 'eval_matthews_correlation': 0.41086901038523405, 'eval_precision': 0.7570740503585687, 'eval_recall': 0.6641680125429614, 'eval_runtime': 39.8835, 'eval_samples_per_second': 963.832, 'eval_steps_per_second': 7.547, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:36:39<46:27, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.3051, 'learning_rate': 5.252361275088548e-06, 'epoch': 3.04} +{'loss': 0.3092, 'learning_rate': 5.1785714285714296e-06, 'epoch': 3.08} +{'loss': 0.3018, 'learning_rate': 5.10478158205431e-06, 'epoch': 3.12} +{'loss': 0.309, 'learning_rate': 5.030991735537191e-06, 'epoch': 3.16} +{'loss': 0.3036, 'learning_rate': 4.957201889020071e-06, 'epoch': 3.2} +{'loss': 0.2965, 'learning_rate': 4.883412042502952e-06, 'epoch': 3.25} +{'loss': 0.3136, 'learning_rate': 4.809622195985833e-06, 'epoch': 3.29} +{'loss': 0.2946, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-9612/special_tokens_map.json + 83%|████████▎ | 12015/14418 [2:02:45<23:13, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.2974, 'learning_rate': 3.482142857142857e-06, 'epoch': 4.04} +{'loss': 0.2943, 'learning_rate': 3.4083530106257382e-06, 'epoch': 4.08} +{'loss': 0.3012, 'learning_rate': 3.334563164108619e-06, 'epoch': 4.12} +{'loss': 0.2894, 'learning_rate': 3.2607733175914995e-06, 'epoch': 4.16} +{'loss': 0.2808, 'learning_rate': 3.1877213695395514e-06, 'epoch': 4.2} +{'loss': 0.2969, 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'eval_recall': 0.6523970770459596, 'eval_runtime': 42.102, 'eval_samples_per_second': 913.045, 'eval_steps_per_second': 7.149, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:29:07<00:00, 1.68it/s]***** Running Evaluation ***** +{'loss': 0.267, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35707855224609375, 'eval_accuracy': 0.862516583855779, 'eval_f1': 0.6840809907431797, 'eval_matthews_correlation': 0.3833010869829014, 'eval_precision': 0.7304690214880062, 'eval_recall': 0.6593703595538539, 'eval_runtime': 41.8749, 'eval_samples_per_second': 917.996, 'eval_steps_per_second': 7.188, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209 (score: 0.6942504227325976). +100%|██████████| 14418/14418 [2:29:51<00:00, 1.68it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 8991.0603, 'train_samples_per_second': 205.223, 'train_steps_per_second': 1.604, 'train_loss': 0.3148110338513473, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:29:51<00:00, 1.60it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:09<00:00, 4.36it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_171152-ht7c7u2r/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_171152-ht7c7u2r/files/requirements.txt new file mode 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+{'loss': 0.6198, 'learning_rate': 8.50744347676863e-06, 'epoch': 1.75} +{'loss': 0.6155, 'learning_rate': 8.46454159337595e-06, 'epoch': 1.79} +{'loss': 0.6209, 'learning_rate': 8.42163970998327e-06, 'epoch': 1.83} +{'loss': 0.6152, 'learning_rate': 8.378737826590588e-06, 'epoch': 1.87} +{'loss': 0.6179, 'learning_rate': 8.335835943197907e-06, 'epoch': 1.91} +{'loss': 0.614, 'learning_rate': 8.292934059805227e-06, 'epoch': 1.96} +{'loss': 0.6147, 'learning_rate': 8.250032176412546e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [52:12<2:56:28, 1.82Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 0.6223277449607849, 'eval_accuracy': 0.651075674410135, 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args.save_total_limit + 30%|███ | 7209/24030 [1:17:33<2:41:16, 1.74it/s]***** Running Evaluation ***** +{'loss': 0.6038, 'learning_rate': 8.207130293019864e-06, 'epoch': 2.04} +{'loss': 0.6015, 'learning_rate': 8.164228409627184e-06, 'epoch': 2.08} +{'loss': 0.5992, 'learning_rate': 8.121326526234501e-06, 'epoch': 2.12} +{'loss': 0.6043, 'learning_rate': 8.078424642841821e-06, 'epoch': 2.16} +{'loss': 0.6038, 'learning_rate': 8.03552275944914e-06, 'epoch': 2.21} +{'loss': 0.5972, 'learning_rate': 7.99262087605646e-06, 'epoch': 2.25} +{'loss': 0.6018, 'learning_rate': 7.949718992663778e-06, 'epoch': 2.29} +{'loss': 0.6074, 'learning_rate': 7.906817109271098e-06, 'epoch': 2.33} +{'loss': 0.6031, 'learning_rate': 7.863915225878417e-06, 'epoch': 2.37} +{'loss': 0.6004, 'learning_rate': 7.821013342485737e-06, 'epoch': 2.41} +{'loss': 0.6072, 'learning_rate': 7.778111459093054e-06, 'epoch': 2.46} +{'loss': 0.607, 'learning_rate': 7.735209575700374e-06, 'epoch': 2.5} +{'loss': 0.6012, 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.6152486801147461, 'eval_accuracy': 0.65560209151687, 'eval_f1': 0.6533242209418757, 'eval_matthews_correlation': 0.3082321226860727, 'eval_precision': 0.6549904109832433, 'eval_recall': 0.6532466441840614, 'eval_runtime': 56.557, 'eval_samples_per_second': 679.685, 'eval_steps_per_second': 5.322, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:44:04<2:10:07, 1.85it/s]***** Running Evaluation ***** +{'loss': 0.5872, 'learning_rate': 7.177914110429448e-06, 'epoch': 3.04} +{'loss': 0.5902, 'learning_rate': 7.135012227036767e-06, 'epoch': 3.08} +{'loss': 0.5864, 'learning_rate': 7.0921103436440866e-06, 'epoch': 3.12} +{'loss': 0.5895, 'learning_rate': 7.049208460251405e-06, 'epoch': 3.16} +{'loss': 0.5822, 'learning_rate': 7.006306576858725e-06, 'epoch': 3.2} +{'loss': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [2:29:30<1:21:03, 1.98it/s]***** Running Evaluation ***** +{'loss': 0.5345, 'learning_rate': 5.119481745248617e-06, 'epoch': 5.04} +{'loss': 0.5395, 'learning_rate': 5.077008880689863e-06, 'epoch': 5.08} +{'loss': 0.5358, 'learning_rate': 5.034106997297181e-06, 'epoch': 5.12} +{'loss': 0.5292, 'learning_rate': 4.991205113904501e-06, 'epoch': 5.16} +{'loss': 0.5311, 'learning_rate': 4.94830323051182e-06, 'epoch': 5.2} +{'loss': 0.533, 'learning_rate': 4.905401347119139e-06, 'epoch': 5.24} +{'loss': 0.5248, 'learning_rate': 4.862499463726458e-06, 'epoch': 5.29} +{'loss': 0.5355, 'learning_rate': 4.819597580333777e-06, 'epoch': 5.33} +{'loss': 0.5409, 'learning_rate': 4.776695696941096e-06, 'epoch': 5.37} +{'loss': 0.5322, 'learning_rate': 4.7337938135484155e-06, 'epoch': 5.41} +{'loss': 0.5336, 'learning_rate': 4.690891930155734e-06, 'epoch': 5.45} +{'loss': 0.5351, 'learning_rate': 4.647990046763054e-06, 'epoch': 5.49} +{'loss': 0.5363, 'learning_rate': 4.6050881633703725e-06, 'epoch': 5.53} +{'loss': 0.5373, 'learning_rate': 4.562186279977691e-06, 'epoch': 5.58} +{'loss': 0.5371, 'learning_rate': 4.51928439658501e-06, 'epoch': 5.62} +{'loss': 0.5324, 'learning_rate': 4.4763825131923294e-06, 'epoch': 5.66} +{'loss': 0.5315, 'learning_rate': 4.433480629799648e-06, 'epoch': 5.7} +{'loss': 0.538, 'learning_rate': 4.390578746406968e-06, 'epoch': 5.74} +{'loss': 0.5417, 'learning_rate': 4.347676863014286e-06, 'epoch': 5.78} +{'loss': 0.5373, 'learning_rate': 4.304774979621606e-06, 'epoch': 5.83} +{'loss': 0.5347, 'learning_rate': 4.261873096228925e-06, 'epoch': 5.87} +{'loss': 0.5322, 'learning_rate': 4.218971212836243e-06, 'epoch': 5.91} +{'loss': 0.5384, 'learning_rate': 4.17649834827749e-06, 'epoch': 5.95} +{'loss': 0.5341, 'learning_rate': 4.1335964648848085e-06, 'epoch': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:52:53<1:02:44, 1.92it/s]***** Running Evaluation ***** +{'loss': 0.514, 'learning_rate': 4.090694581492128e-06, 'epoch': 6.03} +{'loss': 0.5079, 'learning_rate': 4.047792698099447e-06, 'epoch': 6.08} +{'loss': 0.504, 'learning_rate': 4.004890814706766e-06, 'epoch': 6.12} +{'loss': 0.5087, 'learning_rate': 3.961988931314085e-06, 'epoch': 6.16} +{'loss': 0.5096, 'learning_rate': 3.919087047921404e-06, 'epoch': 6.2} +{'loss': 0.49, 'learning_rate': 3.876185164528723e-06, 'epoch': 6.24} +{'loss': 0.5072, 'learning_rate': 3.833283281136042e-06, 'epoch': 6.28} +{'loss': 0.5075, 'learning_rate': 3.790381397743361e-06, 'epoch': 6.33} +{'loss': 0.5149, 'learning_rate': 3.7474795143506802e-06, 'epoch': 6.37} +{'loss': 0.5074, 'learning_rate': 3.7045776309579994e-06, 'epoch': 6.41} +{'loss': 0.5043, 'learning_rate': 3.6616757475653185e-06, 'epoch': 6.45} +{'loss': 0.509, 'learning_rate': 3.618773864172637e-06, 'epoch': 6.49} +{'loss': 0.517, 'learning_rate': 3.5758719807799563e-06, 'epoch': 6.53} +{'loss': 0.5065, 'learning_rate': 3.5329700973872755e-06, 'epoch': 6.58} +{'loss': 0.514, 'learning_rate': 3.4900682139945946e-06, 'epoch': 6.62} +{'loss': 0.4976, 'learning_rate': 3.4471663306019137e-06, 'epoch': 6.66} +{'loss': 0.5128, 'learning_rate': 3.404264447209233e-06, 'epoch': 6.7} +{'loss': 0.5056, 'learning_rate': 3.361362563816552e-06, 'epoch': 6.74} +{'loss': 0.5053, 'learning_rate': 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0.648404175357193, 'eval_recall': 0.6423686094994967, 'eval_runtime': 47.4459, 'eval_samples_per_second': 810.207, 'eval_steps_per_second': 6.344, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:16:06<39:28, 2.03it/s]***** Running Evaluation ***** +{'loss': 0.4796, 'learning_rate': 3.0614783989017123e-06, 'epoch': 7.03} +{'loss': 0.4891, 'learning_rate': 3.0185765155090315e-06, 'epoch': 7.07} +{'loss': 0.488, 'learning_rate': 2.9756746321163498e-06, 'epoch': 7.12} +{'loss': 0.4825, 'learning_rate': 2.932772748723669e-06, 'epoch': 7.16} +{'loss': 0.4765, 'learning_rate': 2.889870865330988e-06, 'epoch': 7.2} +{'loss': 0.481, 'learning_rate': 2.846968981938307e-06, 'epoch': 7.24} +{'loss': 0.4873, 'learning_rate': 2.8040670985456263e-06, 'epoch': 7.28} +{'loss': 0.478, 'learning_rate': 2.7611652151529454e-06, 'epoch': 7.32} +{'loss': 0.4875, 'learning_rate': 2.7182633317602645e-06, 'epoch': 7.37} +{'loss': 0.4847, 'learning_rate': 2.6753614483675837e-06, 'epoch': 7.41} +{'loss': 0.4827, 'learning_rate': 2.6324595649749024e-06, 'epoch': 7.45} +{'loss': 0.4881, 'learning_rate': 2.5895576815822215e-06, 'epoch': 7.49} +{'loss': 0.4818, 'learning_rate': 2.5466557981895406e-06, 'epoch': 7.53} +{'loss': 0.4791, 'learning_rate': 2.5037539147968598e-06, 'epoch': 7.57} +{'loss': 0.4851, 'learning_rate': 2.460852031404179e-06, 'epoch': 7.62} +{'loss': 0.4831, 'learning_rate': 2.4179501480114976e-06, 'epoch': 7.66} +{'loss': 0.4871, 'learning_rate': 2.3750482646188167e-06, 'epoch': 7.7} +{'loss': 0.4808, 'learning_rate': 2.3325754000600627e-06, 'epoch': 7.74} +{'loss': 0.4817, 'learning_rate': 2.289673516667382e-06, 'epoch': 7.78} +{'loss': 0.4917, 'learning_rate': 2.246771633274701e-06, 'epoch': 7.82} +{'loss': 0.4844, 'learning_rate': 2.20386974988202e-06, 'epoch': 7.87} +{'loss': 0.4841, 'learning_rate': 2.1609678664893392e-06, 'epoch': 7.91} +{'loss': 0.4813, 'learning_rate': 2.1180659830966584e-06, 'epoch': 7.95} +{'loss': 0.4755, 'learning_rate': 2.075164099703977e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:16:52<39:28, 2.0Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.7181257605552673, 'eval_accuracy': 0.6413464790197966, 'eval_f1': 0.6373287977985882, 'eval_matthews_correlation': 0.2791543424794894, 'eval_precision': 0.641341971114533, 'eval_recall': 0.6378344067064299, 'eval_runtime': 46.672, 'eval_samples_per_second': 823.641, 'eval_steps_per_second': 6.449, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:39:29<19:09, 2.09it/s]***** Running Evaluation ***** +{'loss': 0.4719, 'learning_rate': 2.032262216311296e-06, 'epoch': 8.03} +{'loss': 0.454, 'learning_rate': 1.9893603329186153e-06, 'epoch': 8.07} +{'loss': 0.4522, 'learning_rate': 1.946458449525934e-06, 'epoch': 8.11} +{'loss': 0.4524, 'learning_rate': 1.9035565661332534e-06, 'epoch': 8.16} +{'loss': 0.4637, 'learning_rate': 1.8606546827405725e-06, 'epoch': 8.2} +{'loss': 0.4672, 'learning_rate': 1.8177527993478916e-06, 'epoch': 8.24} +{'loss': 0.463, 'learning_rate': 1.7748509159552106e-06, 'epoch': 8.28} +{'loss': 0.4665, 'learning_rate': 1.7319490325625297e-06, 'epoch': 8.32} +{'loss': 0.4595, 'learning_rate': 1.6890471491698488e-06, 'epoch': 8.36} +{'loss': 0.4545, 'learning_rate': 1.646145265777168e-06, 'epoch': 8.41} +{'loss': 0.458, 'learning_rate': 1.6032433823844867e-06, 'epoch': 8.45} +{'loss': 0.4527, 'learning_rate': 1.5603414989918058e-06, 'epoch': 8.49} +{'loss': 0.4652, 'learning_rate': 1.517439615599125e-06, 'epoch': 8.53} +{'loss': 0.4535, 'learning_rate': 1.4745377322064438e-06, 'epoch': 8.57} +{'loss': 0.4591, 'learning_rate': 1.431635848813763e-06, 'epoch': 8.61} +{'loss': 0.4617, 'learning_rate': 1.389162984255009e-06, 'epoch': 8.66} +{'loss': 0.4667, 'learning_rate': 1.346261100862328e-06, 'epoch': 8.7} +{'loss': 0.4733, 'learning_rate': 1.3033592174696468e-06, 'epoch': 8.74} +{'loss': 0.4674, 'learning_rate': 1.260457334076966e-06, 'epoch': 8.78} +{'loss': 0.4598, 'learning_rate': 1.217555450684285e-06, 'epoch': 8.82} +{'loss': 0.4568, 'learning_rate': 1.1746535672916042e-06, 'epoch': 8.86} +{'loss': 0.4663, 'learning_rate': 1.1317516838989233e-06, 'epoch': 8.91} +{'loss': 0.4629, 'learning_rate': 1.0888498005062422e-06, 'epoch': 8.95} +{'loss': 0.4739, 'learning_rate': 1.0459479171135614e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:40:18<19:09, 2.0Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.7433251738548279, 'eval_accuracy': 0.6395775344033714, 'eval_f1': 0.6355481056924646, 'eval_matthews_correlation': 0.2755641229057456, 'eval_precision': 0.6395192716985343, 'eval_recall': 0.6360664819066904, 'eval_runtime': 48.2995, 'eval_samples_per_second': 795.888, 'eval_steps_per_second': 6.232, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [4:02:33<00:00, 2.07it/s]***** Running Evaluation ***** +{'loss': 0.4536, 'learning_rate': 1.0030460337208805e-06, 'epoch': 9.03} +{'loss': 0.4343, 'learning_rate': 9.601441503281996e-07, 'epoch': 9.07} +{'loss': 0.4462, 'learning_rate': 9.172422669355185e-07, 'epoch': 9.11} +{'loss': 0.4372, 'learning_rate': 8.743403835428376e-07, 'epoch': 9.16} +{'loss': 0.4433, 'learning_rate': 8.314385001501567e-07, 'epoch': 9.2} +{'loss': 0.4404, 'learning_rate': 7.885366167574756e-07, 'epoch': 9.24} +{'loss': 0.4504, 'learning_rate': 7.456347333647948e-07, 'epoch': 9.28} +{'loss': 0.4427, 'learning_rate': 7.027328499721138e-07, 'epoch': 9.32} +{'loss': 0.4481, 'learning_rate': 6.598309665794329e-07, 'epoch': 9.36} +{'loss': 0.4576, 'learning_rate': 6.169290831867519e-07, 'epoch': 9.4} +{'loss': 0.4395, 'learning_rate': 5.74027199794071e-07, 'epoch': 9.45} +{'loss': 0.448, 'learning_rate': 5.311253164013901e-07, 'epoch': 9.49} +{'loss': 0.4444, 'learning_rate': 4.882234330087091e-07, 'epoch': 9.53} +{'loss': 0.4426, 'learning_rate': 4.453215496160282e-07, 'epoch': 9.57} +{'loss': 0.4467, 'learning_rate': 4.0241966622334727e-07, 'epoch': 9.61} +{'loss': 0.451, 'learning_rate': 3.5951778283066635e-07, 'epoch': 9.65} +{'loss': 0.4481, 'learning_rate': 3.166158994379853e-07, 'epoch': 9.7} +{'loss': 0.4455, 'learning_rate': 2.737140160453044e-07, 'epoch': 9.74} +{'loss': 0.4546, 'learning_rate': 2.3081213265262347e-07, 'epoch': 9.78} +{'loss': 0.444, 'learning_rate': 1.8791024925994252e-07, 'epoch': 9.82} +{'loss': 0.4396, 'learning_rate': 1.4500836586726157e-07, 'epoch': 9.86} +{'loss': 0.4468, 'learning_rate': 1.0210648247458065e-07, 'epoch': 9.9} +{'loss': 0.4406, 'learning_rate': 5.92045990818997e-08, 'epoch': 9.95} +{'loss': 0.4427, 'learning_rate': 1.6302715689218757e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [4:03:20<00:00, 2.0Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.7710901498794556, 'eval_accuracy': 0.6408262011914362, 'eval_f1': 0.6374160706458294, 'eval_matthews_correlation': 0.27814219387634775, 'eval_precision': 0.6404579241742576, 'eval_recall': 0.6376979626980107, 'eval_runtime': 46.9417, 'eval_samples_per_second': 818.91, 'eval_steps_per_second': 6.412, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209 (score: 0.6533242209418757). +100%|██████████| 24030/24030 [4:03:22<00:00, 2.07it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 14602.4476, 'train_samples_per_second': 210.601, 'train_steps_per_second': 1.646, 'train_loss': 0.5441601090464947, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:03:22<00:00, 1.65it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:57<00:00, 5.21it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_175218-kjpgv2kj/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_175218-kjpgv2kj/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260305_175218-kjpgv2kj/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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b/VASC/len2_5120/wandb/run-20260305_194412-7glccrkd/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['classifier.bias', 'bert.pooler.dense.weight', 'bert.pooler.dense.bias', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 8 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 19,224 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 12%|█▎ | 2403/19224 [18:40<1:58:08, 2.37it/s]***** Running Evaluation ***** +{'loss': 0.6042, 'learning_rate': 8.665511265164646e-07, 'epoch': 0.04} +{'loss': 0.3885, 'learning_rate': 1.7331022530329292e-06, 'epoch': 0.08} +{'loss': 0.3627, 'learning_rate': 2.599653379549394e-06, 'epoch': 0.12} +{'loss': 0.3549, 'learning_rate': 3.4662045060658585e-06, 'epoch': 0.17} +{'loss': 0.3596, 'learning_rate': 4.332755632582323e-06, 'epoch': 0.21} +{'loss': 0.3572, 'learning_rate': 5.199306759098788e-06, 'epoch': 0.25} +{'loss': 0.3581, 'learning_rate': 6.065857885615252e-06, 'epoch': 0.29} +{'loss': 0.3485, 'learning_rate': 6.932409012131717e-06, 'epoch': 0.33} +{'loss': 0.3603, 'learning_rate': 7.79896013864818e-06, 'epoch': 0.37} +{'loss': 0.3568, 'learning_rate': 8.665511265164645e-06, 'epoch': 0.42} +{'loss': 0.3546, 'learning_rate': 9.532062391681109e-06, 'epoch': 0.46} +{'loss': 0.359, 'learning_rate': 9.974543442169342e-06, 'epoch': 0.5} +{'loss': 0.3506, 'learning_rate': 9.919203099059215e-06, 'epoch': 0.54} +{'loss': 0.349, 'learning_rate': 9.863862755949087e-06, 'epoch': 0.58} +{'loss': 0.3563, 'learning_rate': 9.80852241283896e-06, 'epoch': 0.62} +{'loss': 0.3446, 'learning_rate': 9.753182069728832e-06, 'epoch': 0.67} +{'loss': 0.3481, 'learning_rate': 9.697841726618706e-06, 'epoch': 0.71} +{'loss': 0.342, 'learning_rate': 9.642501383508579e-06, 'epoch': 0.75} +{'loss': 0.3531, 'learning_rate': 9.587161040398452e-06, 'epoch': 0.79} +{'loss': 0.3456, 'learning_rate': 9.531820697288324e-06, 'epoch': 0.83} +{'loss': 0.3267, 'learning_rate': 9.476480354178197e-06, 'epoch': 0.87} +{'loss': 0.3354, 'learning_rate': 9.421140011068069e-06, 'epoch': 0.92} +{'loss': 0.3465, 'learning_rate': 9.365799667957943e-06, 'epoch': 0.96} +{'loss': 0.3469, 'learning_rate': 9.310459324847814e-06, 'epoch': 1.0} + Num examples = 38441 + Batch size = 128 + 12%|█▎ | 2403/19224 [19:12<1:58:08, 2.37Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-2403 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-2403/config.json +{'eval_loss': 0.3401157855987549, 'eval_accuracy': 0.8739626960797066, 'eval_f1': 0.6681251426140954, 'eval_matthews_correlation': 0.39299627336960347, 'eval_precision': 0.791338502357383, 'eval_recall': 0.6325314622275175, 'eval_runtime': 31.9568, 'eval_samples_per_second': 1202.905, 'eval_steps_per_second': 9.419, 'epoch': 1.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-2403/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-2403/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-2403/special_tokens_map.json + 25%|██▌ | 4806/19224 [37:44<1:39:04, 2.43it/s]***** Running Evaluation ***** +{'loss': 0.3374, 'learning_rate': 9.255118981737688e-06, 'epoch': 1.04} +{'loss': 0.343, 'learning_rate': 9.19977863862756e-06, 'epoch': 1.08} +{'loss': 0.3374, 'learning_rate': 9.144438295517433e-06, 'epoch': 1.12} +{'loss': 0.3295, 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+{'loss': 0.3321, 'learning_rate': 8.314333148865523e-06, 'epoch': 1.75} +{'loss': 0.3451, 'learning_rate': 8.258992805755395e-06, 'epoch': 1.79} +{'loss': 0.3391, 'learning_rate': 8.20365246264527e-06, 'epoch': 1.83} +{'loss': 0.3344, 'learning_rate': 8.148312119535142e-06, 'epoch': 1.87} +{'loss': 0.3342, 'learning_rate': 8.092971776425015e-06, 'epoch': 1.91} +{'loss': 0.3296, 'learning_rate': 8.037631433314887e-06, 'epoch': 1.96} +{'loss': 0.3239, 'learning_rate': 7.98229109020476e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 25%|██▌ | 4806/19224 [38:15<1:39:04, 2.43Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-4806/config.json +{'eval_loss': 0.33811965584754944, 'eval_accuracy': 0.8741708072110507, 'eval_f1': 0.676395627538732, 'eval_matthews_correlation': 0.40066141716002196, 'eval_precision': 0.7849614976650936, 'eval_recall': 0.6408344394909646, 'eval_runtime': 31.3704, 'eval_samples_per_second': 1225.392, 'eval_steps_per_second': 9.595, 'epoch': 2.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-4806/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-4806/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-4806/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-2403] due to args.save_total_limit + 38%|███▊ | 7209/19224 [56:46<1:25:12, 2.35it/s]***** Running Evaluation ***** +{'loss': 0.3217, 'learning_rate': 7.926950747094632e-06, 'epoch': 2.04} +{'loss': 0.3299, 'learning_rate': 7.871610403984505e-06, 'epoch': 2.08} +{'loss': 0.3214, 'learning_rate': 7.816270060874379e-06, 'epoch': 2.12} +{'loss': 0.3175, 'learning_rate': 7.76092971776425e-06, 'epoch': 2.16} +{'loss': 0.3186, 'learning_rate': 7.705589374654124e-06, 'epoch': 2.21} +{'loss': 0.3231, 'learning_rate': 7.650249031543996e-06, 'epoch': 2.25} +{'loss': 0.3195, 'learning_rate': 7.594908688433868e-06, 'epoch': 2.29} +{'loss': 0.3235, 'learning_rate': 7.5395683453237415e-06, 'epoch': 2.33} +{'loss': 0.3225, 'learning_rate': 7.484228002213614e-06, 'epoch': 2.37} +{'loss': 0.318, 'learning_rate': 7.4288876591034875e-06, 'epoch': 2.41} +{'loss': 0.3244, 'learning_rate': 7.37354731599336e-06, 'epoch': 2.46} +{'loss': 0.3238, 'learning_rate': 7.3182069728832326e-06, 'epoch': 2.5} +{'loss': 0.3246, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33617863059043884, 'eval_accuracy': 0.8739366821882886, 'eval_f1': 0.6959037379886726, 'eval_matthews_correlation': 0.41956944617188524, 'eval_precision': 0.7698254420854092, 'eval_recall': 0.6631040783259979, 'eval_runtime': 31.6115, 'eval_samples_per_second': 1216.043, 'eval_steps_per_second': 9.522, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:15:47<1:06:21, 2.41it/s]***** Running Evaluation ***** +{'loss': 0.3034, 'learning_rate': 6.599335915882678e-06, 'epoch': 3.04} +{'loss': 0.3073, 'learning_rate': 6.543995572772552e-06, 'epoch': 3.08} +{'loss': 0.3014, 'learning_rate': 6.488655229662424e-06, 'epoch': 3.12} +{'loss': 0.3075, 'learning_rate': 6.4333148865522976e-06, 'epoch': 3.16} +{'loss': 0.3047, 'learning_rate': 6.37797454344217e-06, 'epoch': 3.2} +{'loss': 0.295, 'learning_rate': 6.322634200332043e-06, 'epoch': 3.25} +{'loss': 0.3137, 'learning_rate': 6.267293857221915e-06, 'epoch': 3.29} +{'loss': 0.2975, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [1:34:44<50:32, 2.38it/s]***** Running Evaluation ***** +{'loss': 0.2944, 'learning_rate': 5.271721084670725e-06, 'epoch': 4.04} +{'loss': 0.2866, 'learning_rate': 5.216380741560599e-06, 'epoch': 4.08} +{'loss': 0.2956, 'learning_rate': 5.161040398450471e-06, 'epoch': 4.12} +{'loss': 0.2843, 'learning_rate': 5.105700055340344e-06, 'epoch': 4.16} +{'loss': 0.2776, 'learning_rate': 5.050359712230216e-06, 'epoch': 4.2} +{'loss': 0.294, 'learning_rate': 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'eval_runtime': 31.5579, 'eval_samples_per_second': 1218.11, 'eval_steps_per_second': 9.538, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [1:54:15<33:20, 2.40it/s]***** Running Evaluation ***** +{'loss': 0.2606, 'learning_rate': 3.9435528500276705e-06, 'epoch': 5.04} +{'loss': 0.2713, 'learning_rate': 3.888212506917543e-06, 'epoch': 5.08} +{'loss': 0.2634, 'learning_rate': 3.832872163807416e-06, 'epoch': 5.12} +{'loss': 0.2733, 'learning_rate': 3.777531820697289e-06, 'epoch': 5.16} +{'loss': 0.2722, 'learning_rate': 3.7221914775871616e-06, 'epoch': 5.2} +{'loss': 0.2663, 'learning_rate': 3.666851134477034e-06, 'epoch': 5.24} +{'loss': 0.2606, 'learning_rate': 3.6115107913669066e-06, 'epoch': 5.29} +{'loss': 0.2629, 'learning_rate': 3.556170448256779e-06, 'epoch': 5.33} +{'loss': 0.2718, 'learning_rate': 3.500830105146652e-06, 'epoch': 5.37} +{'loss': 0.2715, 'learning_rate': 3.4454897620365247e-06, 'epoch': 5.41} +{'loss': 0.2734, 'learning_rate': 3.3901494189263977e-06, 'epoch': 5.45} +{'loss': 0.2685, 'learning_rate': 3.3348090758162706e-06, 'epoch': 5.49} +{'loss': 0.2725, 'learning_rate': 3.280022136137244e-06, 'epoch': 5.53} +{'loss': 0.2715, 'learning_rate': 3.2246817930271166e-06, 'epoch': 5.58} +{'loss': 0.2592, 'learning_rate': 3.16934144991699e-06, 'epoch': 5.62} +{'loss': 0.278, 'learning_rate': 3.1140011068068626e-06, 'epoch': 5.66} +{'loss': 0.2767, 'learning_rate': 3.058660763696735e-06, 'epoch': 5.7} +{'loss': 0.266, 'learning_rate': 3.003320420586608e-06, 'epoch': 5.74} +{'loss': 0.2662, 'learning_rate': 2.9479800774764806e-06, 'epoch': 5.78} +{'loss': 0.2619, 'learning_rate': 2.892639734366353e-06, 'epoch': 5.83} +{'loss': 0.2746, 'learning_rate': 2.8372993912562257e-06, 'epoch': 5.87} +{'loss': 0.2653, 'learning_rate': 2.781959048146099e-06, 'epoch': 5.91} +{'loss': 0.2693, 'learning_rate': 2.7266187050359716e-06, 'epoch': 5.95} +{'loss': 0.2712, 'learning_rate': 2.671278361925844e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [1:54:47<33:20, 2.4Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3597162663936615, 'eval_accuracy': 0.8638432923180979, 'eval_f1': 0.6738705639550554, 'eval_matthews_correlation': 0.37173841714526074, 'eval_precision': 0.7366332357154844, 'eval_recall': 0.6459953949028273, 'eval_runtime': 31.7013, 'eval_samples_per_second': 1212.602, 'eval_steps_per_second': 9.495, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:12:45<07:02, 5.69it/s]***** Running Evaluation ***** +{'loss': 0.257, 'learning_rate': 2.6159380188157167e-06, 'epoch': 6.03} +{'loss': 0.2538, 'learning_rate': 2.5605976757055893e-06, 'epoch': 6.08} +{'loss': 0.2417, 'learning_rate': 2.5052573325954622e-06, 'epoch': 6.12} +{'loss': 0.2562, 'learning_rate': 2.449916989485335e-06, 'epoch': 6.16} +{'loss': 0.2531, 'learning_rate': 2.3945766463752078e-06, 'epoch': 6.2} +{'loss': 0.2505, 'learning_rate': 2.3392363032650807e-06, 'epoch': 6.24} +{'loss': 0.2465, 'learning_rate': 2.2838959601549533e-06, 'epoch': 6.28} +{'loss': 0.2523, 'learning_rate': 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+{'loss': 0.2498, 'learning_rate': 1.454344216934145e-06, 'epoch': 6.91} +{'loss': 0.2486, 'learning_rate': 1.3990038738240178e-06, 'epoch': 6.95} +{'loss': 0.2452, 'learning_rate': 1.3436635307138906e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [2:12:58<07:02, 5.6Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3837572932243347, 'eval_accuracy': 0.8578340834005359, 'eval_f1': 0.6797418041051133, 'eval_matthews_correlation': 0.3708059919185529, 'eval_precision': 0.7173119235260468, 'eval_recall': 0.65817940568068, 'eval_runtime': 12.8925, 'eval_samples_per_second': 2981.654, 'eval_steps_per_second': 23.347, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [2:30:23<00:00, 2.44it/s]***** Running Evaluation ***** +{'loss': 0.2366, 'learning_rate': 1.2883231876037633e-06, 'epoch': 7.03} +{'loss': 0.2324, 'learning_rate': 1.2329828444936359e-06, 'epoch': 7.07} +{'loss': 0.2267, 'learning_rate': 1.1776425013835086e-06, 'epoch': 7.12} +{'loss': 0.2397, 'learning_rate': 1.1223021582733814e-06, 'epoch': 7.16} +{'loss': 0.2279, 'learning_rate': 1.0669618151632542e-06, 'epoch': 7.2} +{'loss': 0.2387, 'learning_rate': 1.011621472053127e-06, 'epoch': 7.24} +{'loss': 0.2336, 'learning_rate': 9.568345323741008e-07, 'epoch': 7.28} +{'loss': 0.2343, 'learning_rate': 9.014941892639735e-07, 'epoch': 7.32} +{'loss': 0.2409, 'learning_rate': 8.461538461538463e-07, 'epoch': 7.37} +{'loss': 0.2256, 'learning_rate': 7.908135030437189e-07, 'epoch': 7.41} +{'loss': 0.2282, 'learning_rate': 7.354731599335917e-07, 'epoch': 7.45} +{'loss': 0.233, 'learning_rate': 6.801328168234643e-07, 'epoch': 7.49} +{'loss': 0.24, 'learning_rate': 6.247924737133371e-07, 'epoch': 7.53} +{'loss': 0.2404, 'learning_rate': 5.694521306032098e-07, 'epoch': 7.57} +{'loss': 0.2435, 'learning_rate': 5.141117874930825e-07, 'epoch': 7.62} +{'loss': 0.2322, 'learning_rate': 4.587714443829552e-07, 'epoch': 7.66} +{'loss': 0.2361, 'learning_rate': 4.034311012728279e-07, 'epoch': 7.7} +{'loss': 0.2392, 'learning_rate': 3.480907581627006e-07, 'epoch': 7.74} +{'loss': 0.2292, 'learning_rate': 2.9275041505257337e-07, 'epoch': 7.78} +{'loss': 0.2414, 'learning_rate': 2.3741007194244607e-07, 'epoch': 7.82} +{'loss': 0.2357, 'learning_rate': 1.8206972883231878e-07, 'epoch': 7.87} +{'loss': 0.238, 'learning_rate': 1.2672938572219148e-07, 'epoch': 7.91} +{'loss': 0.2388, 'learning_rate': 7.138904261206419e-08, 'epoch': 7.95} +{'loss': 0.2287, 'learning_rate': 1.6048699501936912e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [2:30:54<00:00, 2.4Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.39648470282554626, 'eval_accuracy': 0.8567154860695612, 'eval_f1': 0.6779814750667875, 'eval_matthews_correlation': 0.3668341230794449, 'eval_precision': 0.7143446717352311, 'eval_recall': 0.656951969888117, 'eval_runtime': 31.5359, 'eval_samples_per_second': 1218.962, 'eval_steps_per_second': 9.545, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209 (score: 0.6959037379886726). +100%|██████████| 19224/19224 [2:30:56<00:00, 2.44it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 9056.9204, 'train_samples_per_second': 271.641, 'train_steps_per_second': 2.123, 'train_loss': 0.29602202305533815, 'epoch': 8.0} +100%|██████████| 19224/19224 [2:30:57<00:00, 2.12it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:48<00:00, 6.21it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_194412-7glccrkd/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_194412-7glccrkd/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260305_194412-7glccrkd/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 +nvidia-nccl-cu12==2.27.3 +debugpy==1.8.16 +ipython==8.18.1 +anyio==4.12.0 +prompt_toolkit==3.0.51 +mkl_fft==1.3.11 +httpcore==1.0.9 +Jinja2==3.1.6 +ply==3.11 +zipp==3.23.0 +setproctitle==1.3.6 +docker-pycreds==0.4.0 +nvidia-cuda-nvrtc-cu12==12.8.93 +urllib3==2.5.0 +kiwisolver==1.4.4 +nvidia-curand-cu12==10.3.9.90 +llvmlite==0.43.0 +six==1.17.0 +frozenlist==1.8.0 +wcwidth==0.2.13 +numexpr==2.10.1 +click==8.1.8 +multiprocess==0.70.18 +threadpoolctl==3.6.0 +typing_extensions==4.15.0 +decorator==5.2.1 +sip==6.7.12 +pure_eval==0.2.3 +async-timeout==5.0.1 +Pygments==2.19.2 +mkl-service==2.4.0 +transformers==4.35.2 +numba==0.60.0 +pyzmq==27.0.2 +mkl_random==1.2.8 +ptyprocess==0.7.0 +nvidia-cuda-cupti-cu12==12.8.90 +charset-normalizer==3.4.4 +nvidia-cublas-cu12==12.8.4.1 +PyQt5_sip==12.13.0 +Bottleneck==1.4.2 +networkx==3.2.1 +PySocks==1.7.1 +pysam==0.9.1 +tornado==6.5.2 +pandas==2.3.3 +smmap==5.0.2 +PyQt5==5.15.10 +nvidia-cufft-cu12==11.3.3.83 +safetensors==0.7.0 +requests==2.32.5 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.05" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.06" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune_3072 + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "565888729088" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 + host: sn4622116170 + memory: + total: "4316310355968" + os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 + program: /home/n5huang/dna_token/Finetune-screen/train.py + python: CPython 3.9.18 + root: /data/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120 + startedAt: "2026-03-05T21:57:58.915438Z" + writerId: 8itsqh46tcp67vr50vmfj1aeyxi2nm5b + m: + - "1": train/global_step + "6": + - 3 + "7": [] + - "2": '*' + "5": 1 + "6": + - 1 + "7": [] + python_version: 3.9.18 + t: + "1": + - 1 + - 5 + - 11 + - 49 + - 51 + - 53 + - 71 + "2": + - 1 + - 5 + - 11 + - 49 + - 51 + - 53 + - 71 + "3": + - 7 + - 66 + "4": 3.9.18 + "5": 0.23.1 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [1:09:56<1:00:45, 1.98it/s]***** Running Evaluation ***** +{'loss': 0.6032, 'learning_rate': 7.02331759149941e-06, 'epoch': 2.04} +{'loss': 0.6022, 'learning_rate': 6.9495277449822905e-06, 'epoch': 2.08} +{'loss': 0.5986, 'learning_rate': 6.875737898465171e-06, 'epoch': 2.12} +{'loss': 0.6054, 'learning_rate': 6.801948051948053e-06, 'epoch': 2.16} +{'loss': 0.6014, 'learning_rate': 6.728158205430933e-06, 'epoch': 2.21} +{'loss': 0.5977, 'learning_rate': 6.654368358913814e-06, 'epoch': 2.25} +{'loss': 0.6009, 'learning_rate': 6.5805785123966945e-06, 'epoch': 2.29} +{'loss': 0.6066, 'learning_rate': 6.506788665879575e-06, 'epoch': 2.33} +{'loss': 0.601, 'learning_rate': 6.432998819362456e-06, 'epoch': 2.37} +{'loss': 0.5993, 'learning_rate': 6.359208972845336e-06, 'epoch': 2.41} +{'loss': 0.6086, 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Num examples = 38441 + Batch size = 128 + 50%|█████ | 7209/14418 [1:10:49<1:00:45, 1.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.6161000728607178, 'eval_accuracy': 0.6590619390754663, 'eval_f1': 0.6537234719898543, 'eval_matthews_correlation': 0.3155810082300389, 'eval_precision': 0.6609343531243419, 'eval_recall': 0.654708070126179, 'eval_runtime': 52.9903, 'eval_samples_per_second': 725.434, 'eval_steps_per_second': 5.68, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:35:23<43:23, 1.85it/s]***** Running Evaluation ***** +{'loss': 0.5858, 'learning_rate': 5.25309917355372e-06, 'epoch': 3.04} +{'loss': 0.5862, 'learning_rate': 5.1793093270366005e-06, 'epoch': 3.08} +{'loss': 0.5847, 'learning_rate': 5.105519480519481e-06, 'epoch': 3.12} +{'loss': 0.5874, 'learning_rate': 5.031729634002362e-06, 'epoch': 3.16} +{'loss': 0.5826, 'learning_rate': 4.957939787485242e-06, 'epoch': 3.2} +{'loss': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:26:14<00:00, 1.82it/s]***** Running Evaluation ***** +{'loss': 0.5463, 'learning_rate': 1.7126623376623378e-06, 'epoch': 5.04} +{'loss': 0.5512, 'learning_rate': 1.6388724911452187e-06, 'epoch': 5.08} +{'loss': 0.5476, 'learning_rate': 1.5650826446280993e-06, 'epoch': 5.12} +{'loss': 0.542, 'learning_rate': 1.49129279811098e-06, 'epoch': 5.16} +{'loss': 0.543, 'learning_rate': 1.4175029515938607e-06, 'epoch': 5.2} +{'loss': 0.5432, 'learning_rate': 1.3437131050767415e-06, 'epoch': 5.24} +{'loss': 0.5405, 'learning_rate': 1.2699232585596222e-06, 'epoch': 5.29} +{'loss': 0.5452, 'learning_rate': 1.196133412042503e-06, 'epoch': 5.33} +{'loss': 0.546, 'learning_rate': 1.1223435655253838e-06, 'epoch': 5.37} +{'loss': 0.5453, 'learning_rate': 1.0485537190082644e-06, 'epoch': 5.41} +{'loss': 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5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [2:27:10<00:00, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.646594762802124, 'eval_accuracy': 0.6578653000702375, 'eval_f1': 0.6531095278725849, 'eval_matthews_correlation': 0.3129083860409688, 'eval_precision': 0.6591147557225889, 'eval_recall': 0.6538381176687812, 'eval_runtime': 55.9435, 'eval_samples_per_second': 687.14, 'eval_steps_per_second': 5.38, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209 (score: 0.6537234719898543). +100%|██████████| 14418/14418 [2:27:12<00:00, 1.82it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 8832.4625, 'train_samples_per_second': 208.908, 'train_steps_per_second': 1.632, 'train_loss': 0.5920904274373101, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:27:12<00:00, 1.63it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:07<00:00, 4.43it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_215758-igi7bnu4/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_215758-igi7bnu4/files/requirements.txt new file 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+{'loss': 0.3349, 'learning_rate': 8.778997697892687e-06, 'epoch': 1.75} +{'loss': 0.347, 'learning_rate': 8.734726403400036e-06, 'epoch': 1.79} +{'loss': 0.3405, 'learning_rate': 8.690455108907386e-06, 'epoch': 1.83} +{'loss': 0.336, 'learning_rate': 8.646183814414734e-06, 'epoch': 1.87} +{'loss': 0.3359, 'learning_rate': 8.601912519922083e-06, 'epoch': 1.91} +{'loss': 0.3325, 'learning_rate': 8.557641225429433e-06, 'epoch': 1.96} +{'loss': 0.3259, 'learning_rate': 8.51336993093678e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [50:10<2:41:05, 1.99Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 0.3396458625793457, 'eval_accuracy': 0.8745610155823209, 'eval_f1': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33908581733703613, 'eval_accuracy': 0.8725579459431336, 'eval_f1': 0.6885307547641953, 'eval_matthews_correlation': 0.40809757131970154, 'eval_precision': 0.7675727165633044, 'eval_recall': 0.6556059506515837, 'eval_runtime': 40.3702, 'eval_samples_per_second': 952.213, 'eval_steps_per_second': 7.456, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:40:09<2:13:10, 1.80it/s]***** Running Evaluation ***** +{'loss': 0.3102, 'learning_rate': 7.406587568620507e-06, 'epoch': 3.04} +{'loss': 0.3146, 'learning_rate': 7.362316274127856e-06, 'epoch': 3.08} +{'loss': 0.3069, 'learning_rate': 7.318044979635205e-06, 'epoch': 3.12} +{'loss': 0.3147, 'learning_rate': 7.273773685142555e-06, 'epoch': 3.16} +{'loss': 0.3117, 'learning_rate': 7.2295023906499025e-06, 'epoch': 3.2} +{'loss': 0.3026, 'learning_rate': 7.185231096157252e-06, 'epoch': 3.25} +{'loss': 0.32, 'learning_rate': 7.140959801664601e-06, 'epoch': 3.29} +{'loss': 0.3017, 'learning_rate': 7.09668850717195e-06, 'epoch': 3.33} +{'loss': 0.3068, 'learning_rate': 7.052859925624226e-06, 'epoch': 3.37} +{'loss': 0.3109, 'learning_rate': 7.008588631131576e-06, 'epoch': 3.41} +{'loss': 0.3288, 'learning_rate': 6.9643173366389235e-06, 'epoch': 3.45} +{'loss': 0.326, 'learning_rate': 6.920046042146273e-06, 'epoch': 3.5} +{'loss': 0.3092, 'learning_rate': 6.875774747653622e-06, 'epoch': 3.54} +{'loss': 0.3058, 'learning_rate': 6.831503453160971e-06, 'epoch': 3.58} +{'loss': 0.3082, 'learning_rate': 6.78723215866832e-06, 'epoch': 3.62} +{'loss': 0.3187, 'learning_rate': 6.7429608641756695e-06, 'epoch': 3.66} +{'loss': 0.3227, 'learning_rate': 6.698689569683018e-06, 'epoch': 3.7} +{'loss': 0.3122, 'learning_rate': 6.654418275190368e-06, 'epoch': 3.75} +{'loss': 0.3154, 'learning_rate': 6.610146980697716e-06, 'epoch': 3.79} +{'loss': 0.3157, 'learning_rate': 6.565875686205065e-06, 'epoch': 3.83} +{'loss': 0.3188, 'learning_rate': 6.522047104657341e-06, 'epoch': 3.87} +{'loss': 0.3092, 'learning_rate': 6.47777581016469e-06, 'epoch': 3.91} +{'loss': 0.3132, 'learning_rate': 6.433504515672039e-06, 'epoch': 3.95} +{'loss': 0.3145, 'learning_rate': 6.389233221179387e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 40%|████ | 9612/24030 [1:40:49<2:13:10, 1.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-9612/config.json +{'eval_loss': 0.33897697925567627, 'eval_accuracy': 0.8718815847662652, 'eval_f1': 0.6821433596740271, 'eval_matthews_correlation': 0.39950075491568937, 'eval_precision': 0.7680081163341225, 'eval_recall': 0.6488768841791653, 'eval_runtime': 40.1204, 'eval_samples_per_second': 958.141, 'eval_steps_per_second': 7.502, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-9612/special_tokens_map.json + 50%|█████ | 12015/24030 [2:05:24<1:52:23, 1.78it/s]***** Running Evaluation ***** +{'loss': 0.3025, 'learning_rate': 6.344961926686737e-06, 'epoch': 4.04} +{'loss': 0.2995, 'learning_rate': 6.300690632194086e-06, 'epoch': 4.08} +{'loss': 0.3055, 'learning_rate': 6.256419337701435e-06, 'epoch': 4.12} +{'loss': 0.297, 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args.save_total_limit + 60%|██████ | 14418/24030 [2:27:43<1:53:33, 1.41it/s]***** Running Evaluation ***** +{'loss': 0.2678, 'learning_rate': 5.282450858863114e-06, 'epoch': 5.04} +{'loss': 0.2826, 'learning_rate': 5.238179564370463e-06, 'epoch': 5.08} +{'loss': 0.2743, 'learning_rate': 5.193908269877812e-06, 'epoch': 5.12} +{'loss': 0.2765, 'learning_rate': 5.149636975385161e-06, 'epoch': 5.16} +{'loss': 0.2838, 'learning_rate': 5.1053656808925104e-06, 'epoch': 5.2} +{'loss': 0.2749, 'learning_rate': 5.061094386399858e-06, 'epoch': 5.24} +{'loss': 0.2699, 'learning_rate': 5.016823091907208e-06, 'epoch': 5.29} +{'loss': 0.2729, 'learning_rate': 4.972551797414557e-06, 'epoch': 5.33} +{'loss': 0.2827, 'learning_rate': 4.928280502921906e-06, 'epoch': 5.37} +{'loss': 0.281, 'learning_rate': 4.884009208429255e-06, 'epoch': 5.41} +{'loss': 0.2822, 'learning_rate': 4.839737913936604e-06, 'epoch': 5.45} +{'loss': 0.278, 'learning_rate': 4.795466619443953e-06, 'epoch': 5.49} +{'loss': 0.2782, 'learning_rate': 4.751638037896229e-06, 'epoch': 5.53} +{'loss': 0.2789, 'learning_rate': 4.7073667434035775e-06, 'epoch': 5.58} +{'loss': 0.2737, 'learning_rate': 4.663095448910926e-06, 'epoch': 5.62} +{'loss': 0.2913, 'learning_rate': 4.618824154418276e-06, 'epoch': 5.66} +{'loss': 0.2872, 'learning_rate': 4.5745528599256245e-06, 'epoch': 5.7} +{'loss': 0.2758, 'learning_rate': 4.530281565432973e-06, 'epoch': 5.74} +{'loss': 0.2785, 'learning_rate': 4.486010270940323e-06, 'epoch': 5.78} +{'loss': 0.2743, 'learning_rate': 4.4417389764476714e-06, 'epoch': 5.83} +{'loss': 0.2814, 'learning_rate': 4.39746768195502e-06, 'epoch': 5.87} +{'loss': 0.2769, 'learning_rate': 4.35319638746237e-06, 'epoch': 5.91} +{'loss': 0.2809, 'learning_rate': 4.308925092969719e-06, 'epoch': 5.95} +{'loss': 0.2763, 'learning_rate': 4.264653798477068e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [2:28:40<1:53:33, 1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3586450219154358, 'eval_accuracy': 0.8669129315054239, 'eval_f1': 0.6699808773515774, 'eval_matthews_correlation': 0.37361180488781365, 'eval_precision': 0.7504463273050282, 'eval_recall': 0.6393370210830871, 'eval_runtime': 56.5721, 'eval_samples_per_second': 679.504, 'eval_steps_per_second': 5.321, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:52:43<1:06:30, 1.81it/s]***** Running Evaluation ***** +{'loss': 0.2673, 'learning_rate': 4.2203825039844175e-06, 'epoch': 6.03} +{'loss': 0.2629, 'learning_rate': 4.176111209491766e-06, 'epoch': 6.08} +{'loss': 0.2528, 'learning_rate': 4.131839914999115e-06, 'epoch': 6.12} +{'loss': 0.2642, 'learning_rate': 4.0875686205064644e-06, 'epoch': 6.16} +{'loss': 0.2613, 'learning_rate': 4.043297326013813e-06, 'epoch': 6.2} +{'loss': 0.2578, 'learning_rate': 3.999026031521162e-06, 'epoch': 6.24} +{'loss': 0.2603, 'learning_rate': 3.954754737028511e-06, 'epoch': 6.28} +{'loss': 0.258, 'learning_rate': 3.91048344253586e-06, 'epoch': 6.33} +{'loss': 0.2581, 'learning_rate': 3.866654860988136e-06, 'epoch': 6.37} +{'loss': 0.2521, 'learning_rate': 3.8223835664954845e-06, 'epoch': 6.41} +{'loss': 0.2627, 'learning_rate': 3.7781122720028337e-06, 'epoch': 6.45} +{'loss': 0.2561, 'learning_rate': 3.7338409775101824e-06, 'epoch': 6.49} +{'loss': 0.2543, 'learning_rate': 3.6895696830175315e-06, 'epoch': 6.53} +{'loss': 0.2578, 'learning_rate': 3.6452983885248806e-06, 'epoch': 6.58} +{'loss': 0.2544, 'learning_rate': 3.60102709403223e-06, 'epoch': 6.62} +{'loss': 0.2598, 'learning_rate': 3.556755799539579e-06, 'epoch': 6.66} +{'loss': 0.2565, 'learning_rate': 3.512484505046928e-06, 'epoch': 6.7} +{'loss': 0.2522, 'learning_rate': 3.468213210554277e-06, 'epoch': 6.74} +{'loss': 0.2566, 'learning_rate': 3.4239419160616263e-06, 'epoch': 6.78} +{'loss': 0.2725, 'learning_rate': 3.379670621568975e-06, 'epoch': 6.82} +{'loss': 0.2587, 'learning_rate': 3.335399327076324e-06, 'epoch': 6.87} +{'loss': 0.2614, 'learning_rate': 3.2911280325836732e-06, 'epoch': 6.91} +{'loss': 0.2581, 'learning_rate': 3.246856738091022e-06, 'epoch': 6.95} +{'loss': 0.254, 'learning_rate': 3.202585443598371e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [2:53:22<1:06:30, 1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3829362690448761, 'eval_accuracy': 0.8591347779714368, 'eval_f1': 0.6806598157019842, 'eval_matthews_correlation': 0.37376624429027294, 'eval_precision': 0.720819163520416, 'eval_recall': 0.6581624564911684, 'eval_runtime': 39.2263, 'eval_samples_per_second': 979.98, 'eval_steps_per_second': 7.673, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:16:46<40:54, 1.96it/s]***** Running Evaluation ***** +{'loss': 0.2368, 'learning_rate': 3.15831414910572e-06, 'epoch': 7.03} +{'loss': 0.24, 'learning_rate': 3.1140428546130693e-06, 'epoch': 7.07} +{'loss': 0.2291, 'learning_rate': 3.069771560120418e-06, 'epoch': 7.12} +{'loss': 0.2478, 'learning_rate': 3.025500265627767e-06, 'epoch': 7.16} +{'loss': 0.2328, 'learning_rate': 2.9816716840800425e-06, 'epoch': 7.2} +{'loss': 0.2413, 'learning_rate': 2.937400389587392e-06, 'epoch': 7.24} +{'loss': 0.2343, 'learning_rate': 2.893129095094741e-06, 'epoch': 7.28} +{'loss': 0.2373, 'learning_rate': 2.8488578006020903e-06, 'epoch': 7.32} +{'loss': 0.2431, 'learning_rate': 2.804586506109439e-06, 'epoch': 7.37} +{'loss': 0.2298, 'learning_rate': 2.760315211616788e-06, 'epoch': 7.41} +{'loss': 0.2402, 'learning_rate': 2.7160439171241372e-06, 'epoch': 7.45} +{'loss': 0.2385, 'learning_rate': 2.671772622631486e-06, 'epoch': 7.49} +{'loss': 0.2403, 'learning_rate': 2.627501328138835e-06, 'epoch': 7.53} +{'loss': 0.2462, 'learning_rate': 2.583230033646184e-06, 'epoch': 7.57} +{'loss': 0.2494, 'learning_rate': 2.538958739153533e-06, 'epoch': 7.62} +{'loss': 0.2356, 'learning_rate': 2.494687444660882e-06, 'epoch': 7.66} +{'loss': 0.2361, 'learning_rate': 2.450416150168231e-06, 'epoch': 7.7} +{'loss': 0.2418, 'learning_rate': 2.4061448556755803e-06, 'epoch': 7.74} +{'loss': 0.2354, 'learning_rate': 2.361873561182929e-06, 'epoch': 7.78} +{'loss': 0.2429, 'learning_rate': 2.317602266690278e-06, 'epoch': 7.82} +{'loss': 0.2356, 'learning_rate': 2.273330972197627e-06, 'epoch': 7.87} +{'loss': 0.2439, 'learning_rate': 2.2290596777049763e-06, 'epoch': 7.91} +{'loss': 0.2482, 'learning_rate': 2.1847883832123255e-06, 'epoch': 7.95} +{'loss': 0.236, 'learning_rate': 2.1405170887196746e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:17:25<40:54, 1.9Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.40423592925071716, 'eval_accuracy': 0.8560391248926927, 'eval_f1': 0.670527720155867, 'eval_matthews_correlation': 0.35480002938989225, 'eval_precision': 0.7122069070810462, 'eval_recall': 0.6483022661545497, 'eval_runtime': 38.8714, 'eval_samples_per_second': 988.927, 'eval_steps_per_second': 7.743, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:41:00<22:23, 1.79it/s]***** Running Evaluation ***** +{'loss': 0.2175, 'learning_rate': 2.0962457942270233e-06, 'epoch': 8.03} +{'loss': 0.2142, 'learning_rate': 2.0524172126792986e-06, 'epoch': 8.07} +{'loss': 0.2179, 'learning_rate': 2.008145918186648e-06, 'epoch': 8.11} +{'loss': 0.227, 'learning_rate': 1.963874623693997e-06, 'epoch': 8.16} +{'loss': 0.2173, 'learning_rate': 1.919603329201346e-06, 'epoch': 8.2} +{'loss': 0.2265, 'learning_rate': 1.8753320347086951e-06, 'epoch': 8.24} +{'loss': 0.2237, 'learning_rate': 1.831060740216044e-06, 'epoch': 8.28} +{'loss': 0.2228, 'learning_rate': 1.7867894457233932e-06, 'epoch': 8.32} +{'loss': 0.2186, 'learning_rate': 1.742518151230742e-06, 'epoch': 8.36} +{'loss': 0.2237, 'learning_rate': 1.698246856738091e-06, 'epoch': 8.41} +{'loss': 0.2245, 'learning_rate': 1.6539755622454401e-06, 'epoch': 8.45} +{'loss': 0.223, 'learning_rate': 1.609704267752789e-06, 'epoch': 8.49} +{'loss': 0.2199, 'learning_rate': 1.5654329732601384e-06, 'epoch': 8.53} +{'loss': 0.217, 'learning_rate': 1.5211616787674873e-06, 'epoch': 8.57} +{'loss': 0.2242, 'learning_rate': 1.4768903842748364e-06, 'epoch': 8.61} +{'loss': 0.226, 'learning_rate': 1.4326190897821853e-06, 'epoch': 8.66} +{'loss': 0.2258, 'learning_rate': 1.3883477952895345e-06, 'epoch': 8.7} +{'loss': 0.2259, 'learning_rate': 1.3440765007968834e-06, 'epoch': 8.74} +{'loss': 0.2177, 'learning_rate': 1.2998052063042325e-06, 'epoch': 8.78} +{'loss': 0.2199, 'learning_rate': 1.2555339118115814e-06, 'epoch': 8.82} +{'loss': 0.2203, 'learning_rate': 1.2112626173189305e-06, 'epoch': 8.86} +{'loss': 0.2239, 'learning_rate': 1.1669913228262794e-06, 'epoch': 8.91} +{'loss': 0.2301, 'learning_rate': 1.1227200283336286e-06, 'epoch': 8.95} +{'loss': 0.2321, 'learning_rate': 1.0788914467859041e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:41:39<22:23, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.42444247007369995, 'eval_accuracy': 0.8544782914076117, 'eval_f1': 0.6669555595504012, 'eval_matthews_correlation': 0.3474967616025217, 'eval_precision': 0.7078388018376292, 'eval_recall': 0.6452495855641251, 'eval_runtime': 39.2569, 'eval_samples_per_second': 979.216, 'eval_steps_per_second': 7.667, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [4:06:31<00:00, 1.79it/s]***** Running Evaluation ***** +{'loss': 0.2131, 'learning_rate': 1.034620152293253e-06, 'epoch': 9.03} +{'loss': 0.2169, 'learning_rate': 9.903488578006022e-07, 'epoch': 9.07} +{'loss': 0.2069, 'learning_rate': 9.460775633079512e-07, 'epoch': 9.11} +{'loss': 0.2119, 'learning_rate': 9.018062688153002e-07, 'epoch': 9.16} +{'loss': 0.2081, 'learning_rate': 8.575349743226492e-07, 'epoch': 9.2} +{'loss': 0.2138, 'learning_rate': 8.132636798299982e-07, 'epoch': 9.24} +{'loss': 0.2119, 'learning_rate': 7.689923853373474e-07, 'epoch': 9.28} +{'loss': 0.2047, 'learning_rate': 7.247210908446964e-07, 'epoch': 9.32} +{'loss': 0.2097, 'learning_rate': 6.804497963520454e-07, 'epoch': 9.36} +{'loss': 0.21, 'learning_rate': 6.361785018593944e-07, 'epoch': 9.4} +{'loss': 0.2088, 'learning_rate': 5.919072073667434e-07, 'epoch': 9.45} +{'loss': 0.212, 'learning_rate': 5.476359128740925e-07, 'epoch': 9.49} +{'loss': 0.2108, 'learning_rate': 5.033646183814416e-07, 'epoch': 9.53} +{'loss': 0.2087, 'learning_rate': 4.5909332388879056e-07, 'epoch': 9.57} +{'loss': 0.2155, 'learning_rate': 4.1482202939613953e-07, 'epoch': 9.61} +{'loss': 0.2057, 'learning_rate': 3.705507349034886e-07, 'epoch': 9.65} +{'loss': 0.2052, 'learning_rate': 3.262794404108376e-07, 'epoch': 9.7} +{'loss': 0.2172, 'learning_rate': 2.820081459181867e-07, 'epoch': 9.74} +{'loss': 0.2097, 'learning_rate': 2.3773685142553572e-07, 'epoch': 9.78} +{'loss': 0.2102, 'learning_rate': 1.9390826987781125e-07, 'epoch': 9.82} +{'loss': 0.2125, 'learning_rate': 1.4963697538516027e-07, 'epoch': 9.86} +{'loss': 0.2096, 'learning_rate': 1.053656808925093e-07, 'epoch': 9.9} +{'loss': 0.2134, 'learning_rate': 6.109438639985834e-08, 'epoch': 9.95} +{'loss': 0.2038, 'learning_rate': 1.6823091907207366e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [4:07:12<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.44298648834228516, 'eval_accuracy': 0.8501339715408028, 'eval_f1': 0.6711992315604611, 'eval_matthews_correlation': 0.3495700138033143, 'eval_precision': 0.6982797030025074, 'eval_recall': 0.6540742606278063, 'eval_runtime': 40.7043, 'eval_samples_per_second': 944.397, 'eval_steps_per_second': 7.395, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209 (score: 0.6885307547641953). +100%|██████████| 24030/24030 [4:07:14<00:00, 1.79it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 14834.3502, 'train_samples_per_second': 207.309, 'train_steps_per_second': 1.62, 'train_loss': 0.2844814440036286, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:07:14<00:00, 1.62it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:07<00:00, 4.48it/s] diff --git a/VASC/len2_5120/wandb/run-20260305_221716-fdd3q8ae/files/requirements.txt b/VASC/len2_5120/wandb/run-20260305_221716-fdd3q8ae/files/requirements.txt new file mode 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b/VASC/len2_5120/wandb/run-20260306_002740-0lbhek4e/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.weight', 'classifier.bias', 'bert.pooler.dense.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 8 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 19,224 + Number of trainable parameters = 88,402,178 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 12%|█▎ | 2403/19224 [23:36<2:49:06, 1.66it/s]***** Running Evaluation ***** +{'loss': 0.6954, 'learning_rate': 8.665511265164646e-07, 'epoch': 0.04} +{'loss': 0.6789, 'learning_rate': 1.7331022530329292e-06, 'epoch': 0.08} +{'loss': 0.6659, 'learning_rate': 2.599653379549394e-06, 'epoch': 0.12} +{'loss': 0.6634, 'learning_rate': 3.4662045060658585e-06, 'epoch': 0.17} +{'loss': 0.658, 'learning_rate': 4.332755632582323e-06, 'epoch': 0.21} 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-2403] due to args.save_total_limit + 38%|███▊ | 7209/19224 [1:12:25<1:53:00, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.6044, 'learning_rate': 7.926950747094632e-06, 'epoch': 2.04} +{'loss': 0.6031, 'learning_rate': 7.871610403984505e-06, 'epoch': 2.08} +{'loss': 0.5998, 'learning_rate': 7.816270060874379e-06, 'epoch': 2.12} +{'loss': 0.6046, 'learning_rate': 7.76092971776425e-06, 'epoch': 2.16} +{'loss': 0.6037, 'learning_rate': 7.705589374654124e-06, 'epoch': 2.21} +{'loss': 0.5973, 'learning_rate': 7.650249031543996e-06, 'epoch': 2.25} +{'loss': 0.6043, 'learning_rate': 7.594908688433868e-06, 'epoch': 2.29} +{'loss': 0.609, 'learning_rate': 7.5395683453237415e-06, 'epoch': 2.33} +{'loss': 0.6032, 'learning_rate': 7.484228002213614e-06, 'epoch': 2.37} +{'loss': 0.6014, 'learning_rate': 7.4288876591034875e-06, 'epoch': 2.41} +{'loss': 0.6102, 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Num examples = 38441 + Batch size = 128 + 38%|███▊ | 7209/19224 [1:13:20<1:53:00, 1.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.6171724200248718, 'eval_accuracy': 0.6546655914258214, 'eval_f1': 0.6512104643529879, 'eval_matthews_correlation': 0.3061573325636403, 'eval_precision': 0.6547262538431741, 'eval_recall': 0.651448622897391, 'eval_runtime': 54.095, 'eval_samples_per_second': 710.62, 'eval_steps_per_second': 5.564, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:36:50<1:24:16, 1.90it/s]***** Running Evaluation ***** +{'loss': 0.5851, 'learning_rate': 6.599335915882678e-06, 'epoch': 3.04} +{'loss': 0.5937, 'learning_rate': 6.543995572772552e-06, 'epoch': 3.08} +{'loss': 0.5895, 'learning_rate': 6.488655229662424e-06, 'epoch': 3.12} +{'loss': 0.5907, 'learning_rate': 6.4333148865522976e-06, 'epoch': 3.16} +{'loss': 0.5846, 'learning_rate': 6.37797454344217e-06, 'epoch': 3.2} +{'loss': 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'epoch': 3.79} +{'loss': 0.5902, 'learning_rate': 5.548422800221362e-06, 'epoch': 3.83} +{'loss': 0.585, 'learning_rate': 5.493082457111234e-06, 'epoch': 3.87} +{'loss': 0.5826, 'learning_rate': 5.437742114001108e-06, 'epoch': 3.91} +{'loss': 0.5894, 'learning_rate': 5.38240177089098e-06, 'epoch': 3.95} +{'loss': 0.5863, 'learning_rate': 5.327061427780853e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 9612/19224 [1:37:45<1:24:16, 1.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/config.json +{'eval_loss': 0.6301206350326538, 'eval_accuracy': 0.6531827996149944, 'eval_f1': 0.6419559312313153, 'eval_matthews_correlation': 0.30730328158858944, 'eval_precision': 0.6613132209471828, 'eval_recall': 0.646353947805115, 'eval_runtime': 54.9603, 'eval_samples_per_second': 699.432, 'eval_steps_per_second': 5.477, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [1:59:34<1:04:46, 1.85it/s]***** Running Evaluation ***** +{'loss': 0.5604, 'learning_rate': 5.271721084670725e-06, 'epoch': 4.04} +{'loss': 0.5593, 'learning_rate': 5.216380741560599e-06, 'epoch': 4.08} +{'loss': 0.56, 'learning_rate': 5.161040398450471e-06, 'epoch': 4.12} 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [2:24:52<42:20, 1.89it/s]***** Running Evaluation ***** +{'loss': 0.5432, 'learning_rate': 3.9441062534587715e-06, 'epoch': 5.04} +{'loss': 0.5434, 'learning_rate': 3.888765910348645e-06, 'epoch': 5.08} +{'loss': 0.5399, 'learning_rate': 3.833978970669618e-06, 'epoch': 5.12} +{'loss': 0.5317, 'learning_rate': 3.7786386275594913e-06, 'epoch': 5.16} +{'loss': 0.5378, 'learning_rate': 3.723298284449364e-06, 'epoch': 5.2} +{'loss': 0.5351, 'learning_rate': 3.6679579413392364e-06, 'epoch': 5.24} +{'loss': 0.5317, 'learning_rate': 3.6126175982291093e-06, 'epoch': 5.29} +{'loss': 0.545, 'learning_rate': 3.5572772551189823e-06, 'epoch': 5.33} +{'loss': 0.5423, 'learning_rate': 3.501936912008855e-06, 'epoch': 5.37} +{'loss': 0.5422, 'learning_rate': 3.4465965688987274e-06, 'epoch': 5.41} +{'loss': 0.5375, 'learning_rate': 3.3912562257886e-06, 'epoch': 5.45} +{'loss': 0.5416, 'learning_rate': 3.3359158826784725e-06, 'epoch': 5.49} +{'loss': 0.5457, 'learning_rate': 3.280575539568346e-06, 'epoch': 5.53} +{'loss': 0.5423, 'learning_rate': 3.2252351964582184e-06, 'epoch': 5.58} +{'loss': 0.5399, 'learning_rate': 3.169894853348091e-06, 'epoch': 5.62} +{'loss': 0.5369, 'learning_rate': 3.114554510237964e-06, 'epoch': 5.66} +{'loss': 0.5375, 'learning_rate': 3.0592141671278364e-06, 'epoch': 5.7} +{'loss': 0.543, 'learning_rate': 3.003873824017709e-06, 'epoch': 5.74} +{'loss': 0.5458, 'learning_rate': 2.9485334809075815e-06, 'epoch': 5.78} +{'loss': 0.5428, 'learning_rate': 2.893193137797455e-06, 'epoch': 5.83} +{'loss': 0.5403, 'learning_rate': 2.8378527946873275e-06, 'epoch': 5.87} +{'loss': 0.5364, 'learning_rate': 2.7825124515772e-06, 'epoch': 5.91} +{'loss': 0.5473, 'learning_rate': 2.7271721084670726e-06, 'epoch': 5.95} +{'loss': 0.5406, 'learning_rate': 2.6718317653569455e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [2:25:48<42:20, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.651382327079773, 'eval_accuracy': 0.6486303686168414, 'eval_f1': 0.6463243691189446, 'eval_matthews_correlation': 0.2941870118684641, 'eval_precision': 0.6479172157194693, 'eval_recall': 0.6462743831594182, 'eval_runtime': 55.7799, 'eval_samples_per_second': 689.155, 'eval_steps_per_second': 5.396, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:50:21<22:26, 1.78it/s]***** Running Evaluation ***** +{'loss': 0.5247, 'learning_rate': 2.616491422246818e-06, 'epoch': 6.03} +{'loss': 0.5177, 'learning_rate': 2.5611510791366906e-06, 'epoch': 6.08} +{'loss': 0.5126, 'learning_rate': 2.5058107360265636e-06, 'epoch': 6.12} +{'loss': 0.5204, 'learning_rate': 2.4504703929164365e-06, 'epoch': 6.16} +{'loss': 0.5185, 'learning_rate': 2.395130049806309e-06, 'epoch': 6.2} +{'loss': 0.5035, 'learning_rate': 2.340343110127283e-06, 'epoch': 6.24} +{'loss': 0.5252, 'learning_rate': 2.2850027670171555e-06, 'epoch': 6.28} +{'loss': 0.5133, 'learning_rate': 2.2296624239070285e-06, 'epoch': 6.33} +{'loss': 0.5217, 'learning_rate': 2.174322080796901e-06, 'epoch': 6.37} +{'loss': 0.5229, 'learning_rate': 2.118981737686774e-06, 'epoch': 6.41} +{'loss': 0.5129, 'learning_rate': 2.0636413945766465e-06, 'epoch': 6.45} +{'loss': 0.5154, 'learning_rate': 2.0083010514665195e-06, 'epoch': 6.49} +{'loss': 0.5234, 'learning_rate': 1.952960708356392e-06, 'epoch': 6.53} +{'loss': 0.5174, 'learning_rate': 1.8976203652462646e-06, 'epoch': 6.58} +{'loss': 0.5197, 'learning_rate': 1.8422800221361373e-06, 'epoch': 6.62} +{'loss': 0.5066, 'learning_rate': 1.78693967902601e-06, 'epoch': 6.66} +{'loss': 0.5245, 'learning_rate': 1.7315993359158828e-06, 'epoch': 6.7} +{'loss': 0.5223, 'learning_rate': 1.6762589928057554e-06, 'epoch': 6.74} +{'loss': 0.5149, 'learning_rate': 1.6209186496956284e-06, 'epoch': 6.78} +{'loss': 0.525, 'learning_rate': 1.565578306585501e-06, 'epoch': 6.82} +{'loss': 0.5194, 'learning_rate': 1.5102379634753737e-06, 'epoch': 6.87} +{'loss': 0.5201, 'learning_rate': 1.4548976203652464e-06, 'epoch': 6.91} +{'loss': 0.5253, 'learning_rate': 1.3995572772551192e-06, 'epoch': 6.95} +{'loss': 0.5162, 'learning_rate': 1.3442169341449917e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [2:51:16<22:26, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.6855613589286804, 'eval_accuracy': 0.6471735906974324, 'eval_f1': 0.6434584195177324, 'eval_matthews_correlation': 0.29097530885300893, 'eval_precision': 0.6471728058902275, 'eval_recall': 0.6438217982085199, 'eval_runtime': 55.2204, 'eval_samples_per_second': 696.138, 'eval_steps_per_second': 5.451, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [3:15:49<00:00, 1.84it/s]***** Running Evaluation ***** +{'loss': 0.4985, 'learning_rate': 1.2888765910348645e-06, 'epoch': 7.03} +{'loss': 0.5062, 'learning_rate': 1.2335362479247372e-06, 'epoch': 7.07} +{'loss': 0.5058, 'learning_rate': 1.178749308245711e-06, 'epoch': 7.12} +{'loss': 0.5028, 'learning_rate': 1.1234089651355839e-06, 'epoch': 7.16} +{'loss': 0.4938, 'learning_rate': 1.0680686220254566e-06, 'epoch': 7.2} +{'loss': 0.5055, 'learning_rate': 1.0127282789153294e-06, 'epoch': 7.24} +{'loss': 0.5059, 'learning_rate': 9.573879358052021e-07, 'epoch': 7.28} +{'loss': 0.4926, 'learning_rate': 9.020475926950748e-07, 'epoch': 7.32} +{'loss': 0.4991, 'learning_rate': 8.467072495849475e-07, 'epoch': 7.37} +{'loss': 0.5044, 'learning_rate': 7.913669064748202e-07, 'epoch': 7.41} +{'loss': 0.4998, 'learning_rate': 7.360265633646929e-07, 'epoch': 7.45} +{'loss': 0.4962, 'learning_rate': 6.806862202545657e-07, 'epoch': 7.49} +{'loss': 0.4997, 'learning_rate': 6.253458771444383e-07, 'epoch': 7.53} +{'loss': 0.4966, 'learning_rate': 5.700055340343111e-07, 'epoch': 7.57} +{'loss': 0.508, 'learning_rate': 5.146651909241837e-07, 'epoch': 7.62} +{'loss': 0.5006, 'learning_rate': 4.593248478140565e-07, 'epoch': 7.66} +{'loss': 0.5052, 'learning_rate': 4.039845047039292e-07, 'epoch': 7.7} +{'loss': 0.4998, 'learning_rate': 3.486441615938019e-07, 'epoch': 7.74} +{'loss': 0.4959, 'learning_rate': 2.933038184836746e-07, 'epoch': 7.78} +{'loss': 0.5031, 'learning_rate': 2.3796347537354735e-07, 'epoch': 7.82} +{'loss': 0.493, 'learning_rate': 1.8262313226342006e-07, 'epoch': 7.87} +{'loss': 0.503, 'learning_rate': 1.2728278915329276e-07, 'epoch': 7.91} +{'loss': 0.496, 'learning_rate': 7.194244604316547e-08, 'epoch': 7.95} +{'loss': 0.4926, 'learning_rate': 1.6602102933038186e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [3:16:43<00:00, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.6972386837005615, 'eval_accuracy': 0.6464452017377279, 'eval_f1': 0.6430005752732748, 'eval_matthews_correlation': 0.28950939164581735, 'eval_precision': 0.6462537584629178, 'eval_recall': 0.6432709981815314, 'eval_runtime': 53.4936, 'eval_samples_per_second': 718.609, 'eval_steps_per_second': 5.627, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209 (score: 0.6512104643529879). +100%|██████████| 19224/19224 [3:16:44<00:00, 1.84it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 11804.7532, 'train_samples_per_second': 208.41, 'train_steps_per_second': 1.628, 'train_loss': 0.5719506908742974, 'epoch': 8.0} +100%|██████████| 19224/19224 [3:16:44<00:00, 1.63it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:07<00:00, 4.43it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_002740-0lbhek4e/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_002740-0lbhek4e/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_002740-0lbhek4e/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 +nvidia-nccl-cu12==2.27.3 +debugpy==1.8.16 +ipython==8.18.1 +anyio==4.12.0 +prompt_toolkit==3.0.51 +mkl_fft==1.3.11 +httpcore==1.0.9 +Jinja2==3.1.6 +ply==3.11 +zipp==3.23.0 +setproctitle==1.3.6 +docker-pycreds==0.4.0 +nvidia-cuda-nvrtc-cu12==12.8.93 +urllib3==2.5.0 +kiwisolver==1.4.4 +nvidia-curand-cu12==10.3.9.90 +llvmlite==0.43.0 +six==1.17.0 +frozenlist==1.8.0 +wcwidth==0.2.13 +numexpr==2.10.1 +click==8.1.8 +multiprocess==0.70.18 +threadpoolctl==3.6.0 +typing_extensions==4.15.0 +decorator==5.2.1 +sip==6.7.12 +pure_eval==0.2.3 +async-timeout==5.0.1 +Pygments==2.19.2 +mkl-service==2.4.0 +transformers==4.35.2 +numba==0.60.0 +pyzmq==27.0.2 +mkl_random==1.2.8 +ptyprocess==0.7.0 +nvidia-cuda-cupti-cu12==12.8.90 +charset-normalizer==3.4.4 +nvidia-cublas-cu12==12.8.4.1 +PyQt5_sip==12.13.0 +Bottleneck==1.4.2 +networkx==3.2.1 +PySocks==1.7.1 +pysam==0.9.1 +tornado==6.5.2 +pandas==2.3.3 +smmap==5.0.2 +PyQt5==5.15.10 +nvidia-cufft-cu12==11.3.3.83 +safetensors==0.7.0 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.01" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.10" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "571055534080" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 + host: sn4622116170 + memory: + total: "4316310355968" + os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 + program: /home/n5huang/dna_token/Finetune-screen/train.py + python: CPython 3.9.18 + root: /data/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120 + startedAt: "2026-03-06T02:26:58.464838Z" + writerId: ksjn3oqajbeyred44mu71k6jqfkyvnb4 + m: + - "1": train/global_step + "6": + - 3 + "7": [] + - "2": '*' + "5": 1 + "6": + - 1 + "7": [] + python_version: 3.9.18 + t: + "1": + - 1 + - 5 + - 11 + - 49 + - 51 + - 53 + - 71 + "2": + - 1 + - 5 + - 11 + - 49 + - 51 + - 53 + - 71 + "3": + - 7 + - 66 + "4": 3.9.18 + "5": 0.23.1 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due to args.save_total_limit + 50%|█████ | 7209/14418 [1:14:52<1:07:27, 1.78it/s]***** Running Evaluation ***** +{'loss': 0.3212, 'learning_rate': 7.335080147965476e-06, 'epoch': 2.04} +{'loss': 0.33, 'learning_rate': 7.258014796547473e-06, 'epoch': 2.08} +{'loss': 0.3222, 'learning_rate': 7.1809494451294705e-06, 'epoch': 2.12} +{'loss': 0.3185, 'learning_rate': 7.103884093711468e-06, 'epoch': 2.16} +{'loss': 0.3194, 'learning_rate': 7.026818742293465e-06, 'epoch': 2.21} +{'loss': 0.3259, 'learning_rate': 6.949753390875463e-06, 'epoch': 2.25} +{'loss': 0.3214, 'learning_rate': 6.87268803945746e-06, 'epoch': 2.29} +{'loss': 0.3261, 'learning_rate': 6.795622688039458e-06, 'epoch': 2.33} +{'loss': 0.3232, 'learning_rate': 6.718557336621455e-06, 'epoch': 2.37} +{'loss': 0.3199, 'learning_rate': 6.641491985203453e-06, 'epoch': 2.41} +{'loss': 0.3245, 'learning_rate': 6.56442663378545e-06, 'epoch': 2.46} +{'loss': 0.3233, 'learning_rate': 6.487361282367448e-06, 'epoch': 2.5} +{'loss': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3379155099391937, 'eval_accuracy': 0.8721937514632814, 'eval_f1': 0.6908975497699799, 'eval_matthews_correlation': 0.409883019958866, 'eval_precision': 0.7645984832027729, 'eval_recall': 0.6587349330361161, 'eval_runtime': 42.3454, 'eval_samples_per_second': 907.797, 'eval_steps_per_second': 7.108, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:37:17<41:05, 1.95it/s]***** Running Evaluation ***** +{'loss': 0.3067, 'learning_rate': 5.485511713933416e-06, 'epoch': 3.04} +{'loss': 0.3096, 'learning_rate': 5.408446362515414e-06, 'epoch': 3.08} +{'loss': 0.3031, 'learning_rate': 5.331381011097411e-06, 'epoch': 3.12} +{'loss': 0.3092, 'learning_rate': 5.2543156596794085e-06, 'epoch': 3.16} +{'loss': 0.3071, 'learning_rate': 5.1772503082614055e-06, 'epoch': 3.2} +{'loss': 0.2983, 'learning_rate': 5.100184956843403e-06, 'epoch': 3.25} +{'loss': 0.3159, 'learning_rate': 5.023119605425402e-06, 'epoch': 3.29} +{'loss': 0.2976, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-9612/special_tokens_map.json + 83%|████████▎ | 12015/14418 [2:02:49<23:31, 1.70it/s]***** Running Evaluation ***** +{'loss': 0.2995, 'learning_rate': 3.6374845869297166e-06, 'epoch': 4.04} +{'loss': 0.2951, 'learning_rate': 3.560419235511714e-06, 'epoch': 4.08} +{'loss': 0.2996, 'learning_rate': 3.483353884093712e-06, 'epoch': 4.12} +{'loss': 0.291, 'learning_rate': 3.4062885326757093e-06, 'epoch': 4.16} +{'loss': 0.2804, 'learning_rate': 3.3292231812577068e-06, 'epoch': 4.2} +{'loss': 0.2959, 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'eval_recall': 0.6484109495565438, 'eval_runtime': 42.6055, 'eval_samples_per_second': 902.255, 'eval_steps_per_second': 7.065, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:28:39<00:00, 1.92it/s]***** Running Evaluation ***** +{'loss': 0.2671, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3554569482803345, 'eval_accuracy': 0.8637132228610078, 'eval_f1': 0.682133576284622, 'eval_matthews_correlation': 0.3824349156426455, 'eval_precision': 0.7345692541108995, 'eval_recall': 0.6558777015096897, 'eval_runtime': 38.2841, 'eval_samples_per_second': 1004.098, 'eval_steps_per_second': 7.862, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209 (score: 0.6908975497699799). +100%|██████████| 14418/14418 [2:29:20<00:00, 1.92it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 8960.0789, 'train_samples_per_second': 205.933, 'train_steps_per_second': 1.609, 'train_loss': 0.3161125077935392, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:29:20<00:00, 1.61it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:07<00:00, 4.47it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_022658-lme9vree/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_022658-lme9vree/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_022658-lme9vree/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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+{'loss': 0.6214, 'learning_rate': 8.778997697892687e-06, 'epoch': 1.75} +{'loss': 0.6187, 'learning_rate': 8.734726403400036e-06, 'epoch': 1.79} +{'loss': 0.6217, 'learning_rate': 8.690455108907386e-06, 'epoch': 1.83} +{'loss': 0.6181, 'learning_rate': 8.646183814414734e-06, 'epoch': 1.87} +{'loss': 0.6195, 'learning_rate': 8.601912519922083e-06, 'epoch': 1.91} +{'loss': 0.6159, 'learning_rate': 8.557641225429433e-06, 'epoch': 1.96} +{'loss': 0.6183, 'learning_rate': 8.51336993093678e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [51:30<3:03:07, 1.75Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 0.6233178377151489, 'eval_accuracy': 0.6487604380739315, 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args.save_total_limit + 30%|███ | 7209/24030 [1:13:17<2:27:31, 1.90it/s]***** Running Evaluation ***** +{'loss': 0.6075, 'learning_rate': 8.46909863644413e-06, 'epoch': 2.04} +{'loss': 0.6055, 'learning_rate': 8.42482734195148e-06, 'epoch': 2.08} +{'loss': 0.6042, 'learning_rate': 8.38055604745883e-06, 'epoch': 2.12} +{'loss': 0.608, 'learning_rate': 8.336284752966177e-06, 'epoch': 2.16} +{'loss': 0.6077, 'learning_rate': 8.292013458473527e-06, 'epoch': 2.21} +{'loss': 0.6013, 'learning_rate': 8.247742163980875e-06, 'epoch': 2.25} +{'loss': 0.6066, 'learning_rate': 8.203470869488224e-06, 'epoch': 2.29} +{'loss': 0.6124, 'learning_rate': 8.159199574995574e-06, 'epoch': 2.33} +{'loss': 0.604, 'learning_rate': 8.114928280502923e-06, 'epoch': 2.37} +{'loss': 0.6057, 'learning_rate': 8.070656986010271e-06, 'epoch': 2.41} +{'loss': 0.6102, 'learning_rate': 8.02638569151762e-06, 'epoch': 2.46} +{'loss': 0.6106, 'learning_rate': 7.982114397024969e-06, 'epoch': 2.5} +{'loss': 0.6057, 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.6175864338874817, 'eval_accuracy': 0.6543794386202232, 'eval_f1': 0.6518400379013514, 'eval_matthews_correlation': 0.305684296520781, 'eval_precision': 0.6538720034660283, 'eval_recall': 0.6518191858079546, 'eval_runtime': 51.3271, 'eval_samples_per_second': 748.941, 'eval_steps_per_second': 5.864, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:39:52<2:45:08, 1.46it/s]***** Running Evaluation ***** +{'loss': 0.5918, 'learning_rate': 7.407030281565434e-06, 'epoch': 3.04} +{'loss': 0.5974, 'learning_rate': 7.362758987072783e-06, 'epoch': 3.08} +{'loss': 0.5916, 'learning_rate': 7.318487692580132e-06, 'epoch': 3.12} +{'loss': 0.5951, 'learning_rate': 7.27421639808748e-06, 'epoch': 3.16} +{'loss': 0.5891, 'learning_rate': 7.2299451035948296e-06, 'epoch': 3.2} +{'loss': 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'eval_accuracy': 0.6533648968549205, 'eval_f1': 0.6415255987204227, 'eval_matthews_correlation': 0.30822351967555855, 'eval_precision': 0.6623187218147744, 'eval_recall': 0.6463197482998883, 'eval_runtime': 48.9127, 'eval_samples_per_second': 785.911, 'eval_steps_per_second': 6.154, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [2:32:24<1:21:31, 1.96it/s]***** Running Evaluation ***** +{'loss': 0.5512, 'learning_rate': 5.28289357180804e-06, 'epoch': 5.04} +{'loss': 0.5525, 'learning_rate': 5.239064990260315e-06, 'epoch': 5.08} +{'loss': 0.5501, 'learning_rate': 5.194793695767665e-06, 'epoch': 5.12} +{'loss': 0.5401, 'learning_rate': 5.150522401275013e-06, 'epoch': 5.16} +{'loss': 0.5461, 'learning_rate': 5.106251106782363e-06, 'epoch': 5.2} +{'loss': 0.5493, 'learning_rate': 5.0619798122897115e-06, 'epoch': 5.24} +{'loss': 0.54, 'learning_rate': 5.017708517797061e-06, 'epoch': 5.29} +{'loss': 0.5528, 'learning_rate': 4.97343722330441e-06, 'epoch': 5.33} +{'loss': 0.5556, 'learning_rate': 4.9291659288117585e-06, 'epoch': 5.37} +{'loss': 0.5508, 'learning_rate': 4.884894634319108e-06, 'epoch': 5.41} +{'loss': 0.5489, 'learning_rate': 4.840623339826457e-06, 'epoch': 5.45} +{'loss': 0.5459, 'learning_rate': 4.7963520453338055e-06, 'epoch': 5.49} +{'loss': 0.5548, 'learning_rate': 4.752080750841155e-06, 'epoch': 5.53} +{'loss': 0.5485, 'learning_rate': 4.707809456348504e-06, 'epoch': 5.58} +{'loss': 0.5513, 'learning_rate': 4.663538161855853e-06, 'epoch': 5.62} +{'loss': 0.5453, 'learning_rate': 4.619266867363202e-06, 'epoch': 5.66} +{'loss': 0.5484, 'learning_rate': 4.574995572870551e-06, 'epoch': 5.7} +{'loss': 0.5466, 'learning_rate': 4.5307242783779e-06, 'epoch': 5.74} +{'loss': 0.5569, 'learning_rate': 4.48645298388525e-06, 'epoch': 5.78} +{'loss': 0.5505, 'learning_rate': 4.4421816893925985e-06, 'epoch': 5.83} +{'loss': 0.5464, 'learning_rate': 4.397910394899947e-06, 'epoch': 5.87} +{'loss': 0.5441, 'learning_rate': 4.353639100407297e-06, 'epoch': 5.91} +{'loss': 0.556, 'learning_rate': 4.309810518859572e-06, 'epoch': 5.95} +{'loss': 0.5456, 'learning_rate': 4.265539224366921e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [2:33:16<1:21:31, 1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.641571581363678, 'eval_accuracy': 0.6508935771702089, 'eval_f1': 0.6471929207413604, 'eval_matthews_correlation': 0.29851861046117345, 'eval_precision': 0.6510046989293385, 'eval_recall': 0.6475340857329376, 'eval_runtime': 52.2259, 'eval_samples_per_second': 736.052, 'eval_steps_per_second': 5.763, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:56:59<1:06:54, 1.80it/s]***** Running Evaluation ***** +{'loss': 0.5301, 'learning_rate': 4.22126792987427e-06, 'epoch': 6.03} +{'loss': 0.5206, 'learning_rate': 4.176996635381619e-06, 'epoch': 6.08} +{'loss': 0.5235, 'learning_rate': 4.132725340888968e-06, 'epoch': 6.12} +{'loss': 0.5301, 'learning_rate': 4.088454046396317e-06, 'epoch': 6.16} +{'loss': 0.5247, 'learning_rate': 4.0441827519036655e-06, 'epoch': 6.2} +{'loss': 0.5085, 'learning_rate': 3.999911457411015e-06, 'epoch': 6.24} +{'loss': 0.5267, 'learning_rate': 3.955640162918364e-06, 'epoch': 6.28} +{'loss': 0.5197, 'learning_rate': 3.9113688684257125e-06, 'epoch': 6.33} +{'loss': 0.5283, 'learning_rate': 3.867097573933062e-06, 'epoch': 6.37} +{'loss': 0.528, 'learning_rate': 3.822826279440412e-06, 'epoch': 6.41} +{'loss': 0.5207, 'learning_rate': 3.7785549849477603e-06, 'epoch': 6.45} +{'loss': 0.5247, 'learning_rate': 3.7342836904551094e-06, 'epoch': 6.49} +{'loss': 0.5303, 'learning_rate': 3.6900123959624585e-06, 'epoch': 6.53} +{'loss': 0.5226, 'learning_rate': 3.6457411014698073e-06, 'epoch': 6.58} +{'loss': 0.5365, 'learning_rate': 3.6014698069771564e-06, 'epoch': 6.62} +{'loss': 0.516, 'learning_rate': 3.5571985124845055e-06, 'epoch': 6.66} +{'loss': 0.5313, 'learning_rate': 3.5129272179918546e-06, 'epoch': 6.7} +{'loss': 0.5287, 'learning_rate': 3.4686559234992033e-06, 'epoch': 6.74} +{'loss': 0.5217, 'learning_rate': 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0.6462715201494076, 'eval_recall': 0.6440887290497037, 'eval_runtime': 52.0072, 'eval_samples_per_second': 739.147, 'eval_steps_per_second': 5.788, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:21:38<42:14, 1.90it/s]***** Running Evaluation ***** +{'loss': 0.507, 'learning_rate': 3.1591995749955734e-06, 'epoch': 7.03} +{'loss': 0.5044, 'learning_rate': 3.1149282805029225e-06, 'epoch': 7.07} +{'loss': 0.5048, 'learning_rate': 3.0706569860102712e-06, 'epoch': 7.12} +{'loss': 0.5044, 'learning_rate': 3.0263856915176204e-06, 'epoch': 7.16} +{'loss': 0.5, 'learning_rate': 2.9821143970249695e-06, 'epoch': 7.2} +{'loss': 0.5062, 'learning_rate': 2.937843102532318e-06, 'epoch': 7.24} +{'loss': 0.5042, 'learning_rate': 2.8935718080396673e-06, 'epoch': 7.28} +{'loss': 0.4975, 'learning_rate': 2.8493005135470165e-06, 'epoch': 7.32} +{'loss': 0.4997, 'learning_rate': 2.8050292190543656e-06, 'epoch': 7.37} +{'loss': 0.507, 'learning_rate': 2.7607579245617143e-06, 'epoch': 7.41} +{'loss': 0.5038, 'learning_rate': 2.7164866300690634e-06, 'epoch': 7.45} +{'loss': 0.5011, 'learning_rate': 2.6722153355764125e-06, 'epoch': 7.49} +{'loss': 0.4974, 'learning_rate': 2.6279440410837612e-06, 'epoch': 7.53} +{'loss': 0.502, 'learning_rate': 2.5836727465911104e-06, 'epoch': 7.57} +{'loss': 0.5085, 'learning_rate': 2.5394014520984595e-06, 'epoch': 7.62} +{'loss': 0.5, 'learning_rate': 2.4951301576058086e-06, 'epoch': 7.66} +{'loss': 0.507, 'learning_rate': 2.4508588631131577e-06, 'epoch': 7.7} +{'loss': 0.5028, 'learning_rate': 2.406587568620507e-06, 'epoch': 7.74} +{'loss': 0.4982, 'learning_rate': 2.3623162741278556e-06, 'epoch': 7.78} +{'loss': 0.5059, 'learning_rate': 2.3180449796352047e-06, 'epoch': 7.82} +{'loss': 0.5017, 'learning_rate': 2.273773685142554e-06, 'epoch': 7.87} +{'loss': 0.5103, 'learning_rate': 2.229502390649903e-06, 'epoch': 7.91} +{'loss': 0.5021, 'learning_rate': 2.1856738091021783e-06, 'epoch': 7.95} +{'loss': 0.4942, 'learning_rate': 2.1414025146095274e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:22:28<42:14, 1.9Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.699321985244751, 'eval_accuracy': 0.6433235347675659, 'eval_f1': 0.6410907146608064, 'eval_matthews_correlation': 0.28354433391357975, 'eval_precision': 0.6425048587069278, 'eval_recall': 0.641043242356808, 'eval_runtime': 49.4491, 'eval_samples_per_second': 777.386, 'eval_steps_per_second': 6.087, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:46:17<21:21, 1.88it/s]***** Running Evaluation ***** +{'loss': 0.4928, 'learning_rate': 2.0971312201168765e-06, 'epoch': 8.03} +{'loss': 0.4813, 'learning_rate': 2.0528599256242252e-06, 'epoch': 8.07} +{'loss': 0.4791, 'learning_rate': 2.0085886311315744e-06, 'epoch': 8.11} +{'loss': 0.4809, 'learning_rate': 1.9643173366389235e-06, 'epoch': 8.16} +{'loss': 0.4837, 'learning_rate': 1.9200460421462726e-06, 'epoch': 8.2} +{'loss': 0.4873, 'learning_rate': 1.8757747476536215e-06, 'epoch': 8.24} +{'loss': 0.4836, 'learning_rate': 1.8315034531609704e-06, 'epoch': 8.28} +{'loss': 0.4823, 'learning_rate': 1.7872321586683198e-06, 'epoch': 8.32} +{'loss': 0.4816, 'learning_rate': 1.7429608641756687e-06, 'epoch': 8.36} +{'loss': 0.4726, 'learning_rate': 1.6986895696830178e-06, 'epoch': 8.41} +{'loss': 0.4787, 'learning_rate': 1.6544182751903667e-06, 'epoch': 8.45} +{'loss': 0.477, 'learning_rate': 1.6101469806977157e-06, 'epoch': 8.49} +{'loss': 0.4886, 'learning_rate': 1.5658756862050648e-06, 'epoch': 8.53} +{'loss': 0.4715, 'learning_rate': 1.5216043917124137e-06, 'epoch': 8.57} +{'loss': 0.482, 'learning_rate': 1.4773330972197628e-06, 'epoch': 8.61} +{'loss': 0.478, 'learning_rate': 1.4330618027271117e-06, 'epoch': 8.66} +{'loss': 0.4879, 'learning_rate': 1.3887905082344609e-06, 'epoch': 8.7} +{'loss': 0.4952, 'learning_rate': 1.34451921374181e-06, 'epoch': 8.74} +{'loss': 0.4883, 'learning_rate': 1.3002479192491591e-06, 'epoch': 8.78} +{'loss': 0.4832, 'learning_rate': 1.255976624756508e-06, 'epoch': 8.82} +{'loss': 0.4833, 'learning_rate': 1.2117053302638572e-06, 'epoch': 8.86} +{'loss': 0.4789, 'learning_rate': 1.167434035771206e-06, 'epoch': 8.91} +{'loss': 0.4788, 'learning_rate': 1.1236054542234816e-06, 'epoch': 8.95} +{'loss': 0.4915, 'learning_rate': 1.0793341597308305e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:47:05<21:21, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.714907169342041, 'eval_accuracy': 0.6399937566660596, 'eval_f1': 0.637008637292102, 'eval_matthews_correlation': 0.27654658870689075, 'eval_precision': 0.63939900443389, 'eval_recall': 0.6371566748916201, 'eval_runtime': 48.6559, 'eval_samples_per_second': 790.058, 'eval_steps_per_second': 6.186, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [4:10:51<00:00, 1.76it/s]***** Running Evaluation ***** +{'loss': 0.4826, 'learning_rate': 1.0350628652381797e-06, 'epoch': 9.03} +{'loss': 0.4583, 'learning_rate': 9.907915707455288e-07, 'epoch': 9.07} +{'loss': 0.4686, 'learning_rate': 9.465202762528777e-07, 'epoch': 9.11} +{'loss': 0.458, 'learning_rate': 9.022489817602267e-07, 'epoch': 9.16} +{'loss': 0.4661, 'learning_rate': 8.579776872675757e-07, 'epoch': 9.2} +{'loss': 0.4735, 'learning_rate': 8.137063927749248e-07, 'epoch': 9.24} +{'loss': 0.4636, 'learning_rate': 7.694350982822739e-07, 'epoch': 9.28} +{'loss': 0.4689, 'learning_rate': 7.251638037896229e-07, 'epoch': 9.32} +{'loss': 0.4747, 'learning_rate': 6.808925092969719e-07, 'epoch': 9.36} +{'loss': 0.4765, 'learning_rate': 6.366212148043209e-07, 'epoch': 9.4} +{'loss': 0.4702, 'learning_rate': 5.9234992031167e-07, 'epoch': 9.45} +{'loss': 0.465, 'learning_rate': 5.48078625819019e-07, 'epoch': 9.49} +{'loss': 0.4691, 'learning_rate': 5.03807331326368e-07, 'epoch': 9.53} +{'loss': 0.4664, 'learning_rate': 4.595360368337171e-07, 'epoch': 9.57} +{'loss': 0.4678, 'learning_rate': 4.1526474234106605e-07, 'epoch': 9.61} +{'loss': 0.4756, 'learning_rate': 3.709934478484151e-07, 'epoch': 9.65} +{'loss': 0.471, 'learning_rate': 3.2672215335576414e-07, 'epoch': 9.7} +{'loss': 0.4689, 'learning_rate': 2.8245085886311316e-07, 'epoch': 9.74} +{'loss': 0.4722, 'learning_rate': 2.381795643704622e-07, 'epoch': 9.78} +{'loss': 0.4751, 'learning_rate': 1.9390826987781125e-07, 'epoch': 9.82} +{'loss': 0.4623, 'learning_rate': 1.4963697538516027e-07, 'epoch': 9.86} +{'loss': 0.4769, 'learning_rate': 1.053656808925093e-07, 'epoch': 9.9} +{'loss': 0.4575, 'learning_rate': 6.109438639985834e-08, 'epoch': 9.95} +{'loss': 0.4616, 'learning_rate': 1.6823091907207366e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [4:11:45<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.7338143587112427, 'eval_accuracy': 0.6394214510548633, 'eval_f1': 0.6369869930906833, 'eval_matthews_correlation': 0.27559319779073804, 'eval_precision': 0.6386056180328535, 'eval_recall': 0.6369923018750259, 'eval_runtime': 54.0659, 'eval_samples_per_second': 711.003, 'eval_steps_per_second': 5.567, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209 (score: 0.6518400379013514). +100%|██████████| 24030/24030 [4:11:47<00:00, 1.76it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 15107.1539, 'train_samples_per_second': 203.565, 'train_steps_per_second': 1.591, 'train_loss': 0.5565652704020614, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:11:47<00:00, 1.59it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.72it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_034650-5vx3bmnc/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_034650-5vx3bmnc/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_034650-5vx3bmnc/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 5120 +warmup_ratio: + value: 0.1 +warmup_steps: + value: 0 +weight_decay: + value: 0.01 diff --git a/VASC/len2_5120/wandb/run-20260306_045844-9gy218oi/files/output.log b/VASC/len2_5120/wandb/run-20260306_045844-9gy218oi/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..b7fedd9231c4922215f0f94388d49eea348d8560 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_045844-9gy218oi/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['classifier.bias', 'classifier.weight', 'bert.pooler.dense.bias', 'bert.pooler.dense.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 8 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 19,224 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 12%|█▎ | 2403/19224 [25:44<2:31:42, 1.85it/s]***** Running Evaluation ***** +{'loss': 0.6076, 'learning_rate': 5.200208008320333e-07, 'epoch': 0.04} +{'loss': 0.4151, 'learning_rate': 1.0400416016640667e-06, 'epoch': 0.08} +{'loss': 0.3705, 'learning_rate': 1.5600624024961e-06, 'epoch': 0.12} +{'loss': 0.3585, 'learning_rate': 2.0800832033281333e-06, 'epoch': 0.17} +{'loss': 0.3608, 'learning_rate': 2.6001040041601667e-06, 'epoch': 0.21} +{'loss': 0.3598, 'learning_rate': 3.1201248049922e-06, 'epoch': 0.25} +{'loss': 0.3602, 'learning_rate': 3.6401456058242336e-06, 'epoch': 0.29} +{'loss': 0.3519, 'learning_rate': 4.160166406656267e-06, 'epoch': 0.33} +{'loss': 0.3612, 'learning_rate': 4.6801872074883e-06, 'epoch': 0.37} +{'loss': 0.3577, 'learning_rate': 5.2002080083203335e-06, 'epoch': 0.42} +{'loss': 0.3558, 'learning_rate': 5.7202288091523665e-06, 'epoch': 0.46} +{'loss': 0.3614, 'learning_rate': 6.2402496099844e-06, 'epoch': 0.5} +{'loss': 0.3519, 'learning_rate': 6.760270410816433e-06, 'epoch': 0.54} +{'loss': 0.3502, 'learning_rate': 7.280291211648467e-06, 'epoch': 0.58} +{'loss': 0.3573, 'learning_rate': 7.8003120124805e-06, 'epoch': 0.62} +{'loss': 0.3474, 'learning_rate': 8.320332813312533e-06, 'epoch': 0.67} +{'loss': 0.3489, 'learning_rate': 8.840353614144566e-06, 'epoch': 0.71} +{'loss': 0.3445, 'learning_rate': 9.3603744149766e-06, 'epoch': 0.75} +{'loss': 0.3551, 'learning_rate': 9.880395215808634e-06, 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+{'loss': 0.335, 'learning_rate': 8.68389110456043e-06, 'epoch': 1.75} +{'loss': 0.3465, 'learning_rate': 8.62609097740015e-06, 'epoch': 1.79} +{'loss': 0.3402, 'learning_rate': 8.568290850239872e-06, 'epoch': 1.83} +{'loss': 0.3354, 'learning_rate': 8.510490723079593e-06, 'epoch': 1.87} +{'loss': 0.3345, 'learning_rate': 8.452690595919312e-06, 'epoch': 1.91} +{'loss': 0.332, 'learning_rate': 8.394890468759032e-06, 'epoch': 1.96} +{'loss': 0.3259, 'learning_rate': 8.337090341598753e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 25%|██▌ | 4806/19224 [53:37<2:39:33, 1.51Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-4806/config.json +{'eval_loss': 0.3399035632610321, 'eval_accuracy': 0.8738846544054525, 'eval_f1': 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7209/19224 [1:18:07<1:40:04, 2.00it/s]***** Running Evaluation ***** +{'loss': 0.3225, 'learning_rate': 8.279290214438472e-06, 'epoch': 2.04} +{'loss': 0.3342, 'learning_rate': 8.221490087278192e-06, 'epoch': 2.08} +{'loss': 0.3215, 'learning_rate': 8.163689960117913e-06, 'epoch': 2.12} +{'loss': 0.3196, 'learning_rate': 8.105889832957633e-06, 'epoch': 2.16} +{'loss': 0.3193, 'learning_rate': 8.048089705797354e-06, 'epoch': 2.21} +{'loss': 0.3252, 'learning_rate': 7.990289578637073e-06, 'epoch': 2.25} +{'loss': 0.3236, 'learning_rate': 7.932489451476793e-06, 'epoch': 2.29} +{'loss': 0.3268, 'learning_rate': 7.874689324316514e-06, 'epoch': 2.33} +{'loss': 0.3259, 'learning_rate': 7.816889197156234e-06, 'epoch': 2.37} +{'loss': 0.3204, 'learning_rate': 7.759089069995955e-06, 'epoch': 2.41} +{'loss': 0.3272, 'learning_rate': 7.701288942835674e-06, 'epoch': 2.46} +{'loss': 0.3253, 'learning_rate': 7.643488815675396e-06, 'epoch': 2.5} +{'loss': 0.3266, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.34089159965515137, 'eval_accuracy': 0.8710231263494707, 'eval_f1': 0.6943181516508947, 'eval_matthews_correlation': 0.41141785189321783, 'eval_precision': 0.7579919197406763, 'eval_recall': 0.66402126956783, 'eval_runtime': 40.5263, 'eval_samples_per_second': 948.544, 'eval_steps_per_second': 7.427, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:42:33<1:20:04, 2.00it/s]***** Running Evaluation ***** +{'loss': 0.3076, 'learning_rate': 6.892087162591759e-06, 'epoch': 3.04} +{'loss': 0.3112, 'learning_rate': 6.834287035431478e-06, 'epoch': 3.08} +{'loss': 0.3031, 'learning_rate': 6.776486908271199e-06, 'epoch': 3.12} +{'loss': 0.3127, 'learning_rate': 6.718686781110919e-06, 'epoch': 3.16} +{'loss': 0.309, 'learning_rate': 6.660886653950639e-06, 'epoch': 3.2} +{'loss': 0.2985, 'learning_rate': 6.60308652679036e-06, 'epoch': 3.25} +{'loss': 0.3167, 'learning_rate': 6.54528639963008e-06, 'epoch': 3.29} +{'loss': 0.2984, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [2:07:02<1:06:12, 1.81it/s]***** Running Evaluation ***** +{'loss': 0.2988, 'learning_rate': 5.50604011328825e-06, 'epoch': 4.04} +{'loss': 0.2943, 'learning_rate': 5.44823998612797e-06, 'epoch': 4.08} +{'loss': 0.3022, 'learning_rate': 5.39043985896769e-06, 'epoch': 4.12} +{'loss': 0.291, 'learning_rate': 5.332639731807411e-06, 'epoch': 4.16} +{'loss': 0.2809, 'learning_rate': 5.274839604647131e-06, 'epoch': 4.2} +{'loss': 0.2961, 'learning_rate': 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'eval_runtime': 37.7986, 'eval_samples_per_second': 1016.996, 'eval_steps_per_second': 7.963, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [2:31:28<45:10, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.2645, 'learning_rate': 4.118837061441535e-06, 'epoch': 5.04} +{'loss': 0.2736, 'learning_rate': 4.061036934281256e-06, 'epoch': 5.08} +{'loss': 0.2706, 'learning_rate': 4.003236807120976e-06, 'epoch': 5.12} +{'loss': 0.2755, 'learning_rate': 3.9454366799606964e-06, 'epoch': 5.16} +{'loss': 0.2768, 'learning_rate': 3.887636552800417e-06, 'epoch': 5.2} +{'loss': 0.2695, 'learning_rate': 3.829836425640136e-06, 'epoch': 5.24} +{'loss': 0.2661, 'learning_rate': 3.772036298479857e-06, 'epoch': 5.29} +{'loss': 0.2681, 'learning_rate': 3.7142361713195775e-06, 'epoch': 5.33} +{'loss': 0.2771, 'learning_rate': 3.6564360441592974e-06, 'epoch': 5.37} +{'loss': 0.2754, 'learning_rate': 3.5986359169990178e-06, 'epoch': 5.41} +{'loss': 0.2812, 'learning_rate': 3.540835789838738e-06, 'epoch': 5.45} +{'loss': 0.2699, 'learning_rate': 3.4830356626784585e-06, 'epoch': 5.49} +{'loss': 0.2702, 'learning_rate': 3.425813536789781e-06, 'epoch': 5.53} +{'loss': 0.2727, 'learning_rate': 3.3680134096295014e-06, 'epoch': 5.58} +{'loss': 0.2631, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.36378422379493713, 'eval_accuracy': 0.8621523893759268, 'eval_f1': 0.6724645683105058, 'eval_matthews_correlation': 0.3667968767212148, 'eval_precision': 0.7308326779151847, 'eval_recall': 0.6457115495816761, 'eval_runtime': 38.9551, 'eval_samples_per_second': 986.804, 'eval_steps_per_second': 7.727, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:55:51<23:13, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.2643, 'learning_rate': 2.7327900121380267e-06, 'epoch': 6.03} +{'loss': 0.2569, 'learning_rate': 2.6749898849777474e-06, 'epoch': 6.08} +{'loss': 0.2452, 'learning_rate': 2.617189757817468e-06, 'epoch': 6.12} +{'loss': 0.2551, 'learning_rate': 2.5593896306571873e-06, 'epoch': 6.16} +{'loss': 0.257, 'learning_rate': 2.5015895034969077e-06, 'epoch': 6.2} +{'loss': 0.2516, 'learning_rate': 2.4437893763366285e-06, 'epoch': 6.24} +{'loss': 0.258, 'learning_rate': 2.3859892491763484e-06, 'epoch': 6.28} +{'loss': 0.2536, 'learning_rate': 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+{'loss': 0.2576, 'learning_rate': 1.518987341772152e-06, 'epoch': 6.91} +{'loss': 0.2546, 'learning_rate': 1.4611872146118721e-06, 'epoch': 6.95} +{'loss': 0.2502, 'learning_rate': 1.4033870874515925e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [2:56:33<23:13, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.384450763463974, 'eval_accuracy': 0.8540880830363414, 'eval_f1': 0.6753226964873182, 'eval_matthews_correlation': 0.35988011080798166, 'eval_precision': 0.7076824181146517, 'eval_recall': 0.6559035369133495, 'eval_runtime': 41.5488, 'eval_samples_per_second': 925.202, 'eval_steps_per_second': 7.244, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [3:17:29<00:00, 1.71it/s]***** Running Evaluation ***** +{'loss': 0.2385, 'learning_rate': 1.3455869602913126e-06, 'epoch': 7.03} +{'loss': 0.237, 'learning_rate': 1.287786833131033e-06, 'epoch': 7.07} +{'loss': 0.2336, 'learning_rate': 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0.2398, 'learning_rate': 4.2136292699843943e-07, 'epoch': 7.7} +{'loss': 0.2381, 'learning_rate': 3.635627998381597e-07, 'epoch': 7.74} +{'loss': 0.2357, 'learning_rate': 3.0576267267787995e-07, 'epoch': 7.78} +{'loss': 0.2421, 'learning_rate': 2.4796254551760015e-07, 'epoch': 7.82} +{'loss': 0.2354, 'learning_rate': 1.901624183573204e-07, 'epoch': 7.87} +{'loss': 0.245, 'learning_rate': 1.3236229119704064e-07, 'epoch': 7.91} +{'loss': 0.2428, 'learning_rate': 7.456216403676089e-08, 'epoch': 7.95} +{'loss': 0.2361, 'learning_rate': 1.676203687648113e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [3:18:08<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.3981225788593292, 'eval_accuracy': 0.8556749304128405, 'eval_f1': 0.6741656040834971, 'eval_matthews_correlation': 0.35982086510845224, 'eval_precision': 0.7114609313318392, 'eval_recall': 0.6530673469467275, 'eval_runtime': 38.8034, 'eval_samples_per_second': 990.661, 'eval_steps_per_second': 7.757, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209 (score: 0.6943181516508947). +100%|██████████| 19224/19224 [3:18:10<00:00, 1.71it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 11890.294, 'train_samples_per_second': 206.911, 'train_steps_per_second': 1.617, 'train_loss': 0.29957914377221256, 'epoch': 8.0} +100%|██████████| 19224/19224 [3:18:10<00:00, 1.62it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.71it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_045844-9gy218oi/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_045844-9gy218oi/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_045844-9gy218oi/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.05" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.10" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune_3072 + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "572363960320" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [1:10:14<1:01:04, 1.97it/s]***** Running Evaluation ***** +{'loss': 0.6016, 'learning_rate': 7.335080147965476e-06, 'epoch': 2.04} +{'loss': 0.6019, 'learning_rate': 7.258014796547473e-06, 'epoch': 2.08} +{'loss': 0.5984, 'learning_rate': 7.1809494451294705e-06, 'epoch': 2.12} +{'loss': 0.6013, 'learning_rate': 7.103884093711468e-06, 'epoch': 2.16} +{'loss': 0.603, 'learning_rate': 7.026818742293465e-06, 'epoch': 2.21} +{'loss': 0.5965, 'learning_rate': 6.949753390875463e-06, 'epoch': 2.25} +{'loss': 0.6014, 'learning_rate': 6.87268803945746e-06, 'epoch': 2.29} +{'loss': 0.6055, 'learning_rate': 6.795622688039458e-06, 'epoch': 2.33} +{'loss': 0.6008, 'learning_rate': 6.718557336621455e-06, 'epoch': 2.37} +{'loss': 0.5993, 'learning_rate': 6.641491985203453e-06, 'epoch': 2.41} +{'loss': 0.6079, 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Num examples = 38441 + Batch size = 128 + 50%|█████ | 7209/14418 [1:11:05<1:01:04, 1.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.6180990934371948, 'eval_accuracy': 0.6548216747743295, 'eval_f1': 0.6504561052122996, 'eval_matthews_correlation': 0.3065913611733866, 'eval_precision': 0.6555890859511533, 'eval_recall': 0.65103608034509, 'eval_runtime': 50.9086, 'eval_samples_per_second': 755.099, 'eval_steps_per_second': 5.913, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:34:41<40:32, 1.98it/s]***** Running Evaluation ***** +{'loss': 0.5803, 'learning_rate': 5.486282367447596e-06, 'epoch': 3.04} +{'loss': 0.5857, 'learning_rate': 5.409217016029593e-06, 'epoch': 3.08} +{'loss': 0.5842, 'learning_rate': 5.332151664611591e-06, 'epoch': 3.12} +{'loss': 0.5833, 'learning_rate': 5.255086313193588e-06, 'epoch': 3.16} +{'loss': 0.581, 'learning_rate': 5.178020961775586e-06, 'epoch': 3.2} +{'loss': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:24:05<00:00, 2.01it/s]***** Running Evaluation ***** +{'loss': 0.5378, 'learning_rate': 1.7886868064118373e-06, 'epoch': 5.04} +{'loss': 0.5385, 'learning_rate': 1.7116214549938347e-06, 'epoch': 5.08} +{'loss': 0.5376, 'learning_rate': 1.6345561035758326e-06, 'epoch': 5.12} +{'loss': 0.5274, 'learning_rate': 1.55749075215783e-06, 'epoch': 5.16} +{'loss': 0.5336, 'learning_rate': 1.4804254007398274e-06, 'epoch': 5.2} +{'loss': 0.5312, 'learning_rate': 1.4033600493218249e-06, 'epoch': 5.24} +{'loss': 0.5321, 'learning_rate': 1.3262946979038225e-06, 'epoch': 5.29} +{'loss': 0.5353, 'learning_rate': 1.24922934648582e-06, 'epoch': 5.33} +{'loss': 0.5374, 'learning_rate': 1.1729346485819975e-06, 'epoch': 5.37} +{'loss': 0.539, 'learning_rate': 1.0958692971639952e-06, 'epoch': 5.41} +{'loss': 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'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [2:24:55<00:00, 2.0Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.6602907180786133, 'eval_accuracy': 0.6501391743190864, 'eval_f1': 0.6466756214763425, 'eval_matthews_correlation': 0.2969881117903592, 'eval_precision': 0.6500679832066314, 'eval_recall': 0.6469366360833877, 'eval_runtime': 50.1754, 'eval_samples_per_second': 766.133, 'eval_steps_per_second': 5.999, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209 (score: 0.6504561052122996). +100%|██████████| 14418/14418 [2:24:57<00:00, 2.01it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 8697.2068, 'train_samples_per_second': 212.157, 'train_steps_per_second': 1.658, 'train_loss': 0.589636384175809, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:24:57<00:00, 1.66it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.74it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_080101-tzutjz8c/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_080101-tzutjz8c/files/requirements.txt new file 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b/VASC/len2_5120/wandb/run-20260306_081920-oi75mt7c/files/output.log @@ -0,0 +1,368 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.weight', 'bert.pooler.dense.weight', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 10 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 24,030 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 10%|█ | 2403/24030 [23:38<3:17:30, 1.82it/s]***** Running Evaluation ***** +{'loss': 0.5798, 'learning_rate': 4.161464835622139e-07, 'epoch': 0.04} +{'loss': 0.4195, 'learning_rate': 8.322929671244278e-07, 'epoch': 0.08} +{'loss': 0.3723, 'learning_rate': 1.2484394506866417e-06, 'epoch': 0.12} +{'loss': 0.3585, 'learning_rate': 1.6645859342488557e-06, 'epoch': 0.17} +{'loss': 0.3602, 'learning_rate': 2.0807324178110696e-06, 'epoch': 0.21} +{'loss': 0.361, 'learning_rate': 2.4968789013732834e-06, 'epoch': 0.25} +{'loss': 0.36, 'learning_rate': 2.913025384935498e-06, 'epoch': 0.29} +{'loss': 0.3524, 'learning_rate': 3.3291718684977113e-06, 'epoch': 0.33} +{'loss': 0.3601, 'learning_rate': 3.7453183520599255e-06, 'epoch': 0.37} +{'loss': 0.3568, 'learning_rate': 4.161464835622139e-06, 'epoch': 0.42} +{'loss': 0.3547, 'learning_rate': 4.5776113191843534e-06, 'epoch': 0.46} +{'loss': 0.3599, 'learning_rate': 4.993757802746567e-06, 'epoch': 0.5} +{'loss': 0.3518, 'learning_rate': 5.409904286308782e-06, 'epoch': 0.54} +{'loss': 0.3501, 'learning_rate': 5.826050769870996e-06, 'epoch': 0.58} +{'loss': 0.358, 'learning_rate': 6.2421972534332085e-06, 'epoch': 0.62} +{'loss': 0.3474, 'learning_rate': 6.658343736995423e-06, 'epoch': 0.67} +{'loss': 0.3491, 'learning_rate': 7.074490220557637e-06, 'epoch': 0.71} +{'loss': 0.3452, 'learning_rate': 7.490636704119851e-06, 'epoch': 0.75} +{'loss': 0.3572, 'learning_rate': 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'eval_recall': 0.6343484534609721, 'eval_runtime': 41.3183, 'eval_samples_per_second': 930.362, 'eval_steps_per_second': 7.285, 'epoch': 1.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-2403/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-2403/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-2403/special_tokens_map.json + 20%|██ | 4806/24030 [48:13<3:05:08, 1.73it/s]***** Running Evaluation ***** +{'loss': 0.3422, 'learning_rate': 9.95514865677163e-06, 'epoch': 1.04} +{'loss': 0.3494, 'learning_rate': 9.90891015859805e-06, 'epoch': 1.08} +{'loss': 0.3411, 'learning_rate': 9.862671660424469e-06, 'epoch': 1.12} +{'loss': 0.3337, 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+{'loss': 0.3352, 'learning_rate': 9.169094187820781e-06, 'epoch': 1.75} +{'loss': 0.3474, 'learning_rate': 9.122855689647201e-06, 'epoch': 1.79} +{'loss': 0.3411, 'learning_rate': 9.076617191473621e-06, 'epoch': 1.83} +{'loss': 0.3373, 'learning_rate': 9.030378693300042e-06, 'epoch': 1.87} +{'loss': 0.335, 'learning_rate': 8.984140195126462e-06, 'epoch': 1.91} +{'loss': 0.334, 'learning_rate': 8.937901696952884e-06, 'epoch': 1.96} +{'loss': 0.3259, 'learning_rate': 8.891663198779304e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [48:51<3:05:08, 1.73Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 0.3383219242095947, 'eval_accuracy': 0.8740667516453786, 'eval_f1': 0.672976075228713, 'eval_matthews_correlation': 0.3973523486439711, 'eval_precision': 0.7873659508963543, 'eval_recall': 0.637358730636312, 'eval_runtime': 37.4473, 'eval_samples_per_second': 1026.535, 'eval_steps_per_second': 8.038, 'epoch': 2.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-2403] due to args.save_total_limit + 30%|███ | 7209/24030 [1:12:38<2:33:10, 1.83it/s]***** Running Evaluation ***** +{'loss': 0.3244, 'learning_rate': 8.845424700605725e-06, 'epoch': 2.04} +{'loss': 0.3336, 'learning_rate': 8.799186202432147e-06, 'epoch': 2.08} +{'loss': 0.3244, 'learning_rate': 8.752947704258567e-06, 'epoch': 2.12} +{'loss': 0.3218, 'learning_rate': 8.706709206084987e-06, 'epoch': 2.16} +{'loss': 0.322, 'learning_rate': 8.660470707911408e-06, 'epoch': 2.21} +{'loss': 0.3267, 'learning_rate': 8.614232209737828e-06, 'epoch': 2.25} +{'loss': 0.3236, 'learning_rate': 8.567993711564248e-06, 'epoch': 2.29} +{'loss': 0.3286, 'learning_rate': 8.52175521339067e-06, 'epoch': 2.33} +{'loss': 0.3262, 'learning_rate': 8.47551671521709e-06, 'epoch': 2.37} +{'loss': 0.3242, 'learning_rate': 8.429278217043511e-06, 'epoch': 2.41} +{'loss': 0.3285, 'learning_rate': 8.383039718869931e-06, 'epoch': 2.46} +{'loss': 0.327, 'learning_rate': 8.336801220696353e-06, 'epoch': 2.5} +{'loss': 0.3269, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3366641104221344, 'eval_accuracy': 0.8728440987487318, 'eval_f1': 0.6914290483644117, 'eval_matthews_correlation': 0.4119967875063894, 'eval_precision': 0.7672889692329559, 'eval_recall': 0.6587620257980482, 'eval_runtime': 36.5517, 'eval_samples_per_second': 1051.688, 'eval_steps_per_second': 8.235, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:36:52<2:04:43, 1.93it/s]***** Running Evaluation ***** +{'loss': 0.3086, 'learning_rate': 7.735700744439821e-06, 'epoch': 3.04} +{'loss': 0.3139, 'learning_rate': 7.689462246266241e-06, 'epoch': 3.08} +{'loss': 0.3052, 'learning_rate': 7.643223748092663e-06, 'epoch': 3.12} +{'loss': 0.3144, 'learning_rate': 7.596985249919083e-06, 'epoch': 3.16} +{'loss': 0.3095, 'learning_rate': 7.550746751745504e-06, 'epoch': 3.2} +{'loss': 0.3006, 'learning_rate': 7.504508253571925e-06, 'epoch': 3.25} +{'loss': 0.3173, 'learning_rate': 7.458269755398345e-06, 'epoch': 3.29} +{'loss': 0.2994, 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3.87} +{'loss': 0.3081, 'learning_rate': 6.765617052758126e-06, 'epoch': 3.91} +{'loss': 0.3126, 'learning_rate': 6.719378554584548e-06, 'epoch': 3.95} +{'loss': 0.3131, 'learning_rate': 6.673140056410969e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 40%|████ | 9612/24030 [1:37:31<2:04:43, 1.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612/config.json +{'eval_loss': 0.3399481773376465, 'eval_accuracy': 0.8702427096069301, 'eval_f1': 0.6947547896463387, 'eval_matthews_correlation': 0.4104421759936678, 'eval_precision': 0.7547212653092816, 'eval_recall': 0.6653403178076533, 'eval_runtime': 39.1478, 'eval_samples_per_second': 981.945, 'eval_steps_per_second': 7.689, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209] due to args.save_total_limit + 50%|█████ | 12015/24030 [2:01:34<1:38:55, 2.02it/s]***** Running Evaluation ***** +{'loss': 0.3005, 'learning_rate': 6.6269015582373886e-06, 'epoch': 4.04} +{'loss': 0.2967, 'learning_rate': 6.58066306006381e-06, 'epoch': 4.08} +{'loss': 0.3003, 'learning_rate': 6.53442456189023e-06, 'epoch': 4.12} +{'loss': 0.2909, 'learning_rate': 6.488186063716651e-06, 'epoch': 4.16} +{'loss': 0.2859, 'learning_rate': 6.4419475655430715e-06, 'epoch': 4.2} +{'loss': 0.2971, 'learning_rate': 6.395709067369492e-06, 'epoch': 4.24} +{'loss': 0.2945, 'learning_rate': 6.349470569195914e-06, 'epoch': 4.29} +{'loss': 0.2929, 'learning_rate': 6.303232071022334e-06, 'epoch': 4.33} +{'loss': 0.3013, 'learning_rate': 6.2569935728487545e-06, 'epoch': 4.37} +{'loss': 0.3015, 'learning_rate': 6.210755074675175e-06, 'epoch': 4.41} +{'loss': 0.2961, 'learning_rate': 6.164516576501596e-06, 'epoch': 4.45} +{'loss': 0.2916, 'learning_rate': 6.118278078328016e-06, 'epoch': 4.49} +{'loss': 0.2942, 'learning_rate': 6.0720395801544375e-06, 'epoch': 4.54} +{'loss': 0.2958, 'learning_rate': 6.025801081980857e-06, 'epoch': 4.58} +{'loss': 0.2999, 'learning_rate': 5.979562583807278e-06, 'epoch': 4.62} +{'loss': 0.2825, 'learning_rate': 5.9333240856337e-06, 'epoch': 4.66} +{'loss': 0.294, 'learning_rate': 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'eval_accuracy': 0.863895320100934, 'eval_f1': 0.6875578875234374, 'eval_matthews_correlation': 0.39022015207090466, 'eval_precision': 0.7343246262848148, 'eval_recall': 0.662458134998963, 'eval_runtime': 39.1329, 'eval_samples_per_second': 982.32, 'eval_steps_per_second': 7.692, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/special_tokens_map.json + 60%|██████ | 14418/24030 [2:23:14<1:23:36, 1.92it/s]***** Running Evaluation ***** +{'loss': 0.2663, 'learning_rate': 5.5176399870532206e-06, 'epoch': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3548859655857086, 'eval_accuracy': 0.8650139174319086, 'eval_f1': 0.6782947412555678, 'eval_matthews_correlation': 0.37963664867620733, 'eval_precision': 0.7399347552299731, 'eval_recall': 0.6501699752501069, 'eval_runtime': 37.2519, 'eval_samples_per_second': 1031.921, 'eval_steps_per_second': 8.08, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:47:52<1:08:49, 1.75it/s]***** Running Evaluation ***** +{'loss': 0.2591, 'learning_rate': 4.407916030887317e-06, 'epoch': 6.03} +{'loss': 0.256, 'learning_rate': 4.361677532713738e-06, 'epoch': 6.08} +{'loss': 0.2446, 'learning_rate': 4.315439034540159e-06, 'epoch': 6.12} +{'loss': 0.2586, 'learning_rate': 4.269200536366579e-06, 'epoch': 6.16} +{'loss': 0.2586, 'learning_rate': 4.222962038193e-06, 'epoch': 6.2} +{'loss': 0.2518, 'learning_rate': 4.17672354001942e-06, 'epoch': 6.24} +{'loss': 0.2523, 'learning_rate': 4.130485041845841e-06, 'epoch': 6.28} +{'loss': 0.2498, 'learning_rate': 4.084246543672262e-06, 'epoch': 6.33} +{'loss': 0.2534, 'learning_rate': 4.038008045498683e-06, 'epoch': 6.37} +{'loss': 0.2502, 'learning_rate': 3.991769547325103e-06, 'epoch': 6.41} +{'loss': 0.2585, 'learning_rate': 3.945531049151523e-06, 'epoch': 6.45} +{'loss': 0.2497, 'learning_rate': 3.899292550977945e-06, 'epoch': 6.49} +{'loss': 0.2491, 'learning_rate': 3.8530540528043656e-06, 'epoch': 6.53} +{'loss': 0.2494, 'learning_rate': 3.8068155546307863e-06, 'epoch': 6.58} +{'loss': 0.244, 'learning_rate': 3.760577056457206e-06, 'epoch': 6.62} +{'loss': 0.2573, 'learning_rate': 3.7143385582836274e-06, 'epoch': 6.66} +{'loss': 0.2534, 'learning_rate': 3.668100060110048e-06, 'epoch': 6.7} +{'loss': 0.2476, 'learning_rate': 3.6223239469182043e-06, 'epoch': 6.74} +{'loss': 0.2521, 'learning_rate': 3.576085448744625e-06, 'epoch': 6.78} +{'loss': 0.2664, 'learning_rate': 3.529846950571046e-06, 'epoch': 6.82} +{'loss': 0.253, 'learning_rate': 3.483608452397466e-06, 'epoch': 6.87} +{'loss': 0.2486, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:12:30<39:53, 2.01it/s]***** Running Evaluation ***** +{'loss': 0.234, 'learning_rate': 3.298654459703149e-06, 'epoch': 7.03} +{'loss': 0.2274, 'learning_rate': 3.25241596152957e-06, 'epoch': 7.07} +{'loss': 0.2253, 'learning_rate': 3.2061774633559906e-06, 'epoch': 7.12} +{'loss': 0.2406, 'learning_rate': 3.1599389651824113e-06, 'epoch': 7.16} +{'loss': 0.2278, 'learning_rate': 3.1137004670088316e-06, 'epoch': 7.2} +{'loss': 0.2384, 'learning_rate': 3.0674619688352524e-06, 'epoch': 7.24} +{'loss': 0.2299, 'learning_rate': 3.021223470661673e-06, 'epoch': 7.28} +{'loss': 0.2299, 'learning_rate': 2.9749849724880934e-06, 'epoch': 7.32} +{'loss': 0.2346, 'learning_rate': 2.9287464743145146e-06, 'epoch': 7.37} +{'loss': 0.2212, 'learning_rate': 2.8825079761409353e-06, 'epoch': 7.41} +{'loss': 0.2284, 'learning_rate': 2.836269477967356e-06, 'epoch': 7.45} +{'loss': 0.2324, 'learning_rate': 2.7900309797937764e-06, 'epoch': 7.49} +{'loss': 0.236, 'learning_rate': 2.743792481620197e-06, 'epoch': 7.53} +{'loss': 0.237, 'learning_rate': 2.698016368428354e-06, 'epoch': 7.57} +{'loss': 0.2394, 'learning_rate': 2.651777870254774e-06, 'epoch': 7.62} +{'loss': 0.2321, 'learning_rate': 2.605539372081195e-06, 'epoch': 7.66} +{'loss': 0.235, 'learning_rate': 2.559300873907616e-06, 'epoch': 7.7} +{'loss': 0.2327, 'learning_rate': 2.513062375734036e-06, 'epoch': 7.74} +{'loss': 0.2218, 'learning_rate': 2.466823877560457e-06, 'epoch': 7.78} +{'loss': 0.2377, 'learning_rate': 2.420585379386878e-06, 'epoch': 7.82} +{'loss': 0.2333, 'learning_rate': 2.374346881213298e-06, 'epoch': 7.87} +{'loss': 0.2368, 'learning_rate': 2.3281083830397193e-06, 'epoch': 7.91} +{'loss': 0.2317, 'learning_rate': 2.2818698848661396e-06, 'epoch': 7.95} +{'loss': 0.225, 'learning_rate': 2.2356313866925604e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:13:07<39:53, 2.0Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.40971046686172485, 'eval_accuracy': 0.8513566244374496, 'eval_f1': 0.6701792083587723, 'eval_matthews_correlation': 0.34903572591121906, 'eval_precision': 0.7007214598537079, 'eval_recall': 0.6517350686508088, 'eval_runtime': 37.2314, 'eval_samples_per_second': 1032.489, 'eval_steps_per_second': 8.085, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:37:04<22:32, 1.78it/s]***** Running Evaluation ***** +{'loss': 0.2064, 'learning_rate': 2.189392888518981e-06, 'epoch': 8.03} +{'loss': 0.2094, 'learning_rate': 2.1431543903454014e-06, 'epoch': 8.07} +{'loss': 0.2149, 'learning_rate': 2.0969158921718226e-06, 'epoch': 8.11} +{'loss': 0.2101, 'learning_rate': 2.050677393998243e-06, 'epoch': 8.16} +{'loss': 0.2095, 'learning_rate': 2.0044388958246636e-06, 'epoch': 8.2} +{'loss': 0.2119, 'learning_rate': 1.9582003976510844e-06, 'epoch': 8.24} +{'loss': 0.2182, 'learning_rate': 1.911961899477505e-06, 'epoch': 8.28} +{'loss': 0.216, 'learning_rate': 1.8657234013039259e-06, 'epoch': 8.32} +{'loss': 0.2105, 'learning_rate': 1.8194849031303466e-06, 'epoch': 8.36} +{'loss': 0.2168, 'learning_rate': 1.773708789938503e-06, 'epoch': 8.41} +{'loss': 0.2147, 'learning_rate': 1.7274702917649236e-06, 'epoch': 8.45} +{'loss': 0.2135, 'learning_rate': 1.6812317935913443e-06, 'epoch': 8.49} +{'loss': 0.2126, 'learning_rate': 1.634993295417765e-06, 'epoch': 8.53} +{'loss': 0.21, 'learning_rate': 1.5887547972441856e-06, 'epoch': 8.57} +{'loss': 0.214, 'learning_rate': 1.5425162990706063e-06, 'epoch': 8.61} +{'loss': 0.2155, 'learning_rate': 1.4962778008970269e-06, 'epoch': 8.66} +{'loss': 0.2168, 'learning_rate': 1.4500393027234478e-06, 'epoch': 8.7} +{'loss': 0.2171, 'learning_rate': 1.4038008045498683e-06, 'epoch': 8.74} +{'loss': 0.2165, 'learning_rate': 1.357562306376289e-06, 'epoch': 8.78} +{'loss': 0.211, 'learning_rate': 1.3113238082027096e-06, 'epoch': 8.82} +{'loss': 0.2117, 'learning_rate': 1.2650853100291306e-06, 'epoch': 8.86} +{'loss': 0.2126, 'learning_rate': 1.218846811855551e-06, 'epoch': 8.91} +{'loss': 0.2209, 'learning_rate': 1.1726083136819716e-06, 'epoch': 8.95} +{'loss': 0.2223, 'learning_rate': 1.1263698155083924e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:37:44<22:32, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.42344996333122253, 'eval_accuracy': 0.853489763533727, 'eval_f1': 0.6722154314118796, 'eval_matthews_correlation': 0.3543951414921603, 'eval_precision': 0.7059049372874981, 'eval_recall': 0.6524925992156795, 'eval_runtime': 39.5805, 'eval_samples_per_second': 971.211, 'eval_steps_per_second': 7.605, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [4:01:39<00:00, 2.01it/s]***** Running Evaluation ***** +{'loss': 0.1988, 'learning_rate': 1.0805937023165488e-06, 'epoch': 9.03} +{'loss': 0.209, 'learning_rate': 1.0343552041429696e-06, 'epoch': 9.07} +{'loss': 0.193, 'learning_rate': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612 (score: 0.6947547896463387). +100%|██████████| 24030/24030 [4:02:21<00:00, 2.01it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 14541.6685, 'train_samples_per_second': 211.481, 'train_steps_per_second': 1.652, 'train_loss': 0.2808723733467804, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:02:21<00:00, 1.65it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.78it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_081920-oi75mt7c/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_081920-oi75mt7c/files/requirements.txt new file 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b/VASC/len2_5120/wandb/run-20260306_102817-i0tfydre/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['classifier.bias', 'classifier.weight', 'bert.pooler.dense.weight', 'bert.pooler.dense.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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args.save_total_limit + 38%|███▊ | 7209/19224 [1:13:09<1:50:01, 1.82it/s]***** Running Evaluation ***** +{'loss': 0.609, 'learning_rate': 8.279290214438472e-06, 'epoch': 2.04} +{'loss': 0.6069, 'learning_rate': 8.221490087278192e-06, 'epoch': 2.08} +{'loss': 0.604, 'learning_rate': 8.163689960117913e-06, 'epoch': 2.12} +{'loss': 0.6106, 'learning_rate': 8.105889832957633e-06, 'epoch': 2.16} +{'loss': 0.6073, 'learning_rate': 8.048089705797354e-06, 'epoch': 2.21} +{'loss': 0.6013, 'learning_rate': 7.990289578637073e-06, 'epoch': 2.25} +{'loss': 0.608, 'learning_rate': 7.932489451476793e-06, 'epoch': 2.29} +{'loss': 0.6129, 'learning_rate': 7.874689324316514e-06, 'epoch': 2.33} +{'loss': 0.6067, 'learning_rate': 7.816889197156234e-06, 'epoch': 2.37} +{'loss': 0.6078, 'learning_rate': 7.759089069995955e-06, 'epoch': 2.41} +{'loss': 0.6125, 'learning_rate': 7.701288942835674e-06, 'epoch': 2.46} +{'loss': 0.613, 'learning_rate': 7.643488815675396e-06, 'epoch': 2.5} +{'loss': 0.6085, 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.617188572883606, 'eval_accuracy': 0.6534689524205926, 'eval_f1': 0.6496757958185565, 'eval_matthews_correlation': 0.30375001885390207, 'eval_precision': 0.6537337310707122, 'eval_recall': 0.6500387607052021, 'eval_runtime': 53.9166, 'eval_samples_per_second': 712.972, 'eval_steps_per_second': 5.583, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:37:49<1:29:32, 1.79it/s]***** Running Evaluation ***** +{'loss': 0.5918, 'learning_rate': 6.892665163863361e-06, 'epoch': 3.04} +{'loss': 0.5984, 'learning_rate': 6.834865036703081e-06, 'epoch': 3.08} +{'loss': 0.5932, 'learning_rate': 6.777064909542802e-06, 'epoch': 3.12} +{'loss': 0.5971, 'learning_rate': 6.7192647823825215e-06, 'epoch': 3.16} +{'loss': 0.5929, 'learning_rate': 6.661464655222242e-06, 'epoch': 3.2} +{'loss': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [2:24:23<46:15, 1.73it/s]***** Running Evaluation ***** +{'loss': 0.5556, 'learning_rate': 4.119415062713139e-06, 'epoch': 5.04} +{'loss': 0.5571, 'learning_rate': 4.061614935552858e-06, 'epoch': 5.08} +{'loss': 0.5528, 'learning_rate': 4.004392809664181e-06, 'epoch': 5.12} +{'loss': 0.5471, 'learning_rate': 3.9465926825039016e-06, 'epoch': 5.16} +{'loss': 0.5455, 'learning_rate': 3.888792555343622e-06, 'epoch': 5.2} +{'loss': 0.5515, 'learning_rate': 3.830992428183342e-06, 'epoch': 5.24} +{'loss': 0.5449, 'learning_rate': 3.7731923010230627e-06, 'epoch': 5.29} +{'loss': 0.5546, 'learning_rate': 3.715392173862783e-06, 'epoch': 5.33} +{'loss': 0.554, 'learning_rate': 3.657592046702503e-06, 'epoch': 5.37} +{'loss': 0.5524, 'learning_rate': 3.5997919195422233e-06, 'epoch': 5.41} +{'loss': 0.5546, 'learning_rate': 3.5419917923819437e-06, 'epoch': 5.45} +{'loss': 0.5552, 'learning_rate': 3.484191665221664e-06, 'epoch': 5.49} +{'loss': 0.5572, 'learning_rate': 3.426391538061384e-06, 'epoch': 5.53} +{'loss': 0.5526, 'learning_rate': 3.3685914109011044e-06, 'epoch': 5.58} +{'loss': 0.5555, 'learning_rate': 3.3107912837408247e-06, 'epoch': 5.62} +{'loss': 0.5477, 'learning_rate': 3.252991156580545e-06, 'epoch': 5.66} +{'loss': 0.5505, 'learning_rate': 3.195191029420265e-06, 'epoch': 5.7} +{'loss': 0.5565, 'learning_rate': 3.1373909022599854e-06, 'epoch': 5.74} +{'loss': 0.5597, 'learning_rate': 3.0795907750997057e-06, 'epoch': 5.78} +{'loss': 0.5524, 'learning_rate': 3.0217906479394253e-06, 'epoch': 5.83} +{'loss': 0.5537, 'learning_rate': 2.963990520779146e-06, 'epoch': 5.87} +{'loss': 0.5461, 'learning_rate': 2.9061903936188664e-06, 'epoch': 5.91} +{'loss': 0.5512, 'learning_rate': 2.8483902664585868e-06, 'epoch': 5.95} +{'loss': 0.5513, 'learning_rate': 2.7905901392983063e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [2:25:15<46:15, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.6433835029602051, 'eval_accuracy': 0.6515439244556593, 'eval_f1': 0.6467590153475338, 'eval_matthews_correlation': 0.3000076442267874, 'eval_precision': 0.652513163484879, 'eval_recall': 0.6475357676313465, 'eval_runtime': 51.5383, 'eval_samples_per_second': 745.872, 'eval_steps_per_second': 5.84, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:49:10<23:13, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.5391, 'learning_rate': 2.7327900121380267e-06, 'epoch': 6.03} +{'loss': 0.5309, 'learning_rate': 2.6749898849777474e-06, 'epoch': 6.08} +{'loss': 0.5287, 'learning_rate': 2.617189757817468e-06, 'epoch': 6.12} +{'loss': 0.5326, 'learning_rate': 2.5593896306571873e-06, 'epoch': 6.16} +{'loss': 0.5321, 'learning_rate': 2.5015895034969077e-06, 'epoch': 6.2} +{'loss': 0.5176, 'learning_rate': 2.4437893763366285e-06, 'epoch': 6.24} +{'loss': 0.5348, 'learning_rate': 2.3859892491763484e-06, 'epoch': 6.28} +{'loss': 0.5263, 'learning_rate': 2.3281891220160684e-06, 'epoch': 6.33} +{'loss': 0.5365, 'learning_rate': 2.2703889948557887e-06, 'epoch': 6.37} +{'loss': 0.5356, 'learning_rate': 2.212588867695509e-06, 'epoch': 6.41} +{'loss': 0.5276, 'learning_rate': 2.1547887405352294e-06, 'epoch': 6.45} +{'loss': 0.5308, 'learning_rate': 2.0969886133749494e-06, 'epoch': 6.49} +{'loss': 0.5392, 'learning_rate': 2.0391884862146698e-06, 'epoch': 6.53} +{'loss': 0.5283, 'learning_rate': 1.98138835905439e-06, 'epoch': 6.58} +{'loss': 0.5351, 'learning_rate': 1.9235882318941105e-06, 'epoch': 6.62} +{'loss': 0.5215, 'learning_rate': 1.8657881047338306e-06, 'epoch': 6.66} +{'loss': 0.5375, 'learning_rate': 1.8085659788451538e-06, 'epoch': 6.7} +{'loss': 0.535, 'learning_rate': 1.750765851684874e-06, 'epoch': 6.74} +{'loss': 0.5318, 'learning_rate': 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'eval_precision': 0.6509402510812907, 'eval_recall': 0.646667111863367, 'eval_runtime': 49.7077, 'eval_samples_per_second': 773.341, 'eval_steps_per_second': 6.055, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [3:13:50<00:00, 1.71it/s]***** Running Evaluation ***** +{'loss': 0.5143, 'learning_rate': 1.3461649615629154e-06, 'epoch': 7.03} +{'loss': 0.5206, 'learning_rate': 1.2883648344026358e-06, 'epoch': 7.07} +{'loss': 0.5183, 'learning_rate': 1.230564707242356e-06, 'epoch': 7.12} +{'loss': 0.5192, 'learning_rate': 1.1727645800820763e-06, 'epoch': 7.16} +{'loss': 0.5077, 'learning_rate': 1.1149644529217964e-06, 'epoch': 7.2} +{'loss': 0.5155, 'learning_rate': 1.0571643257615168e-06, 'epoch': 7.24} +{'loss': 0.5208, 'learning_rate': 9.99364198601237e-07, 'epoch': 7.28} +{'loss': 0.5102, 'learning_rate': 9.415640714409572e-07, 'epoch': 7.32} +{'loss': 0.5162, 'learning_rate': 8.837639442806775e-07, 'epoch': 7.37} +{'loss': 0.5185, 'learning_rate': 8.259638171203977e-07, 'epoch': 7.41} +{'loss': 0.5152, 'learning_rate': 7.68163689960118e-07, 'epoch': 7.45} +{'loss': 0.5111, 'learning_rate': 7.103635627998383e-07, 'epoch': 7.49} +{'loss': 0.511, 'learning_rate': 6.525634356395584e-07, 'epoch': 7.53} +{'loss': 0.5141, 'learning_rate': 5.947633084792788e-07, 'epoch': 7.57} +{'loss': 0.516, 'learning_rate': 5.36963181318999e-07, 'epoch': 7.62} +{'loss': 0.5179, 'learning_rate': 4.791630541587192e-07, 'epoch': 7.66} +{'loss': 0.5206, 'learning_rate': 4.2136292699843943e-07, 'epoch': 7.7} +{'loss': 0.5125, 'learning_rate': 3.6414080110976247e-07, 'epoch': 7.74} +{'loss': 0.5089, 'learning_rate': 3.0634067394948273e-07, 'epoch': 7.78} +{'loss': 0.5187, 'learning_rate': 2.4854054678920293e-07, 'epoch': 7.82} +{'loss': 0.508, 'learning_rate': 1.907404196289232e-07, 'epoch': 7.87} +{'loss': 0.5207, 'learning_rate': 1.3294029246864345e-07, 'epoch': 7.91} +{'loss': 0.5123, 'learning_rate': 7.514016530836368e-08, 'epoch': 7.95} +{'loss': 0.5069, 'learning_rate': 1.734003814808393e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [3:14:42<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.6793354153633118, 'eval_accuracy': 0.6477719102000469, 'eval_f1': 0.6440151241637564, 'eval_matthews_correlation': 0.29218892616208525, 'eval_precision': 0.6478178728187801, 'eval_recall': 0.6443911465909449, 'eval_runtime': 51.8251, 'eval_samples_per_second': 741.745, 'eval_steps_per_second': 5.808, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209 (score: 0.6496757958185565). +100%|██████████| 19224/19224 [3:14:44<00:00, 1.71it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 11684.5633, 'train_samples_per_second': 210.554, 'train_steps_per_second': 1.645, 'train_loss': 0.5804523634900661, 'epoch': 8.0} +100%|██████████| 19224/19224 [3:14:44<00:00, 1.65it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:04<00:00, 4.65it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_102817-i0tfydre/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_102817-i0tfydre/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_102817-i0tfydre/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.05" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.03" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "573043793920" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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due to args.save_total_limit + 50%|█████ | 7209/14418 [1:13:08<1:09:40, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.3188, 'learning_rate': 6.80586342509832e-06, 'epoch': 2.04} +{'loss': 0.3283, 'learning_rate': 6.7343582409724705e-06, 'epoch': 2.08} +{'loss': 0.3178, 'learning_rate': 6.662853056846622e-06, 'epoch': 2.12} +{'loss': 0.3157, 'learning_rate': 6.5913478727207724e-06, 'epoch': 2.16} +{'loss': 0.3147, 'learning_rate': 6.519842688594924e-06, 'epoch': 2.21} +{'loss': 0.3215, 'learning_rate': 6.448337504469074e-06, 'epoch': 2.25} +{'loss': 0.3185, 'learning_rate': 6.376832320343226e-06, 'epoch': 2.29} +{'loss': 0.3221, 'learning_rate': 6.305327136217376e-06, 'epoch': 2.33} +{'loss': 0.3222, 'learning_rate': 6.2338219520915265e-06, 'epoch': 2.37} +{'loss': 0.3167, 'learning_rate': 6.162316767965678e-06, 'epoch': 2.41} +{'loss': 0.3224, 'learning_rate': 6.0908115838398285e-06, 'epoch': 2.46} +{'loss': 0.321, 'learning_rate': 6.01930639971398e-06, 'epoch': 2.5} +{'loss': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3373173177242279, 'eval_accuracy': 0.8715694180692489, 'eval_f1': 0.6932223251264789, 'eval_matthews_correlation': 0.41121767668795767, 'eval_precision': 0.7607352639270459, 'eval_recall': 0.6621376171693791, 'eval_runtime': 38.6177, 'eval_samples_per_second': 995.424, 'eval_steps_per_second': 7.794, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:35:02<42:59, 1.86it/s]***** Running Evaluation ***** +{'loss': 0.3026, 'learning_rate': 5.0897390060779406e-06, 'epoch': 3.04} +{'loss': 0.3085, 'learning_rate': 5.018233821952092e-06, 'epoch': 3.08} +{'loss': 0.3014, 'learning_rate': 4.946728637826243e-06, 'epoch': 3.12} +{'loss': 0.306, 'learning_rate': 4.8752234537003935e-06, 'epoch': 3.16} +{'loss': 0.3012, 'learning_rate': 4.8037182695745445e-06, 'epoch': 3.2} +{'loss': 0.2942, 'learning_rate': 4.7322130854486955e-06, 'epoch': 3.25} +{'loss': 0.3145, 'learning_rate': 4.6607079013228465e-06, 'epoch': 3.29} +{'loss': 0.2934, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612/special_tokens_map.json + 83%|████████▎ | 12015/14418 [1:59:39<21:06, 1.90it/s]***** Running Evaluation ***** +{'loss': 0.2942, 'learning_rate': 3.3743296388988207e-06, 'epoch': 4.04} +{'loss': 0.2891, 'learning_rate': 3.3028244547729717e-06, 'epoch': 4.08} +{'loss': 0.2974, 'learning_rate': 3.231319270647122e-06, 'epoch': 4.12} +{'loss': 0.2879, 'learning_rate': 3.159814086521273e-06, 'epoch': 4.16} +{'loss': 0.2777, 'learning_rate': 3.0890239542366825e-06, 'epoch': 4.2} +{'loss': 0.2923, 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0.6430254405455149, 'eval_runtime': 40.0385, 'eval_samples_per_second': 960.1, 'eval_steps_per_second': 7.518, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:24:09<00:00, 1.92it/s]***** Running Evaluation ***** +{'loss': 0.2636, 'learning_rate': 1.6596353235609582e-06, 'epoch': 5.04} +{'loss': 0.2794, 'learning_rate': 1.5881301394351092e-06, 'epoch': 5.08} +{'loss': 0.2669, 'learning_rate': 1.5166249553092602e-06, 'epoch': 5.12} +{'loss': 0.276, 'learning_rate': 1.4451197711834108e-06, 'epoch': 5.16} +{'loss': 0.2805, 'learning_rate': 1.3736145870575618e-06, 'epoch': 5.2} +{'loss': 0.2711, 'learning_rate': 1.3021094029317127e-06, 'epoch': 5.24} +{'loss': 0.2681, 'learning_rate': 1.2306042188058635e-06, 'epoch': 5.29} +{'loss': 0.2673, 'learning_rate': 1.1590990346800143e-06, 'epoch': 5.33} +{'loss': 0.2758, 'learning_rate': 1.0875938505541653e-06, 'epoch': 5.37} +{'loss': 0.2775, 'learning_rate': 1.016088666428316e-06, 'epoch': 5.41} +{'loss': 0.2745, 'learning_rate': 9.44583482302467e-07, 'epoch': 5.45} +{'loss': 0.2742, 'learning_rate': 8.730782981766178e-07, 'epoch': 5.49} +{'loss': 0.272, 'learning_rate': 8.015731140507688e-07, 'epoch': 5.53} +{'loss': 0.2771, 'learning_rate': 7.300679299249196e-07, 'epoch': 5.58} +{'loss': 0.2597, 'learning_rate': 6.585627457990705e-07, 'epoch': 5.62} +{'loss': 0.2818, 'learning_rate': 5.870575616732214e-07, 'epoch': 5.66} +{'loss': 0.2795, 'learning_rate': 5.155523775473722e-07, 'epoch': 5.7} +{'loss': 0.2701, 'learning_rate': 4.4404719342152313e-07, 'epoch': 5.74} +{'loss': 0.2698, 'learning_rate': 3.72542009295674e-07, 'epoch': 5.78} +{'loss': 0.265, 'learning_rate': 3.0103682516982484e-07, 'epoch': 5.83} +{'loss': 0.2772, 'learning_rate': 2.302466928852342e-07, 'epoch': 5.87} +{'loss': 0.2707, 'learning_rate': 1.5874150875938507e-07, 'epoch': 5.91} +{'loss': 0.2708, 'learning_rate': 8.723632463353595e-08, 'epoch': 5.95} +{'loss': 0.2718, 'learning_rate': 1.5731140507686808e-08, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [2:24:49<00:00, 1.9Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35984426736831665, 'eval_accuracy': 0.8629588200098853, 'eval_f1': 0.6819767398034526, 'eval_matthews_correlation': 0.3810204200258709, 'eval_precision': 0.7321213950927524, 'eval_recall': 0.6563584438421548, 'eval_runtime': 39.8774, 'eval_samples_per_second': 963.979, 'eval_steps_per_second': 7.548, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209 (score: 0.6932223251264789). +100%|██████████| 14418/14418 [2:24:51<00:00, 1.92it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 8691.181, 'train_samples_per_second': 212.304, 'train_steps_per_second': 1.659, 'train_loss': 0.3124597797877978, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:24:51<00:00, 1.66it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.72it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_122404-z8wzr6oa/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_122404-z8wzr6oa/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_122404-z8wzr6oa/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-2403] due to args.save_total_limit + 30%|███ | 7209/24030 [1:10:24<2:38:27, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.6103, 'learning_rate': 8.845424700605725e-06, 'epoch': 2.04} +{'loss': 0.609, 'learning_rate': 8.799186202432147e-06, 'epoch': 2.08} +{'loss': 0.6048, 'learning_rate': 8.752947704258567e-06, 'epoch': 2.12} +{'loss': 0.6105, 'learning_rate': 8.706709206084987e-06, 'epoch': 2.16} +{'loss': 0.6078, 'learning_rate': 8.660470707911408e-06, 'epoch': 2.21} +{'loss': 0.6022, 'learning_rate': 8.614232209737828e-06, 'epoch': 2.25} +{'loss': 0.6086, 'learning_rate': 8.567993711564248e-06, 'epoch': 2.29} +{'loss': 0.6133, 'learning_rate': 8.52175521339067e-06, 'epoch': 2.33} +{'loss': 0.6068, 'learning_rate': 8.47551671521709e-06, 'epoch': 2.37} +{'loss': 0.6079, 'learning_rate': 8.429278217043511e-06, 'epoch': 2.41} +{'loss': 0.613, 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examples = 38441 + Batch size = 128 + 30%|███ | 7209/24030 [1:11:15<2:38:27, 1.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.6166539192199707, 'eval_accuracy': 0.6536250357691007, 'eval_f1': 0.6509998048711372, 'eval_matthews_correlation': 0.3041407850485982, 'eval_precision': 0.6531469383750805, 'eval_recall': 0.6510014142486917, 'eval_runtime': 51.2322, 'eval_samples_per_second': 750.329, 'eval_steps_per_second': 5.875, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:35:03<2:14:22, 1.79it/s]***** Running Evaluation ***** +{'loss': 0.5922, 'learning_rate': 7.736163129421557e-06, 'epoch': 3.04} +{'loss': 0.5975, 'learning_rate': 7.689924631247978e-06, 'epoch': 3.08} +{'loss': 0.5927, 'learning_rate': 7.643686133074398e-06, 'epoch': 3.12} +{'loss': 0.5964, 'learning_rate': 7.597447634900819e-06, 'epoch': 3.16} +{'loss': 0.5902, 'learning_rate': 7.55120913672724e-06, 'epoch': 3.2} +{'loss': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [2:24:26<1:25:25, 1.88it/s]***** Running Evaluation ***** +{'loss': 0.551, 'learning_rate': 5.5176399870532206e-06, 'epoch': 5.04} +{'loss': 0.5513, 'learning_rate': 5.471863873861377e-06, 'epoch': 5.08} +{'loss': 0.5485, 'learning_rate': 5.425625375687799e-06, 'epoch': 5.12} +{'loss': 0.5421, 'learning_rate': 5.379386877514219e-06, 'epoch': 5.16} +{'loss': 0.5451, 'learning_rate': 5.3331483793406395e-06, 'epoch': 5.2} +{'loss': 0.549, 'learning_rate': 5.28690988116706e-06, 'epoch': 5.24} +{'loss': 0.5396, 'learning_rate': 5.240671382993481e-06, 'epoch': 5.29} +{'loss': 0.5511, 'learning_rate': 5.194432884819901e-06, 'epoch': 5.33} +{'loss': 0.5543, 'learning_rate': 5.148194386646322e-06, 'epoch': 5.37} +{'loss': 0.5487, 'learning_rate': 5.101955888472742e-06, 'epoch': 5.41} +{'loss': 0.5527, 'learning_rate': 5.055717390299163e-06, 'epoch': 5.45} +{'loss': 0.5496, 'learning_rate': 5.009478892125585e-06, 'epoch': 5.49} +{'loss': 0.5511, 'learning_rate': 4.9632403939520045e-06, 'epoch': 5.53} +{'loss': 0.5475, 'learning_rate': 4.917001895778425e-06, 'epoch': 5.58} +{'loss': 0.5521, 'learning_rate': 4.870763397604846e-06, 'epoch': 5.62} +{'loss': 0.5479, 'learning_rate': 4.824524899431267e-06, 'epoch': 5.66} +{'loss': 0.5486, 'learning_rate': 4.7782864012576875e-06, 'epoch': 5.7} +{'loss': 0.5515, 'learning_rate': 4.732047903084108e-06, 'epoch': 5.74} +{'loss': 0.5531, 'learning_rate': 4.685809404910529e-06, 'epoch': 5.78} +{'loss': 0.5498, 'learning_rate': 4.63957090673695e-06, 'epoch': 5.83} +{'loss': 0.5458, 'learning_rate': 4.5933324085633705e-06, 'epoch': 5.87} +{'loss': 0.5459, 'learning_rate': 4.547093910389791e-06, 'epoch': 5.91} +{'loss': 0.5539, 'learning_rate': 4.501317797197947e-06, 'epoch': 5.95} +{'loss': 0.5496, 'learning_rate': 4.455079299024368e-06, 'epoch': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:49:00<1:07:48, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.5312, 'learning_rate': 4.4088408008507885e-06, 'epoch': 6.03} +{'loss': 0.5227, 'learning_rate': 4.362602302677209e-06, 'epoch': 6.08} +{'loss': 0.5197, 'learning_rate': 4.31636380450363e-06, 'epoch': 6.12} +{'loss': 0.5279, 'learning_rate': 4.270125306330051e-06, 'epoch': 6.16} +{'loss': 0.5266, 'learning_rate': 4.2238868081564715e-06, 'epoch': 6.2} +{'loss': 0.5115, 'learning_rate': 4.177648309982892e-06, 'epoch': 6.24} +{'loss': 0.5249, 'learning_rate': 4.131409811809313e-06, 'epoch': 6.28} +{'loss': 0.5189, 'learning_rate': 4.085171313635734e-06, 'epoch': 6.33} +{'loss': 0.5264, 'learning_rate': 4.0389328154621544e-06, 'epoch': 6.37} +{'loss': 0.5255, 'learning_rate': 3.992694317288574e-06, 'epoch': 6.41} +{'loss': 0.5182, 'learning_rate': 3.946455819114995e-06, 'epoch': 6.45} +{'loss': 0.5271, 'learning_rate': 3.900217320941417e-06, 'epoch': 6.49} +{'loss': 0.5295, 'learning_rate': 3.853978822767837e-06, 'epoch': 6.53} +{'loss': 0.5222, 'learning_rate': 3.8077403245942573e-06, 'epoch': 6.58} +{'loss': 0.532, 'learning_rate': 3.761501826420678e-06, 'epoch': 6.62} +{'loss': 0.514, 'learning_rate': 3.715263328247099e-06, 'epoch': 6.66} +{'loss': 0.5306, 'learning_rate': 3.669024830073519e-06, 'epoch': 6.7} +{'loss': 0.5273, 'learning_rate': 3.6227863318999402e-06, 'epoch': 6.74} +{'loss': 0.5244, 'learning_rate': 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'eval_precision': 0.6508761617864367, 'eval_recall': 0.6435267159145329, 'eval_runtime': 52.8476, 'eval_samples_per_second': 727.394, 'eval_steps_per_second': 5.696, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:13:46<46:56, 1.71it/s]***** Running Evaluation ***** +{'loss': 0.4997, 'learning_rate': 3.2995792296666205e-06, 'epoch': 7.03} +{'loss': 0.5027, 'learning_rate': 3.2533407314930417e-06, 'epoch': 7.07} +{'loss': 0.4989, 'learning_rate': 3.207102233319462e-06, 'epoch': 7.12} +{'loss': 0.5072, 'learning_rate': 3.1608637351458827e-06, 'epoch': 7.16} +{'loss': 0.4917, 'learning_rate': 3.1146252369723035e-06, 'epoch': 7.2} +{'loss': 0.5011, 'learning_rate': 3.068386738798724e-06, 'epoch': 7.24} +{'loss': 0.5061, 'learning_rate': 3.0221482406251445e-06, 'epoch': 7.28} +{'loss': 0.4965, 'learning_rate': 2.9759097424515653e-06, 'epoch': 7.32} +{'loss': 0.4989, 'learning_rate': 2.929671244277986e-06, 'epoch': 7.37} +{'loss': 0.5031, 'learning_rate': 2.8834327461044063e-06, 'epoch': 7.41} +{'loss': 0.5022, 'learning_rate': 2.8371942479308275e-06, 'epoch': 7.45} +{'loss': 0.497, 'learning_rate': 2.7909557497572482e-06, 'epoch': 7.49} +{'loss': 0.4933, 'learning_rate': 2.744717251583669e-06, 'epoch': 7.53} +{'loss': 0.4997, 'learning_rate': 2.6984787534100893e-06, 'epoch': 7.57} +{'loss': 0.501, 'learning_rate': 2.65224025523651e-06, 'epoch': 7.62} +{'loss': 0.4987, 'learning_rate': 2.6060017570629308e-06, 'epoch': 7.66} +{'loss': 0.5024, 'learning_rate': 2.559763258889352e-06, 'epoch': 7.7} +{'loss': 0.4957, 'learning_rate': 2.5139871456975078e-06, 'epoch': 7.74} +{'loss': 0.4955, 'learning_rate': 2.467748647523929e-06, 'epoch': 7.78} +{'loss': 0.505, 'learning_rate': 2.4215101493503492e-06, 'epoch': 7.82} +{'loss': 0.497, 'learning_rate': 2.37527165117677e-06, 'epoch': 7.87} +{'loss': 0.5066, 'learning_rate': 2.3290331530031907e-06, 'epoch': 7.91} +{'loss': 0.4996, 'learning_rate': 2.282794654829611e-06, 'epoch': 7.95} +{'loss': 0.4966, 'learning_rate': 2.236556156656032e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:14:39<46:56, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.6952338814735413, 'eval_accuracy': 0.6420748679795011, 'eval_f1': 0.6384406272501664, 'eval_matthews_correlation': 0.28064553621172056, 'eval_precision': 0.6418655160514251, 'eval_recall': 0.6387967971142008, 'eval_runtime': 53.0036, 'eval_samples_per_second': 725.252, 'eval_steps_per_second': 5.679, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:38:28<20:28, 1.96it/s]***** Running Evaluation ***** +{'loss': 0.4887, 'learning_rate': 2.1903176584824525e-06, 'epoch': 8.03} +{'loss': 0.4764, 'learning_rate': 2.1440791603088733e-06, 'epoch': 8.07} +{'loss': 0.4746, 'learning_rate': 2.097840662135294e-06, 'epoch': 8.11} +{'loss': 0.4784, 'learning_rate': 2.0516021639617147e-06, 'epoch': 8.16} +{'loss': 0.4831, 'learning_rate': 2.0053636657881355e-06, 'epoch': 8.2} +{'loss': 0.4857, 'learning_rate': 1.9591251676145562e-06, 'epoch': 8.24} +{'loss': 0.4794, 'learning_rate': 1.9128866694409765e-06, 'epoch': 8.28} +{'loss': 0.4835, 'learning_rate': 1.8666481712673973e-06, 'epoch': 8.32} +{'loss': 0.4742, 'learning_rate': 1.820409673093818e-06, 'epoch': 8.36} +{'loss': 0.479, 'learning_rate': 1.7741711749202388e-06, 'epoch': 8.41} +{'loss': 0.4716, 'learning_rate': 1.7279326767466595e-06, 'epoch': 8.45} +{'loss': 0.4766, 'learning_rate': 1.68169417857308e-06, 'epoch': 8.49} +{'loss': 0.478, 'learning_rate': 1.6354556803995008e-06, 'epoch': 8.53} +{'loss': 0.4758, 'learning_rate': 1.5892171822259215e-06, 'epoch': 8.57} +{'loss': 0.4792, 'learning_rate': 1.542978684052342e-06, 'epoch': 8.61} +{'loss': 0.4781, 'learning_rate': 1.4972025708604987e-06, 'epoch': 8.66} +{'loss': 0.4847, 'learning_rate': 1.4509640726869192e-06, 'epoch': 8.7} +{'loss': 0.4889, 'learning_rate': 1.4047255745133398e-06, 'epoch': 8.74} +{'loss': 0.4822, 'learning_rate': 1.3584870763397607e-06, 'epoch': 8.78} +{'loss': 0.478, 'learning_rate': 1.3122485781661812e-06, 'epoch': 8.82} +{'loss': 0.4693, 'learning_rate': 1.266010079992602e-06, 'epoch': 8.86} +{'loss': 0.4776, 'learning_rate': 1.2197715818190225e-06, 'epoch': 8.91} +{'loss': 0.4787, 'learning_rate': 1.1735330836454432e-06, 'epoch': 8.95} +{'loss': 0.4904, 'learning_rate': 1.127294585471864e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:39:22<20:28, 1.9Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.7240051627159119, 'eval_accuracy': 0.6392913815977732, 'eval_f1': 0.6349690703203934, 'eval_matthews_correlation': 0.2749851630877595, 'eval_precision': 0.6394023032277475, 'eval_recall': 0.6356090218159152, 'eval_runtime': 53.9249, 'eval_samples_per_second': 712.862, 'eval_steps_per_second': 5.582, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [4:03:05<00:00, 1.81it/s]***** Running Evaluation ***** +{'loss': 0.4733, 'learning_rate': 1.0810560872982845e-06, 'epoch': 9.03} +{'loss': 0.4623, 'learning_rate': 1.0348175891247053e-06, 'epoch': 9.07} +{'loss': 0.4615, 'learning_rate': 9.88579090951126e-07, 'epoch': 9.11} +{'loss': 0.4574, 'learning_rate': 9.423405927775467e-07, 'epoch': 9.16} +{'loss': 0.4613, 'learning_rate': 8.961020946039674e-07, 'epoch': 9.2} +{'loss': 0.4608, 'learning_rate': 8.498635964303881e-07, 'epoch': 9.24} +{'loss': 0.4656, 'learning_rate': 8.036250982568086e-07, 'epoch': 9.28} +{'loss': 0.4634, 'learning_rate': 7.573866000832293e-07, 'epoch': 9.32} +{'loss': 0.4635, 'learning_rate': 7.1114810190965e-07, 'epoch': 9.36} +{'loss': 0.4678, 'learning_rate': 6.649096037360707e-07, 'epoch': 9.4} +{'loss': 0.4638, 'learning_rate': 6.186711055624914e-07, 'epoch': 9.45} +{'loss': 0.4692, 'learning_rate': 5.72432607388912e-07, 'epoch': 9.49} +{'loss': 0.4671, 'learning_rate': 5.261941092153328e-07, 'epoch': 9.53} +{'loss': 0.4611, 'learning_rate': 4.799556110417534e-07, 'epoch': 9.57} +{'loss': 0.4633, 'learning_rate': 4.3371711286817404e-07, 'epoch': 9.61} +{'loss': 0.4632, 'learning_rate': 3.874786146945948e-07, 'epoch': 9.65} +{'loss': 0.466, 'learning_rate': 3.4124011652101547e-07, 'epoch': 9.7} +{'loss': 0.464, 'learning_rate': 2.950016183474361e-07, 'epoch': 9.74} +{'loss': 0.4716, 'learning_rate': 2.4876312017385674e-07, 'epoch': 9.78} +{'loss': 0.4619, 'learning_rate': 2.0252462200027746e-07, 'epoch': 9.82} +{'loss': 0.4559, 'learning_rate': 1.5628612382669814e-07, 'epoch': 9.86} +{'loss': 0.4749, 'learning_rate': 1.1004762565311879e-07, 'epoch': 9.9} +{'loss': 0.4523, 'learning_rate': 6.380912747953947e-08, 'epoch': 9.95} +{'loss': 0.4625, 'learning_rate': 1.7570629305960146e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [4:03:57<00:00, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.7481071352958679, 'eval_accuracy': 0.6391352982492651, 'eval_f1': 0.6347733707322911, 'eval_matthews_correlation': 0.2746692853358322, 'eval_precision': 0.6392652375137695, 'eval_recall': 0.6354308111157989, 'eval_runtime': 51.476, 'eval_samples_per_second': 746.775, 'eval_steps_per_second': 5.847, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209 (score: 0.6509998048711372). +100%|██████████| 24030/24030 [4:03:58<00:00, 1.81it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/INH/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 14638.7593, 'train_samples_per_second': 210.079, 'train_steps_per_second': 1.642, 'train_loss': 0.5562604137822285, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:03:58<00:00, 1.64it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.73it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_134526-s42xzxdh/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_134526-s42xzxdh/files/requirements.txt new 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b/VASC/len2_5120/wandb/run-20260306_145116-6qinnif0/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['classifier.weight', 'bert.pooler.dense.weight', 'classifier.bias', 'bert.pooler.dense.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 8 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 19,224 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 12%|█▎ | 2403/19224 [23:53<2:24:46, 1.94it/s]***** Running Evaluation ***** +{'loss': 0.5409, 'learning_rate': 1.7331022530329292e-06, 'epoch': 0.04} +{'loss': 0.3749, 'learning_rate': 3.4662045060658585e-06, 'epoch': 0.08} +{'loss': 0.3587, 'learning_rate': 5.199306759098788e-06, 'epoch': 0.12} +{'loss': 0.355, 'learning_rate': 6.932409012131717e-06, 'epoch': 0.17} +{'loss': 0.3593, 'learning_rate': 8.665511265164645e-06, 'epoch': 0.21} +{'loss': 0.358, 'learning_rate': 9.987665576232103e-06, 'epoch': 0.25} +{'loss': 0.3554, 'learning_rate': 9.934037646806459e-06, 'epoch': 0.29} +{'loss': 0.3485, 'learning_rate': 9.880409717380811e-06, 'epoch': 0.33} +{'loss': 0.3594, 'learning_rate': 9.826781787955167e-06, 'epoch': 0.37} +{'loss': 0.3537, 'learning_rate': 9.773153858529523e-06, 'epoch': 0.42} +{'loss': 0.353, 'learning_rate': 9.719525929103878e-06, 'epoch': 0.46} +{'loss': 0.3565, 'learning_rate': 9.665897999678234e-06, 'epoch': 0.5} +{'loss': 0.3488, 'learning_rate': 9.612270070252588e-06, 'epoch': 0.54} +{'loss': 0.3465, 'learning_rate': 9.558642140826944e-06, 'epoch': 0.58} +{'loss': 0.3549, 'learning_rate': 9.505014211401298e-06, 'epoch': 0.62} +{'loss': 0.3435, 'learning_rate': 9.451386281975654e-06, 'epoch': 0.67} +{'loss': 0.3456, 'learning_rate': 9.397758352550009e-06, 'epoch': 0.71} +{'loss': 0.3405, 'learning_rate': 9.344130423124363e-06, 'epoch': 0.75} +{'loss': 0.3504, 'learning_rate': 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'eval_recall': 0.6341522499820105, 'eval_runtime': 40.3192, 'eval_samples_per_second': 953.417, 'eval_steps_per_second': 7.465, 'epoch': 1.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-2403/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-2403/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-2403/special_tokens_map.json + 25%|██▌ | 4806/19224 [48:27<2:00:19, 2.00it/s]***** Running Evaluation ***** +{'loss': 0.3345, 'learning_rate': 8.96873491714485e-06, 'epoch': 1.04} +{'loss': 0.3418, 'learning_rate': 8.915106987719206e-06, 'epoch': 1.08} +{'loss': 0.3346, 'learning_rate': 8.86147905829356e-06, 'epoch': 1.12} +{'loss': 0.3286, 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38%|███▊ | 7209/19224 [1:13:00<1:43:19, 1.94it/s]***** Running Evaluation ***** +{'loss': 0.3196, 'learning_rate': 7.681664610929372e-06, 'epoch': 2.04} +{'loss': 0.3285, 'learning_rate': 7.628036681503728e-06, 'epoch': 2.08} +{'loss': 0.3196, 'learning_rate': 7.574408752078083e-06, 'epoch': 2.12} +{'loss': 0.317, 'learning_rate': 7.520780822652438e-06, 'epoch': 2.16} +{'loss': 0.3171, 'learning_rate': 7.4671528932267935e-06, 'epoch': 2.21} +{'loss': 0.3207, 'learning_rate': 7.413524963801149e-06, 'epoch': 2.25} +{'loss': 0.3186, 'learning_rate': 7.359897034375504e-06, 'epoch': 2.29} +{'loss': 0.3226, 'learning_rate': 7.306269104949858e-06, 'epoch': 2.33} +{'loss': 0.3212, 'learning_rate': 7.252641175524213e-06, 'epoch': 2.37} +{'loss': 0.3184, 'learning_rate': 7.199013246098568e-06, 'epoch': 2.41} +{'loss': 0.3232, 'learning_rate': 7.1453853166729235e-06, 'epoch': 2.46} +{'loss': 0.3209, 'learning_rate': 7.091757387247279e-06, 'epoch': 2.5} +{'loss': 0.3222, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3371447026729584, 'eval_accuracy': 0.8726880154002237, 'eval_f1': 0.6945327651056161, 'eval_matthews_correlation': 0.4151759762142593, 'eval_precision': 0.7649356962815601, 'eval_recall': 0.6626537058281833, 'eval_runtime': 41.4343, 'eval_samples_per_second': 927.758, 'eval_steps_per_second': 7.265, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:37:34<1:26:03, 1.86it/s]***** Running Evaluation ***** +{'loss': 0.3029, 'learning_rate': 6.394594304713896e-06, 'epoch': 3.04} +{'loss': 0.3074, 'learning_rate': 6.340966375288251e-06, 'epoch': 3.08} +{'loss': 0.3003, 'learning_rate': 6.287338445862605e-06, 'epoch': 3.12} +{'loss': 0.3065, 'learning_rate': 6.23371051643696e-06, 'epoch': 3.16} +{'loss': 0.3021, 'learning_rate': 6.1800825870113155e-06, 'epoch': 3.2} +{'loss': 0.2953, 'learning_rate': 6.126454657585671e-06, 'epoch': 3.25} +{'loss': 0.3121, 'learning_rate': 6.072826728160026e-06, 'epoch': 3.29} +{'loss': 0.2952, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [2:02:08<1:02:05, 1.94it/s]***** Running Evaluation ***** +{'loss': 0.2968, 'learning_rate': 5.108596557086931e-06, 'epoch': 4.04} +{'loss': 0.289, 'learning_rate': 5.054968627661287e-06, 'epoch': 4.08} +{'loss': 0.2959, 'learning_rate': 5.001340698235642e-06, 'epoch': 4.12} +{'loss': 0.2887, 'learning_rate': 4.947712768809997e-06, 'epoch': 4.16} +{'loss': 0.2773, 'learning_rate': 4.894084839384351e-06, 'epoch': 4.2} +{'loss': 0.2928, 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3617689907550812, 'eval_accuracy': 0.864155459015114, 'eval_f1': 0.6781621096797208, 'eval_matthews_correlation': 0.3778847914618249, 'eval_precision': 0.7368394862503496, 'eval_recall': 0.6507317443967139, 'eval_runtime': 39.2206, 'eval_samples_per_second': 980.122, 'eval_steps_per_second': 7.675, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:51:23<23:50, 1.68it/s]***** Running Evaluation ***** +{'loss': 0.2573, 'learning_rate': 2.5349922239502335e-06, 'epoch': 6.03} +{'loss': 0.2517, 'learning_rate': 2.4813642945245886e-06, 'epoch': 6.08} +{'loss': 0.2433, 'learning_rate': 2.4277363650989438e-06, 'epoch': 6.12} +{'loss': 0.2593, 'learning_rate': 2.374108435673299e-06, 'epoch': 6.16} +{'loss': 0.2524, 'learning_rate': 2.320480506247654e-06, 'epoch': 6.2} +{'loss': 0.2486, 'learning_rate': 2.266852576822009e-06, 'epoch': 6.24} +{'loss': 0.2541, 'learning_rate': 2.2132246473963644e-06, 'epoch': 6.28} +{'loss': 0.2537, 'learning_rate': 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+{'loss': 0.2501, 'learning_rate': 1.4093419853059476e-06, 'epoch': 6.91} +{'loss': 0.2508, 'learning_rate': 1.3557140558803025e-06, 'epoch': 6.95} +{'loss': 0.2484, 'learning_rate': 1.3020861264546577e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [2:52:03<23:50, 1.6Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.38355910778045654, 'eval_accuracy': 0.856455347155381, 'eval_f1': 0.6827942856677309, 'eval_matthews_correlation': 0.3740166185778508, 'eval_precision': 0.7140087380258848, 'eval_recall': 0.6634143917005503, 'eval_runtime': 40.0261, 'eval_samples_per_second': 960.399, 'eval_steps_per_second': 7.52, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [3:13:11<00:00, 1.98it/s]***** Running Evaluation ***** +{'loss': 0.2366, 'learning_rate': 1.2484581970290129e-06, 'epoch': 7.03} +{'loss': 0.2374, 'learning_rate': 1.194830267603368e-06, 'epoch': 7.07} +{'loss': 0.2319, 'learning_rate': 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0.2364, 'learning_rate': 3.9094760551295117e-07, 'epoch': 7.7} +{'loss': 0.2373, 'learning_rate': 3.3731967608730633e-07, 'epoch': 7.74} +{'loss': 0.2291, 'learning_rate': 2.8369174666166143e-07, 'epoch': 7.78} +{'loss': 0.238, 'learning_rate': 2.3006381723601653e-07, 'epoch': 7.82} +{'loss': 0.2377, 'learning_rate': 1.7643588781037166e-07, 'epoch': 7.87} +{'loss': 0.2371, 'learning_rate': 1.228079583847268e-07, 'epoch': 7.91} +{'loss': 0.2384, 'learning_rate': 6.918002895908189e-08, 'epoch': 7.95} +{'loss': 0.2332, 'learning_rate': 1.5552099533437016e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [3:13:53<00:00, 1.9Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.3974858522415161, 'eval_accuracy': 0.8562732499154548, 'eval_f1': 0.6796895995900201, 'eval_matthews_correlation': 0.3689753842559364, 'eval_precision': 0.713340429187685, 'eval_recall': 0.6595370773195608, 'eval_runtime': 41.1948, 'eval_samples_per_second': 933.151, 'eval_steps_per_second': 7.307, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209 (score: 0.6945327651056161). +100%|██████████| 19224/19224 [3:13:54<00:00, 1.98it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 11634.9144, 'train_samples_per_second': 211.453, 'train_steps_per_second': 1.652, 'train_loss': 0.2950773642205021, 'epoch': 8.0} +100%|██████████| 19224/19224 [3:13:55<00:00, 1.65it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:02<00:00, 4.82it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_145116-6qinnif0/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_145116-6qinnif0/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_145116-6qinnif0/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.0" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.03" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune_3072 + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "573709545472" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [1:10:02<1:02:04, 1.94it/s]***** Running Evaluation ***** +{'loss': 0.3204, 'learning_rate': 6.80586342509832e-06, 'epoch': 2.04} +{'loss': 0.3287, 'learning_rate': 6.7343582409724705e-06, 'epoch': 2.08} +{'loss': 0.3207, 'learning_rate': 6.662853056846622e-06, 'epoch': 2.12} +{'loss': 0.3191, 'learning_rate': 6.5913478727207724e-06, 'epoch': 2.16} +{'loss': 0.3202, 'learning_rate': 6.519842688594924e-06, 'epoch': 2.21} +{'loss': 0.3232, 'learning_rate': 6.448337504469074e-06, 'epoch': 2.25} +{'loss': 0.3226, 'learning_rate': 6.376832320343226e-06, 'epoch': 2.29} +{'loss': 0.3279, 'learning_rate': 6.305327136217376e-06, 'epoch': 2.33} +{'loss': 0.3257, 'learning_rate': 6.2338219520915265e-06, 'epoch': 2.37} +{'loss': 0.322, 'learning_rate': 6.162316767965678e-06, 'epoch': 2.41} +{'loss': 0.3258, 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3.0} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 7209/14418 [1:10:43<1:02:04, 1.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.337352454662323, 'eval_accuracy': 0.8714133347207409, 'eval_f1': 0.685610395425335, 'eval_matthews_correlation': 0.40208933482934134, 'eval_precision': 0.7637881900809965, 'eval_recall': 0.653225048791854, 'eval_runtime': 40.9158, 'eval_samples_per_second': 939.515, 'eval_steps_per_second': 7.357, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:34:33<44:33, 1.80it/s]***** Running Evaluation ***** +{'loss': 0.3058, 'learning_rate': 5.0897390060779406e-06, 'epoch': 3.04} +{'loss': 0.3091, 'learning_rate': 5.018233821952092e-06, 'epoch': 3.08} +{'loss': 0.3002, 'learning_rate': 4.946728637826243e-06, 'epoch': 3.12} +{'loss': 0.3101, 'learning_rate': 4.8752234537003935e-06, 'epoch': 3.16} +{'loss': 0.3035, 'learning_rate': 4.8037182695745445e-06, 'epoch': 3.2} +{'loss': 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'epoch': 4.7} +{'loss': 0.2896, 'learning_rate': 2.1594565606006436e-06, 'epoch': 4.74} +{'loss': 0.2813, 'learning_rate': 2.0879513764747945e-06, 'epoch': 4.79} +{'loss': 0.2954, 'learning_rate': 2.0164461923489455e-06, 'epoch': 4.83} +{'loss': 0.2915, 'learning_rate': 1.944941008223096e-06, 'epoch': 4.87} +{'loss': 0.2919, 'learning_rate': 1.8734358240972473e-06, 'epoch': 4.91} +{'loss': 0.2844, 'learning_rate': 1.801930639971398e-06, 'epoch': 4.95} +{'loss': 0.2881, 'learning_rate': 1.7304254558455488e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 83%|████████▎ | 12015/14418 [1:59:44<20:17, 1.9Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-12015/config.json +{'eval_loss': 0.34969809651374817, 'eval_accuracy': 0.8692541817330455, 'eval_f1': 0.6717211838180908, 'eval_matthews_correlation': 0.38148257802644725, 'eval_precision': 0.7607939461278186, 'eval_recall': 0.6395056897394187, 'eval_runtime': 40.5887, 'eval_samples_per_second': 947.087, 'eval_steps_per_second': 7.416, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:23:31<00:00, 1.99it/s]***** Running Evaluation ***** +{'loss': 0.2746, 'learning_rate': 1.6589202717196998e-06, 'epoch': 5.04} +{'loss': 0.284, 'learning_rate': 1.5874150875938508e-06, 'epoch': 5.08} +{'loss': 0.2745, 'learning_rate': 1.5159099034680016e-06, 'epoch': 5.12} +{'loss': 0.273, 'learning_rate': 1.4444047193421524e-06, 'epoch': 5.16} +{'loss': 0.2799, 'learning_rate': 1.3728995352163033e-06, 'epoch': 5.2} +{'loss': 0.2707, 'learning_rate': 1.3013943510904541e-06, 'epoch': 5.24} +{'loss': 0.268, 'learning_rate': 1.229889166964605e-06, 'epoch': 5.29} +{'loss': 0.2685, 'learning_rate': 1.1583839828387559e-06, 'epoch': 5.33} +{'loss': 0.2807, 'learning_rate': 1.0868787987129069e-06, 'epoch': 5.37} +{'loss': 0.2772, 'learning_rate': 1.0153736145870576e-06, 'epoch': 5.41} +{'loss': 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'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [2:24:13<00:00, 1.9Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.36215001344680786, 'eval_accuracy': 0.8674071954423662, 'eval_f1': 0.675180028533375, 'eval_matthews_correlation': 0.38078260091435423, 'eval_precision': 0.7505475952584528, 'eval_recall': 0.644678488142672, 'eval_runtime': 42.2726, 'eval_samples_per_second': 909.359, 'eval_steps_per_second': 7.12, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-7209 (score: 0.685610395425335). +100%|██████████| 14418/14418 [2:24:15<00:00, 1.99it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 8655.5246, 'train_samples_per_second': 213.179, 'train_steps_per_second': 1.666, 'train_loss': 0.31414960607739556, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:24:15<00:00, 1.67it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.73it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_175144-ul5ram0z/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_175144-ul5ram0z/files/requirements.txt new file 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value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 5120 +warmup_ratio: + value: 0.03 +warmup_steps: + value: 0 +weight_decay: + value: 0.05 diff --git a/VASC/len2_5120/wandb/run-20260306_180730-9eaiow92/files/output.log b/VASC/len2_5120/wandb/run-20260306_180730-9eaiow92/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..1713f31665db34526fd9b086163b370a7c5c630f --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_180730-9eaiow92/files/output.log @@ -0,0 +1,368 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['classifier.bias', 'bert.pooler.dense.weight', 'bert.pooler.dense.bias', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 10 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 24,030 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 10%|█ | 2403/24030 [23:53<3:11:46, 1.88it/s]***** Running Evaluation ***** +{'loss': 0.5359, 'learning_rate': 1.3869625520110958e-06, 'epoch': 0.04} +{'loss': 0.381, 'learning_rate': 2.7739251040221917e-06, 'epoch': 0.08} +{'loss': 0.3582, 'learning_rate': 4.160887656033287e-06, 'epoch': 0.12} +{'loss': 0.3554, 'learning_rate': 5.547850208044383e-06, 'epoch': 0.17} +{'loss': 0.3588, 'learning_rate': 6.93481276005548e-06, 'epoch': 0.21} +{'loss': 0.3598, 'learning_rate': 8.321775312066574e-06, 'epoch': 0.25} +{'loss': 0.3581, 'learning_rate': 9.708737864077671e-06, 'epoch': 0.29} +{'loss': 0.3485, 'learning_rate': 9.966107512119783e-06, 'epoch': 0.33} +{'loss': 0.3604, 'learning_rate': 9.923205628727102e-06, 'epoch': 0.37} +{'loss': 0.3551, 'learning_rate': 9.88030374533442e-06, 'epoch': 0.42} +{'loss': 0.3544, 'learning_rate': 9.83740186194174e-06, 'epoch': 0.46} +{'loss': 0.3577, 'learning_rate': 9.79449997854906e-06, 'epoch': 0.5} +{'loss': 0.3491, 'learning_rate': 9.751598095156379e-06, 'epoch': 0.54} +{'loss': 0.3475, 'learning_rate': 9.708696211763697e-06, 'epoch': 0.58} +{'loss': 0.3546, 'learning_rate': 9.665794328371016e-06, 'epoch': 0.62} +{'loss': 0.3446, 'learning_rate': 9.622892444978336e-06, 'epoch': 0.67} +{'loss': 0.3468, 'learning_rate': 9.579990561585655e-06, 'epoch': 0.71} +{'loss': 0.3414, 'learning_rate': 9.537088678192973e-06, 'epoch': 0.75} +{'loss': 0.352, 'learning_rate': 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args.save_total_limit + 30%|███ | 7209/24030 [1:13:08<2:20:57, 1.99it/s]***** Running Evaluation ***** +{'loss': 0.3214, 'learning_rate': 8.207130293019864e-06, 'epoch': 2.04} +{'loss': 0.3311, 'learning_rate': 8.164228409627184e-06, 'epoch': 2.08} +{'loss': 0.3196, 'learning_rate': 8.121326526234501e-06, 'epoch': 2.12} +{'loss': 0.3174, 'learning_rate': 8.078424642841821e-06, 'epoch': 2.16} +{'loss': 0.3175, 'learning_rate': 8.03552275944914e-06, 'epoch': 2.21} +{'loss': 0.3241, 'learning_rate': 7.99262087605646e-06, 'epoch': 2.25} +{'loss': 0.3206, 'learning_rate': 7.949718992663778e-06, 'epoch': 2.29} +{'loss': 0.3249, 'learning_rate': 7.906817109271098e-06, 'epoch': 2.33} +{'loss': 0.3241, 'learning_rate': 7.863915225878417e-06, 'epoch': 2.37} +{'loss': 0.3201, 'learning_rate': 7.821013342485737e-06, 'epoch': 2.41} +{'loss': 0.3248, 'learning_rate': 7.778111459093054e-06, 'epoch': 2.46} +{'loss': 0.3228, 'learning_rate': 7.735209575700374e-06, 'epoch': 2.5} +{'loss': 0.325, 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3367833197116852, 'eval_accuracy': 0.8721677375718634, 'eval_f1': 0.6925807640998711, 'eval_matthews_correlation': 0.4117597383162273, 'eval_precision': 0.7636264074803816, 'eval_recall': 0.6607825290708644, 'eval_runtime': 39.8699, 'eval_samples_per_second': 964.161, 'eval_steps_per_second': 7.55, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:37:42<2:14:48, 1.78it/s]***** Running Evaluation ***** +{'loss': 0.3056, 'learning_rate': 7.1774850915955215e-06, 'epoch': 3.04} +{'loss': 0.3098, 'learning_rate': 7.134583208202841e-06, 'epoch': 3.08} +{'loss': 0.3034, 'learning_rate': 7.09168132481016e-06, 'epoch': 3.12} +{'loss': 0.311, 'learning_rate': 7.048779441417479e-06, 'epoch': 3.16} +{'loss': 0.3066, 'learning_rate': 7.005877558024799e-06, 'epoch': 3.2} +{'loss': 0.2982, 'learning_rate': 6.962975674632117e-06, 'epoch': 3.25} +{'loss': 0.3145, 'learning_rate': 6.920073791239435e-06, 'epoch': 3.29} +{'loss': 0.2975, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-9612/special_tokens_map.json + 50%|█████ | 12015/24030 [2:02:17<1:42:50, 1.95it/s]***** Running Evaluation ***** +{'loss': 0.3004, 'learning_rate': 6.148697927839033e-06, 'epoch': 4.04} +{'loss': 0.2938, 'learning_rate': 6.105796044446351e-06, 'epoch': 4.08} +{'loss': 0.2999, 'learning_rate': 6.062894161053671e-06, 'epoch': 4.12} +{'loss': 0.2912, 'learning_rate': 6.0199922776609896e-06, 'epoch': 4.16} +{'loss': 0.279, 'learning_rate': 5.977090394268309e-06, 'epoch': 4.2} +{'loss': 0.2963, 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0.6507447229811549, 'eval_runtime': 40.1816, 'eval_samples_per_second': 956.681, 'eval_steps_per_second': 7.491, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [2:23:02<1:22:49, 1.93it/s]***** Running Evaluation ***** +{'loss': 0.2635, 'learning_rate': 5.119481745248617e-06, 'epoch': 5.04} +{'loss': 0.274, 'learning_rate': 5.076579861855936e-06, 'epoch': 5.08} +{'loss': 0.2668, 'learning_rate': 5.033677978463255e-06, 'epoch': 5.12} +{'loss': 0.2758, 'learning_rate': 4.990776095070574e-06, 'epoch': 5.16} +{'loss': 0.2794, 'learning_rate': 4.947874211677893e-06, 'epoch': 5.2} +{'loss': 0.2694, 'learning_rate': 4.904972328285212e-06, 'epoch': 5.24} +{'loss': 0.264, 'learning_rate': 4.862070444892531e-06, 'epoch': 5.29} +{'loss': 0.267, 'learning_rate': 4.81916856149985e-06, 'epoch': 5.33} +{'loss': 0.2771, 'learning_rate': 4.776266678107169e-06, 'epoch': 5.37} +{'loss': 0.2751, 'learning_rate': 4.733364794714489e-06, 'epoch': 5.41} +{'loss': 0.281, 'learning_rate': 4.690462911321807e-06, 'epoch': 5.45} +{'loss': 0.271, 'learning_rate': 4.647561027929127e-06, 'epoch': 5.49} +{'loss': 0.2726, 'learning_rate': 4.604659144536446e-06, 'epoch': 5.53} +{'loss': 0.2751, 'learning_rate': 4.561757261143764e-06, 'epoch': 5.58} +{'loss': 0.2649, 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35617581009864807, 'eval_accuracy': 0.8635051117296636, 'eval_f1': 0.676893777397209, 'eval_matthews_correlation': 0.3750556338185711, 'eval_precision': 0.7347890606818959, 'eval_recall': 0.6497799003608952, 'eval_runtime': 38.8357, 'eval_samples_per_second': 989.836, 'eval_steps_per_second': 7.751, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:45:55<1:04:41, 1.86it/s]***** Running Evaluation ***** +{'loss': 0.2606, 'learning_rate': 4.089836543824274e-06, 'epoch': 6.03} +{'loss': 0.2554, 'learning_rate': 4.046934660431593e-06, 'epoch': 6.08} +{'loss': 0.246, 'learning_rate': 4.004032777038913e-06, 'epoch': 6.12} +{'loss': 0.2607, 'learning_rate': 3.961130893646231e-06, 'epoch': 6.16} +{'loss': 0.2553, 'learning_rate': 3.91822901025355e-06, 'epoch': 6.2} +{'loss': 0.2509, 'learning_rate': 3.8753271268608696e-06, 'epoch': 6.24} +{'loss': 0.2535, 'learning_rate': 3.832425243468188e-06, 'epoch': 6.28} +{'loss': 0.2533, 'learning_rate': 3.789523360075508e-06, 'epoch': 6.33} +{'loss': 0.2526, 'learning_rate': 3.746621476682827e-06, 'epoch': 6.37} +{'loss': 0.2514, 'learning_rate': 3.703719593290146e-06, 'epoch': 6.41} +{'loss': 0.2585, 'learning_rate': 3.6608177098974644e-06, 'epoch': 6.45} +{'loss': 0.253, 'learning_rate': 3.6183448453387104e-06, 'epoch': 6.49} +{'loss': 0.2502, 'learning_rate': 3.5754429619460295e-06, 'epoch': 6.53} +{'loss': 0.2478, 'learning_rate': 3.5325410785533486e-06, 'epoch': 6.58} +{'loss': 0.2468, 'learning_rate': 3.4896391951606677e-06, 'epoch': 6.62} +{'loss': 0.253, 'learning_rate': 3.446737311767987e-06, 'epoch': 6.66} +{'loss': 0.2583, 'learning_rate': 3.403835428375306e-06, 'epoch': 6.7} +{'loss': 0.2489, 'learning_rate': 3.360933544982625e-06, 'epoch': 6.74} +{'loss': 0.251, 'learning_rate': 3.318031661589944e-06, 'epoch': 6.78} +{'loss': 0.2691, 'learning_rate': 3.275129778197263e-06, 'epoch': 6.82} +{'loss': 0.2516, 'learning_rate': 3.232227894804582e-06, 'epoch': 6.87} +{'loss': 0.2502, 'learning_rate': 3.1893260114119012e-06, 'epoch': 6.91} +{'loss': 0.2533, 'learning_rate': 3.1464241280192204e-06, 'epoch': 6.95} +{'loss': 0.2523, 'learning_rate': 3.1035222446265395e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [2:46:32<1:04:41, 1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3822759985923767, 'eval_accuracy': 0.8555448609557503, 'eval_f1': 0.6804287960260046, 'eval_matthews_correlation': 0.3693828540788926, 'eval_precision': 0.7116439232314513, 'eval_recall': 0.6611712857191926, 'eval_runtime': 36.771, 'eval_samples_per_second': 1045.417, 'eval_steps_per_second': 8.186, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:08:46<37:12, 2.15it/s]***** Running Evaluation ***** +{'loss': 0.2349, 'learning_rate': 3.0606203612338586e-06, 'epoch': 7.03} +{'loss': 0.228, 'learning_rate': 3.0177184778411773e-06, 'epoch': 7.07} +{'loss': 0.2242, 'learning_rate': 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0.2305, 'learning_rate': 2.3746192457848903e-06, 'epoch': 7.7} +{'loss': 0.2364, 'learning_rate': 2.3317173623922094e-06, 'epoch': 7.74} +{'loss': 0.2303, 'learning_rate': 2.288815478999528e-06, 'epoch': 7.78} +{'loss': 0.238, 'learning_rate': 2.2459135956068473e-06, 'epoch': 7.82} +{'loss': 0.2319, 'learning_rate': 2.2030117122141664e-06, 'epoch': 7.87} +{'loss': 0.2376, 'learning_rate': 2.1601098288214855e-06, 'epoch': 7.91} +{'loss': 0.2364, 'learning_rate': 2.1172079454288042e-06, 'epoch': 7.95} +{'loss': 0.2324, 'learning_rate': 2.0743060620361234e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:09:22<37:12, 2.1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.40386033058166504, 'eval_accuracy': 0.8543742358419396, 'eval_f1': 0.6675487212712516, 'eval_matthews_correlation': 0.34825711259004205, 'eval_precision': 0.7076167302787492, 'eval_recall': 0.6460419595120259, 'eval_runtime': 36.6543, 'eval_samples_per_second': 1048.746, 'eval_steps_per_second': 8.212, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:31:38<21:31, 1.86it/s]***** Running Evaluation ***** +{'loss': 0.2114, 'learning_rate': 2.0314041786434425e-06, 'epoch': 8.03} +{'loss': 0.2107, 'learning_rate': 1.9885022952507616e-06, 'epoch': 8.07} +{'loss': 0.2164, 'learning_rate': 1.9456004118580808e-06, 'epoch': 8.11} +{'loss': 0.2217, 'learning_rate': 1.9031275472993265e-06, 'epoch': 8.16} +{'loss': 0.2147, 'learning_rate': 1.8602256639066457e-06, 'epoch': 8.2} +{'loss': 0.2134, 'learning_rate': 1.8173237805139646e-06, 'epoch': 8.24} +{'loss': 0.2214, 'learning_rate': 1.7744218971212837e-06, 'epoch': 8.28} +{'loss': 0.218, 'learning_rate': 1.7315200137286028e-06, 'epoch': 8.32} +{'loss': 0.2141, 'learning_rate': 1.688618130335922e-06, 'epoch': 8.36} +{'loss': 0.2199, 'learning_rate': 1.6457162469432409e-06, 'epoch': 8.41} +{'loss': 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1.0455188982796345e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:32:16<21:31, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.4202464520931244, 'eval_accuracy': 0.8546083608647017, 'eval_f1': 0.6659089228502614, 'eval_matthews_correlation': 0.34610166454886515, 'eval_precision': 0.7081019717210073, 'eval_recall': 0.6439034445623697, 'eval_runtime': 37.2085, 'eval_samples_per_second': 1033.125, 'eval_steps_per_second': 8.09, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [3:54:26<00:00, 2.10it/s]***** Running Evaluation ***** +{'loss': 0.2087, 'learning_rate': 1.0026170148869536e-06, 'epoch': 9.03} +{'loss': 0.2158, 'learning_rate': 9.597151314942726e-07, 'epoch': 9.07} +{'loss': 0.2015, 'learning_rate': 9.168132481015918e-07, 'epoch': 9.11} +{'loss': 0.2071, 'learning_rate': 8.739113647089108e-07, 'epoch': 9.16} +{'loss': 0.2065, 'learning_rate': 8.3100948131623e-07, 'epoch': 9.2} +{'loss': 0.2077, 'learning_rate': 7.881075979235489e-07, 'epoch': 9.24} +{'loss': 0.2041, 'learning_rate': 7.452057145308679e-07, 'epoch': 9.28} +{'loss': 0.1986, 'learning_rate': 7.02303831138187e-07, 'epoch': 9.32} +{'loss': 0.2061, 'learning_rate': 6.594019477455061e-07, 'epoch': 9.36} +{'loss': 0.2119, 'learning_rate': 6.165000643528252e-07, 'epoch': 9.4} +{'loss': 0.2077, 'learning_rate': 5.735981809601442e-07, 'epoch': 9.45} +{'loss': 0.2096, 'learning_rate': 5.306962975674632e-07, 'epoch': 9.49} +{'loss': 0.2077, 'learning_rate': 4.877944141747823e-07, 'epoch': 9.53} +{'loss': 0.2051, 'learning_rate': 4.4489253078210134e-07, 'epoch': 9.57} +{'loss': 0.2096, 'learning_rate': 4.019906473894204e-07, 'epoch': 9.61} +{'loss': 0.2032, 'learning_rate': 3.590887639967395e-07, 'epoch': 9.65} +{'loss': 0.2, 'learning_rate': 3.166158994379853e-07, 'epoch': 9.7} +{'loss': 0.2056, 'learning_rate': 2.737140160453044e-07, 'epoch': 9.74} +{'loss': 0.2073, 'learning_rate': 2.3081213265262347e-07, 'epoch': 9.78} +{'loss': 0.2012, 'learning_rate': 1.8791024925994252e-07, 'epoch': 9.82} +{'loss': 0.2029, 'learning_rate': 1.4500836586726157e-07, 'epoch': 9.86} +{'loss': 0.2099, 'learning_rate': 1.0210648247458065e-07, 'epoch': 9.9} +{'loss': 0.2073, 'learning_rate': 5.92045990818997e-08, 'epoch': 9.95} +{'loss': 0.2062, 'learning_rate': 1.6302715689218757e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [3:55:02<00:00, 2.1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.43687567114830017, 'eval_accuracy': 0.848911318644156, 'eval_f1': 0.6685446845438405, 'eval_matthews_correlation': 0.3441903189521737, 'eval_precision': 0.6952084413271092, 'eval_recall': 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Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209 (score: 0.6925807640998711). +100%|██████████| 24030/24030 [3:55:04<00:00, 2.10it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 14104.1627, 'train_samples_per_second': 218.041, 'train_steps_per_second': 1.704, 'train_loss': 0.28019440629509057, 'epoch': 10.0} +100%|██████████| 24030/24030 [3:55:04<00:00, 1.70it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:58<00:00, 5.16it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_180730-9eaiow92/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_180730-9eaiow92/files/requirements.txt new file 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.03 +warmup_steps: + value: 0 +weight_decay: + value: 0 diff --git a/VASC/len2_5120/wandb/run-20260306_201818-oiqn6lhu/files/output.log b/VASC/len2_5120/wandb/run-20260306_201818-oiqn6lhu/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..419d4b2612ac91699931419c37e9db9f78ae6a2e --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_201818-oiqn6lhu/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['classifier.bias', 'bert.pooler.dense.bias', 'bert.pooler.dense.weight', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33938461542129517, 'eval_accuracy': 0.8703467651726021, 'eval_f1': 0.6889152638509175, 'eval_matthews_correlation': 0.4034879580617068, 'eval_precision': 0.7574772367251238, 'eval_recall': 0.6580746849425465, 'eval_runtime': 32.9515, 'eval_samples_per_second': 1166.594, 'eval_steps_per_second': 9.135, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:15:29<1:06:23, 2.41it/s]***** Running Evaluation ***** +{'loss': 0.3096, 'learning_rate': 6.394594304713896e-06, 'epoch': 3.04} +{'loss': 0.3102, 'learning_rate': 6.340966375288251e-06, 'epoch': 3.08} +{'loss': 0.303, 'learning_rate': 6.287338445862605e-06, 'epoch': 3.12} +{'loss': 0.3117, 'learning_rate': 6.23371051643696e-06, 'epoch': 3.16} +{'loss': 0.3067, 'learning_rate': 6.1800825870113155e-06, 'epoch': 3.2} +{'loss': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [1:51:32<33:08, 2.42it/s]***** Running Evaluation ***** +{'loss': 0.2699, 'learning_rate': 3.821526250871454e-06, 'epoch': 5.04} +{'loss': 0.281, 'learning_rate': 3.7678983214458092e-06, 'epoch': 5.08} +{'loss': 0.2721, 'learning_rate': 3.7142703920201644e-06, 'epoch': 5.12} +{'loss': 0.2695, 'learning_rate': 3.6606424625945195e-06, 'epoch': 5.16} +{'loss': 0.2769, 'learning_rate': 3.6070145331688743e-06, 'epoch': 5.2} +{'loss': 0.2697, 'learning_rate': 3.55338660374323e-06, 'epoch': 5.24} +{'loss': 0.2721, 'learning_rate': 3.499758674317585e-06, 'epoch': 5.29} +{'loss': 0.267, 'learning_rate': 3.44613074489194e-06, 'epoch': 5.33} +{'loss': 0.2771, 'learning_rate': 3.3925028154662953e-06, 'epoch': 5.37} +{'loss': 0.2789, 'learning_rate': 3.33887488604065e-06, 'epoch': 5.41} +{'loss': 0.2816, 'learning_rate': 3.285246956615005e-06, 'epoch': 5.45} +{'loss': 0.2806, 'learning_rate': 3.2316190271893603e-06, 'epoch': 5.49} +{'loss': 0.2708, 'learning_rate': 3.178527377057972e-06, 'epoch': 5.53} +{'loss': 0.2773, 'learning_rate': 3.1248994476323276e-06, 'epoch': 5.58} +{'loss': 0.2622, 'learning_rate': 3.071271518206682e-06, 'epoch': 5.62} +{'loss': 0.2775, 'learning_rate': 3.0176435887810375e-06, 'epoch': 5.66} +{'loss': 0.2762, 'learning_rate': 2.9640156593553926e-06, 'epoch': 5.7} +{'loss': 0.2735, 'learning_rate': 2.910387729929748e-06, 'epoch': 5.74} +{'loss': 0.2743, 'learning_rate': 2.8567598005041025e-06, 'epoch': 5.78} +{'loss': 0.2685, 'learning_rate': 2.8031318710784577e-06, 'epoch': 5.83} +{'loss': 0.2814, 'learning_rate': 2.749503941652813e-06, 'epoch': 5.87} +{'loss': 0.2699, 'learning_rate': 2.6958760122271684e-06, 'epoch': 5.91} +{'loss': 0.273, 'learning_rate': 2.6422480828015236e-06, 'epoch': 5.95} +{'loss': 0.2779, 'learning_rate': 2.5886201533758783e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [1:52:05<33:08, 2.4Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.36066821217536926, 'eval_accuracy': 0.8649879035404906, 'eval_f1': 0.6761809030682012, 'eval_matthews_correlation': 0.37689164184082946, 'eval_precision': 0.7403734171004523, 'eval_recall': 0.6477360843421741, 'eval_runtime': 33.2065, 'eval_samples_per_second': 1157.636, 'eval_steps_per_second': 9.064, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:10:30<16:14, 2.46it/s]***** Running Evaluation ***** +{'loss': 0.2608, 'learning_rate': 2.5349922239502335e-06, 'epoch': 6.03} +{'loss': 0.2603, 'learning_rate': 2.4813642945245886e-06, 'epoch': 6.08} +{'loss': 0.2543, 'learning_rate': 2.4277363650989438e-06, 'epoch': 6.12} +{'loss': 0.2595, 'learning_rate': 2.374108435673299e-06, 'epoch': 6.16} +{'loss': 0.2584, 'learning_rate': 2.320480506247654e-06, 'epoch': 6.2} +{'loss': 0.255, 'learning_rate': 2.266852576822009e-06, 'epoch': 6.24} +{'loss': 0.2586, 'learning_rate': 2.2132246473963644e-06, 'epoch': 6.28} +{'loss': 0.2549, 'learning_rate': 2.1595967179707195e-06, 'epoch': 6.33} +{'loss': 0.2542, 'learning_rate': 2.106505067839331e-06, 'epoch': 6.37} +{'loss': 0.2558, 'learning_rate': 2.052877138413686e-06, 'epoch': 6.41} +{'loss': 0.2516, 'learning_rate': 1.999249208988041e-06, 'epoch': 6.45} +{'loss': 0.2537, 'learning_rate': 1.9456212795623963e-06, 'epoch': 6.49} +{'loss': 0.2525, 'learning_rate': 1.8919933501367512e-06, 'epoch': 6.53} +{'loss': 0.2588, 'learning_rate': 1.8383654207111066e-06, 'epoch': 6.58} +{'loss': 0.247, 'learning_rate': 1.7847374912854615e-06, 'epoch': 6.62} +{'loss': 0.2635, 'learning_rate': 1.7311095618598167e-06, 'epoch': 6.66} +{'loss': 0.2561, 'learning_rate': 1.677481632434172e-06, 'epoch': 6.7} +{'loss': 0.2541, 'learning_rate': 1.623853703008527e-06, 'epoch': 6.74} +{'loss': 0.2525, 'learning_rate': 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'eval_precision': 0.7192845971734292, 'eval_recall': 0.6517080367714877, 'eval_runtime': 33.0228, 'eval_samples_per_second': 1164.073, 'eval_steps_per_second': 9.115, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [2:29:34<00:00, 2.40it/s]***** Running Evaluation ***** +{'loss': 0.2396, 'learning_rate': 1.2484581970290129e-06, 'epoch': 7.03} +{'loss': 0.2412, 'learning_rate': 1.194830267603368e-06, 'epoch': 7.07} +{'loss': 0.2365, 'learning_rate': 1.141202338177723e-06, 'epoch': 7.12} +{'loss': 0.2508, 'learning_rate': 1.0875744087520781e-06, 'epoch': 7.16} +{'loss': 0.2376, 'learning_rate': 1.0339464793264333e-06, 'epoch': 7.2} +{'loss': 0.2421, 'learning_rate': 9.808548291950447e-07, 'epoch': 7.24} +{'loss': 0.2403, 'learning_rate': 9.272268997693999e-07, 'epoch': 7.28} +{'loss': 0.2378, 'learning_rate': 8.735989703437551e-07, 'epoch': 7.32} +{'loss': 0.2419, 'learning_rate': 8.199710409181102e-07, 'epoch': 7.37} +{'loss': 0.2279, 'learning_rate': 7.663431114924654e-07, 'epoch': 7.41} +{'loss': 0.2459, 'learning_rate': 7.127151820668204e-07, 'epoch': 7.45} +{'loss': 0.2452, 'learning_rate': 6.590872526411756e-07, 'epoch': 7.49} +{'loss': 0.2461, 'learning_rate': 6.054593232155307e-07, 'epoch': 7.53} +{'loss': 0.2421, 'learning_rate': 5.518313937898858e-07, 'epoch': 7.57} +{'loss': 0.2489, 'learning_rate': 4.982034643642409e-07, 'epoch': 7.62} +{'loss': 0.2403, 'learning_rate': 4.4457553493859607e-07, 'epoch': 7.66} +{'loss': 0.2472, 'learning_rate': 3.9094760551295117e-07, 'epoch': 7.7} +{'loss': 0.2472, 'learning_rate': 3.3731967608730633e-07, 'epoch': 7.74} +{'loss': 0.2358, 'learning_rate': 2.8369174666166143e-07, 'epoch': 7.78} +{'loss': 0.2428, 'learning_rate': 2.3006381723601653e-07, 'epoch': 7.82} +{'loss': 0.2411, 'learning_rate': 1.7643588781037166e-07, 'epoch': 7.87} +{'loss': 0.2438, 'learning_rate': 1.228079583847268e-07, 'epoch': 7.91} +{'loss': 0.2457, 'learning_rate': 6.918002895908189e-08, 'epoch': 7.95} +{'loss': 0.2356, 'learning_rate': 1.5552099533437016e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [2:30:07<00:00, 2.4Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.39606449007987976, 'eval_accuracy': 0.8586665279259125, 'eval_f1': 0.6713871034814642, 'eval_matthews_correlation': 0.35966899723174484, 'eval_precision': 0.7196792631453846, 'eval_recall': 0.6472166577280405, 'eval_runtime': 33.2071, 'eval_samples_per_second': 1157.614, 'eval_steps_per_second': 9.064, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-7209 (score: 0.6889152638509175). +100%|██████████| 19224/19224 [2:30:09<00:00, 2.40it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 9009.7815, 'train_samples_per_second': 273.062, 'train_steps_per_second': 2.134, 'train_loss': 0.2988235318457341, 'epoch': 8.0} +100%|██████████| 19224/19224 [2:30:09<00:00, 2.13it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:52<00:00, 5.70it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_201818-oiqn6lhu/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_201818-oiqn6lhu/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_201818-oiqn6lhu/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.05" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.06" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "573365972992" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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b/VASC/len2_5120/wandb/run-20260306_220450-j97i5qhu/files/output.log @@ -0,0 +1,232 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['classifier.weight', 'bert.pooler.dense.bias', 'bert.pooler.dense.weight', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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+{'loss': 0.3316, 'learning_rate': 7.539846517119245e-06, 'epoch': 1.75} +{'loss': 0.3445, 'learning_rate': 7.466056670602125e-06, 'epoch': 1.79} +{'loss': 0.3376, 'learning_rate': 7.392266824085006e-06, 'epoch': 1.83} +{'loss': 0.3348, 'learning_rate': 7.3184769775678874e-06, 'epoch': 1.87} +{'loss': 0.3334, 'learning_rate': 7.244687131050768e-06, 'epoch': 1.91} +{'loss': 0.3305, 'learning_rate': 7.170897284533649e-06, 'epoch': 1.96} +{'loss': 0.3237, 'learning_rate': 7.097107438016529e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 33%|███▎ | 4806/14418 [44:46<32:33, 4.92itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-4806/config.json +{'eval_loss': 0.33994558453559875, 'eval_accuracy': 0.8740927655367966, 'eval_f1': 0.6718260275313136, 'eval_matthews_correlation': 0.39647733921926426, 'eval_precision': 0.78861045015843, 'eval_recall': 0.6361647511620744, 'eval_runtime': 12.9244, 'eval_samples_per_second': 2974.29, 'eval_steps_per_second': 23.289, 'epoch': 2.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-4806/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-4806/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-4806/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [1:06:28<1:07:42, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.322, 'learning_rate': 7.02331759149941e-06, 'epoch': 2.04} +{'loss': 0.3315, 'learning_rate': 6.9495277449822905e-06, 'epoch': 2.08} +{'loss': 0.3204, 'learning_rate': 6.875737898465171e-06, 'epoch': 2.12} +{'loss': 0.3184, 'learning_rate': 6.801948051948053e-06, 'epoch': 2.16} +{'loss': 0.3185, 'learning_rate': 6.728158205430933e-06, 'epoch': 2.21} +{'loss': 0.3246, 'learning_rate': 6.654368358913814e-06, 'epoch': 2.25} +{'loss': 0.3213, 'learning_rate': 6.5805785123966945e-06, 'epoch': 2.29} +{'loss': 0.325, 'learning_rate': 6.506788665879575e-06, 'epoch': 2.33} +{'loss': 0.3239, 'learning_rate': 6.432998819362456e-06, 'epoch': 2.37} +{'loss': 0.3203, 'learning_rate': 6.359208972845336e-06, 'epoch': 2.41} +{'loss': 0.3258, 'learning_rate': 6.285419126328219e-06, 'epoch': 2.46} +{'loss': 0.3234, 'learning_rate': 6.211629279811099e-06, 'epoch': 2.5} +{'loss': 0.3252, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3387947082519531, 'eval_accuracy': 0.871621445852085, 'eval_f1': 0.6918267718109511, 'eval_matthews_correlation': 0.40967886179359747, 'eval_precision': 0.761607496049214, 'eval_recall': 0.6603898706412868, 'eval_runtime': 41.5214, 'eval_samples_per_second': 925.811, 'eval_steps_per_second': 7.249, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:31:01<40:41, 1.97it/s]***** Running Evaluation ***** +{'loss': 0.3066, 'learning_rate': 5.252361275088548e-06, 'epoch': 3.04} +{'loss': 0.3119, 'learning_rate': 5.1785714285714296e-06, 'epoch': 3.08} +{'loss': 0.3047, 'learning_rate': 5.10478158205431e-06, 'epoch': 3.12} +{'loss': 0.3107, 'learning_rate': 5.030991735537191e-06, 'epoch': 3.16} +{'loss': 0.3064, 'learning_rate': 4.957201889020071e-06, 'epoch': 3.2} +{'loss': 0.2991, 'learning_rate': 4.883412042502952e-06, 'epoch': 3.25} +{'loss': 0.3164, 'learning_rate': 4.809622195985833e-06, 'epoch': 3.29} +{'loss': 0.2987, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-9612/special_tokens_map.json + 83%|████████▎ | 12015/14418 [1:55:24<19:38, 2.04it/s]***** Running Evaluation ***** +{'loss': 0.299, 'learning_rate': 3.482142857142857e-06, 'epoch': 4.04} +{'loss': 0.2968, 'learning_rate': 3.4083530106257382e-06, 'epoch': 4.08} +{'loss': 0.3036, 'learning_rate': 3.334563164108619e-06, 'epoch': 4.12} +{'loss': 0.2967, 'learning_rate': 3.2607733175914995e-06, 'epoch': 4.16} +{'loss': 0.2864, 'learning_rate': 3.1877213695395514e-06, 'epoch': 4.2} +{'loss': 0.2991, 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'epoch': 4.79} +{'loss': 0.2959, 'learning_rate': 2.0808736717827628e-06, 'epoch': 4.83} +{'loss': 0.2961, 'learning_rate': 2.0070838252656434e-06, 'epoch': 4.87} +{'loss': 0.2988, 'learning_rate': 1.9332939787485244e-06, 'epoch': 4.91} +{'loss': 0.2875, 'learning_rate': 1.859504132231405e-06, 'epoch': 4.95} +{'loss': 0.2914, 'learning_rate': 1.7857142857142859e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 83%|████████▎ | 12015/14418 [1:56:03<19:38, 2.0Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015/config.json +{'eval_loss': 0.34559524059295654, 'eval_accuracy': 0.868603834447595, 'eval_f1': 0.6769069254398168, 'eval_matthews_correlation': 0.38556122534964815, 'eval_precision': 0.7551317988013188, 'eval_recall': 0.645667317041189, 'eval_runtime': 39.0827, 'eval_samples_per_second': 983.58, 'eval_steps_per_second': 7.702, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:19:55<00:00, 1.86it/s]***** Running Evaluation ***** +{'loss': 0.2726, 'learning_rate': 1.7126623376623378e-06, 'epoch': 5.04} +{'loss': 0.2859, 'learning_rate': 1.6388724911452187e-06, 'epoch': 5.08} +{'loss': 0.275, 'learning_rate': 1.5650826446280993e-06, 'epoch': 5.12} +{'loss': 0.2859, 'learning_rate': 1.49129279811098e-06, 'epoch': 5.16} +{'loss': 0.2887, 'learning_rate': 1.4175029515938607e-06, 'epoch': 5.2} +{'loss': 0.2803, 'learning_rate': 1.3437131050767415e-06, 'epoch': 5.24} +{'loss': 0.2725, 'learning_rate': 1.2699232585596222e-06, 'epoch': 5.29} +{'loss': 0.2751, 'learning_rate': 1.196133412042503e-06, 'epoch': 5.33} +{'loss': 0.2859, 'learning_rate': 1.1223435655253838e-06, 'epoch': 5.37} +{'loss': 0.2839, 'learning_rate': 1.0485537190082644e-06, 'epoch': 5.41} +{'loss': 0.2857, 'learning_rate': 9.747638724911453e-07, 'epoch': 5.45} +{'loss': 0.2822, 'learning_rate': 9.00974025974026e-07, 'epoch': 5.49} +{'loss': 0.2839, 'learning_rate': 8.271841794569067e-07, 'epoch': 5.53} +{'loss': 0.2817, 'learning_rate': 7.533943329397877e-07, 'epoch': 5.58} +{'loss': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3545328974723816, 'eval_accuracy': 0.8646237090606383, 'eval_f1': 0.6799310438927837, 'eval_matthews_correlation': 0.38104389794261656, 'eval_precision': 0.738132951489792, 'eval_recall': 0.652430030420976, 'eval_runtime': 39.6122, 'eval_samples_per_second': 970.433, 'eval_steps_per_second': 7.599, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209 (score: 0.6918267718109511). +100%|██████████| 14418/14418 [2:20:36<00:00, 1.86it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 8436.7024, 'train_samples_per_second': 218.708, 'train_steps_per_second': 1.709, 'train_loss': 0.3170995739730325, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:20:36<00:00, 1.71it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.72it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_220450-j97i5qhu/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_220450-j97i5qhu/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260306_220450-j97i5qhu/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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0.6285568653752269, 'eval_runtime': 39.3046, 'eval_samples_per_second': 978.028, 'eval_steps_per_second': 7.658, 'epoch': 1.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-2403/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-2403/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-2403/special_tokens_map.json + 20%|██ | 4806/24030 [47:55<2:37:36, 2.03it/s]***** Running Evaluation ***** +{'loss': 0.3356, 'learning_rate': 9.236775494444207e-06, 'epoch': 1.04} +{'loss': 0.3447, 'learning_rate': 9.193873611051526e-06, 'epoch': 1.08} +{'loss': 0.3378, 'learning_rate': 9.150971727658846e-06, 'epoch': 1.12} +{'loss': 0.3283, 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+{'loss': 0.3311, 'learning_rate': 8.50744347676863e-06, 'epoch': 1.75} +{'loss': 0.346, 'learning_rate': 8.46454159337595e-06, 'epoch': 1.79} +{'loss': 0.3376, 'learning_rate': 8.42163970998327e-06, 'epoch': 1.83} +{'loss': 0.3344, 'learning_rate': 8.378737826590588e-06, 'epoch': 1.87} +{'loss': 0.3339, 'learning_rate': 8.335835943197907e-06, 'epoch': 1.91} +{'loss': 0.3318, 'learning_rate': 8.292934059805227e-06, 'epoch': 1.96} +{'loss': 0.3226, 'learning_rate': 8.250032176412546e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [48:34<2:37:36, 2.03Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 0.3390704393386841, 'eval_accuracy': 0.8737545849483624, 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+{'loss': 0.3178, 'learning_rate': 7.56360204212965e-06, 'epoch': 2.66} +{'loss': 0.3165, 'learning_rate': 7.520700158736968e-06, 'epoch': 2.7} +{'loss': 0.3239, 'learning_rate': 7.477798275344288e-06, 'epoch': 2.75} +{'loss': 0.3269, 'learning_rate': 7.434896391951607e-06, 'epoch': 2.79} +{'loss': 0.3309, 'learning_rate': 7.391994508558926e-06, 'epoch': 2.83} +{'loss': 0.3157, 'learning_rate': 7.349092625166245e-06, 'epoch': 2.87} +{'loss': 0.3218, 'learning_rate': 7.3061907417735645e-06, 'epoch': 2.91} +{'loss': 0.3215, 'learning_rate': 7.263288858380883e-06, 'epoch': 2.95} +{'loss': 0.3276, 'learning_rate': 7.220386974988203e-06, 'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 30%|███ | 7209/24030 [1:12:51<2:16:52, 2.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.337472140789032, 'eval_accuracy': 0.8719596264405193, 'eval_f1': 0.689703138264441, 'eval_matthews_correlation': 0.40798456423516904, 'eval_precision': 0.7641580676725463, 'eval_recall': 0.6575301164571055, 'eval_runtime': 42.6508, 'eval_samples_per_second': 901.296, 'eval_steps_per_second': 7.057, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:36:06<41:21, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.3079, 'learning_rate': 7.1774850915955215e-06, 'epoch': 3.04} +{'loss': 0.3111, 'learning_rate': 7.134583208202841e-06, 'epoch': 3.08} +{'loss': 0.3028, 'learning_rate': 7.09168132481016e-06, 'epoch': 3.12} +{'loss': 0.3106, 'learning_rate': 7.048779441417479e-06, 'epoch': 3.16} +{'loss': 0.307, 'learning_rate': 7.005877558024799e-06, 'epoch': 3.2} +{'loss': 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0.65885597031402, 'eval_runtime': 13.3476, 'eval_samples_per_second': 2879.997, 'eval_steps_per_second': 22.551, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-9612/special_tokens_map.json + 50%|█████ | 12015/24030 [1:58:27<1:40:20, 2.00it/s]***** Running Evaluation ***** +{'loss': 0.2979, 'learning_rate': 6.148697927839033e-06, 'epoch': 4.04} +{'loss': 0.2879, 'learning_rate': 6.105796044446351e-06, 'epoch': 4.08} +{'loss': 0.2957, 'learning_rate': 6.062894161053671e-06, 'epoch': 4.12} +{'loss': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [2:22:31<1:17:15, 2.07it/s]***** Running Evaluation ***** +{'loss': 0.2674, 'learning_rate': 5.119052726414691e-06, 'epoch': 5.04} +{'loss': 0.2764, 'learning_rate': 5.076150843022009e-06, 'epoch': 5.08} +{'loss': 0.2674, 'learning_rate': 5.0332489596293275e-06, 'epoch': 5.12} +{'loss': 0.2609, 'learning_rate': 4.990347076236647e-06, 'epoch': 5.16} +{'loss': 0.2732, 'learning_rate': 4.9474451928439666e-06, 'epoch': 5.2} +{'loss': 0.2656, 'learning_rate': 4.904543309451285e-06, 'epoch': 5.24} +{'loss': 0.2683, 'learning_rate': 4.861641426058604e-06, 'epoch': 5.29} +{'loss': 0.2665, 'learning_rate': 4.8187395426659235e-06, 'epoch': 5.33} +{'loss': 0.2762, 'learning_rate': 4.775837659273242e-06, 'epoch': 5.37} +{'loss': 0.27, 'learning_rate': 4.732935775880562e-06, 'epoch': 5.41} +{'loss': 0.2788, 'learning_rate': 4.6900338924878805e-06, 'epoch': 5.45} +{'loss': 0.2712, 'learning_rate': 4.6471320090952e-06, 'epoch': 5.49} +{'loss': 0.273, 'learning_rate': 4.604659144536446e-06, 'epoch': 5.53} +{'loss': 0.2759, 'learning_rate': 4.561757261143764e-06, 'epoch': 5.58} +{'loss': 0.2628, 'learning_rate': 4.518855377751084e-06, 'epoch': 5.62} +{'loss': 0.2767, 'learning_rate': 4.475953494358403e-06, 'epoch': 5.66} +{'loss': 0.2776, 'learning_rate': 4.433051610965722e-06, 'epoch': 5.7} +{'loss': 0.2688, 'learning_rate': 4.390149727573041e-06, 'epoch': 5.74} +{'loss': 0.2706, 'learning_rate': 4.34724784418036e-06, 'epoch': 5.78} +{'loss': 0.2652, 'learning_rate': 4.304345960787679e-06, 'epoch': 5.83} +{'loss': 0.2783, 'learning_rate': 4.261444077394998e-06, 'epoch': 5.87} +{'loss': 0.2661, 'learning_rate': 4.2185421940023165e-06, 'epoch': 5.91} +{'loss': 0.2732, 'learning_rate': 4.175640310609636e-06, 'epoch': 5.95} +{'loss': 0.2744, 'learning_rate': 4.132738427216955e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [2:23:11<1:17:15, 2Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.36177554726600647, 'eval_accuracy': 0.8674592232252023, 'eval_f1': 0.6807994283895142, 'eval_matthews_correlation': 0.3876155803936117, 'eval_precision': 0.7486853478295963, 'eval_recall': 0.6510400989394313, 'eval_runtime': 39.8472, 'eval_samples_per_second': 964.71, 'eval_steps_per_second': 7.554, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:46:09<59:37, 2.02it/s] ***** Running Evaluation ***** +{'loss': 0.2546, 'learning_rate': 4.089836543824274e-06, 'epoch': 6.03} +{'loss': 0.2479, 'learning_rate': 4.046934660431593e-06, 'epoch': 6.08} +{'loss': 0.2426, 'learning_rate': 4.004032777038913e-06, 'epoch': 6.12} +{'loss': 0.2525, 'learning_rate': 3.961130893646231e-06, 'epoch': 6.16} +{'loss': 0.2502, 'learning_rate': 3.91822901025355e-06, 'epoch': 6.2} +{'loss': 0.2484, 'learning_rate': 3.8753271268608696e-06, 'epoch': 6.24} +{'loss': 0.2511, 'learning_rate': 3.832425243468188e-06, 'epoch': 6.28} +{'loss': 0.2443, 'learning_rate': 3.789523360075508e-06, 'epoch': 6.33} +{'loss': 0.2504, 'learning_rate': 3.746621476682827e-06, 'epoch': 6.37} +{'loss': 0.2491, 'learning_rate': 3.7041486121240725e-06, 'epoch': 6.41} +{'loss': 0.2453, 'learning_rate': 3.661246728731392e-06, 'epoch': 6.45} +{'loss': 0.243, 'learning_rate': 3.6183448453387104e-06, 'epoch': 6.49} +{'loss': 0.2479, 'learning_rate': 3.5754429619460295e-06, 'epoch': 6.53} +{'loss': 0.2443, 'learning_rate': 3.5325410785533486e-06, 'epoch': 6.58} +{'loss': 0.2428, 'learning_rate': 3.4896391951606677e-06, 'epoch': 6.62} +{'loss': 0.2557, 'learning_rate': 3.446737311767987e-06, 'epoch': 6.66} +{'loss': 0.2516, 'learning_rate': 3.403835428375306e-06, 'epoch': 6.7} +{'loss': 0.2492, 'learning_rate': 3.360933544982625e-06, 'epoch': 6.74} +{'loss': 0.2478, 'learning_rate': 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0.7108093275334941, 'eval_recall': 0.668913187368385, 'eval_runtime': 39.0387, 'eval_samples_per_second': 984.69, 'eval_steps_per_second': 7.71, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:09:52<39:07, 2.05it/s]***** Running Evaluation ***** +{'loss': 0.2254, 'learning_rate': 3.0606203612338586e-06, 'epoch': 7.03} +{'loss': 0.228, 'learning_rate': 3.0177184778411773e-06, 'epoch': 7.07} +{'loss': 0.218, 'learning_rate': 2.9748165944484965e-06, 'epoch': 7.12} +{'loss': 0.2392, 'learning_rate': 2.9319147110558156e-06, 'epoch': 7.16} +{'loss': 0.2232, 'learning_rate': 2.8890128276631347e-06, 'epoch': 7.2} +{'loss': 0.228, 'learning_rate': 2.8465399631043807e-06, 'epoch': 7.24} +{'loss': 0.2252, 'learning_rate': 2.8036380797117e-06, 'epoch': 7.28} +{'loss': 0.2251, 'learning_rate': 2.760736196319019e-06, 'epoch': 7.32} +{'loss': 0.2296, 'learning_rate': 2.717834312926338e-06, 'epoch': 7.37} +{'loss': 0.2123, 'learning_rate': 2.6749324295336564e-06, 'epoch': 7.41} +{'loss': 0.2303, 'learning_rate': 2.6320305461409755e-06, 'epoch': 7.45} +{'loss': 0.2312, 'learning_rate': 2.5891286627482946e-06, 'epoch': 7.49} +{'loss': 0.2305, 'learning_rate': 2.5462267793556138e-06, 'epoch': 7.53} +{'loss': 0.2314, 'learning_rate': 2.503324895962933e-06, 'epoch': 7.57} +{'loss': 0.2417, 'learning_rate': 2.460423012570252e-06, 'epoch': 7.62} +{'loss': 0.2279, 'learning_rate': 2.417521129177571e-06, 'epoch': 7.66} +{'loss': 0.2324, 'learning_rate': 2.3746192457848903e-06, 'epoch': 7.7} +{'loss': 0.2297, 'learning_rate': 2.3317173623922094e-06, 'epoch': 7.74} +{'loss': 0.2252, 'learning_rate': 2.288815478999528e-06, 'epoch': 7.78} +{'loss': 0.2341, 'learning_rate': 2.2459135956068473e-06, 'epoch': 7.82} +{'loss': 0.2265, 'learning_rate': 2.2030117122141664e-06, 'epoch': 7.87} +{'loss': 0.2344, 'learning_rate': 2.1601098288214855e-06, 'epoch': 7.91} +{'loss': 0.2342, 'learning_rate': 2.1172079454288042e-06, 'epoch': 7.95} +{'loss': 0.2208, 'learning_rate': 2.0743060620361234e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:10:32<39:07, 2.0Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.40614116191864014, 'eval_accuracy': 0.856481361046799, 'eval_f1': 0.6738388892906713, 'eval_matthews_correlation': 0.36029276866610516, 'eval_precision': 0.7135370280074134, 'eval_recall': 0.6519770135001843, 'eval_runtime': 39.4535, 'eval_samples_per_second': 974.337, 'eval_steps_per_second': 7.629, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:35:06<22:38, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.2095, 'learning_rate': 2.0314041786434425e-06, 'epoch': 8.03} +{'loss': 0.2103, 'learning_rate': 1.9885022952507616e-06, 'epoch': 8.07} +{'loss': 0.2114, 'learning_rate': 1.9460294306920076e-06, 'epoch': 8.11} +{'loss': 0.2096, 'learning_rate': 1.9031275472993265e-06, 'epoch': 8.16} +{'loss': 0.2064, 'learning_rate': 1.8602256639066457e-06, 'epoch': 8.2} +{'loss': 0.2113, 'learning_rate': 1.8173237805139646e-06, 'epoch': 8.24} +{'loss': 0.2061, 'learning_rate': 1.7744218971212837e-06, 'epoch': 8.28} +{'loss': 0.2112, 'learning_rate': 1.7315200137286028e-06, 'epoch': 8.32} +{'loss': 0.2011, 'learning_rate': 1.688618130335922e-06, 'epoch': 8.36} +{'loss': 0.2157, 'learning_rate': 1.6457162469432409e-06, 'epoch': 8.41} +{'loss': 0.2192, 'learning_rate': 1.60281436355056e-06, 'epoch': 8.45} +{'loss': 0.2105, 'learning_rate': 1.5599124801578792e-06, 'epoch': 8.49} +{'loss': 0.2128, 'learning_rate': 1.5170105967651983e-06, 'epoch': 8.53} +{'loss': 0.2062, 'learning_rate': 1.4741087133725172e-06, 'epoch': 8.57} +{'loss': 0.2153, 'learning_rate': 1.4312068299798363e-06, 'epoch': 8.61} +{'loss': 0.2089, 'learning_rate': 1.3883049465871555e-06, 'epoch': 8.66} +{'loss': 0.2133, 'learning_rate': 1.3454030631944742e-06, 'epoch': 8.7} +{'loss': 0.2169, 'learning_rate': 1.3025011798017933e-06, 'epoch': 8.74} +{'loss': 0.2118, 'learning_rate': 1.2595992964091124e-06, 'epoch': 8.78} +{'loss': 0.2101, 'learning_rate': 1.2166974130164316e-06, 'epoch': 8.82} +{'loss': 0.2067, 'learning_rate': 1.1737955296237507e-06, 'epoch': 8.86} +{'loss': 0.2091, 'learning_rate': 1.1308936462310696e-06, 'epoch': 8.91} +{'loss': 0.2135, 'learning_rate': 1.0879917628383887e-06, 'epoch': 8.95} +{'loss': 0.2221, 'learning_rate': 1.0455188982796345e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:35:49<22:38, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.43407806754112244, 'eval_accuracy': 0.8568455555266512, 'eval_f1': 0.6725780934234025, 'eval_matthews_correlation': 0.35887598185828273, 'eval_precision': 0.7144696179252895, 'eval_recall': 0.650128455956418, 'eval_runtime': 42.7856, 'eval_samples_per_second': 898.457, 'eval_steps_per_second': 7.035, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [3:59:32<00:00, 1.96it/s]***** Running Evaluation ***** +{'loss': 0.1955, 'learning_rate': 1.0026170148869536e-06, 'epoch': 9.03} +{'loss': 0.2022, 'learning_rate': 9.597151314942726e-07, 'epoch': 9.07} +{'loss': 0.1937, 'learning_rate': 9.168132481015918e-07, 'epoch': 9.11} +{'loss': 0.1971, 'learning_rate': 8.739113647089108e-07, 'epoch': 9.16} +{'loss': 0.2025, 'learning_rate': 8.3100948131623e-07, 'epoch': 9.2} +{'loss': 0.2051, 'learning_rate': 7.881075979235489e-07, 'epoch': 9.24} +{'loss': 0.1978, 'learning_rate': 7.452057145308679e-07, 'epoch': 9.28} +{'loss': 0.1972, 'learning_rate': 7.02303831138187e-07, 'epoch': 9.32} +{'loss': 0.196, 'learning_rate': 6.594019477455061e-07, 'epoch': 9.36} +{'loss': 0.2025, 'learning_rate': 6.165000643528252e-07, 'epoch': 9.4} +{'loss': 0.1946, 'learning_rate': 5.735981809601442e-07, 'epoch': 9.45} +{'loss': 0.2025, 'learning_rate': 5.306962975674632e-07, 'epoch': 9.49} +{'loss': 0.2041, 'learning_rate': 4.877944141747823e-07, 'epoch': 9.53} +{'loss': 0.1996, 'learning_rate': 4.4489253078210134e-07, 'epoch': 9.57} +{'loss': 0.2043, 'learning_rate': 4.019906473894204e-07, 'epoch': 9.61} +{'loss': 0.1892, 'learning_rate': 3.590887639967395e-07, 'epoch': 9.65} +{'loss': 0.1952, 'learning_rate': 3.1618688060405857e-07, 'epoch': 9.7} +{'loss': 0.1981, 'learning_rate': 2.732849972113776e-07, 'epoch': 9.74} +{'loss': 0.1971, 'learning_rate': 2.3038311381869664e-07, 'epoch': 9.78} +{'loss': 0.1921, 'learning_rate': 1.8748123042601572e-07, 'epoch': 9.82} +{'loss': 0.1976, 'learning_rate': 1.4457934703333477e-07, 'epoch': 9.86} +{'loss': 0.1983, 'learning_rate': 1.0167746364065382e-07, 'epoch': 9.9} +{'loss': 0.1989, 'learning_rate': 5.8775580247972894e-08, 'epoch': 9.95} +{'loss': 0.199, 'learning_rate': 1.5873696855291948e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [4:00:15<00:00, 1.9Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.44686874747276306, 'eval_accuracy': 0.8531515829452928, 'eval_f1': 0.6729015755233342, 'eval_matthews_correlation': 0.35512079628213966, 'eval_precision': 0.7051981535814343, 'eval_recall': 0.6536451202788394, 'eval_runtime': 43.0928, 'eval_samples_per_second': 892.051, 'eval_steps_per_second': 6.985, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-7209 (score: 0.689703138264441). +100%|██████████| 24030/24030 [4:00:17<00:00, 1.96it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.03_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 14417.357, 'train_samples_per_second': 213.305, 'train_steps_per_second': 1.667, 'train_loss': 0.2774329545048441, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:00:17<00:00, 1.67it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.73it/s] diff --git a/VASC/len2_5120/wandb/run-20260306_225041-sh09dizm/files/requirements.txt b/VASC/len2_5120/wandb/run-20260306_225041-sh09dizm/files/requirements.txt new 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 5120 +warmup_ratio: + value: 0.06 +warmup_steps: + value: 0 +weight_decay: + value: 0.05 diff --git a/VASC/len2_5120/wandb/run-20260307_002750-uymuu765/files/output.log b/VASC/len2_5120/wandb/run-20260307_002750-uymuu765/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..4ed01ca301b70895090e68db7490bc8d30248933 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_002750-uymuu765/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.weight', 'classifier.bias', 'classifier.weight', 'bert.pooler.dense.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 8 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 19,224 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 12%|█▎ | 2403/19224 [23:57<2:25:38, 1.92it/s]***** Running Evaluation ***** +{'loss': 0.5509, 'learning_rate': 8.665511265164646e-07, 'epoch': 0.04} +{'loss': 0.3922, 'learning_rate': 1.7331022530329292e-06, 'epoch': 0.08} +{'loss': 0.3619, 'learning_rate': 2.599653379549394e-06, 'epoch': 0.12} +{'loss': 0.3558, 'learning_rate': 3.4662045060658585e-06, 'epoch': 0.17} +{'loss': 0.3598, 'learning_rate': 4.332755632582323e-06, 'epoch': 0.21} +{'loss': 0.3584, 'learning_rate': 5.199306759098788e-06, 'epoch': 0.25} +{'loss': 0.3591, 'learning_rate': 6.065857885615252e-06, 'epoch': 0.29} +{'loss': 0.3498, 'learning_rate': 6.932409012131717e-06, 'epoch': 0.33} +{'loss': 0.3601, 'learning_rate': 7.79896013864818e-06, 'epoch': 0.37} +{'loss': 0.3572, 'learning_rate': 8.665511265164645e-06, 'epoch': 0.42} +{'loss': 0.3559, 'learning_rate': 9.532062391681109e-06, 'epoch': 0.46} +{'loss': 0.3596, 'learning_rate': 9.974543442169342e-06, 'epoch': 0.5} +{'loss': 0.351, 'learning_rate': 9.919203099059215e-06, 'epoch': 0.54} +{'loss': 0.3487, 'learning_rate': 9.863862755949087e-06, 'epoch': 0.58} +{'loss': 0.3567, 'learning_rate': 9.80852241283896e-06, 'epoch': 0.62} +{'loss': 0.345, 'learning_rate': 9.753182069728832e-06, 'epoch': 0.67} +{'loss': 0.348, 'learning_rate': 9.697841726618706e-06, 'epoch': 0.71} +{'loss': 0.3415, 'learning_rate': 9.642501383508579e-06, 'epoch': 0.75} +{'loss': 0.3531, 'learning_rate': 9.587161040398452e-06, 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7209/19224 [1:12:39<1:44:06, 1.92it/s]***** Running Evaluation ***** +{'loss': 0.3205, 'learning_rate': 7.926950747094632e-06, 'epoch': 2.04} +{'loss': 0.3325, 'learning_rate': 7.871610403984505e-06, 'epoch': 2.08} +{'loss': 0.3198, 'learning_rate': 7.816270060874379e-06, 'epoch': 2.12} +{'loss': 0.3197, 'learning_rate': 7.76092971776425e-06, 'epoch': 2.16} +{'loss': 0.3192, 'learning_rate': 7.705589374654124e-06, 'epoch': 2.21} +{'loss': 0.325, 'learning_rate': 7.650249031543996e-06, 'epoch': 2.25} +{'loss': 0.3227, 'learning_rate': 7.594908688433868e-06, 'epoch': 2.29} +{'loss': 0.3278, 'learning_rate': 7.5395683453237415e-06, 'epoch': 2.33} +{'loss': 0.3249, 'learning_rate': 7.484228002213614e-06, 'epoch': 2.37} +{'loss': 0.3199, 'learning_rate': 7.4288876591034875e-06, 'epoch': 2.41} +{'loss': 0.3256, 'learning_rate': 7.37354731599336e-06, 'epoch': 2.46} +{'loss': 0.3255, 'learning_rate': 7.3182069728832326e-06, 'epoch': 2.5} +{'loss': 0.3263, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3384457528591156, 'eval_accuracy': 0.8717255014177571, 'eval_f1': 0.6908962677811549, 'eval_matthews_correlation': 0.40882263201186025, 'eval_precision': 0.7625105572379323, 'eval_recall': 0.6591706884131306, 'eval_runtime': 39.2916, 'eval_samples_per_second': 978.353, 'eval_steps_per_second': 7.661, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:37:01<1:19:44, 2.01it/s]***** Running Evaluation ***** +{'loss': 0.3088, 'learning_rate': 6.598782512451578e-06, 'epoch': 3.04} +{'loss': 0.3118, 'learning_rate': 6.543442169341451e-06, 'epoch': 3.08} +{'loss': 0.3061, 'learning_rate': 6.488101826231323e-06, 'epoch': 3.12} +{'loss': 0.3141, 'learning_rate': 6.432761483121196e-06, 'epoch': 3.16} +{'loss': 0.3092, 'learning_rate': 6.377421140011068e-06, 'epoch': 3.2} +{'loss': 0.3001, 'learning_rate': 6.322080796900941e-06, 'epoch': 3.25} +{'loss': 0.3171, 'learning_rate': 6.266740453790814e-06, 'epoch': 3.29} +{'loss': 0.3009, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [2:03:01<1:01:32, 1.95it/s]***** Running Evaluation ***** +{'loss': 0.3017, 'learning_rate': 5.271721084670725e-06, 'epoch': 4.04} +{'loss': 0.2974, 'learning_rate': 5.216380741560599e-06, 'epoch': 4.08} +{'loss': 0.3055, 'learning_rate': 5.161040398450471e-06, 'epoch': 4.12} +{'loss': 0.295, 'learning_rate': 5.105700055340344e-06, 'epoch': 4.16} +{'loss': 0.283, 'learning_rate': 5.050359712230216e-06, 'epoch': 4.2} +{'loss': 0.2997, 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0.6404485866784781, 'eval_runtime': 37.352, 'eval_samples_per_second': 1029.155, 'eval_steps_per_second': 8.058, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [2:25:16<13:56, 5.74it/s]***** Running Evaluation ***** +{'loss': 0.2719, 'learning_rate': 3.9435528500276705e-06, 'epoch': 5.04} +{'loss': 0.2791, 'learning_rate': 3.888212506917543e-06, 'epoch': 5.08} +{'loss': 0.2726, 'learning_rate': 3.832872163807416e-06, 'epoch': 5.12} +{'loss': 0.2846, 'learning_rate': 3.777531820697289e-06, 'epoch': 5.16} +{'loss': 0.2844, 'learning_rate': 3.7221914775871616e-06, 'epoch': 5.2} +{'loss': 0.2724, 'learning_rate': 3.666851134477034e-06, 'epoch': 5.24} +{'loss': 0.2733, 'learning_rate': 3.6115107913669066e-06, 'epoch': 5.29} +{'loss': 0.2703, 'learning_rate': 3.556170448256779e-06, 'epoch': 5.33} +{'loss': 0.2827, 'learning_rate': 3.500830105146652e-06, 'epoch': 5.37} +{'loss': 0.2811, 'learning_rate': 3.4454897620365247e-06, 'epoch': 5.41} +{'loss': 0.2843, 'learning_rate': 3.3901494189263977e-06, 'epoch': 5.45} +{'loss': 0.2778, 'learning_rate': 3.3348090758162706e-06, 'epoch': 5.49} +{'loss': 0.2772, 'learning_rate': 3.280022136137244e-06, 'epoch': 5.53} +{'loss': 0.2803, 'learning_rate': 3.2246817930271166e-06, 'epoch': 5.58} +{'loss': 0.272, 'learning_rate': 3.16934144991699e-06, 'epoch': 5.62} +{'loss': 0.2902, 'learning_rate': 3.1140011068068626e-06, 'epoch': 5.66} +{'loss': 0.2828, 'learning_rate': 3.058660763696735e-06, 'epoch': 5.7} +{'loss': 0.2778, 'learning_rate': 3.003320420586608e-06, 'epoch': 5.74} +{'loss': 0.2754, 'learning_rate': 2.9479800774764806e-06, 'epoch': 5.78} +{'loss': 0.2723, 'learning_rate': 2.892639734366353e-06, 'epoch': 5.83} +{'loss': 0.2793, 'learning_rate': 2.8372993912562257e-06, 'epoch': 5.87} +{'loss': 0.274, 'learning_rate': 2.781959048146099e-06, 'epoch': 5.91} +{'loss': 0.2794, 'learning_rate': 2.7266187050359716e-06, 'epoch': 5.95} +{'loss': 0.282, 'learning_rate': 2.671278361925844e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [2:25:29<13:56, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3530832827091217, 'eval_accuracy': 0.866990973179678, 'eval_f1': 0.6695484666121381, 'eval_matthews_correlation': 0.3733086783556562, 'eval_precision': 0.750982419802759, 'eval_recall': 0.6388138753355372, 'eval_runtime': 12.9022, 'eval_samples_per_second': 2979.404, 'eval_steps_per_second': 23.329, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:49:31<19:23, 2.06it/s]***** Running Evaluation ***** +{'loss': 0.2713, 'learning_rate': 2.6159380188157167e-06, 'epoch': 6.03} +{'loss': 0.2667, 'learning_rate': 2.5605976757055893e-06, 'epoch': 6.08} +{'loss': 0.2562, 'learning_rate': 2.5052573325954622e-06, 'epoch': 6.12} +{'loss': 0.2678, 'learning_rate': 2.449916989485335e-06, 'epoch': 6.16} +{'loss': 0.2642, 'learning_rate': 2.3945766463752078e-06, 'epoch': 6.2} +{'loss': 0.2579, 'learning_rate': 2.3392363032650807e-06, 'epoch': 6.24} +{'loss': 0.2624, 'learning_rate': 2.2838959601549533e-06, 'epoch': 6.28} +{'loss': 0.2642, 'learning_rate': 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+{'loss': 0.2637, 'learning_rate': 1.454344216934145e-06, 'epoch': 6.91} +{'loss': 0.2589, 'learning_rate': 1.3990038738240178e-06, 'epoch': 6.95} +{'loss': 0.259, 'learning_rate': 1.3436635307138906e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [2:50:08<19:23, 2.0Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3726886808872223, 'eval_accuracy': 0.8602793891938295, 'eval_f1': 0.6811716140879938, 'eval_matthews_correlation': 0.3760045715385199, 'eval_precision': 0.7240290300178271, 'eval_recall': 0.6577691045292385, 'eval_runtime': 37.1953, 'eval_samples_per_second': 1033.492, 'eval_steps_per_second': 8.092, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [3:14:08<00:00, 1.79it/s]***** Running Evaluation ***** +{'loss': 0.2471, 'learning_rate': 1.2883231876037633e-06, 'epoch': 7.03} +{'loss': 0.249, 'learning_rate': 1.2329828444936359e-06, 'epoch': 7.07} +{'loss': 0.2442, 'learning_rate': 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+{'eval_loss': 0.3843921720981598, 'eval_accuracy': 0.8603314169766655, 'eval_f1': 0.6791174214691019, 'eval_matthews_correlation': 0.3731051158873488, 'eval_precision': 0.7242853865901154, 'eval_recall': 0.6551677414406355, 'eval_runtime': 37.1467, 'eval_samples_per_second': 1034.843, 'eval_steps_per_second': 8.103, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209 (score: 0.6908962677811549). +100%|██████████| 19224/19224 [3:14:47<00:00, 1.79it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 11687.0626, 'train_samples_per_second': 210.509, 'train_steps_per_second': 1.645, 'train_loss': 0.30205514415621115, 'epoch': 8.0} +100%|██████████| 19224/19224 [3:14:47<00:00, 1.64it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:03<00:00, 4.73it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_002750-uymuu765/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_002750-uymuu765/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_002750-uymuu765/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.0" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.06" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune_3072 + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "574648340480" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3382768929004669, 'eval_accuracy': 0.8704508207382743, 'eval_f1': 0.6919213245860417, 'eval_matthews_correlation': 0.4073335173389597, 'eval_precision': 0.7566498966393458, 'eval_recall': 0.661621528510575, 'eval_runtime': 40.5346, 'eval_samples_per_second': 948.351, 'eval_steps_per_second': 7.426, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:34:45<43:13, 1.85it/s]***** Running Evaluation ***** +{'loss': 0.3092, 'learning_rate': 5.252361275088548e-06, 'epoch': 3.04} +{'loss': 0.3115, 'learning_rate': 5.1785714285714296e-06, 'epoch': 3.08} +{'loss': 0.3031, 'learning_rate': 5.10478158205431e-06, 'epoch': 3.12} +{'loss': 0.3125, 'learning_rate': 5.030991735537191e-06, 'epoch': 3.16} +{'loss': 0.3069, 'learning_rate': 4.957201889020071e-06, 'epoch': 3.2} +{'loss': 0.3003, 'learning_rate': 4.883412042502952e-06, 'epoch': 3.25} +{'loss': 0.3176, 'learning_rate': 4.809622195985833e-06, 'epoch': 3.29} +{'loss': 0.2978, 'learning_rate': 4.735832349468713e-06, 'epoch': 3.33} +{'loss': 0.3027, 'learning_rate': 4.662780401416766e-06, 'epoch': 3.37} +{'loss': 0.3081, 'learning_rate': 4.588990554899646e-06, 'epoch': 3.41} +{'loss': 0.3222, 'learning_rate': 4.515200708382527e-06, 'epoch': 3.45} +{'loss': 0.3214, 'learning_rate': 4.4414108618654075e-06, 'epoch': 3.5} +{'loss': 0.3039, 'learning_rate': 4.367621015348288e-06, 'epoch': 3.54} +{'loss': 0.3057, 'learning_rate': 4.293831168831169e-06, 'epoch': 3.58} +{'loss': 0.3058, 'learning_rate': 4.22004132231405e-06, 'epoch': 3.62} +{'loss': 0.3161, 'learning_rate': 4.146251475796931e-06, 'epoch': 3.66} +{'loss': 0.3174, 'learning_rate': 4.072461629279811e-06, 'epoch': 3.7} +{'loss': 0.3075, 'learning_rate': 3.998671782762692e-06, 'epoch': 3.75} +{'loss': 0.3124, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-12015/config.json +{'eval_loss': 0.3456884026527405, 'eval_accuracy': 0.8691501261673734, 'eval_f1': 0.6816013626005616, 'eval_matthews_correlation': 0.39223848094699043, 'eval_precision': 0.7554960996610114, 'eval_recall': 0.6505414624134477, 'eval_runtime': 45.7642, 'eval_samples_per_second': 839.98, 'eval_steps_per_second': 6.577, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:27:17<00:00, 1.75it/s]***** Running Evaluation ***** +{'loss': 0.2753, 'learning_rate': 1.7119244391971665e-06, 'epoch': 5.04} +{'loss': 0.2862, 'learning_rate': 1.6381345926800473e-06, 'epoch': 5.08} +{'loss': 0.2805, 'learning_rate': 1.564344746162928e-06, 'epoch': 5.12} +{'loss': 0.2751, 'learning_rate': 1.4905548996458088e-06, 'epoch': 5.16} +{'loss': 0.2847, 'learning_rate': 1.4167650531286898e-06, 'epoch': 5.2} +{'loss': 0.2762, 'learning_rate': 1.3429752066115702e-06, 'epoch': 5.24} +{'loss': 0.2752, 'learning_rate': 1.2691853600944513e-06, 'epoch': 5.29} +{'loss': 0.2725, 'learning_rate': 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0.2785, 'learning_rate': 1.6307556080283354e-07, 'epoch': 5.91} +{'loss': 0.2812, 'learning_rate': 8.928571428571429e-08, 'epoch': 5.95} +{'loss': 0.2814, 'learning_rate': 1.5495867768595042e-08, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [2:28:02<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35327523946762085, 'eval_accuracy': 0.8657162925001951, 'eval_f1': 0.6820387270173697, 'eval_matthews_correlation': 0.3857690948880244, 'eval_precision': 0.7415907344507765, 'eval_recall': 0.6539978291272661, 'eval_runtime': 45.4997, 'eval_samples_per_second': 844.862, 'eval_steps_per_second': 6.615, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-7209 (score: 0.6919213245860417). +100%|██████████| 14418/14418 [2:28:04<00:00, 1.75it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 8884.657, 'train_samples_per_second': 207.681, 'train_steps_per_second': 1.623, 'train_loss': 0.317418872640374, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:28:04<00:00, 1.62it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:10<00:00, 4.28it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_025318-q1zgv2ta/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_025318-q1zgv2ta/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_025318-q1zgv2ta/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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b/VASC/len2_5120/wandb/run-20260307_034456-hf9t43nv/files/output.log @@ -0,0 +1,368 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['classifier.bias', 'classifier.weight', 'bert.pooler.dense.weight', 'bert.pooler.dense.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 10 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 24,030 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 10%|█ | 2403/24030 [23:51<3:16:25, 1.84it/s]***** Running Evaluation ***** +{'loss': 0.5855, 'learning_rate': 6.934812760055479e-07, 'epoch': 0.04} +{'loss': 0.3984, 'learning_rate': 1.3869625520110958e-06, 'epoch': 0.08} +{'loss': 0.3648, 'learning_rate': 2.0804438280166435e-06, 'epoch': 0.12} +{'loss': 0.3552, 'learning_rate': 2.7739251040221917e-06, 'epoch': 0.17} +{'loss': 0.357, 'learning_rate': 3.46740638002774e-06, 'epoch': 0.21} +{'loss': 0.3577, 'learning_rate': 4.160887656033287e-06, 'epoch': 0.25} +{'loss': 0.3583, 'learning_rate': 4.854368932038836e-06, 'epoch': 0.29} +{'loss': 0.3514, 'learning_rate': 5.547850208044383e-06, 'epoch': 0.33} +{'loss': 0.36, 'learning_rate': 6.24133148404993e-06, 'epoch': 0.37} +{'loss': 0.3565, 'learning_rate': 6.93481276005548e-06, 'epoch': 0.42} +{'loss': 0.3551, 'learning_rate': 7.628294036061027e-06, 'epoch': 0.46} +{'loss': 0.3608, 'learning_rate': 8.321775312066574e-06, 'epoch': 0.5} +{'loss': 0.3518, 'learning_rate': 9.015256588072124e-06, 'epoch': 0.54} +{'loss': 0.3503, 'learning_rate': 9.708737864077671e-06, 'epoch': 0.58} +{'loss': 0.358, 'learning_rate': 9.974322649194264e-06, 'epoch': 0.62} +{'loss': 0.3459, 'learning_rate': 9.930051354701612e-06, 'epoch': 0.67} +{'loss': 0.3491, 'learning_rate': 9.885780060208962e-06, 'epoch': 0.71} +{'loss': 0.3436, 'learning_rate': 9.84150876571631e-06, 'epoch': 0.75} +{'loss': 0.3539, 'learning_rate': 9.797237471223659e-06, 'epoch': 0.79} +{'loss': 0.3452, 'learning_rate': 9.752966176731009e-06, 'epoch': 0.83} +{'loss': 0.327, 'learning_rate': 9.708694882238358e-06, 'epoch': 0.87} +{'loss': 0.3355, 'learning_rate': 9.664423587745706e-06, 'epoch': 0.92} +{'loss': 0.3478, 'learning_rate': 9.620152293253056e-06, 'epoch': 0.96} +{'loss': 0.3476, 'learning_rate': 9.575880998760403e-06, 'epoch': 1.0} + Num examples = 38441 + Batch size = 128 + 10%|█ | 2403/24030 [24:29<3:16:25, 1.84Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-2403 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-2403/config.json +{'eval_loss': 0.3401639461517334, 'eval_accuracy': 0.8735724877084363, 'eval_f1': 0.662166041715491, 'eval_matthews_correlation': 0.38691152325504247, 'eval_precision': 0.7947633672699534, 'eval_recall': 0.6269666989270388, 'eval_runtime': 37.6923, 'eval_samples_per_second': 1019.864, 'eval_steps_per_second': 7.986, 'epoch': 1.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-2403/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-2403/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-2403/special_tokens_map.json + 20%|██ | 4806/24030 [48:22<3:04:32, 1.74it/s]***** Running Evaluation ***** +{'loss': 0.3379, 'learning_rate': 9.531609704267753e-06, 'epoch': 1.04} +{'loss': 0.3458, 'learning_rate': 9.487338409775103e-06, 'epoch': 1.08} +{'loss': 0.3378, 'learning_rate': 9.443067115282452e-06, 'epoch': 1.12} +{'loss': 0.3314, 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+{'loss': 0.3333, 'learning_rate': 8.778997697892687e-06, 'epoch': 1.75} +{'loss': 0.3449, 'learning_rate': 8.734726403400036e-06, 'epoch': 1.79} +{'loss': 0.3393, 'learning_rate': 8.690455108907386e-06, 'epoch': 1.83} +{'loss': 0.3357, 'learning_rate': 8.646183814414734e-06, 'epoch': 1.87} +{'loss': 0.3344, 'learning_rate': 8.601912519922083e-06, 'epoch': 1.91} +{'loss': 0.3306, 'learning_rate': 8.557641225429433e-06, 'epoch': 1.96} +{'loss': 0.3242, 'learning_rate': 8.51336993093678e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [49:05<3:04:32, 1.74Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 0.33776307106018066, 'eval_accuracy': 0.8746910850394111, 'eval_f1': 0.669257761898532, 'eval_matthews_correlation': 0.3966149199921006, 'eval_precision': 0.7952977101100571, 'eval_recall': 0.6331735646559141, 'eval_runtime': 43.2023, 'eval_samples_per_second': 889.791, 'eval_steps_per_second': 6.967, 'epoch': 2.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-2403] due to args.save_total_limit + 30%|███ | 7209/24030 [1:14:49<2:39:07, 1.76it/s]***** Running Evaluation ***** +{'loss': 0.3221, 'learning_rate': 8.46909863644413e-06, 'epoch': 2.04} +{'loss': 0.3323, 'learning_rate': 8.42482734195148e-06, 'epoch': 2.08} +{'loss': 0.3206, 'learning_rate': 8.38055604745883e-06, 'epoch': 2.12} +{'loss': 0.3194, 'learning_rate': 8.336284752966177e-06, 'epoch': 2.16} +{'loss': 0.3188, 'learning_rate': 8.292013458473527e-06, 'epoch': 2.21} +{'loss': 0.3261, 'learning_rate': 8.247742163980875e-06, 'epoch': 2.25} +{'loss': 0.3214, 'learning_rate': 8.203470869488224e-06, 'epoch': 2.29} +{'loss': 0.3262, 'learning_rate': 8.159199574995574e-06, 'epoch': 2.33} +{'loss': 0.3232, 'learning_rate': 8.114928280502923e-06, 'epoch': 2.37} +{'loss': 0.3197, 'learning_rate': 8.070656986010271e-06, 'epoch': 2.41} +{'loss': 0.3257, 'learning_rate': 8.02638569151762e-06, 'epoch': 2.46} +{'loss': 0.3241, 'learning_rate': 7.982114397024969e-06, 'epoch': 2.5} +{'loss': 0.325, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33656424283981323, 'eval_accuracy': 0.8730522098800759, 'eval_f1': 0.690735686719143, 'eval_matthews_correlation': 0.411725081359093, 'eval_precision': 0.7686552439919055, 'eval_recall': 0.6577463556092537, 'eval_runtime': 43.0787, 'eval_samples_per_second': 892.344, 'eval_steps_per_second': 6.987, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:38:40<46:43, 5.14it/s]***** Running Evaluation ***** +{'loss': 0.3056, 'learning_rate': 7.406587568620507e-06, 'epoch': 3.04} +{'loss': 0.3108, 'learning_rate': 7.362316274127856e-06, 'epoch': 3.08} +{'loss': 0.3048, 'learning_rate': 7.318044979635205e-06, 'epoch': 3.12} +{'loss': 0.3117, 'learning_rate': 7.273773685142555e-06, 'epoch': 3.16} +{'loss': 0.3073, 'learning_rate': 7.2295023906499025e-06, 'epoch': 3.2} +{'loss': 0.2994, 'learning_rate': 7.185231096157252e-06, 'epoch': 3.25} +{'loss': 0.3177, 'learning_rate': 7.140959801664601e-06, 'epoch': 3.29} +{'loss': 0.2994, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-9612/special_tokens_map.json + 50%|█████ | 12015/24030 [2:04:40<1:50:19, 1.82it/s]***** Running Evaluation ***** +{'loss': 0.2999, 'learning_rate': 6.344961926686737e-06, 'epoch': 4.04} +{'loss': 0.2903, 'learning_rate': 6.300690632194086e-06, 'epoch': 4.08} +{'loss': 0.2996, 'learning_rate': 6.256419337701435e-06, 'epoch': 4.12} +{'loss': 0.2923, 'learning_rate': 6.212148043208784e-06, 'epoch': 4.16} +{'loss': 0.2812, 'learning_rate': 6.167876748716133e-06, 'epoch': 4.2} +{'loss': 0.2981, 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0.6534746833797164, 'eval_runtime': 38.0385, 'eval_samples_per_second': 1010.582, 'eval_steps_per_second': 7.913, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [2:31:01<1:30:26, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.2691, 'learning_rate': 5.282450858863114e-06, 'epoch': 5.04} +{'loss': 0.2729, 'learning_rate': 5.238179564370463e-06, 'epoch': 5.08} +{'loss': 0.2679, 'learning_rate': 5.193908269877812e-06, 'epoch': 5.12} +{'loss': 0.2774, 'learning_rate': 5.149636975385161e-06, 'epoch': 5.16} +{'loss': 0.2751, 'learning_rate': 5.1053656808925104e-06, 'epoch': 5.2} +{'loss': 0.2724, 'learning_rate': 5.061094386399858e-06, 'epoch': 5.24} +{'loss': 0.2698, 'learning_rate': 5.016823091907208e-06, 'epoch': 5.29} +{'loss': 0.2666, 'learning_rate': 4.972551797414557e-06, 'epoch': 5.33} +{'loss': 0.2801, 'learning_rate': 4.928280502921906e-06, 'epoch': 5.37} +{'loss': 0.2761, 'learning_rate': 4.884009208429255e-06, 'epoch': 5.41} +{'loss': 0.2793, 'learning_rate': 4.839737913936604e-06, 'epoch': 5.45} +{'loss': 0.2742, 'learning_rate': 4.795466619443953e-06, 'epoch': 5.49} +{'loss': 0.2746, 'learning_rate': 4.751638037896229e-06, 'epoch': 5.53} +{'loss': 0.2723, 'learning_rate': 4.7073667434035775e-06, 'epoch': 5.58} +{'loss': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35850220918655396, 'eval_accuracy': 0.86105980593637, 'eval_f1': 0.6747508966915934, 'eval_matthews_correlation': 0.368050895179609, 'eval_precision': 0.7268801340600137, 'eval_recall': 0.6492654502384502, 'eval_runtime': 37.6077, 'eval_samples_per_second': 1022.157, 'eval_steps_per_second': 8.004, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:57:15<1:06:37, 1.80it/s]***** Running Evaluation ***** +{'loss': 0.258, 'learning_rate': 4.2203825039844175e-06, 'epoch': 6.03} +{'loss': 0.2583, 'learning_rate': 4.176111209491766e-06, 'epoch': 6.08} +{'loss': 0.2447, 'learning_rate': 4.131839914999115e-06, 'epoch': 6.12} +{'loss': 0.2582, 'learning_rate': 4.0875686205064644e-06, 'epoch': 6.16} +{'loss': 0.2577, 'learning_rate': 4.043297326013813e-06, 'epoch': 6.2} +{'loss': 0.2495, 'learning_rate': 3.999026031521162e-06, 'epoch': 6.24} +{'loss': 0.2574, 'learning_rate': 3.954754737028511e-06, 'epoch': 6.28} +{'loss': 0.2528, 'learning_rate': 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0.255, 'learning_rate': 3.2911280325836732e-06, 'epoch': 6.91} +{'loss': 0.2552, 'learning_rate': 3.246856738091022e-06, 'epoch': 6.95} +{'loss': 0.2529, 'learning_rate': 3.202585443598371e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [2:57:52<1:06:37, 1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3756933808326721, 'eval_accuracy': 0.8580942223147161, 'eval_f1': 0.6743285377643958, 'eval_matthews_correlation': 0.3630957304840496, 'eval_precision': 0.717959505517993, 'eval_recall': 0.6512190408746157, 'eval_runtime': 36.8864, 'eval_samples_per_second': 1042.146, 'eval_steps_per_second': 8.16, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:23:13<43:48, 1.83it/s]***** Running Evaluation ***** +{'loss': 0.2337, 'learning_rate': 3.15831414910572e-06, 'epoch': 7.03} +{'loss': 0.2302, 'learning_rate': 3.1140428546130693e-06, 'epoch': 7.07} +{'loss': 0.2245, 'learning_rate': 3.069771560120418e-06, 'epoch': 7.12} +{'loss': 0.241, 'learning_rate': 3.025500265627767e-06, 'epoch': 7.16} +{'loss': 0.2262, 'learning_rate': 2.9816716840800425e-06, 'epoch': 7.2} +{'loss': 0.2343, 'learning_rate': 2.937400389587392e-06, 'epoch': 7.24} +{'loss': 0.2329, 'learning_rate': 2.893129095094741e-06, 'epoch': 7.28} +{'loss': 0.2329, 'learning_rate': 2.8488578006020903e-06, 'epoch': 7.32} +{'loss': 0.2385, 'learning_rate': 2.804586506109439e-06, 'epoch': 7.37} +{'loss': 0.22, 'learning_rate': 2.760315211616788e-06, 'epoch': 7.41} +{'loss': 0.2325, 'learning_rate': 2.7160439171241372e-06, 'epoch': 7.45} +{'loss': 0.2359, 'learning_rate': 2.671772622631486e-06, 'epoch': 7.49} +{'loss': 0.2383, 'learning_rate': 2.627501328138835e-06, 'epoch': 7.53} +{'loss': 0.2407, 'learning_rate': 2.583230033646184e-06, 'epoch': 7.57} +{'loss': 0.2414, 'learning_rate': 2.5394014520984595e-06, 'epoch': 7.62} +{'loss': 0.2329, 'learning_rate': 2.4951301576058086e-06, 'epoch': 7.66} +{'loss': 0.2353, 'learning_rate': 2.4508588631131577e-06, 'epoch': 7.7} +{'loss': 0.2358, 'learning_rate': 2.406587568620507e-06, 'epoch': 7.74} +{'loss': 0.2268, 'learning_rate': 2.3623162741278556e-06, 'epoch': 7.78} +{'loss': 0.2392, 'learning_rate': 2.3180449796352047e-06, 'epoch': 7.82} +{'loss': 0.2357, 'learning_rate': 2.273773685142554e-06, 'epoch': 7.87} +{'loss': 0.2408, 'learning_rate': 2.229502390649903e-06, 'epoch': 7.91} +{'loss': 0.2368, 'learning_rate': 2.1852310961572517e-06, 'epoch': 7.95} +{'loss': 0.231, 'learning_rate': 2.1409598016646008e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:23:50<43:48, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.4030454754829407, 'eval_accuracy': 0.851980957831482, 'eval_f1': 0.6677461753485375, 'eval_matthews_correlation': 0.3458240789224372, 'eval_precision': 0.7017582169520525, 'eval_recall': 0.6481901150907938, 'eval_runtime': 37.417, 'eval_samples_per_second': 1027.368, 'eval_steps_per_second': 8.044, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:49:16<21:28, 1.86it/s]***** Running Evaluation ***** +{'loss': 0.2152, 'learning_rate': 2.09668850717195e-06, 'epoch': 8.03} +{'loss': 0.2125, 'learning_rate': 2.0524172126792986e-06, 'epoch': 8.07} +{'loss': 0.2187, 'learning_rate': 2.008145918186648e-06, 'epoch': 8.11} +{'loss': 0.2193, 'learning_rate': 1.963874623693997e-06, 'epoch': 8.16} +{'loss': 0.2134, 'learning_rate': 1.919603329201346e-06, 'epoch': 8.2} +{'loss': 0.2155, 'learning_rate': 1.8753320347086951e-06, 'epoch': 8.24} +{'loss': 0.2184, 'learning_rate': 1.831060740216044e-06, 'epoch': 8.28} +{'loss': 0.2163, 'learning_rate': 1.7867894457233932e-06, 'epoch': 8.32} +{'loss': 0.2165, 'learning_rate': 1.742518151230742e-06, 'epoch': 8.36} +{'loss': 0.2196, 'learning_rate': 1.698246856738091e-06, 'epoch': 8.41} +{'loss': 0.2154, 'learning_rate': 1.6539755622454401e-06, 'epoch': 8.45} +{'loss': 0.2179, 'learning_rate': 1.609704267752789e-06, 'epoch': 8.49} +{'loss': 0.2161, 'learning_rate': 1.5654329732601384e-06, 'epoch': 8.53} +{'loss': 0.2107, 'learning_rate': 1.5211616787674873e-06, 'epoch': 8.57} +{'loss': 0.2142, 'learning_rate': 1.4768903842748364e-06, 'epoch': 8.61} +{'loss': 0.2171, 'learning_rate': 1.4326190897821853e-06, 'epoch': 8.66} +{'loss': 0.2245, 'learning_rate': 1.3883477952895345e-06, 'epoch': 8.7} +{'loss': 0.2222, 'learning_rate': 1.3440765007968834e-06, 'epoch': 8.74} +{'loss': 0.2164, 'learning_rate': 1.2998052063042325e-06, 'epoch': 8.78} +{'loss': 0.2173, 'learning_rate': 1.2555339118115814e-06, 'epoch': 8.82} +{'loss': 0.2144, 'learning_rate': 1.2112626173189305e-06, 'epoch': 8.86} +{'loss': 0.213, 'learning_rate': 1.1669913228262794e-06, 'epoch': 8.91} +{'loss': 0.2212, 'learning_rate': 1.1227200283336286e-06, 'epoch': 8.95} +{'loss': 0.2316, 'learning_rate': 1.0784487338409775e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:49:53<21:28, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.4184388518333435, 'eval_accuracy': 0.8530995551624567, 'eval_f1': 0.6675055752613811, 'eval_matthews_correlation': 0.3466802846997334, 'eval_precision': 0.704401464999313, 'eval_recall': 0.6469989706285767, 'eval_runtime': 37.3281, 'eval_samples_per_second': 1029.815, 'eval_steps_per_second': 8.064, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [4:15:11<00:00, 1.89it/s]***** Running Evaluation ***** +{'loss': 0.2069, 'learning_rate': 1.0341774393483266e-06, 'epoch': 9.03} +{'loss': 0.2123, 'learning_rate': 9.899061448556757e-07, 'epoch': 9.07} +{'loss': 0.1983, 'learning_rate': 9.456348503630248e-07, 'epoch': 9.11} +{'loss': 0.2075, 'learning_rate': 9.013635558703737e-07, 'epoch': 9.16} +{'loss': 0.2015, 'learning_rate': 8.570922613777227e-07, 'epoch': 9.2} +{'loss': 0.211, 'learning_rate': 8.128209668850717e-07, 'epoch': 9.24} +{'loss': 0.2104, 'learning_rate': 7.689923853373474e-07, 'epoch': 9.28} +{'loss': 0.1983, 'learning_rate': 7.251638037896229e-07, 'epoch': 9.32} +{'loss': 0.2007, 'learning_rate': 6.808925092969719e-07, 'epoch': 9.36} +{'loss': 0.2069, 'learning_rate': 6.366212148043209e-07, 'epoch': 9.4} +{'loss': 0.2042, 'learning_rate': 5.9234992031167e-07, 'epoch': 9.45} +{'loss': 0.2016, 'learning_rate': 5.48078625819019e-07, 'epoch': 9.49} +{'loss': 0.2102, 'learning_rate': 5.03807331326368e-07, 'epoch': 9.53} +{'loss': 0.2015, 'learning_rate': 4.595360368337171e-07, 'epoch': 9.57} +{'loss': 0.2081, 'learning_rate': 4.1526474234106605e-07, 'epoch': 9.61} +{'loss': 0.1964, 'learning_rate': 3.709934478484151e-07, 'epoch': 9.65} +{'loss': 0.1991, 'learning_rate': 3.2672215335576414e-07, 'epoch': 9.7} +{'loss': 0.2046, 'learning_rate': 2.8245085886311316e-07, 'epoch': 9.74} +{'loss': 0.2064, 'learning_rate': 2.381795643704622e-07, 'epoch': 9.78} +{'loss': 0.1991, 'learning_rate': 1.9390826987781125e-07, 'epoch': 9.82} +{'loss': 0.1981, 'learning_rate': 1.4963697538516027e-07, 'epoch': 9.86} +{'loss': 0.2048, 'learning_rate': 1.053656808925093e-07, 'epoch': 9.9} +{'loss': 0.2046, 'learning_rate': 6.109438639985834e-08, 'epoch': 9.95} +{'loss': 0.2016, 'learning_rate': 1.6823091907207366e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [4:15:48<00:00, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.4355672597885132, 'eval_accuracy': 0.8492234853411722, 'eval_f1': 0.6691180653273854, 'eval_matthews_correlation': 0.3453930956785309, 'eval_precision': 0.6959702951019764, 'eval_recall': 0.6521868282133281, 'eval_runtime': 37.602, 'eval_samples_per_second': 1022.313, 'eval_steps_per_second': 8.005, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209 (score: 0.690735686719143). +100%|██████████| 24030/24030 [4:15:50<00:00, 1.89it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 15350.8719, 'train_samples_per_second': 200.333, 'train_steps_per_second': 1.565, 'train_loss': 0.28093050890449084, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:15:51<00:00, 1.57it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:08<00:00, 4.39it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_034456-hf9t43nv/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_034456-hf9t43nv/files/requirements.txt new file 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/home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.06 +warmup_steps: + value: 0 +weight_decay: + value: 0 diff --git a/VASC/len2_5120/wandb/run-20260307_052350-icyx189y/files/output.log b/VASC/len2_5120/wandb/run-20260307_052350-icyx189y/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..4831a9d1a786a11578a3cf20fd1f7bdb6b4e705b --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_052350-icyx189y/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.weight', 'classifier.bias', 'classifier.weight', 'bert.pooler.dense.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 8 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 19,224 + Number of trainable parameters = 88,402,178 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 12%|█▎ | 2403/19224 [25:33<2:36:29, 1.79it/s]***** Running Evaluation ***** +{'loss': 0.5331, 'learning_rate': 8.665511265164646e-07, 'epoch': 0.04} +{'loss': 0.389, 'learning_rate': 1.7331022530329292e-06, 'epoch': 0.08} +{'loss': 0.3637, 'learning_rate': 2.599653379549394e-06, 'epoch': 0.12} +{'loss': 0.3559, 'learning_rate': 3.4662045060658585e-06, 'epoch': 0.17} +{'loss': 0.3593, 'learning_rate': 4.332755632582323e-06, 'epoch': 0.21} 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33860915899276733, 'eval_accuracy': 0.8712312374808148, 'eval_f1': 0.6922103437227975, 'eval_matthews_correlation': 0.4092961877372573, 'eval_precision': 0.7597628323877017, 'eval_recall': 0.6612272315446382, 'eval_runtime': 42.8927, 'eval_samples_per_second': 896.213, 'eval_steps_per_second': 7.018, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:44:12<1:28:51, 1.80it/s]***** Running Evaluation ***** +{'loss': 0.3065, 'learning_rate': 6.598782512451578e-06, 'epoch': 3.04} +{'loss': 0.3118, 'learning_rate': 6.543442169341451e-06, 'epoch': 3.08} +{'loss': 0.3049, 'learning_rate': 6.488101826231323e-06, 'epoch': 3.12} +{'loss': 0.3126, 'learning_rate': 6.432761483121196e-06, 'epoch': 3.16} +{'loss': 0.3067, 'learning_rate': 6.377421140011068e-06, 'epoch': 3.2} +{'loss': 0.3009, 'learning_rate': 6.322080796900941e-06, 'epoch': 3.25} +{'loss': 0.316, 'learning_rate': 6.266740453790814e-06, 'epoch': 3.29} +{'loss': 0.2958, 'learning_rate': 6.211400110680687e-06, 'epoch': 3.33} +{'loss': 0.2998, 'learning_rate': 6.156613171001661e-06, 'epoch': 3.37} +{'loss': 0.3089, 'learning_rate': 6.101272827891534e-06, 'epoch': 3.41} +{'loss': 0.3238, 'learning_rate': 6.045932484781406e-06, 'epoch': 3.45} +{'loss': 0.3209, 'learning_rate': 5.990592141671279e-06, 'epoch': 3.5} +{'loss': 0.3032, 'learning_rate': 5.935251798561151e-06, 'epoch': 3.54} +{'loss': 0.3026, 'learning_rate': 5.879911455451024e-06, 'epoch': 3.58} +{'loss': 0.3059, 'learning_rate': 5.824571112340896e-06, 'epoch': 3.62} +{'loss': 0.3154, 'learning_rate': 5.769230769230769e-06, 'epoch': 3.66} +{'loss': 0.3175, 'learning_rate': 5.713890426120643e-06, 'epoch': 3.7} +{'loss': 0.3091, 'learning_rate': 5.658550083010516e-06, 'epoch': 3.75} +{'loss': 0.3125, 'learning_rate': 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+{'eval_loss': 0.3506777882575989, 'eval_accuracy': 0.8686818761218491, 'eval_f1': 0.673324988417146, 'eval_matthews_correlation': 0.38173314822654786, 'eval_precision': 0.7571679851544342, 'eval_recall': 0.6416585703382206, 'eval_runtime': 42.6727, 'eval_samples_per_second': 900.833, 'eval_steps_per_second': 7.054, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [2:36:10<44:03, 1.82it/s]***** Running Evaluation ***** +{'loss': 0.2703, 'learning_rate': 3.9435528500276705e-06, 'epoch': 5.04} +{'loss': 0.2799, 'learning_rate': 3.888212506917543e-06, 'epoch': 5.08} +{'loss': 0.2722, 'learning_rate': 3.832872163807416e-06, 'epoch': 5.12} +{'loss': 0.2695, 'learning_rate': 3.777531820697289e-06, 'epoch': 5.16} +{'loss': 0.2783, 'learning_rate': 3.7221914775871616e-06, 'epoch': 5.2} +{'loss': 0.2684, 'learning_rate': 3.666851134477034e-06, 'epoch': 5.24} +{'loss': 0.2678, 'learning_rate': 3.6115107913669066e-06, 'epoch': 5.29} +{'loss': 0.2657, 'learning_rate': 3.556170448256779e-06, 'epoch': 5.33} +{'loss': 0.2785, 'learning_rate': 3.500830105146652e-06, 'epoch': 5.37} +{'loss': 0.2736, 'learning_rate': 3.4454897620365247e-06, 'epoch': 5.41} +{'loss': 0.2805, 'learning_rate': 3.3901494189263977e-06, 'epoch': 5.45} +{'loss': 0.2751, 'learning_rate': 3.3348090758162706e-06, 'epoch': 5.49} +{'loss': 0.2742, 'learning_rate': 3.280022136137244e-06, 'epoch': 5.53} +{'loss': 0.278, 'learning_rate': 3.2246817930271166e-06, 'epoch': 5.58} +{'loss': 0.2616, 'learning_rate': 3.16934144991699e-06, 'epoch': 5.62} +{'loss': 0.2802, 'learning_rate': 3.1140011068068626e-06, 'epoch': 5.66} +{'loss': 0.2758, 'learning_rate': 3.058660763696735e-06, 'epoch': 5.7} +{'loss': 0.2703, 'learning_rate': 3.003320420586608e-06, 'epoch': 5.74} +{'loss': 0.2741, 'learning_rate': 2.9479800774764806e-06, 'epoch': 5.78} +{'loss': 0.2669, 'learning_rate': 2.892639734366353e-06, 'epoch': 5.83} +{'loss': 0.282, 'learning_rate': 2.8372993912562257e-06, 'epoch': 5.87} +{'loss': 0.2717, 'learning_rate': 2.781959048146099e-06, 'epoch': 5.91} +{'loss': 0.276, 'learning_rate': 2.7266187050359716e-06, 'epoch': 5.95} +{'loss': 0.2775, 'learning_rate': 2.671278361925844e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [2:36:53<44:03, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3601917624473572, 'eval_accuracy': 0.865534195260269, 'eval_f1': 0.6751668170263271, 'eval_matthews_correlation': 0.3767150862271216, 'eval_precision': 0.7427761014494094, 'eval_recall': 0.6461369707972268, 'eval_runtime': 43.2117, 'eval_samples_per_second': 889.597, 'eval_steps_per_second': 6.966, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:59:14<23:20, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.2632, 'learning_rate': 2.6159380188157167e-06, 'epoch': 6.03} +{'loss': 0.2609, 'learning_rate': 2.5605976757055893e-06, 'epoch': 6.08} +{'loss': 0.247, 'learning_rate': 2.5052573325954622e-06, 'epoch': 6.12} +{'loss': 0.2556, 'learning_rate': 2.449916989485335e-06, 'epoch': 6.16} +{'loss': 0.2604, 'learning_rate': 2.3945766463752078e-06, 'epoch': 6.2} +{'loss': 0.2547, 'learning_rate': 2.3392363032650807e-06, 'epoch': 6.24} +{'loss': 0.2558, 'learning_rate': 2.2838959601549533e-06, 'epoch': 6.28} +{'loss': 0.2551, 'learning_rate': 2.228555617044826e-06, 'epoch': 6.33} +{'loss': 0.2557, 'learning_rate': 2.1732152739346983e-06, 'epoch': 6.37} +{'loss': 0.2523, 'learning_rate': 2.1184283342556726e-06, 'epoch': 6.41} +{'loss': 0.2536, 'learning_rate': 2.063087991145545e-06, 'epoch': 6.45} +{'loss': 0.2558, 'learning_rate': 2.007747648035418e-06, 'epoch': 6.49} +{'loss': 0.2489, 'learning_rate': 1.9524073049252907e-06, 'epoch': 6.53} +{'loss': 0.2486, 'learning_rate': 1.8970669618151635e-06, 'epoch': 6.58} +{'loss': 0.2502, 'learning_rate': 1.8417266187050362e-06, 'epoch': 6.62} +{'loss': 0.2601, 'learning_rate': 1.7863862755949088e-06, 'epoch': 6.66} +{'loss': 0.2566, 'learning_rate': 1.7310459324847815e-06, 'epoch': 6.7} +{'loss': 0.2506, 'learning_rate': 1.6757055893746543e-06, 'epoch': 6.74} +{'loss': 0.2526, 'learning_rate': 1.620365246264527e-06, 'epoch': 6.78} +{'loss': 0.2681, 'learning_rate': 1.5650249031543996e-06, 'epoch': 6.82} +{'loss': 0.2493, 'learning_rate': 1.5096845600442725e-06, 'epoch': 6.87} +{'loss': 0.2582, 'learning_rate': 1.454344216934145e-06, 'epoch': 6.91} +{'loss': 0.2597, 'learning_rate': 1.3990038738240178e-06, 'epoch': 6.95} +{'loss': 0.2553, 'learning_rate': 1.3436635307138906e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [2:59:58<23:20, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.38140520453453064, 'eval_accuracy': 0.8581462500975521, 'eval_f1': 0.6795482824877521, 'eval_matthews_correlation': 0.3708875050477732, 'eval_precision': 0.7181350819978206, 'eval_recall': 0.6576517863847507, 'eval_runtime': 44.1088, 'eval_samples_per_second': 871.504, 'eval_steps_per_second': 6.824, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [3:25:32<00:00, 1.81it/s]***** Running Evaluation ***** +{'loss': 0.2388, 'learning_rate': 1.2883231876037633e-06, 'epoch': 7.03} +{'loss': 0.2389, 'learning_rate': 1.2329828444936359e-06, 'epoch': 7.07} +{'loss': 0.2387, 'learning_rate': 1.1776425013835086e-06, 'epoch': 7.12} +{'loss': 0.2495, 'learning_rate': 1.1223021582733814e-06, 'epoch': 7.16} +{'loss': 0.2332, 'learning_rate': 1.0669618151632542e-06, 'epoch': 7.2} +{'loss': 0.2391, 'learning_rate': 1.011621472053127e-06, 'epoch': 7.24} +{'loss': 0.2362, 'learning_rate': 9.568345323741008e-07, 'epoch': 7.28} +{'loss': 0.2398, 'learning_rate': 9.014941892639735e-07, 'epoch': 7.32} +{'loss': 0.2394, 'learning_rate': 8.461538461538463e-07, 'epoch': 7.37} +{'loss': 0.2223, 'learning_rate': 7.908135030437189e-07, 'epoch': 7.41} +{'loss': 0.2431, 'learning_rate': 7.354731599335917e-07, 'epoch': 7.45} +{'loss': 0.2413, 'learning_rate': 6.801328168234643e-07, 'epoch': 7.49} +{'loss': 0.2457, 'learning_rate': 6.247924737133371e-07, 'epoch': 7.53} +{'loss': 0.2443, 'learning_rate': 5.694521306032098e-07, 'epoch': 7.57} +{'loss': 0.2555, 'learning_rate': 5.141117874930825e-07, 'epoch': 7.62} +{'loss': 0.2383, 'learning_rate': 4.587714443829552e-07, 'epoch': 7.66} +{'loss': 0.2487, 'learning_rate': 4.034311012728279e-07, 'epoch': 7.7} +{'loss': 0.246, 'learning_rate': 3.480907581627006e-07, 'epoch': 7.74} +{'loss': 0.2358, 'learning_rate': 2.9275041505257337e-07, 'epoch': 7.78} +{'loss': 0.2421, 'learning_rate': 2.3741007194244607e-07, 'epoch': 7.82} +{'loss': 0.2375, 'learning_rate': 1.8206972883231878e-07, 'epoch': 7.87} +{'loss': 0.247, 'learning_rate': 1.2672938572219148e-07, 'epoch': 7.91} +{'loss': 0.2418, 'learning_rate': 7.138904261206419e-08, 'epoch': 7.95} +{'loss': 0.2337, 'learning_rate': 1.6048699501936912e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [3:26:17<00:00, 1.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.39542725682258606, 'eval_accuracy': 0.8587705834915845, 'eval_f1': 0.6766345281536936, 'eval_matthews_correlation': 0.3673697946770687, 'eval_precision': 0.719853290711489, 'eval_recall': 0.6534666204043529, 'eval_runtime': 44.5941, 'eval_samples_per_second': 862.021, 'eval_steps_per_second': 6.75, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-7209 (score: 0.6922103437227975). +100%|██████████| 19224/19224 [3:26:19<00:00, 1.81it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 12379.3267, 'train_samples_per_second': 198.737, 'train_steps_per_second': 1.553, 'train_loss': 0.29882224596791895, 'epoch': 8.0} +100%|██████████| 19224/19224 [3:26:19<00:00, 1.55it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:08<00:00, 4.39it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_052350-icyx189y/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_052350-icyx189y/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_052350-icyx189y/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.05" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.10" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "574550298624" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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b/VASC/len2_5120/wandb/run-20260307_080314-mvrosw49/files/output.log @@ -0,0 +1,232 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['classifier.bias', 'bert.pooler.dense.weight', 'bert.pooler.dense.bias', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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+{'loss': 0.3301, 'learning_rate': 7.258014796547473e-06, 'epoch': 2.08} +{'loss': 0.3211, 'learning_rate': 7.1809494451294705e-06, 'epoch': 2.12} +{'loss': 0.3195, 'learning_rate': 7.103884093711468e-06, 'epoch': 2.16} +{'loss': 0.3189, 'learning_rate': 7.026818742293465e-06, 'epoch': 2.21} +{'loss': 0.3246, 'learning_rate': 6.949753390875463e-06, 'epoch': 2.25} +{'loss': 0.3222, 'learning_rate': 6.87268803945746e-06, 'epoch': 2.29} +{'loss': 0.3261, 'learning_rate': 6.795622688039458e-06, 'epoch': 2.33} +{'loss': 0.3247, 'learning_rate': 6.718557336621455e-06, 'epoch': 2.37} +{'loss': 0.3206, 'learning_rate': 6.641491985203453e-06, 'epoch': 2.41} +{'loss': 0.3267, 'learning_rate': 6.56442663378545e-06, 'epoch': 2.46} +{'loss': 0.3248, 'learning_rate': 6.487361282367448e-06, 'epoch': 2.5} +{'loss': 0.3245, 'learning_rate': 6.4102959309494466e-06, 'epoch': 2.54} +{'loss': 0.3247, 'learning_rate': 6.333230579531443e-06, 'epoch': 2.58} +{'loss': 0.33, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3392159342765808, 'eval_accuracy': 0.8723758487032075, 'eval_f1': 0.6958687755626012, 'eval_matthews_correlation': 0.41607080464790686, 'eval_precision': 0.7629263172311681, 'eval_recall': 0.6646040193916305, 'eval_runtime': 38.1932, 'eval_samples_per_second': 1006.488, 'eval_steps_per_second': 7.881, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:41:29<44:52, 1.79it/s]***** Running Evaluation ***** +{'loss': 0.3071, 'learning_rate': 5.485511713933416e-06, 'epoch': 3.04} +{'loss': 0.3106, 'learning_rate': 5.408446362515414e-06, 'epoch': 3.08} +{'loss': 0.3066, 'learning_rate': 5.331381011097411e-06, 'epoch': 3.12} +{'loss': 0.3115, 'learning_rate': 5.2543156596794085e-06, 'epoch': 3.16} +{'loss': 0.311, 'learning_rate': 5.1772503082614055e-06, 'epoch': 3.2} +{'loss': 0.2982, 'learning_rate': 5.100184956843403e-06, 'epoch': 3.25} +{'loss': 0.3179, 'learning_rate': 5.023119605425402e-06, 'epoch': 3.29} +{'loss': 0.2985, 'learning_rate': 4.946054254007398e-06, 'epoch': 3.33} +{'loss': 0.3033, 'learning_rate': 4.869759556103576e-06, 'epoch': 3.37} +{'loss': 0.3078, 'learning_rate': 4.792694204685574e-06, 'epoch': 3.41} +{'loss': 0.3253, 'learning_rate': 4.7156288532675715e-06, 'epoch': 3.45} +{'loss': 0.324, 'learning_rate': 4.6385635018495685e-06, 'epoch': 3.5} +{'loss': 0.3016, 'learning_rate': 4.561498150431566e-06, 'epoch': 3.54} +{'loss': 0.3027, 'learning_rate': 4.484432799013564e-06, 'epoch': 3.58} +{'loss': 0.303, 'learning_rate': 4.407367447595561e-06, 'epoch': 3.62} +{'loss': 0.3147, 'learning_rate': 4.330302096177559e-06, 'epoch': 3.66} +{'loss': 0.3194, 'learning_rate': 4.253236744759556e-06, 'epoch': 3.7} +{'loss': 0.306, 'learning_rate': 4.176171393341554e-06, 'epoch': 3.75} +{'loss': 0.3118, 'learning_rate': 4.099106041923552e-06, 'epoch': 3.79} +{'loss': 0.3107, 'learning_rate': 4.022040690505549e-06, 'epoch': 3.83} +{'loss': 0.3148, 'learning_rate': 3.944975339087547e-06, 'epoch': 3.87} +{'loss': 0.3057, 'learning_rate': 3.8679099876695446e-06, 'epoch': 3.91} +{'loss': 0.3108, 'learning_rate': 3.7908446362515416e-06, 'epoch': 3.95} +{'loss': 0.3084, 'learning_rate': 3.713779284833539e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 67%|██████▋ | 9612/14418 [1:42:08<44:52, 1.79Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-9612/config.json +{'eval_loss': 0.33910509943962097, 'eval_accuracy': 0.871517390286413, 'eval_f1': 0.6786079347197363, 'eval_matthews_correlation': 0.39482642463629963, 'eval_precision': 0.7683132156016127, 'eval_recall': 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'epoch': 4.7} +{'loss': 0.2929, 'learning_rate': 2.328144266337855e-06, 'epoch': 4.74} +{'loss': 0.285, 'learning_rate': 2.2510789149198523e-06, 'epoch': 4.79} +{'loss': 0.2995, 'learning_rate': 2.1740135635018497e-06, 'epoch': 4.83} +{'loss': 0.2948, 'learning_rate': 2.096948212083847e-06, 'epoch': 4.87} +{'loss': 0.2989, 'learning_rate': 2.019882860665845e-06, 'epoch': 4.91} +{'loss': 0.2894, 'learning_rate': 1.9428175092478424e-06, 'epoch': 4.95} +{'loss': 0.2923, 'learning_rate': 1.8657521578298398e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 83%|████████▎ | 12015/14418 [2:08:39<22:41, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-12015/config.json +{'eval_loss': 0.3466635048389435, 'eval_accuracy': 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args.save_total_limit +100%|██████████| 14418/14418 [2:34:26<00:00, 2.17it/s]***** Running Evaluation ***** +{'loss': 0.2723, 'learning_rate': 1.7886868064118373e-06, 'epoch': 5.04} +{'loss': 0.2862, 'learning_rate': 1.7116214549938347e-06, 'epoch': 5.08} +{'loss': 0.2756, 'learning_rate': 1.6345561035758326e-06, 'epoch': 5.12} +{'loss': 0.2832, 'learning_rate': 1.55749075215783e-06, 'epoch': 5.16} +{'loss': 0.2882, 'learning_rate': 1.4804254007398274e-06, 'epoch': 5.2} +{'loss': 0.2796, 'learning_rate': 1.4033600493218249e-06, 'epoch': 5.24} +{'loss': 0.2735, 'learning_rate': 1.3262946979038225e-06, 'epoch': 5.29} +{'loss': 0.2759, 'learning_rate': 1.24922934648582e-06, 'epoch': 5.33} +{'loss': 0.2851, 'learning_rate': 1.1721639950678176e-06, 'epoch': 5.37} +{'loss': 0.2839, 'learning_rate': 1.095098643649815e-06, 'epoch': 5.41} +{'loss': 0.2855, 'learning_rate': 1.0180332922318127e-06, 'epoch': 5.45} +{'loss': 0.2844, 'learning_rate': 9.409679408138102e-07, 'epoch': 5.49} +{'loss': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35622912645339966, 'eval_accuracy': 0.8624385421815249, 'eval_f1': 0.679072288258511, 'eval_matthews_correlation': 0.37619713562182905, 'eval_precision': 0.730829450615335, 'eval_recall': 0.6532779769574458, 'eval_runtime': 42.396, 'eval_samples_per_second': 906.712, 'eval_steps_per_second': 7.1, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209 (score: 0.6958687755626012). +100%|██████████| 14418/14418 [2:35:11<00:00, 2.17it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 9311.5779, 'train_samples_per_second': 198.159, 'train_steps_per_second': 1.548, 'train_loss': 0.31782937258221533, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:35:11<00:00, 1.55it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:10<00:00, 4.29it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_080314-mvrosw49/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_080314-mvrosw49/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_080314-mvrosw49/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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'epoch': 2.04} +{'loss': 0.3299, 'learning_rate': 8.42482734195148e-06, 'epoch': 2.08} +{'loss': 0.3235, 'learning_rate': 8.38055604745883e-06, 'epoch': 2.12} +{'loss': 0.3224, 'learning_rate': 8.336284752966177e-06, 'epoch': 2.16} +{'loss': 0.3206, 'learning_rate': 8.292013458473527e-06, 'epoch': 2.21} +{'loss': 0.3257, 'learning_rate': 8.247742163980875e-06, 'epoch': 2.25} +{'loss': 0.3227, 'learning_rate': 8.203470869488224e-06, 'epoch': 2.29} +{'loss': 0.3307, 'learning_rate': 8.159199574995574e-06, 'epoch': 2.33} +{'loss': 0.3262, 'learning_rate': 8.114928280502923e-06, 'epoch': 2.37} +{'loss': 0.3257, 'learning_rate': 8.070656986010271e-06, 'epoch': 2.41} +{'loss': 0.3288, 'learning_rate': 8.02638569151762e-06, 'epoch': 2.46} +{'loss': 0.3249, 'learning_rate': 7.982114397024969e-06, 'epoch': 2.5} +{'loss': 0.3248, 'learning_rate': 7.937843102532318e-06, 'epoch': 2.54} +{'loss': 0.3247, 'learning_rate': 7.893571808039668e-06, 'epoch': 2.58} +{'loss': 0.3324, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33754318952560425, 'eval_accuracy': 0.871621445852085, 'eval_f1': 0.6921790772356471, 'eval_matthews_correlation': 0.41009311128760384, 'eval_precision': 0.7614411033938766, 'eval_recall': 0.6608166789215422, 'eval_runtime': 45.4869, 'eval_samples_per_second': 845.1, 'eval_steps_per_second': 6.617, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:44:21<2:19:13, 1.73it/s]***** Running Evaluation ***** +{'loss': 0.3103, 'learning_rate': 7.406587568620507e-06, 'epoch': 3.04} +{'loss': 0.3121, 'learning_rate': 7.362316274127856e-06, 'epoch': 3.08} +{'loss': 0.3025, 'learning_rate': 7.318044979635205e-06, 'epoch': 3.12} +{'loss': 0.3118, 'learning_rate': 7.273773685142555e-06, 'epoch': 3.16} +{'loss': 0.3088, 'learning_rate': 7.2295023906499025e-06, 'epoch': 3.2} +{'loss': 0.2995, 'learning_rate': 7.185231096157252e-06, 'epoch': 3.25} +{'loss': 0.3168, 'learning_rate': 7.140959801664601e-06, 'epoch': 3.29} +{'loss': 0.3011, 'learning_rate': 7.09668850717195e-06, 'epoch': 3.33} +{'loss': 0.3021, 'learning_rate': 7.052859925624226e-06, 'epoch': 3.37} +{'loss': 0.3099, 'learning_rate': 7.008588631131576e-06, 'epoch': 3.41} +{'loss': 0.3247, 'learning_rate': 6.9643173366389235e-06, 'epoch': 3.45} +{'loss': 0.3219, 'learning_rate': 6.920046042146273e-06, 'epoch': 3.5} +{'loss': 0.3031, 'learning_rate': 6.875774747653622e-06, 'epoch': 3.54} +{'loss': 0.3069, 'learning_rate': 6.831503453160971e-06, 'epoch': 3.58} +{'loss': 0.3048, 'learning_rate': 6.78723215866832e-06, 'epoch': 3.62} +{'loss': 0.3173, 'learning_rate': 6.7429608641756695e-06, 'epoch': 3.66} +{'loss': 0.3207, 'learning_rate': 6.698689569683018e-06, 'epoch': 3.7} +{'loss': 0.3112, 'learning_rate': 6.654418275190368e-06, 'epoch': 3.75} +{'loss': 0.3152, 'learning_rate': 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+{'eval_loss': 0.34661051630973816, 'eval_accuracy': 0.8713092791550688, 'eval_f1': 0.6770447728402287, 'eval_matthews_correlation': 0.39264181798891334, 'eval_precision': 0.7682054584711995, 'eval_recall': 0.6437028893002505, 'eval_runtime': 45.0848, 'eval_samples_per_second': 852.638, 'eval_steps_per_second': 6.676, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [2:34:06<1:30:37, 1.77it/s]***** Running Evaluation ***** +{'loss': 0.2712, 'learning_rate': 5.282450858863114e-06, 'epoch': 5.04} +{'loss': 0.2783, 'learning_rate': 5.238179564370463e-06, 'epoch': 5.08} +{'loss': 0.2664, 'learning_rate': 5.193908269877812e-06, 'epoch': 5.12} +{'loss': 0.264, 'learning_rate': 5.149636975385161e-06, 'epoch': 5.16} +{'loss': 0.2774, 'learning_rate': 5.1053656808925104e-06, 'epoch': 5.2} +{'loss': 0.27, 'learning_rate': 5.061094386399858e-06, 'epoch': 5.24} +{'loss': 0.2677, 'learning_rate': 5.016823091907208e-06, 'epoch': 5.29} +{'loss': 0.2667, 'learning_rate': 4.972551797414557e-06, 'epoch': 5.33} +{'loss': 0.2767, 'learning_rate': 4.928280502921906e-06, 'epoch': 5.37} +{'loss': 0.272, 'learning_rate': 4.884009208429255e-06, 'epoch': 5.41} +{'loss': 0.2764, 'learning_rate': 4.839737913936604e-06, 'epoch': 5.45} +{'loss': 0.2739, 'learning_rate': 4.795466619443953e-06, 'epoch': 5.49} +{'loss': 0.2735, 'learning_rate': 4.751638037896229e-06, 'epoch': 5.53} +{'loss': 0.2775, 'learning_rate': 4.7073667434035775e-06, 'epoch': 5.58} +{'loss': 0.2653, 'learning_rate': 4.663095448910926e-06, 'epoch': 5.62} +{'loss': 0.2805, 'learning_rate': 4.618824154418276e-06, 'epoch': 5.66} +{'loss': 0.2793, 'learning_rate': 4.5745528599256245e-06, 'epoch': 5.7} +{'loss': 0.2682, 'learning_rate': 4.530281565432973e-06, 'epoch': 5.74} +{'loss': 0.2712, 'learning_rate': 4.486010270940323e-06, 'epoch': 5.78} +{'loss': 0.2677, 'learning_rate': 4.4417389764476714e-06, 'epoch': 5.83} +{'loss': 0.2755, 'learning_rate': 4.39746768195502e-06, 'epoch': 5.87} +{'loss': 0.27, 'learning_rate': 4.35319638746237e-06, 'epoch': 5.91} +{'loss': 0.2735, 'learning_rate': 4.308925092969719e-06, 'epoch': 5.95} +{'loss': 0.277, 'learning_rate': 4.264653798477068e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [2:34:51<1:30:37, 1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3584495782852173, 'eval_accuracy': 0.8631409172498113, 'eval_f1': 0.6834079646108647, 'eval_matthews_correlation': 0.38328632655927125, 'eval_precision': 0.7325096892745948, 'eval_recall': 0.6579594473951158, 'eval_runtime': 45.4532, 'eval_samples_per_second': 845.728, 'eval_steps_per_second': 6.622, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [3:00:27<1:06:15, 1.81it/s]***** Running Evaluation ***** +{'loss': 0.2551, 'learning_rate': 4.2203825039844175e-06, 'epoch': 6.03} +{'loss': 0.2528, 'learning_rate': 4.176111209491766e-06, 'epoch': 6.08} +{'loss': 0.2431, 'learning_rate': 4.131839914999115e-06, 'epoch': 6.12} +{'loss': 0.2538, 'learning_rate': 4.0875686205064644e-06, 'epoch': 6.16} +{'loss': 0.2532, 'learning_rate': 4.043297326013813e-06, 'epoch': 6.2} +{'loss': 0.2478, 'learning_rate': 3.999026031521162e-06, 'epoch': 6.24} +{'loss': 0.2555, 'learning_rate': 3.954754737028511e-06, 'epoch': 6.28} +{'loss': 0.2525, 'learning_rate': 3.91048344253586e-06, 'epoch': 6.33} +{'loss': 0.2526, 'learning_rate': 3.866654860988136e-06, 'epoch': 6.37} +{'loss': 0.2523, 'learning_rate': 3.8223835664954845e-06, 'epoch': 6.41} +{'loss': 0.2543, 'learning_rate': 3.7781122720028337e-06, 'epoch': 6.45} +{'loss': 0.2461, 'learning_rate': 3.7338409775101824e-06, 'epoch': 6.49} +{'loss': 0.2467, 'learning_rate': 3.6895696830175315e-06, 'epoch': 6.53} +{'loss': 0.247, 'learning_rate': 3.6452983885248806e-06, 'epoch': 6.58} +{'loss': 0.2463, 'learning_rate': 3.60102709403223e-06, 'epoch': 6.62} +{'loss': 0.2545, 'learning_rate': 3.556755799539579e-06, 'epoch': 6.66} +{'loss': 0.2506, 'learning_rate': 3.512484505046928e-06, 'epoch': 6.7} +{'loss': 0.247, 'learning_rate': 3.468213210554277e-06, 'epoch': 6.74} +{'loss': 0.2486, 'learning_rate': 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0.7140283510206107, 'eval_recall': 0.6648217753149156, 'eval_runtime': 45.4143, 'eval_samples_per_second': 846.452, 'eval_steps_per_second': 6.628, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:26:47<45:36, 1.76it/s]***** Running Evaluation ***** +{'loss': 0.2302, 'learning_rate': 3.15831414910572e-06, 'epoch': 7.03} +{'loss': 0.2304, 'learning_rate': 3.1140428546130693e-06, 'epoch': 7.07} +{'loss': 0.2233, 'learning_rate': 3.069771560120418e-06, 'epoch': 7.12} +{'loss': 0.2389, 'learning_rate': 3.025500265627767e-06, 'epoch': 7.16} +{'loss': 0.2252, 'learning_rate': 2.9816716840800425e-06, 'epoch': 7.2} +{'loss': 0.2281, 'learning_rate': 2.937400389587392e-06, 'epoch': 7.24} +{'loss': 0.223, 'learning_rate': 2.893129095094741e-06, 'epoch': 7.28} +{'loss': 0.2278, 'learning_rate': 2.8488578006020903e-06, 'epoch': 7.32} +{'loss': 0.2298, 'learning_rate': 2.804586506109439e-06, 'epoch': 7.37} +{'loss': 0.2171, 'learning_rate': 2.760315211616788e-06, 'epoch': 7.41} +{'loss': 0.2306, 'learning_rate': 2.7160439171241372e-06, 'epoch': 7.45} +{'loss': 0.2317, 'learning_rate': 2.671772622631486e-06, 'epoch': 7.49} +{'loss': 0.2345, 'learning_rate': 2.627501328138835e-06, 'epoch': 7.53} +{'loss': 0.2356, 'learning_rate': 2.583230033646184e-06, 'epoch': 7.57} +{'loss': 0.2402, 'learning_rate': 2.538958739153533e-06, 'epoch': 7.62} +{'loss': 0.2298, 'learning_rate': 2.494687444660882e-06, 'epoch': 7.66} +{'loss': 0.2345, 'learning_rate': 2.450416150168231e-06, 'epoch': 7.7} +{'loss': 0.2324, 'learning_rate': 2.4061448556755803e-06, 'epoch': 7.74} +{'loss': 0.2269, 'learning_rate': 2.361873561182929e-06, 'epoch': 7.78} +{'loss': 0.236, 'learning_rate': 2.317602266690278e-06, 'epoch': 7.82} +{'loss': 0.2293, 'learning_rate': 2.273330972197627e-06, 'epoch': 7.87} +{'loss': 0.2397, 'learning_rate': 2.2290596777049763e-06, 'epoch': 7.91} +{'loss': 0.2356, 'learning_rate': 2.1847883832123255e-06, 'epoch': 7.95} +{'loss': 0.2215, 'learning_rate': 2.1405170887196746e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:27:32<45:36, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.4050333797931671, 'eval_accuracy': 0.8584063890117323, 'eval_f1': 0.6734619192974411, 'eval_matthews_correlation': 0.36226617658423776, 'eval_precision': 0.7188608346706566, 'eval_recall': 0.6499089397315515, 'eval_runtime': 45.127, 'eval_samples_per_second': 851.84, 'eval_steps_per_second': 6.67, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:53:06<22:47, 1.76it/s]***** Running Evaluation ***** +{'loss': 0.2142, 'learning_rate': 2.0962457942270233e-06, 'epoch': 8.03} +{'loss': 0.2117, 'learning_rate': 2.0519744997343724e-06, 'epoch': 8.07} +{'loss': 0.2114, 'learning_rate': 2.008145918186648e-06, 'epoch': 8.11} +{'loss': 0.2125, 'learning_rate': 1.963874623693997e-06, 'epoch': 8.16} +{'loss': 0.2017, 'learning_rate': 1.919603329201346e-06, 'epoch': 8.2} +{'loss': 0.2173, 'learning_rate': 1.8753320347086951e-06, 'epoch': 8.24} +{'loss': 0.208, 'learning_rate': 1.831060740216044e-06, 'epoch': 8.28} +{'loss': 0.2145, 'learning_rate': 1.7867894457233932e-06, 'epoch': 8.32} +{'loss': 0.2043, 'learning_rate': 1.742518151230742e-06, 'epoch': 8.36} +{'loss': 0.215, 'learning_rate': 1.698246856738091e-06, 'epoch': 8.41} +{'loss': 0.217, 'learning_rate': 1.6539755622454401e-06, 'epoch': 8.45} +{'loss': 0.2082, 'learning_rate': 1.609704267752789e-06, 'epoch': 8.49} +{'loss': 0.2154, 'learning_rate': 1.5654329732601384e-06, 'epoch': 8.53} +{'loss': 0.2135, 'learning_rate': 1.5211616787674873e-06, 'epoch': 8.57} +{'loss': 0.2179, 'learning_rate': 1.4768903842748364e-06, 'epoch': 8.61} +{'loss': 0.209, 'learning_rate': 1.4326190897821853e-06, 'epoch': 8.66} +{'loss': 0.2125, 'learning_rate': 1.3883477952895345e-06, 'epoch': 8.7} +{'loss': 0.2165, 'learning_rate': 1.3440765007968834e-06, 'epoch': 8.74} +{'loss': 0.2081, 'learning_rate': 1.2998052063042325e-06, 'epoch': 8.78} +{'loss': 0.2125, 'learning_rate': 1.2555339118115814e-06, 'epoch': 8.82} +{'loss': 0.2111, 'learning_rate': 1.2112626173189305e-06, 'epoch': 8.86} +{'loss': 0.2104, 'learning_rate': 1.1669913228262794e-06, 'epoch': 8.91} +{'loss': 0.2177, 'learning_rate': 1.123162741278555e-06, 'epoch': 8.95} +{'loss': 0.2225, 'learning_rate': 1.0788914467859041e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:53:51<22:47, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.43474891781806946, 'eval_accuracy': 0.8562732499154548, 'eval_f1': 0.6690802499319979, 'eval_matthews_correlation': 0.35297176637158406, 'eval_precision': 0.7127877597460668, 'eval_recall': 0.646377155345021, 'eval_runtime': 45.3827, 'eval_samples_per_second': 847.041, 'eval_steps_per_second': 6.632, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [4:19:21<00:00, 1.71it/s]***** Running Evaluation ***** +{'loss': 0.1926, 'learning_rate': 1.034620152293253e-06, 'epoch': 9.03} +{'loss': 0.2041, 'learning_rate': 9.903488578006022e-07, 'epoch': 9.07} +{'loss': 0.1953, 'learning_rate': 9.460775633079512e-07, 'epoch': 9.11} +{'loss': 0.1985, 'learning_rate': 9.018062688153002e-07, 'epoch': 9.16} +{'loss': 0.2031, 'learning_rate': 8.575349743226492e-07, 'epoch': 9.2} +{'loss': 0.2082, 'learning_rate': 8.132636798299982e-07, 'epoch': 9.24} +{'loss': 0.2031, 'learning_rate': 7.689923853373474e-07, 'epoch': 9.28} +{'loss': 0.1967, 'learning_rate': 7.247210908446964e-07, 'epoch': 9.32} +{'loss': 0.1999, 'learning_rate': 6.804497963520454e-07, 'epoch': 9.36} +{'loss': 0.1994, 'learning_rate': 6.361785018593944e-07, 'epoch': 9.4} +{'loss': 0.1942, 'learning_rate': 5.919072073667434e-07, 'epoch': 9.45} +{'loss': 0.2021, 'learning_rate': 5.476359128740925e-07, 'epoch': 9.49} +{'loss': 0.1991, 'learning_rate': 5.033646183814416e-07, 'epoch': 9.53} +{'loss': 0.1973, 'learning_rate': 4.5909332388879056e-07, 'epoch': 9.57} +{'loss': 0.2015, 'learning_rate': 4.1482202939613953e-07, 'epoch': 9.61} +{'loss': 0.1932, 'learning_rate': 3.705507349034886e-07, 'epoch': 9.65} +{'loss': 0.1942, 'learning_rate': 3.262794404108376e-07, 'epoch': 9.7} +{'loss': 0.1979, 'learning_rate': 2.820081459181867e-07, 'epoch': 9.74} +{'loss': 0.1988, 'learning_rate': 2.3773685142553572e-07, 'epoch': 9.78} +{'loss': 0.1963, 'learning_rate': 1.9346555693288474e-07, 'epoch': 9.82} +{'loss': 0.2039, 'learning_rate': 1.4919426244023376e-07, 'epoch': 9.86} +{'loss': 0.2023, 'learning_rate': 1.053656808925093e-07, 'epoch': 9.9} +{'loss': 0.1983, 'learning_rate': 6.109438639985834e-08, 'epoch': 9.95} +{'loss': 0.1973, 'learning_rate': 1.6823091907207366e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [4:20:07<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.44855570793151855, 'eval_accuracy': 0.8522671106370802, 'eval_f1': 0.672002989080965, 'eval_matthews_correlation': 0.35281977071567056, 'eval_precision': 0.7030475097573736, 'eval_recall': 0.6532668274984075, 'eval_runtime': 45.3238, 'eval_samples_per_second': 848.141, 'eval_steps_per_second': 6.641, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-7209 (score: 0.6921790772356471). +100%|██████████| 24030/24030 [4:20:09<00:00, 1.71it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.06_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 15609.166, 'train_samples_per_second': 197.018, 'train_steps_per_second': 1.539, 'train_loss': 0.2792122056074456, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:20:09<00:00, 1.54it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:10<00:00, 4.27it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_085233-inzb7bjn/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_085233-inzb7bjn/files/requirements.txt new 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/home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 5120 +warmup_ratio: + value: 0.1 +warmup_steps: + value: 0 +weight_decay: + value: 0.05 diff --git a/VASC/len2_5120/wandb/run-20260307_104055-hh05kzkl/files/output.log b/VASC/len2_5120/wandb/run-20260307_104055-hh05kzkl/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..efe90f201fc5638e1dccb0f668aaa5d8c9986c5e --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_104055-hh05kzkl/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['classifier.weight', 'bert.pooler.dense.bias', 'bert.pooler.dense.weight', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 8 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 19,224 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 12%|█▎ | 2403/19224 [25:46<2:43:34, 1.71it/s]***** Running Evaluation ***** +{'loss': 0.611, 'learning_rate': 5.200208008320333e-07, 'epoch': 0.04} +{'loss': 0.4134, 'learning_rate': 1.0400416016640667e-06, 'epoch': 0.08} +{'loss': 0.3675, 'learning_rate': 1.5600624024961e-06, 'epoch': 0.12} +{'loss': 0.3577, 'learning_rate': 2.0800832033281333e-06, 'epoch': 0.17} +{'loss': 0.358, 'learning_rate': 2.6001040041601667e-06, 'epoch': 0.21} +{'loss': 0.3589, 'learning_rate': 3.1201248049922e-06, 'epoch': 0.25} +{'loss': 0.3588, 'learning_rate': 3.6401456058242336e-06, 'epoch': 0.29} +{'loss': 0.3522, 'learning_rate': 4.160166406656267e-06, 'epoch': 0.33} +{'loss': 0.3615, 'learning_rate': 4.6801872074883e-06, 'epoch': 0.37} +{'loss': 0.3555, 'learning_rate': 5.2002080083203335e-06, 'epoch': 0.42} +{'loss': 0.3555, 'learning_rate': 5.7202288091523665e-06, 'epoch': 0.46} +{'loss': 0.3599, 'learning_rate': 6.2402496099844e-06, 'epoch': 0.5} +{'loss': 0.3514, 'learning_rate': 6.760270410816433e-06, 'epoch': 0.54} +{'loss': 0.3497, 'learning_rate': 7.280291211648467e-06, 'epoch': 0.58} +{'loss': 0.3573, 'learning_rate': 7.8003120124805e-06, 'epoch': 0.62} +{'loss': 0.3471, 'learning_rate': 8.320332813312533e-06, 'epoch': 0.67} +{'loss': 0.3497, 'learning_rate': 8.840353614144566e-06, 'epoch': 0.71} +{'loss': 0.3437, 'learning_rate': 9.3603744149766e-06, 'epoch': 0.75} +{'loss': 0.3555, 'learning_rate': 9.880395215808634e-06, 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7209/19224 [1:18:43<1:55:24, 1.74it/s]***** Running Evaluation ***** +{'loss': 0.3239, 'learning_rate': 8.279290214438472e-06, 'epoch': 2.04} +{'loss': 0.3325, 'learning_rate': 8.221490087278192e-06, 'epoch': 2.08} +{'loss': 0.3199, 'learning_rate': 8.163689960117913e-06, 'epoch': 2.12} +{'loss': 0.3197, 'learning_rate': 8.105889832957633e-06, 'epoch': 2.16} +{'loss': 0.3189, 'learning_rate': 8.048089705797354e-06, 'epoch': 2.21} +{'loss': 0.3247, 'learning_rate': 7.990289578637073e-06, 'epoch': 2.25} +{'loss': 0.3223, 'learning_rate': 7.932489451476793e-06, 'epoch': 2.29} +{'loss': 0.3263, 'learning_rate': 7.874689324316514e-06, 'epoch': 2.33} +{'loss': 0.3234, 'learning_rate': 7.816889197156234e-06, 'epoch': 2.37} +{'loss': 0.3204, 'learning_rate': 7.759089069995955e-06, 'epoch': 2.41} +{'loss': 0.3274, 'learning_rate': 7.701288942835674e-06, 'epoch': 2.46} +{'loss': 0.3231, 'learning_rate': 7.643488815675396e-06, 'epoch': 2.5} +{'loss': 0.3257, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3387642800807953, 'eval_accuracy': 0.8705808901953643, 'eval_f1': 0.6923754977917358, 'eval_matthews_correlation': 0.4081514611470621, 'eval_precision': 0.7569943764704227, 'eval_recall': 0.6620537553432168, 'eval_runtime': 42.5627, 'eval_samples_per_second': 903.162, 'eval_steps_per_second': 7.072, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [2:11:31<1:04:50, 1.85it/s]***** Running Evaluation ***** +{'loss': 0.2986, 'learning_rate': 5.50604011328825e-06, 'epoch': 4.04} +{'loss': 0.2922, 'learning_rate': 5.44823998612797e-06, 'epoch': 4.08} +{'loss': 0.2992, 'learning_rate': 5.39043985896769e-06, 'epoch': 4.12} +{'loss': 0.2902, 'learning_rate': 5.332639731807411e-06, 'epoch': 4.16} +{'loss': 0.2777, 'learning_rate': 5.274839604647131e-06, 'epoch': 4.2} +{'loss': 0.2946, 'learning_rate': 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+{'loss': 0.272, 'learning_rate': 4.061614935552858e-06, 'epoch': 5.08} +{'loss': 0.2678, 'learning_rate': 4.003814808392579e-06, 'epoch': 5.12} +{'loss': 0.2758, 'learning_rate': 3.946014681232299e-06, 'epoch': 5.16} +{'loss': 0.2728, 'learning_rate': 3.888214554072019e-06, 'epoch': 5.2} +{'loss': 0.2684, 'learning_rate': 3.83041442691174e-06, 'epoch': 5.24} +{'loss': 0.2644, 'learning_rate': 3.7726142997514597e-06, 'epoch': 5.29} +{'loss': 0.2642, 'learning_rate': 3.71481417259118e-06, 'epoch': 5.33} +{'loss': 0.2766, 'learning_rate': 3.6570140454309e-06, 'epoch': 5.37} +{'loss': 0.275, 'learning_rate': 3.5992139182706203e-06, 'epoch': 5.41} +{'loss': 0.2773, 'learning_rate': 3.5414137911103407e-06, 'epoch': 5.45} +{'loss': 0.2736, 'learning_rate': 3.483613663950061e-06, 'epoch': 5.49} +{'loss': 0.2718, 'learning_rate': 3.425813536789781e-06, 'epoch': 5.53} +{'loss': 0.2714, 'learning_rate': 3.3680134096295014e-06, 'epoch': 5.58} +{'loss': 0.264, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3577874004840851, 'eval_accuracy': 0.8630628755755574, 'eval_f1': 0.6711250103105888, 'eval_matthews_correlation': 0.36672133714392463, 'eval_precision': 0.7343374381597622, 'eval_recall': 0.6434731686203526, 'eval_runtime': 42.6935, 'eval_samples_per_second': 900.395, 'eval_steps_per_second': 7.05, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [3:01:18<23:07, 1.73it/s]***** Running Evaluation ***** +{'loss': 0.261, 'learning_rate': 2.732212010866424e-06, 'epoch': 6.03} +{'loss': 0.2585, 'learning_rate': 2.6744118837061445e-06, 'epoch': 6.08} +{'loss': 0.2468, 'learning_rate': 2.616611756545865e-06, 'epoch': 6.12} +{'loss': 0.2628, 'learning_rate': 2.5588116293855848e-06, 'epoch': 6.16} +{'loss': 0.2565, 'learning_rate': 2.501011502225305e-06, 'epoch': 6.2} +{'loss': 0.2496, 'learning_rate': 2.4432113750650255e-06, 'epoch': 6.24} +{'loss': 0.2562, 'learning_rate': 2.3854112479047454e-06, 'epoch': 6.28} +{'loss': 0.2533, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [3:27:46<00:00, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.2395, 'learning_rate': 1.3455869602913126e-06, 'epoch': 7.03} +{'loss': 0.2389, 'learning_rate': 1.287786833131033e-06, 'epoch': 7.07} +{'loss': 0.2313, 'learning_rate': 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0.2424, 'learning_rate': 4.2136292699843943e-07, 'epoch': 7.7} +{'loss': 0.2394, 'learning_rate': 3.635627998381597e-07, 'epoch': 7.74} +{'loss': 0.2377, 'learning_rate': 3.0576267267787995e-07, 'epoch': 7.78} +{'loss': 0.2429, 'learning_rate': 2.4796254551760015e-07, 'epoch': 7.82} +{'loss': 0.239, 'learning_rate': 1.901624183573204e-07, 'epoch': 7.87} +{'loss': 0.2418, 'learning_rate': 1.3236229119704064e-07, 'epoch': 7.91} +{'loss': 0.2418, 'learning_rate': 7.456216403676089e-08, 'epoch': 7.95} +{'loss': 0.2332, 'learning_rate': 1.676203687648113e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [3:28:29<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.39331895112991333, 'eval_accuracy': 0.8555448609557503, 'eval_f1': 0.6756048943951996, 'eval_matthews_correlation': 0.3618734618293475, 'eval_precision': 0.7112373121171731, 'eval_recall': 0.6549825656554902, 'eval_runtime': 43.0024, 'eval_samples_per_second': 893.927, 'eval_steps_per_second': 7.0, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209 (score: 0.6923754977917358). +100%|██████████| 19224/19224 [3:28:31<00:00, 1.72it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 12511.0098, 'train_samples_per_second': 196.645, 'train_steps_per_second': 1.537, 'train_loss': 0.2988487142004473, 'epoch': 8.0} +100%|██████████| 19224/19224 [3:28:31<00:00, 1.54it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:09<00:00, 4.32it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_104055-hh05kzkl/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_104055-hh05kzkl/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_104055-hh05kzkl/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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--per_device_eval_batch_size + - "128" + - --gradient_accumulation_steps + - "1" + - --learning_rate + - "1e-5" + - --weight_decay + - "0.0" + - --num_train_epochs + - "6" + - --lr_scheduler_type + - linear + - --warmup_steps + - "0" + - --warmup_ratio + - "0.10" + - --fp16 + - --output_dir + - /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42 + - --evaluation_strategy + - epoch + - --save_strategy + - epoch + - --load_best_model_at_end + - "True" + - --metric_for_best_model + - eval_f1 + - --greater_is_better + - "True" + - --save_total_limit + - "1" + - --logging_steps + - "100" + - --overwrite_output_dir + - "True" + - --log_level + - info + - --seed + - "42" + - --find_unused_parameters + - "False" + - --project_name + - super_binary_tune_3072 + cpu_count: 128 + cpu_count_logical: 255 + cudaVersion: "12.2" + disk: + /: + total: "1876350566400" + used: "575103508480" + email: n5huang@ucsd.edu + executable: /home/n5huang/miniconda3/envs/bpe/bin/python + gpu: NVIDIA A100 80GB PCIe + gpu_count: 8 + gpu_nvidia: + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 + - architecture: Ampere + cudaCores: 6912 + memoryTotal: "85899345920" + name: NVIDIA A100 80GB PCIe + uuid: 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'epoch': 2.04} +{'loss': 0.3313, 'learning_rate': 7.258014796547473e-06, 'epoch': 2.08} +{'loss': 0.3226, 'learning_rate': 7.1809494451294705e-06, 'epoch': 2.12} +{'loss': 0.3208, 'learning_rate': 7.103884093711468e-06, 'epoch': 2.16} +{'loss': 0.3224, 'learning_rate': 7.026818742293465e-06, 'epoch': 2.21} +{'loss': 0.3251, 'learning_rate': 6.949753390875463e-06, 'epoch': 2.25} +{'loss': 0.3238, 'learning_rate': 6.87268803945746e-06, 'epoch': 2.29} +{'loss': 0.3306, 'learning_rate': 6.795622688039458e-06, 'epoch': 2.33} +{'loss': 0.3256, 'learning_rate': 6.718557336621455e-06, 'epoch': 2.37} +{'loss': 0.3242, 'learning_rate': 6.641491985203453e-06, 'epoch': 2.41} +{'loss': 0.3278, 'learning_rate': 6.56442663378545e-06, 'epoch': 2.46} +{'loss': 0.324, 'learning_rate': 6.487361282367448e-06, 'epoch': 2.5} +{'loss': 0.3242, 'learning_rate': 6.4102959309494466e-06, 'epoch': 2.54} +{'loss': 0.3259, 'learning_rate': 6.333230579531443e-06, 'epoch': 2.58} +{'loss': 0.3311, 'learning_rate': 6.256165228113441e-06, 'epoch': 2.62} +{'loss': 0.3183, 'learning_rate': 6.179099876695438e-06, 'epoch': 2.66} +{'loss': 0.3169, 'learning_rate': 6.102034525277436e-06, 'epoch': 2.7} +{'loss': 0.3244, 'learning_rate': 6.024969173859433e-06, 'epoch': 2.75} +{'loss': 0.3267, 'learning_rate': 5.947903822441431e-06, 'epoch': 2.79} +{'loss': 0.329, 'learning_rate': 5.870838471023428e-06, 'epoch': 2.83} +{'loss': 0.3148, 'learning_rate': 5.793773119605426e-06, 'epoch': 2.87} +{'loss': 0.3227, 'learning_rate': 5.716707768187424e-06, 'epoch': 2.91} +{'loss': 0.3209, 'learning_rate': 5.639642416769421e-06, 'epoch': 2.95} +{'loss': 0.3246, 'learning_rate': 5.562577065351419e-06, 'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 7209/14418 [1:15:40<1:07:44, 1.Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33997613191604614, 'eval_accuracy': 0.8707369735438725, 'eval_f1': 0.6902942830285763, 'eval_matthews_correlation': 0.40596300597582674, 'eval_precision': 0.7585250521093252, 'eval_recall': 0.6593713654404718, 'eval_runtime': 44.661, 'eval_samples_per_second': 860.728, 'eval_steps_per_second': 6.74, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [1:40:53<44:36, 1.80it/s]***** Running Evaluation ***** +{'loss': 0.31, 'learning_rate': 5.485511713933416e-06, 'epoch': 3.04} +{'loss': 0.311, 'learning_rate': 5.408446362515414e-06, 'epoch': 3.08} +{'loss': 0.3023, 'learning_rate': 5.331381011097411e-06, 'epoch': 3.12} +{'loss': 0.3111, 'learning_rate': 5.2543156596794085e-06, 'epoch': 3.16} +{'loss': 0.3101, 'learning_rate': 5.1772503082614055e-06, 'epoch': 3.2} +{'loss': 0.3004, 'learning_rate': 5.100184956843403e-06, 'epoch': 3.25} +{'loss': 0.3177, 'learning_rate': 5.023119605425402e-06, 'epoch': 3.29} +{'loss': 0.2959, 'learning_rate': 4.946054254007398e-06, 'epoch': 3.33} +{'loss': 0.3006, 'learning_rate': 4.869759556103576e-06, 'epoch': 3.37} +{'loss': 0.3082, 'learning_rate': 4.792694204685574e-06, 'epoch': 3.41} +{'loss': 0.3199, 'learning_rate': 4.7156288532675715e-06, 'epoch': 3.45} +{'loss': 0.3207, 'learning_rate': 4.6385635018495685e-06, 'epoch': 3.5} +{'loss': 0.3018, 'learning_rate': 4.561498150431566e-06, 'epoch': 3.54} +{'loss': 0.302, 'learning_rate': 4.484432799013564e-06, 'epoch': 3.58} +{'loss': 0.3038, 'learning_rate': 4.407367447595561e-06, 'epoch': 3.62} +{'loss': 0.3146, 'learning_rate': 4.330302096177559e-06, 'epoch': 3.66} +{'loss': 0.3178, 'learning_rate': 4.253236744759556e-06, 'epoch': 3.7} +{'loss': 0.3078, 'learning_rate': 4.176171393341554e-06, 'epoch': 3.75} +{'loss': 0.3141, 'learning_rate': 4.099106041923552e-06, 'epoch': 3.79} +{'loss': 0.3123, 'learning_rate': 4.022040690505549e-06, 'epoch': 3.83} +{'loss': 0.3114, 'learning_rate': 3.9457459926017264e-06, 'epoch': 3.87} +{'loss': 0.303, 'learning_rate': 3.868680641183724e-06, 'epoch': 3.91} +{'loss': 0.3081, 'learning_rate': 3.7916152897657217e-06, 'epoch': 3.95} +{'loss': 0.3124, 'learning_rate': 3.714549938347719e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 67%|██████▋ | 9612/14418 [1:41:38<44:36, 1.80Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-9612/config.json +{'eval_loss': 0.3370780050754547, 'eval_accuracy': 0.8713613069379048, 'eval_f1': 0.6799584717733966, 'eval_matthews_correlation': 0.39582089792836095, 'eval_precision': 0.7667004554973834, 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [2:33:17<00:00, 1.75it/s]***** Running Evaluation ***** +{'loss': 0.2732, 'learning_rate': 1.7879161528976574e-06, 'epoch': 5.04} +{'loss': 0.2851, 'learning_rate': 1.7108508014796548e-06, 'epoch': 5.08} +{'loss': 0.2789, 'learning_rate': 1.6337854500616524e-06, 'epoch': 5.12} +{'loss': 0.2757, 'learning_rate': 1.5567200986436499e-06, 'epoch': 5.16} +{'loss': 0.2813, 'learning_rate': 1.4796547472256475e-06, 'epoch': 5.2} +{'loss': 0.2732, 'learning_rate': 1.402589395807645e-06, 'epoch': 5.24} +{'loss': 0.2735, 'learning_rate': 1.3255240443896426e-06, 'epoch': 5.29} +{'loss': 0.2732, 'learning_rate': 1.24845869297164e-06, 'epoch': 5.33} +{'loss': 0.2859, 'learning_rate': 1.1713933415536375e-06, 'epoch': 5.37} +{'loss': 0.2793, 'learning_rate': 1.0943279901356351e-06, 'epoch': 5.41} +{'loss': 0.2838, 'learning_rate': 1.0172626387176325e-06, 'epoch': 5.45} +{'loss': 0.2805, 'learning_rate': 9.401972872996301e-07, 'epoch': 5.49} +{'loss': 0.2779, 'learning_rate': 8.639025893958077e-07, 'epoch': 5.53} +{'loss': 0.2786, 'learning_rate': 7.868372379778052e-07, 'epoch': 5.58} +{'loss': 0.2694, 'learning_rate': 7.097718865598027e-07, 'epoch': 5.62} +{'loss': 0.2874, 'learning_rate': 6.327065351418003e-07, 'epoch': 5.66} +{'loss': 0.2835, 'learning_rate': 5.556411837237978e-07, 'epoch': 5.7} +{'loss': 0.2734, 'learning_rate': 4.785758323057954e-07, 'epoch': 5.74} +{'loss': 0.2768, 'learning_rate': 4.0151048088779286e-07, 'epoch': 5.78} +{'loss': 0.2697, 'learning_rate': 3.244451294697904e-07, 'epoch': 5.83} +{'loss': 0.2801, 'learning_rate': 2.4737977805178794e-07, 'epoch': 5.87} +{'loss': 0.2763, 'learning_rate': 1.7031442663378545e-07, 'epoch': 5.91} +{'loss': 0.2801, 'learning_rate': 9.324907521578299e-08, 'epoch': 5.95} +{'loss': 0.2803, 'learning_rate': 1.6183723797780518e-08, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [2:34:01<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3561706840991974, 'eval_accuracy': 0.8643895840378762, 'eval_f1': 0.6820179037310703, 'eval_matthews_correlation': 0.3834012021054672, 'eval_precision': 0.7368807753718646, 'eval_recall': 0.6551376230776395, 'eval_runtime': 44.6507, 'eval_samples_per_second': 860.928, 'eval_steps_per_second': 6.741, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-7209 (score: 0.6902942830285763). +100%|██████████| 14418/14418 [2:34:03<00:00, 1.75it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 9243.7911, 'train_samples_per_second': 199.612, 'train_steps_per_second': 1.56, 'train_loss': 0.3171644860025682, 'epoch': 6.0} +100%|██████████| 14418/14418 [2:34:03<00:00, 1.56it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:09<00:00, 4.33it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_131510-at1htxdp/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_131510-at1htxdp/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_131510-at1htxdp/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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b/VASC/len2_5120/wandb/run-20260307_141152-q05v6wzc/files/output.log @@ -0,0 +1,368 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.weight', 'classifier.bias', 'bert.pooler.dense.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 10 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 24,030 + Number of trainable parameters = 89,975,042 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 10%|█ | 2403/24030 [25:10<3:19:22, 1.81it/s]***** Running Evaluation ***** +{'loss': 0.6029, 'learning_rate': 4.161464835622139e-07, 'epoch': 0.04} +{'loss': 0.4164, 'learning_rate': 8.322929671244278e-07, 'epoch': 0.08} +{'loss': 0.3688, 'learning_rate': 1.2484394506866417e-06, 'epoch': 0.12} +{'loss': 0.3576, 'learning_rate': 1.6645859342488557e-06, 'epoch': 0.17} +{'loss': 0.361, 'learning_rate': 2.0807324178110696e-06, 'epoch': 0.21} 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+{'loss': 0.3357, 'learning_rate': 9.169094187820781e-06, 'epoch': 1.75} +{'loss': 0.349, 'learning_rate': 9.122855689647201e-06, 'epoch': 1.79} +{'loss': 0.3418, 'learning_rate': 9.076617191473621e-06, 'epoch': 1.83} +{'loss': 0.3379, 'learning_rate': 9.030378693300042e-06, 'epoch': 1.87} +{'loss': 0.3381, 'learning_rate': 8.984140195126462e-06, 'epoch': 1.91} +{'loss': 0.334, 'learning_rate': 8.937901696952884e-06, 'epoch': 1.96} +{'loss': 0.3273, 'learning_rate': 8.891663198779304e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [51:45<3:04:14, 1.74Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 0.3383144736289978, 'eval_accuracy': 0.8744049322338129, 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3379461467266083, 'eval_accuracy': 0.8716734736349211, 'eval_f1': 0.690770896159894, 'eval_matthews_correlation': 0.4085612763300843, 'eval_precision': 0.7623427372096656, 'eval_recall': 0.6590689323934499, 'eval_runtime': 42.2612, 'eval_samples_per_second': 909.606, 'eval_steps_per_second': 7.122, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [1:40:24<2:16:21, 1.76it/s]***** Running Evaluation ***** +{'loss': 0.3102, 'learning_rate': 7.735700744439821e-06, 'epoch': 3.04} +{'loss': 0.3144, 'learning_rate': 7.689462246266241e-06, 'epoch': 3.08} +{'loss': 0.3087, 'learning_rate': 7.643223748092663e-06, 'epoch': 3.12} +{'loss': 0.3155, 'learning_rate': 7.596985249919083e-06, 'epoch': 3.16} +{'loss': 0.3113, 'learning_rate': 7.550746751745504e-06, 'epoch': 3.2} +{'loss': 0.3037, 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0.6633843342201653, 'eval_runtime': 42.3053, 'eval_samples_per_second': 908.657, 'eval_steps_per_second': 7.115, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-9612/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209] due to args.save_total_limit + 50%|█████ | 12015/24030 [2:06:38<1:55:57, 1.73it/s]***** Running Evaluation ***** +{'loss': 0.3034, 'learning_rate': 6.6269015582373886e-06, 'epoch': 4.04} +{'loss': 0.2977, 'learning_rate': 6.58066306006381e-06, 'epoch': 4.08} +{'loss': 0.308, 'learning_rate': 6.53442456189023e-06, 'epoch': 4.12} +{'loss': 0.2987, 'learning_rate': 6.488186063716651e-06, 'epoch': 4.16} +{'loss': 0.2864, 'learning_rate': 6.4419475655430715e-06, 'epoch': 4.2} +{'loss': 0.3024, 'learning_rate': 6.395709067369492e-06, 'epoch': 4.24} +{'loss': 0.2991, 'learning_rate': 6.349470569195914e-06, 'epoch': 4.29} +{'loss': 0.2966, 'learning_rate': 6.303232071022334e-06, 'epoch': 4.33} +{'loss': 0.3065, 'learning_rate': 6.2569935728487545e-06, 'epoch': 4.37} +{'loss': 0.3023, 'learning_rate': 6.210755074675175e-06, 'epoch': 4.41} +{'loss': 0.3027, 'learning_rate': 6.164516576501596e-06, 'epoch': 4.45} +{'loss': 0.2912, 'learning_rate': 6.118278078328016e-06, 'epoch': 4.49} +{'loss': 0.2975, 'learning_rate': 6.0720395801544375e-06, 'epoch': 4.54} +{'loss': 0.2978, 'learning_rate': 6.025801081980857e-06, 'epoch': 4.58} +{'loss': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015/config.json +{'eval_loss': 0.34391534328460693, 'eval_accuracy': 0.8672771259852762, 'eval_f1': 0.6841359833320622, 'eval_matthews_correlation': 0.39138957506950983, 'eval_precision': 0.7468670234935011, 'eval_recall': 0.6551298724565415, 'eval_runtime': 42.4173, 'eval_samples_per_second': 906.258, 'eval_steps_per_second': 7.096, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015/special_tokens_map.json + 60%|██████ | 14418/24030 [2:32:50<1:29:19, 1.79it/s]***** Running Evaluation ***** +{'loss': 0.2696, 'learning_rate': 5.5171776020714855e-06, 'epoch': 5.04} +{'loss': 0.2813, 'learning_rate': 5.470939103897905e-06, 'epoch': 5.08} +{'loss': 0.2739, 'learning_rate': 5.424700605724327e-06, 'epoch': 5.12} +{'loss': 0.2791, 'learning_rate': 5.378462107550747e-06, 'epoch': 5.16} +{'loss': 0.2817, 'learning_rate': 5.332223609377168e-06, 'epoch': 5.2} +{'loss': 0.2783, 'learning_rate': 5.285985111203588e-06, 'epoch': 5.24} +{'loss': 0.2735, 'learning_rate': 5.239746613030009e-06, 'epoch': 5.29} +{'loss': 0.271, 'learning_rate': 5.193508114856431e-06, 'epoch': 5.33} +{'loss': 0.2831, 'learning_rate': 5.147269616682851e-06, 'epoch': 5.37} +{'loss': 0.2823, 'learning_rate': 5.101031118509271e-06, 'epoch': 5.41} +{'loss': 0.284, 'learning_rate': 5.054792620335692e-06, 'epoch': 5.45} +{'loss': 0.2787, 'learning_rate': 5.008554122162113e-06, 'epoch': 5.49} +{'loss': 0.2815, 'learning_rate': 4.9627780089702695e-06, 'epoch': 5.53} +{'loss': 0.2787, 'learning_rate': 4.916539510796689e-06, 'epoch': 5.58} +{'loss': 0.2687, 'learning_rate': 4.87030101262311e-06, 'epoch': 5.62} +{'loss': 0.2904, 'learning_rate': 4.824062514449531e-06, 'epoch': 5.66} +{'loss': 0.2899, 'learning_rate': 4.777824016275952e-06, 'epoch': 5.7} +{'loss': 0.2806, 'learning_rate': 4.731585518102372e-06, 'epoch': 5.74} +{'loss': 0.28, 'learning_rate': 4.685347019928793e-06, 'epoch': 5.78} +{'loss': 0.2744, 'learning_rate': 4.639108521755214e-06, 'epoch': 5.83} +{'loss': 0.2839, 'learning_rate': 4.5928700235816345e-06, 'epoch': 5.87} +{'loss': 0.2781, 'learning_rate': 4.546631525408055e-06, 'epoch': 5.91} +{'loss': 0.28, 'learning_rate': 4.500393027234476e-06, 'epoch': 5.95} +{'loss': 0.2774, 'learning_rate': 4.454154529060897e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [2:33:33<1:29:19, 1Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3548985719680786, 'eval_accuracy': 0.8628807783356313, 'eval_f1': 0.6802506859734745, 'eval_matthews_correlation': 0.37852084626090465, 'eval_precision': 0.7321107829370959, 'eval_recall': 0.6543207399081725, 'eval_runtime': 42.3765, 'eval_samples_per_second': 907.13, 'eval_steps_per_second': 7.103, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [2:59:02<1:09:56, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.2649, 'learning_rate': 4.407916030887317e-06, 'epoch': 6.03} +{'loss': 0.2645, 'learning_rate': 4.361677532713738e-06, 'epoch': 6.08} +{'loss': 0.2497, 'learning_rate': 4.315439034540159e-06, 'epoch': 6.12} +{'loss': 0.2637, 'learning_rate': 4.269200536366579e-06, 'epoch': 6.16} +{'loss': 0.26, 'learning_rate': 4.222962038193e-06, 'epoch': 6.2} +{'loss': 0.2551, 'learning_rate': 4.17672354001942e-06, 'epoch': 6.24} +{'loss': 0.2608, 'learning_rate': 4.130485041845841e-06, 'epoch': 6.28} +{'loss': 0.2604, 'learning_rate': 4.084246543672262e-06, 'epoch': 6.33} +{'loss': 0.2573, 'learning_rate': 4.0384704304804185e-06, 'epoch': 6.37} +{'loss': 0.2547, 'learning_rate': 3.992231932306839e-06, 'epoch': 6.41} +{'loss': 0.2594, 'learning_rate': 3.945993434133259e-06, 'epoch': 6.45} +{'loss': 0.2567, 'learning_rate': 3.899754935959681e-06, 'epoch': 6.49} +{'loss': 0.2529, 'learning_rate': 3.853978822767837e-06, 'epoch': 6.53} +{'loss': 0.257, 'learning_rate': 3.8077403245942573e-06, 'epoch': 6.58} +{'loss': 0.2473, 'learning_rate': 3.761501826420678e-06, 'epoch': 6.62} +{'loss': 0.2606, 'learning_rate': 3.715263328247099e-06, 'epoch': 6.66} +{'loss': 0.2617, 'learning_rate': 3.669024830073519e-06, 'epoch': 6.7} +{'loss': 0.2533, 'learning_rate': 3.6227863318999402e-06, 'epoch': 6.74} +{'loss': 0.2574, 'learning_rate': 3.576547833726361e-06, 'epoch': 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0.6612749317468871, 'eval_runtime': 42.748, 'eval_samples_per_second': 899.247, 'eval_steps_per_second': 7.041, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [3:25:15<46:27, 1.72it/s]***** Running Evaluation ***** +{'loss': 0.2436, 'learning_rate': 3.299116844684885e-06, 'epoch': 7.03} +{'loss': 0.2353, 'learning_rate': 3.2528783465113058e-06, 'epoch': 7.07} +{'loss': 0.2304, 'learning_rate': 3.2066398483377265e-06, 'epoch': 7.12} +{'loss': 0.2449, 'learning_rate': 3.160401350164147e-06, 'epoch': 7.16} +{'loss': 0.2343, 'learning_rate': 3.1141628519905676e-06, 'epoch': 7.2} +{'loss': 0.2467, 'learning_rate': 3.0679243538169883e-06, 'epoch': 7.24} +{'loss': 0.2355, 'learning_rate': 3.021685855643409e-06, 'epoch': 7.28} +{'loss': 0.2361, 'learning_rate': 2.9754473574698293e-06, 'epoch': 7.32} +{'loss': 0.2392, 'learning_rate': 2.9292088592962505e-06, 'epoch': 7.37} +{'loss': 0.2282, 'learning_rate': 2.8829703611226713e-06, 'epoch': 7.41} +{'loss': 0.2405, 'learning_rate': 2.8367318629490916e-06, 'epoch': 7.45} +{'loss': 0.2385, 'learning_rate': 2.7904933647755123e-06, 'epoch': 7.49} +{'loss': 0.2418, 'learning_rate': 2.744254866601933e-06, 'epoch': 7.53} +{'loss': 0.243, 'learning_rate': 2.698016368428354e-06, 'epoch': 7.57} +{'loss': 0.2502, 'learning_rate': 2.651777870254774e-06, 'epoch': 7.62} +{'loss': 0.2396, 'learning_rate': 2.605539372081195e-06, 'epoch': 7.66} +{'loss': 0.2453, 'learning_rate': 2.559300873907616e-06, 'epoch': 7.7} +{'loss': 0.238, 'learning_rate': 2.513062375734036e-06, 'epoch': 7.74} +{'loss': 0.2384, 'learning_rate': 2.466823877560457e-06, 'epoch': 7.78} +{'loss': 0.2426, 'learning_rate': 2.420585379386878e-06, 'epoch': 7.82} +{'loss': 0.2423, 'learning_rate': 2.374346881213298e-06, 'epoch': 7.87} +{'loss': 0.2421, 'learning_rate': 2.3281083830397193e-06, 'epoch': 7.91} +{'loss': 0.2451, 'learning_rate': 2.2818698848661396e-06, 'epoch': 7.95} +{'loss': 0.2355, 'learning_rate': 2.2356313866925604e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [3:25:57<46:27, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.3963141143321991, 'eval_accuracy': 0.8557269581956765, 'eval_f1': 0.6698132880347739, 'eval_matthews_correlation': 0.35333937583241815, 'eval_precision': 0.7113332860323628, 'eval_recall': 0.6476917300364647, 'eval_runtime': 42.4286, 'eval_samples_per_second': 906.016, 'eval_steps_per_second': 7.094, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [3:51:30<22:52, 1.75it/s]***** Running Evaluation ***** +{'loss': 0.2186, 'learning_rate': 2.189392888518981e-06, 'epoch': 8.03} +{'loss': 0.2222, 'learning_rate': 2.1431543903454014e-06, 'epoch': 8.07} +{'loss': 0.2233, 'learning_rate': 2.0969158921718226e-06, 'epoch': 8.11} +{'loss': 0.2224, 'learning_rate': 2.050677393998243e-06, 'epoch': 8.16} +{'loss': 0.2189, 'learning_rate': 2.0044388958246636e-06, 'epoch': 8.2} +{'loss': 0.2235, 'learning_rate': 1.9586627826328203e-06, 'epoch': 8.24} +{'loss': 0.218, 'learning_rate': 1.912424284459241e-06, 'epoch': 8.28} +{'loss': 0.2229, 'learning_rate': 1.8661857862856616e-06, 'epoch': 8.32} +{'loss': 0.22, 'learning_rate': 1.8199472881120823e-06, 'epoch': 8.36} +{'loss': 0.2286, 'learning_rate': 1.773708789938503e-06, 'epoch': 8.41} +{'loss': 0.2213, 'learning_rate': 1.7274702917649236e-06, 'epoch': 8.45} +{'loss': 0.2228, 'learning_rate': 1.6812317935913443e-06, 'epoch': 8.49} +{'loss': 0.2197, 'learning_rate': 1.634993295417765e-06, 'epoch': 8.53} +{'loss': 0.219, 'learning_rate': 1.5887547972441856e-06, 'epoch': 8.57} +{'loss': 0.2243, 'learning_rate': 1.542978684052342e-06, 'epoch': 8.61} +{'loss': 0.2214, 'learning_rate': 1.4967401858787628e-06, 'epoch': 8.66} +{'loss': 0.2273, 'learning_rate': 1.4505016877051833e-06, 'epoch': 8.7} +{'loss': 0.2285, 'learning_rate': 1.4042631895316043e-06, 'epoch': 8.74} +{'loss': 0.2177, 'learning_rate': 1.3580246913580248e-06, 'epoch': 8.78} +{'loss': 0.2209, 'learning_rate': 1.3117861931844455e-06, 'epoch': 8.82} +{'loss': 0.219, 'learning_rate': 1.265547695010866e-06, 'epoch': 8.86} +{'loss': 0.2179, 'learning_rate': 1.2193091968372868e-06, 'epoch': 8.91} +{'loss': 0.2274, 'learning_rate': 1.1730706986637075e-06, 'epoch': 8.95} +{'loss': 0.229, 'learning_rate': 1.126832200490128e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [3:52:13<22:52, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.41426530480384827, 'eval_accuracy': 0.8500299159751307, 'eval_f1': 0.6705824939107204, 'eval_matthews_correlation': 0.34847508075018246, 'eval_precision': 0.6979406998406514, 'eval_recall': 0.6533728055948134, 'eval_runtime': 42.4549, 'eval_samples_per_second': 905.454, 'eval_steps_per_second': 7.09, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [4:17:45<00:00, 1.71it/s]***** Running Evaluation ***** +{'loss': 0.2128, 'learning_rate': 1.0805937023165488e-06, 'epoch': 9.03} +{'loss': 0.2093, 'learning_rate': 1.0343552041429696e-06, 'epoch': 9.07} +{'loss': 0.2047, 'learning_rate': 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0.2042, 'learning_rate': 3.407777315392796e-07, 'epoch': 9.7} +{'loss': 0.2075, 'learning_rate': 2.945392333657003e-07, 'epoch': 9.74} +{'loss': 0.2078, 'learning_rate': 2.48300735192121e-07, 'epoch': 9.78} +{'loss': 0.204, 'learning_rate': 2.0206223701854164e-07, 'epoch': 9.82} +{'loss': 0.205, 'learning_rate': 1.5582373884496233e-07, 'epoch': 9.86} +{'loss': 0.2125, 'learning_rate': 1.09585240671383e-07, 'epoch': 9.9} +{'loss': 0.2158, 'learning_rate': 6.334674249780367e-08, 'epoch': 9.95} +{'loss': 0.2045, 'learning_rate': 1.7108244324224352e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [4:18:28<00:00, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030/config.json 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-9612 (score: 0.6917207637115). +100%|██████████| 24030/24030 [4:18:30<00:00, 1.71it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu/VASC/len2_5120/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 15510.4419, 'train_samples_per_second': 198.272, 'train_steps_per_second': 1.549, 'train_loss': 0.2851774517516518, 'epoch': 10.0} +100%|██████████| 24030/24030 [4:18:30<00:00, 1.55it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [01:10<00:00, 4.26it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_141152-q05v6wzc/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_141152-q05v6wzc/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_141152-q05v6wzc/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.1 +warmup_steps: + value: 0 +weight_decay: + value: 0 diff --git a/VASC/len2_5120/wandb/run-20260307_155139-ssfl0igb/files/output.log b/VASC/len2_5120/wandb/run-20260307_155139-ssfl0igb/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..31d28eac5373f3f21c082534b7fc64131fe63b42 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_155139-ssfl0igb/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.weight', 'bert.pooler.dense.weight', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33843931555747986, 'eval_accuracy': 0.8713092791550688, 'eval_f1': 0.6911952409496127, 'eval_matthews_correlation': 0.40825830005662217, 'eval_precision': 0.7605571033687273, 'eval_recall': 0.6599216039499537, 'eval_runtime': 45.4432, 'eval_samples_per_second': 845.914, 'eval_steps_per_second': 6.624, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [1:44:11<1:28:05, 1.82it/s]***** Running Evaluation ***** +{'loss': 0.3083, 'learning_rate': 6.892087162591759e-06, 'epoch': 3.04} +{'loss': 0.3127, 'learning_rate': 6.834287035431478e-06, 'epoch': 3.08} +{'loss': 0.3022, 'learning_rate': 6.776486908271199e-06, 'epoch': 3.12} +{'loss': 0.3115, 'learning_rate': 6.718686781110919e-06, 'epoch': 3.16} +{'loss': 0.3082, 'learning_rate': 6.660886653950639e-06, 'epoch': 3.2} 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [2:36:45<46:25, 1.73it/s]***** Running Evaluation ***** +{'loss': 0.2651, 'learning_rate': 4.118837061441535e-06, 'epoch': 5.04} +{'loss': 0.2754, 'learning_rate': 4.061036934281256e-06, 'epoch': 5.08} +{'loss': 0.2666, 'learning_rate': 4.003236807120976e-06, 'epoch': 5.12} +{'loss': 0.2647, 'learning_rate': 3.9454366799606964e-06, 'epoch': 5.16} +{'loss': 0.2744, 'learning_rate': 3.887636552800417e-06, 'epoch': 5.2} +{'loss': 0.2687, 'learning_rate': 3.829836425640136e-06, 'epoch': 5.24} +{'loss': 0.263, 'learning_rate': 3.772036298479857e-06, 'epoch': 5.29} +{'loss': 0.2624, 'learning_rate': 3.7142361713195775e-06, 'epoch': 5.33} +{'loss': 0.2715, 'learning_rate': 3.6564360441592974e-06, 'epoch': 5.37} +{'loss': 0.2713, 'learning_rate': 3.5986359169990178e-06, 'epoch': 5.41} +{'loss': 0.273, 'learning_rate': 3.540835789838738e-06, 'epoch': 5.45} +{'loss': 0.2695, 'learning_rate': 3.4830356626784585e-06, 'epoch': 5.49} +{'loss': 0.2707, 'learning_rate': 3.425813536789781e-06, 'epoch': 5.53} +{'loss': 0.2736, 'learning_rate': 3.3680134096295014e-06, 'epoch': 5.58} +{'loss': 0.2598, 'learning_rate': 3.3102132824692217e-06, 'epoch': 5.62} +{'loss': 0.2744, 'learning_rate': 3.252413155308942e-06, 'epoch': 5.66} +{'loss': 0.2736, 'learning_rate': 3.194613028148662e-06, 'epoch': 5.7} +{'loss': 0.2662, 'learning_rate': 3.1368129009883824e-06, 'epoch': 5.74} +{'loss': 0.2733, 'learning_rate': 3.0790127738281028e-06, 'epoch': 5.78} +{'loss': 0.2663, 'learning_rate': 3.0212126466678227e-06, 'epoch': 5.83} +{'loss': 0.2761, 'learning_rate': 2.963412519507543e-06, 'epoch': 5.87} +{'loss': 0.2674, 'learning_rate': 2.9056123923472634e-06, 'epoch': 5.91} +{'loss': 0.2695, 'learning_rate': 2.8478122651869838e-06, 'epoch': 5.95} +{'loss': 0.2765, 'learning_rate': 2.7900121380267037e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [2:37:30<46:25, 1.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.36573296785354614, 'eval_accuracy': 0.865508181368851, 'eval_f1': 0.6757588855130654, 'eval_matthews_correlation': 0.3773970403957949, 'eval_precision': 0.7425008666988719, 'eval_recall': 0.6468330072778332, 'eval_runtime': 45.1814, 'eval_samples_per_second': 850.815, 'eval_steps_per_second': 6.662, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [2:46:46<06:52, 5.83it/s]***** Running Evaluation ***** +{'loss': 0.2522, 'learning_rate': 2.732212010866424e-06, 'epoch': 6.03} +{'loss': 0.2543, 'learning_rate': 2.6744118837061445e-06, 'epoch': 6.08} +{'loss': 0.244, 'learning_rate': 2.616611756545865e-06, 'epoch': 6.12} +{'loss': 0.2505, 'learning_rate': 2.5588116293855848e-06, 'epoch': 6.16} +{'loss': 0.2539, 'learning_rate': 2.501011502225305e-06, 'epoch': 6.2} +{'loss': 0.2468, 'learning_rate': 2.4432113750650255e-06, 'epoch': 6.24} +{'loss': 0.2528, 'learning_rate': 2.3854112479047454e-06, 'epoch': 6.28} +{'loss': 0.2489, 'learning_rate': 2.327611120744466e-06, 'epoch': 6.33} +{'loss': 0.2542, 'learning_rate': 2.269810993584186e-06, 'epoch': 6.37} +{'loss': 0.2505, 'learning_rate': 2.212588867695509e-06, 'epoch': 6.41} +{'loss': 0.2476, 'learning_rate': 2.1547887405352294e-06, 'epoch': 6.45} +{'loss': 0.2497, 'learning_rate': 2.0969886133749494e-06, 'epoch': 6.49} +{'loss': 0.2466, 'learning_rate': 2.0391884862146698e-06, 'epoch': 6.53} +{'loss': 0.2511, 'learning_rate': 1.98138835905439e-06, 'epoch': 6.58} +{'loss': 0.2452, 'learning_rate': 1.9235882318941105e-06, 'epoch': 6.62} +{'loss': 0.2579, 'learning_rate': 1.8657881047338306e-06, 'epoch': 6.66} +{'loss': 0.25, 'learning_rate': 1.807987977573551e-06, 'epoch': 6.7} +{'loss': 0.2421, 'learning_rate': 1.7501878504132711e-06, 'epoch': 6.74} +{'loss': 0.2438, 'learning_rate': 1.692387723252991e-06, 'epoch': 6.78} +{'loss': 0.2564, 'learning_rate': 1.6345875960927117e-06, 'epoch': 6.82} +{'loss': 0.2412, 'learning_rate': 1.5767874689324316e-06, 'epoch': 6.87} +{'loss': 0.2449, 'learning_rate': 1.518987341772152e-06, 'epoch': 6.91} +{'loss': 0.2521, 'learning_rate': 1.4611872146118721e-06, 'epoch': 6.95} +{'loss': 0.2478, 'learning_rate': 1.4033870874515925e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [2:47:00<06:52, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3907715082168579, 'eval_accuracy': 0.8546343747561198, 'eval_f1': 0.6781128333080129, 'eval_matthews_correlation': 0.36482441383280323, 'eval_precision': 0.7092726836399181, 'eval_recall': 0.658999314451211, 'eval_runtime': 13.2878, 'eval_samples_per_second': 2892.956, 'eval_steps_per_second': 22.652, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [2:54:37<00:00, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.2337, 'learning_rate': 1.3455869602913126e-06, 'epoch': 7.03} +{'loss': 0.2326, 'learning_rate': 1.287786833131033e-06, 'epoch': 7.07} +{'loss': 0.2242, 'learning_rate': 1.2299867059707532e-06, 'epoch': 7.12} +{'loss': 0.2392, 'learning_rate': 1.1721865788104735e-06, 'epoch': 7.16} +{'loss': 0.2314, 'learning_rate': 1.1143864516501937e-06, 'epoch': 7.2} +{'loss': 0.2346, 'learning_rate': 1.056586324489914e-06, 'epoch': 7.24} +{'loss': 0.2296, 'learning_rate': 9.99364198601237e-07, 'epoch': 7.28} +{'loss': 0.2352, 'learning_rate': 9.415640714409572e-07, 'epoch': 7.32} +{'loss': 0.2311, 'learning_rate': 8.837639442806775e-07, 'epoch': 7.37} +{'loss': 0.2238, 'learning_rate': 8.259638171203977e-07, 'epoch': 7.41} +{'loss': 0.2373, 'learning_rate': 7.68163689960118e-07, 'epoch': 7.45} +{'loss': 0.2362, 'learning_rate': 7.103635627998383e-07, 'epoch': 7.49} +{'loss': 0.234, 'learning_rate': 6.525634356395584e-07, 'epoch': 7.53} +{'loss': 0.2333, 'learning_rate': 5.947633084792788e-07, 'epoch': 7.57} +{'loss': 0.24, 'learning_rate': 5.36963181318999e-07, 'epoch': 7.62} +{'loss': 0.2338, 'learning_rate': 4.791630541587192e-07, 'epoch': 7.66} +{'loss': 0.2379, 'learning_rate': 4.2136292699843943e-07, 'epoch': 7.7} +{'loss': 0.2316, 'learning_rate': 3.635627998381597e-07, 'epoch': 7.74} +{'loss': 0.2333, 'learning_rate': 3.0576267267787995e-07, 'epoch': 7.78} +{'loss': 0.2416, 'learning_rate': 2.4796254551760015e-07, 'epoch': 7.82} +{'loss': 0.2309, 'learning_rate': 1.901624183573204e-07, 'epoch': 7.87} +{'loss': 0.2395, 'learning_rate': 1.3236229119704064e-07, 'epoch': 7.91} +{'loss': 0.2398, 'learning_rate': 7.456216403676089e-08, 'epoch': 7.95} +{'loss': 0.2235, 'learning_rate': 1.676203687648113e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [2:54:50<00:00, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.4034731984138489, 'eval_accuracy': 0.8583543612288962, 'eval_f1': 0.677180955062954, 'eval_matthews_correlation': 0.3676242523822757, 'eval_precision': 0.7186824855252383, 'eval_recall': 0.6545020747946795, 'eval_runtime': 13.3818, 'eval_samples_per_second': 2872.632, 'eval_steps_per_second': 22.493, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-7209 (score: 0.6911952409496127). +100%|██████████| 19224/19224 [2:54:52<00:00, 5.81it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 10492.2678, 'train_samples_per_second': 234.48, 'train_steps_per_second': 1.832, 'train_loss': 0.2975114335926483, 'epoch': 8.0} +100%|██████████| 19224/19224 [2:54:52<00:00, 1.83it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.99it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_155139-ssfl0igb/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_155139-ssfl0igb/files/requirements.txt new 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.1 +warmup_steps: + value: 0 +weight_decay: + value: 0 diff --git a/VASC/len2_5120/wandb/run-20260307_184807-tobhmrlp/files/output.log b/VASC/len2_5120/wandb/run-20260307_184807-tobhmrlp/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..9b102c5398e8caf80dbdb97830c58bda1bf9e8ee --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_184807-tobhmrlp/files/output.log @@ -0,0 +1,368 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['classifier.weight', 'classifier.bias', 'bert.pooler.dense.weight', 'bert.pooler.dense.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 10 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 24,030 + Number of trainable parameters = 88,402,178 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 10%|█ | 2403/24030 [07:34<1:01:57, 5.82it/s]***** Running Evaluation ***** +{'loss': 0.582, 'learning_rate': 4.161464835622139e-07, 'epoch': 0.04} +{'loss': 0.4232, 'learning_rate': 8.322929671244278e-07, 'epoch': 0.08} +{'loss': 0.3715, 'learning_rate': 1.2484394506866417e-06, 'epoch': 0.12} +{'loss': 0.3583, 'learning_rate': 1.6645859342488557e-06, 'epoch': 0.17} +{'loss': 0.3611, 'learning_rate': 2.0807324178110696e-06, 'epoch': 0.21} 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2.04} +{'loss': 0.3343, 'learning_rate': 8.799186202432147e-06, 'epoch': 2.08} +{'loss': 0.3257, 'learning_rate': 8.752947704258567e-06, 'epoch': 2.12} +{'loss': 0.3249, 'learning_rate': 8.706709206084987e-06, 'epoch': 2.16} +{'loss': 0.3268, 'learning_rate': 8.660470707911408e-06, 'epoch': 2.21} +{'loss': 0.3295, 'learning_rate': 8.614232209737828e-06, 'epoch': 2.25} +{'loss': 0.3265, 'learning_rate': 8.567993711564248e-06, 'epoch': 2.29} +{'loss': 0.3331, 'learning_rate': 8.52175521339067e-06, 'epoch': 2.33} +{'loss': 0.3295, 'learning_rate': 8.47551671521709e-06, 'epoch': 2.37} +{'loss': 0.3282, 'learning_rate': 8.429278217043511e-06, 'epoch': 2.41} +{'loss': 0.3314, 'learning_rate': 8.383039718869931e-06, 'epoch': 2.46} +{'loss': 0.3299, 'learning_rate': 8.336801220696353e-06, 'epoch': 2.5} +{'loss': 0.3286, 'learning_rate': 8.290562722522774e-06, 'epoch': 2.54} +{'loss': 0.3294, 'learning_rate': 8.244324224349194e-06, 'epoch': 2.58} +{'loss': 0.337, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.34139522910118103, 'eval_accuracy': 0.8710491402408886, 'eval_f1': 0.6917458494847358, 'eval_matthews_correlation': 0.4083570924274669, 'eval_precision': 0.7592019425901385, 'eval_recall': 0.6608355181190674, 'eval_runtime': 13.3097, 'eval_samples_per_second': 2888.199, 'eval_steps_per_second': 22.615, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [31:03<43:42, 5.50it/s]***** Running Evaluation ***** +{'loss': 0.3122, 'learning_rate': 7.735700744439821e-06, 'epoch': 3.04} +{'loss': 0.3163, 'learning_rate': 7.689462246266241e-06, 'epoch': 3.08} +{'loss': 0.308, 'learning_rate': 7.643223748092663e-06, 'epoch': 3.12} +{'loss': 0.3171, 'learning_rate': 7.596985249919083e-06, 'epoch': 3.16} +{'loss': 0.3146, 'learning_rate': 7.550746751745504e-06, 'epoch': 3.2} +{'loss': 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+{'loss': 0.2968, 'learning_rate': 6.488186063716651e-06, 'epoch': 4.16} +{'loss': 0.2872, 'learning_rate': 6.4419475655430715e-06, 'epoch': 4.2} +{'loss': 0.304, 'learning_rate': 6.395709067369492e-06, 'epoch': 4.24} +{'loss': 0.3008, 'learning_rate': 6.349470569195914e-06, 'epoch': 4.29} +{'loss': 0.2999, 'learning_rate': 6.303232071022334e-06, 'epoch': 4.33} +{'loss': 0.3066, 'learning_rate': 6.2569935728487545e-06, 'epoch': 4.37} +{'loss': 0.2988, 'learning_rate': 6.210755074675175e-06, 'epoch': 4.41} +{'loss': 0.3024, 'learning_rate': 6.164516576501596e-06, 'epoch': 4.45} +{'loss': 0.2932, 'learning_rate': 6.118278078328016e-06, 'epoch': 4.49} +{'loss': 0.299, 'learning_rate': 6.0720395801544375e-06, 'epoch': 4.54} +{'loss': 0.3004, 'learning_rate': 6.025801081980857e-06, 'epoch': 4.58} +{'loss': 0.3048, 'learning_rate': 5.979562583807278e-06, 'epoch': 4.62} +{'loss': 0.2886, 'learning_rate': 5.9333240856337e-06, 'epoch': 4.66} +{'loss': 0.3024, 'learning_rate': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [46:44<28:16, 5.67it/s]***** Running Evaluation ***** +{'loss': 0.2732, 'learning_rate': 5.5171776020714855e-06, 'epoch': 5.04} +{'loss': 0.2839, 'learning_rate': 5.470939103897905e-06, 'epoch': 5.08} +{'loss': 0.2776, 'learning_rate': 5.424700605724327e-06, 'epoch': 5.12} +{'loss': 0.2771, 'learning_rate': 5.378462107550747e-06, 'epoch': 5.16} +{'loss': 0.2799, 'learning_rate': 5.332223609377168e-06, 'epoch': 5.2} +{'loss': 0.2762, 'learning_rate': 5.285985111203588e-06, 'epoch': 5.24} +{'loss': 0.2727, 'learning_rate': 5.239746613030009e-06, 'epoch': 5.29} +{'loss': 0.273, 'learning_rate': 5.193508114856431e-06, 'epoch': 5.33} +{'loss': 0.2842, 'learning_rate': 5.147269616682851e-06, 'epoch': 5.37} +{'loss': 0.2771, 'learning_rate': 5.101031118509271e-06, 'epoch': 5.41} +{'loss': 0.2854, 'learning_rate': 5.054792620335692e-06, 'epoch': 5.45} +{'loss': 0.2814, 'learning_rate': 5.008554122162113e-06, 'epoch': 5.49} +{'loss': 0.2803, 'learning_rate': 4.9627780089702695e-06, 'epoch': 5.53} +{'loss': 0.2832, 'learning_rate': 4.916539510796689e-06, 'epoch': 5.58} +{'loss': 0.2677, 'learning_rate': 4.87030101262311e-06, 'epoch': 5.62} +{'loss': 0.2849, 'learning_rate': 4.824062514449531e-06, 'epoch': 5.66} +{'loss': 0.2825, 'learning_rate': 4.777824016275952e-06, 'epoch': 5.7} +{'loss': 0.2725, 'learning_rate': 4.731585518102372e-06, 'epoch': 5.74} +{'loss': 0.2791, 'learning_rate': 4.685347019928793e-06, 'epoch': 5.78} +{'loss': 0.2718, 'learning_rate': 4.639108521755214e-06, 'epoch': 5.83} +{'loss': 0.2855, 'learning_rate': 4.5928700235816345e-06, 'epoch': 5.87} +{'loss': 0.2739, 'learning_rate': 4.546631525408055e-06, 'epoch': 5.91} +{'loss': 0.2806, 'learning_rate': 4.500393027234476e-06, 'epoch': 5.95} +{'loss': 0.2838, 'learning_rate': 4.454154529060897e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [46:58<28:16, 5.67iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3553777039051056, 'eval_accuracy': 0.8660284591972113, 'eval_f1': 0.6795920493273825, 'eval_matthews_correlation': 0.38323400515665096, 'eval_precision': 0.7434202309849933, 'eval_recall': 0.6508382254364288, 'eval_runtime': 13.3044, 'eval_samples_per_second': 2889.339, 'eval_steps_per_second': 22.624, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [54:34<20:41, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.2602, 'learning_rate': 4.407916030887317e-06, 'epoch': 6.03} +{'loss': 0.2574, 'learning_rate': 4.361677532713738e-06, 'epoch': 6.08} +{'loss': 0.2452, 'learning_rate': 4.315439034540159e-06, 'epoch': 6.12} +{'loss': 0.2646, 'learning_rate': 4.269200536366579e-06, 'epoch': 6.16} +{'loss': 0.2591, 'learning_rate': 4.222962038193e-06, 'epoch': 6.2} +{'loss': 0.2592, 'learning_rate': 4.17672354001942e-06, 'epoch': 6.24} +{'loss': 0.2535, 'learning_rate': 4.130485041845841e-06, 'epoch': 6.28} +{'loss': 0.2561, 'learning_rate': 4.084246543672262e-06, 'epoch': 6.33} +{'loss': 0.2571, 'learning_rate': 4.0384704304804185e-06, 'epoch': 6.37} +{'loss': 0.2593, 'learning_rate': 3.992231932306839e-06, 'epoch': 6.41} +{'loss': 0.2548, 'learning_rate': 3.945993434133259e-06, 'epoch': 6.45} +{'loss': 0.2575, 'learning_rate': 3.899754935959681e-06, 'epoch': 6.49} +{'loss': 0.25, 'learning_rate': 3.8535164377861015e-06, 'epoch': 6.53} +{'loss': 0.254, 'learning_rate': 3.8072779396125214e-06, 'epoch': 6.58} +{'loss': 0.2508, 'learning_rate': 3.761039441438942e-06, 'epoch': 6.62} +{'loss': 0.2598, 'learning_rate': 3.7148009432653633e-06, 'epoch': 6.66} +{'loss': 0.2592, 'learning_rate': 3.668562445091784e-06, 'epoch': 6.7} +{'loss': 0.2557, 'learning_rate': 3.6223239469182043e-06, 'epoch': 6.74} +{'loss': 0.254, 'learning_rate': 3.576085448744625e-06, 'epoch': 6.78} +{'loss': 0.2718, 'learning_rate': 3.529846950571046e-06, 'epoch': 6.82} +{'loss': 0.2466, 'learning_rate': 3.483608452397466e-06, 'epoch': 6.87} +{'loss': 0.256, 'learning_rate': 3.437369954223887e-06, 'epoch': 6.91} +{'loss': 0.2626, 'learning_rate': 3.3911314560503076e-06, 'epoch': 6.95} +{'loss': 0.2604, 'learning_rate': 3.3448929578767288e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [54:48<20:41, 5.81iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.37641802430152893, 'eval_accuracy': 0.8621784032673447, 'eval_f1': 0.6812103179977371, 'eval_matthews_correlation': 0.37875897782730017, 'eval_precision': 0.7297355067629478, 'eval_recall': 0.6561125283877086, 'eval_runtime': 13.3225, 'eval_samples_per_second': 2885.414, 'eval_steps_per_second': 22.593, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [1:02:24<13:44, 5.83it/s]***** Running Evaluation ***** +{'loss': 0.2382, 'learning_rate': 3.298654459703149e-06, 'epoch': 7.03} +{'loss': 0.2307, 'learning_rate': 3.25241596152957e-06, 'epoch': 7.07} +{'loss': 0.2286, 'learning_rate': 3.2061774633559906e-06, 'epoch': 7.12} +{'loss': 0.2424, 'learning_rate': 3.1599389651824113e-06, 'epoch': 7.16} +{'loss': 0.2293, 'learning_rate': 3.1141628519905676e-06, 'epoch': 7.2} +{'loss': 0.2358, 'learning_rate': 3.0679243538169883e-06, 'epoch': 7.24} +{'loss': 0.2305, 'learning_rate': 3.021685855643409e-06, 'epoch': 7.28} +{'loss': 0.2296, 'learning_rate': 2.9754473574698293e-06, 'epoch': 7.32} +{'loss': 0.2311, 'learning_rate': 2.9292088592962505e-06, 'epoch': 7.37} +{'loss': 0.2217, 'learning_rate': 2.8829703611226713e-06, 'epoch': 7.41} +{'loss': 0.2351, 'learning_rate': 2.8367318629490916e-06, 'epoch': 7.45} +{'loss': 0.2381, 'learning_rate': 2.7904933647755123e-06, 'epoch': 7.49} +{'loss': 0.238, 'learning_rate': 2.744254866601933e-06, 'epoch': 7.53} +{'loss': 0.2373, 'learning_rate': 2.698016368428354e-06, 'epoch': 7.57} +{'loss': 0.2414, 'learning_rate': 2.651777870254774e-06, 'epoch': 7.62} +{'loss': 0.2332, 'learning_rate': 2.605539372081195e-06, 'epoch': 7.66} +{'loss': 0.2403, 'learning_rate': 2.559300873907616e-06, 'epoch': 7.7} +{'loss': 0.2371, 'learning_rate': 2.513062375734036e-06, 'epoch': 7.74} +{'loss': 0.2347, 'learning_rate': 2.466823877560457e-06, 'epoch': 7.78} +{'loss': 0.2416, 'learning_rate': 2.420585379386878e-06, 'epoch': 7.82} +{'loss': 0.235, 'learning_rate': 2.374346881213298e-06, 'epoch': 7.87} +{'loss': 0.2393, 'learning_rate': 2.3281083830397193e-06, 'epoch': 7.91} +{'loss': 0.2412, 'learning_rate': 2.2818698848661396e-06, 'epoch': 7.95} +{'loss': 0.2317, 'learning_rate': 2.2356313866925604e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [1:02:37<13:44, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.4045044183731079, 'eval_accuracy': 0.8575739444863557, 'eval_f1': 0.673075861096121, 'eval_matthews_correlation': 0.36056661387899686, 'eval_precision': 0.716492345716313, 'eval_recall': 0.6501303459644316, 'eval_runtime': 13.2889, 'eval_samples_per_second': 2892.713, 'eval_steps_per_second': 22.65, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [1:10:14<07:00, 5.71it/s]***** Running Evaluation ***** +{'loss': 0.2153, 'learning_rate': 2.189392888518981e-06, 'epoch': 8.03} +{'loss': 0.218, 'learning_rate': 2.1436167753271373e-06, 'epoch': 8.07} +{'loss': 0.2128, 'learning_rate': 2.0973782771535585e-06, 'epoch': 8.11} +{'loss': 0.2196, 'learning_rate': 2.051139778979979e-06, 'epoch': 8.16} +{'loss': 0.2099, 'learning_rate': 2.0049012808063996e-06, 'epoch': 8.2} +{'loss': 0.2215, 'learning_rate': 1.9586627826328203e-06, 'epoch': 8.24} +{'loss': 0.2119, 'learning_rate': 1.912424284459241e-06, 'epoch': 8.28} +{'loss': 0.2158, 'learning_rate': 1.8661857862856616e-06, 'epoch': 8.32} +{'loss': 0.2167, 'learning_rate': 1.8199472881120823e-06, 'epoch': 8.36} +{'loss': 0.2183, 'learning_rate': 1.773708789938503e-06, 'epoch': 8.41} +{'loss': 0.2204, 'learning_rate': 1.7274702917649236e-06, 'epoch': 8.45} +{'loss': 0.2141, 'learning_rate': 1.6812317935913443e-06, 'epoch': 8.49} +{'loss': 0.22, 'learning_rate': 1.634993295417765e-06, 'epoch': 8.53} +{'loss': 0.216, 'learning_rate': 1.5887547972441856e-06, 'epoch': 8.57} +{'loss': 0.2281, 'learning_rate': 1.5425162990706063e-06, 'epoch': 8.61} +{'loss': 0.2153, 'learning_rate': 1.4962778008970269e-06, 'epoch': 8.66} +{'loss': 0.2161, 'learning_rate': 1.4500393027234478e-06, 'epoch': 8.7} +{'loss': 0.2214, 'learning_rate': 1.4038008045498683e-06, 'epoch': 8.74} +{'loss': 0.2203, 'learning_rate': 1.357562306376289e-06, 'epoch': 8.78} +{'loss': 0.2147, 'learning_rate': 1.3113238082027096e-06, 'epoch': 8.82} +{'loss': 0.2163, 'learning_rate': 1.2650853100291306e-06, 'epoch': 8.86} +{'loss': 0.212, 'learning_rate': 1.218846811855551e-06, 'epoch': 8.91} +{'loss': 0.2146, 'learning_rate': 1.1726083136819716e-06, 'epoch': 8.95} +{'loss': 0.228, 'learning_rate': 1.1263698155083924e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [1:10:27<07:00, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.4330947697162628, 'eval_accuracy': 0.8560911526755287, 'eval_f1': 0.6689889719032989, 'eval_matthews_correlation': 0.3525949233398742, 'eval_precision': 0.7122827492157855, 'eval_recall': 0.6464122501997056, 'eval_runtime': 13.2835, 'eval_samples_per_second': 2893.891, 'eval_steps_per_second': 22.66, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [1:18:04<00:00, 5.70it/s]***** Running Evaluation ***** +{'loss': 0.2041, 'learning_rate': 1.0805937023165488e-06, 'epoch': 9.03} +{'loss': 0.2068, 'learning_rate': 1.0343552041429696e-06, 'epoch': 9.07} +{'loss': 0.2004, 'learning_rate': 9.881167059693903e-07, 'epoch': 9.11} +{'loss': 0.2093, 'learning_rate': 9.418782077958109e-07, 'epoch': 9.16} +{'loss': 0.2051, 'learning_rate': 8.956397096222315e-07, 'epoch': 9.2} +{'loss': 0.2089, 'learning_rate': 8.494012114486522e-07, 'epoch': 9.24} +{'loss': 0.2053, 'learning_rate': 8.031627132750728e-07, 'epoch': 9.28} +{'loss': 0.2037, 'learning_rate': 7.569242151014936e-07, 'epoch': 9.32} +{'loss': 0.2033, 'learning_rate': 7.106857169279142e-07, 'epoch': 9.36} +{'loss': 0.2098, 'learning_rate': 6.64447218754335e-07, 'epoch': 9.4} +{'loss': 0.2047, 'learning_rate': 6.182087205807556e-07, 'epoch': 9.45} +{'loss': 0.1986, 'learning_rate': 5.719702224071762e-07, 'epoch': 9.49} +{'loss': 0.2025, 'learning_rate': 5.25731724233597e-07, 'epoch': 9.53} +{'loss': 0.2059, 'learning_rate': 4.794932260600176e-07, 'epoch': 9.57} +{'loss': 0.2052, 'learning_rate': 4.3325472788643834e-07, 'epoch': 9.61} +{'loss': 0.2023, 'learning_rate': 3.870162297128589e-07, 'epoch': 9.65} +{'loss': 0.1998, 'learning_rate': 3.407777315392796e-07, 'epoch': 9.7} +{'loss': 0.2044, 'learning_rate': 2.945392333657003e-07, 'epoch': 9.74} +{'loss': 0.1978, 'learning_rate': 2.48300735192121e-07, 'epoch': 9.78} +{'loss': 0.1984, 'learning_rate': 2.0206223701854164e-07, 'epoch': 9.82} +{'loss': 0.2049, 'learning_rate': 1.5582373884496233e-07, 'epoch': 9.86} +{'loss': 0.2011, 'learning_rate': 1.1004762565311879e-07, 'epoch': 9.9} +{'loss': 0.2018, 'learning_rate': 6.380912747953947e-08, 'epoch': 9.95} +{'loss': 0.2002, 'learning_rate': 1.7570629305960146e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [1:18:18<00:00, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.44831061363220215, 'eval_accuracy': 0.8512005410889415, 'eval_f1': 0.6753143534726418, 'eval_matthews_correlation': 0.35720057380367126, 'eval_precision': 0.7012849895369593, 'eval_recall': 0.6584721372159794, 'eval_runtime': 13.2956, 'eval_samples_per_second': 2891.26, 'eval_steps_per_second': 22.639, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-7209 (score: 0.6917458494847358). +100%|██████████| 24030/24030 [1:18:19<00:00, 5.70it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.0_wr0.10_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 4699.5584, 'train_samples_per_second': 654.379, 'train_steps_per_second': 5.113, 'train_loss': 0.2839201034430013, 'epoch': 10.0} +100%|██████████| 24030/24030 [1:18:19<00:00, 5.11it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.73it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_184807-tobhmrlp/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_184807-tobhmrlp/files/requirements.txt new 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [23:16<20:41, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.3228, 'learning_rate': 6.80586342509832e-06, 'epoch': 2.04} +{'loss': 0.3327, 'learning_rate': 6.7343582409724705e-06, 'epoch': 2.08} +{'loss': 0.3221, 'learning_rate': 6.662853056846622e-06, 'epoch': 2.12} +{'loss': 0.3226, 'learning_rate': 6.5913478727207724e-06, 'epoch': 2.16} +{'loss': 0.3234, 'learning_rate': 6.519842688594924e-06, 'epoch': 2.21} +{'loss': 0.3271, 'learning_rate': 6.448337504469074e-06, 'epoch': 2.25} +{'loss': 0.3244, 'learning_rate': 6.376832320343226e-06, 'epoch': 2.29} +{'loss': 0.3306, 'learning_rate': 6.305327136217376e-06, 'epoch': 2.33} +{'loss': 0.3265, 'learning_rate': 6.2338219520915265e-06, 'epoch': 2.37} +{'loss': 0.3242, 'learning_rate': 6.162316767965678e-06, 'epoch': 2.41} +{'loss': 0.3285, 'learning_rate': 6.0908115838398285e-06, 'epoch': 2.46} +{'loss': 0.3275, 'learning_rate': 6.01930639971398e-06, 'epoch': 2.5} +{'loss': 0.3265, 'learning_rate': 5.9478012155881304e-06, 'epoch': 2.54} +{'loss': 0.3257, 'learning_rate': 5.876296031462282e-06, 'epoch': 2.58} +{'loss': 0.3332, 'learning_rate': 5.804790847336432e-06, 'epoch': 2.62} +{'loss': 0.3204, 'learning_rate': 5.733285663210583e-06, 'epoch': 2.66} +{'loss': 0.3175, 'learning_rate': 5.661780479084734e-06, 'epoch': 2.7} +{'loss': 0.3256, 'learning_rate': 5.5902752949588845e-06, 'epoch': 2.75} +{'loss': 0.3279, 'learning_rate': 5.518770110833036e-06, 'epoch': 2.79} +{'loss': 0.3319, 'learning_rate': 5.4472649267071865e-06, 'epoch': 2.83} +{'loss': 0.3168, 'learning_rate': 5.375759742581338e-06, 'epoch': 2.87} +{'loss': 0.3234, 'learning_rate': 5.3042545584554885e-06, 'epoch': 2.91} +{'loss': 0.3229, 'learning_rate': 5.2327493743296394e-06, 'epoch': 2.95} +{'loss': 0.3268, 'learning_rate': 5.1612441902037904e-06, 'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 7209/14418 [23:29<20:41, 5.81itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.34049439430236816, 'eval_accuracy': 0.8716994875263391, 'eval_f1': 0.6896124226612061, 'eval_matthews_correlation': 0.40728395705599424, 'eval_precision': 0.7630321453768358, 'eval_recall': 0.6576615487790844, 'eval_runtime': 13.3806, 'eval_samples_per_second': 2872.881, 'eval_steps_per_second': 22.495, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [31:07<13:59, 5.73it/s]***** Running Evaluation ***** +{'loss': 0.3122, 'learning_rate': 5.0897390060779406e-06, 'epoch': 3.04} +{'loss': 0.3165, 'learning_rate': 5.018233821952092e-06, 'epoch': 3.08} +{'loss': 0.3066, 'learning_rate': 4.946728637826243e-06, 'epoch': 3.12} +{'loss': 0.3166, 'learning_rate': 4.8752234537003935e-06, 'epoch': 3.16} +{'loss': 0.3106, 'learning_rate': 4.8037182695745445e-06, 'epoch': 3.2} +{'loss': 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'epoch': 3.79} +{'loss': 0.3159, 'learning_rate': 3.731855559528066e-06, 'epoch': 3.83} +{'loss': 0.3183, 'learning_rate': 3.6610654272434754e-06, 'epoch': 3.87} +{'loss': 0.3091, 'learning_rate': 3.5895602431176264e-06, 'epoch': 3.91} +{'loss': 0.3107, 'learning_rate': 3.5180550589917774e-06, 'epoch': 3.95} +{'loss': 0.3154, 'learning_rate': 3.4465498748659284e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 67%|██████▋ | 9612/14418 [31:21<13:59, 5.73itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612/config.json +{'eval_loss': 0.3399066627025604, 'eval_accuracy': 0.8725319320517156, 'eval_f1': 0.6748641005407918, 'eval_matthews_correlation': 0.3940470218247109, 'eval_precision': 0.7764066873485779, 'eval_recall': 0.6404389460493666, 'eval_runtime': 13.4895, 'eval_samples_per_second': 2849.693, 'eval_steps_per_second': 22.314, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612/special_tokens_map.json + 83%|████████▎ | 12015/14418 [38:58<06:53, 5.82it/s]***** Running Evaluation ***** +{'loss': 0.306, 'learning_rate': 3.375044690740079e-06, 'epoch': 4.04} +{'loss': 0.2987, 'learning_rate': 3.30353950661423e-06, 'epoch': 4.08} +{'loss': 0.3096, 'learning_rate': 3.2320343224883805e-06, 'epoch': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [46:51<00:00, 5.65it/s]***** Running Evaluation ***** +{'loss': 0.2804, 'learning_rate': 1.6589202717196998e-06, 'epoch': 5.04} +{'loss': 0.2956, 'learning_rate': 1.5874150875938508e-06, 'epoch': 5.08} +{'loss': 0.288, 'learning_rate': 1.5159099034680016e-06, 'epoch': 5.12} +{'loss': 0.2854, 'learning_rate': 1.4444047193421524e-06, 'epoch': 5.16} +{'loss': 0.2913, 'learning_rate': 1.3728995352163033e-06, 'epoch': 5.2} +{'loss': 0.2874, 'learning_rate': 1.3013943510904541e-06, 'epoch': 5.24} +{'loss': 0.2819, 'learning_rate': 1.229889166964605e-06, 'epoch': 5.29} +{'loss': 0.2787, 'learning_rate': 1.1583839828387559e-06, 'epoch': 5.33} +{'loss': 0.2943, 'learning_rate': 1.0868787987129069e-06, 'epoch': 5.37} +{'loss': 0.2898, 'learning_rate': 1.0153736145870576e-06, 'epoch': 5.41} +{'loss': 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'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [47:04<00:00, 5.65iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35439959168434143, 'eval_accuracy': 0.87011264014984, 'eval_f1': 0.6790978509184904, 'eval_matthews_correlation': 0.3916871080418913, 'eval_precision': 0.7610743609041924, 'eval_recall': 0.6469110084909113, 'eval_runtime': 13.3088, 'eval_samples_per_second': 2888.384, 'eval_steps_per_second': 22.617, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-7209 (score: 0.6896124226612061). +100%|██████████| 14418/14418 [47:06<00:00, 5.65it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 2826.0664, 'train_samples_per_second': 652.912, 'train_steps_per_second': 5.102, 'train_loss': 0.31988689078919547, 'epoch': 6.0} +100%|██████████| 14418/14418 [47:06<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.96it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_200804-tymqq6xu/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_200804-tymqq6xu/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_200804-tymqq6xu/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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+push_to_hub_organization: + value: null +push_to_hub_token: + value: +ray_scope: + value: last +remove_invalid_values: + value: false +remove_unused_columns: + value: true +repetition_penalty: + value: 1 +report_to: + value: + - wandb +resume_from_checkpoint: + value: null +return_dict: + value: true +return_dict_in_generate: + value: false +run_name: + value: hg38_len2_3072_binary_VASC_lr1e-5_wd0.01_wr0.03_ep8_seed42 +save_model: + value: false +save_on_each_node: + value: false +save_safetensors: + value: true +save_steps: + value: 100 +save_strategy: + value: epoch +save_total_limit: + value: 1 +seed: + value: 42 +sep_token_id: + value: null +skip_memory_metrics: + value: true +split_batches: + value: false +suppress_tokens: + value: null +task_specific_params: + value: null +temperature: + value: 1 +tf_legacy_loss: + value: false +tf32: + value: null +tie_encoder_decoder: + value: false +tie_word_embeddings: + value: true +tokenizer_class: + value: null +top_k: + value: 50 +top_p: + value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.03 +warmup_steps: + value: 0 +weight_decay: + value: 0.01 diff --git a/VASC/len2_5120/wandb/run-20260307_205648-smymbkb0/files/output.log b/VASC/len2_5120/wandb/run-20260307_205648-smymbkb0/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..95a7b068d0b69cd795c8df867abf0ee2c491383b --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_205648-smymbkb0/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.weight', 'bert.pooler.dense.weight', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3402101397514343, 'eval_accuracy': 0.8708150152181264, 'eval_f1': 0.6895651152444551, 'eval_matthews_correlation': 0.4052646100653909, 'eval_precision': 0.7591811970157737, 'eval_recall': 0.6584214114126667, 'eval_runtime': 13.3745, 'eval_samples_per_second': 2874.191, 'eval_steps_per_second': 22.505, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [31:11<27:38, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.3114, 'learning_rate': 6.394594304713896e-06, 'epoch': 3.04} +{'loss': 0.3142, 'learning_rate': 6.340966375288251e-06, 'epoch': 3.08} +{'loss': 0.3064, 'learning_rate': 6.287338445862605e-06, 'epoch': 3.12} +{'loss': 0.3146, 'learning_rate': 6.23371051643696e-06, 'epoch': 3.16} +{'loss': 0.3126, 'learning_rate': 6.1800825870113155e-06, 'epoch': 3.2} +{'loss': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [46:55<13:48, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.2765, 'learning_rate': 3.821526250871454e-06, 'epoch': 5.04} +{'loss': 0.2849, 'learning_rate': 3.7678983214458092e-06, 'epoch': 5.08} +{'loss': 0.2798, 'learning_rate': 3.7142703920201644e-06, 'epoch': 5.12} +{'loss': 0.2776, 'learning_rate': 3.6606424625945195e-06, 'epoch': 5.16} +{'loss': 0.2802, 'learning_rate': 3.6070145331688743e-06, 'epoch': 5.2} +{'loss': 0.2757, 'learning_rate': 3.55338660374323e-06, 'epoch': 5.24} +{'loss': 0.2721, 'learning_rate': 3.499758674317585e-06, 'epoch': 5.29} +{'loss': 0.2726, 'learning_rate': 3.44613074489194e-06, 'epoch': 5.33} +{'loss': 0.2883, 'learning_rate': 3.3925028154662953e-06, 'epoch': 5.37} +{'loss': 0.2788, 'learning_rate': 3.33887488604065e-06, 'epoch': 5.41} +{'loss': 0.2864, 'learning_rate': 3.285246956615005e-06, 'epoch': 5.45} +{'loss': 0.2829, 'learning_rate': 3.2316190271893603e-06, 'epoch': 5.49} +{'loss': 0.2822, 'learning_rate': 3.178527377057972e-06, 'epoch': 5.53} +{'loss': 0.2815, 'learning_rate': 3.1248994476323276e-06, 'epoch': 5.58} +{'loss': 0.2702, 'learning_rate': 3.071271518206682e-06, 'epoch': 5.62} +{'loss': 0.2859, 'learning_rate': 3.0176435887810375e-06, 'epoch': 5.66} +{'loss': 0.2863, 'learning_rate': 2.9640156593553926e-06, 'epoch': 5.7} +{'loss': 0.2763, 'learning_rate': 2.910387729929748e-06, 'epoch': 5.74} +{'loss': 0.2774, 'learning_rate': 2.8567598005041025e-06, 'epoch': 5.78} +{'loss': 0.2778, 'learning_rate': 2.8031318710784577e-06, 'epoch': 5.83} +{'loss': 0.2833, 'learning_rate': 2.749503941652813e-06, 'epoch': 5.87} +{'loss': 0.2765, 'learning_rate': 2.6958760122271684e-06, 'epoch': 5.91} +{'loss': 0.2813, 'learning_rate': 2.6422480828015236e-06, 'epoch': 5.95} +{'loss': 0.2844, 'learning_rate': 2.5886201533758783e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [47:09<13:48, 5.80iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35765042901039124, 'eval_accuracy': 0.8661845425457194, 'eval_f1': 0.6718308178429155, 'eval_matthews_correlation': 0.3740686671807624, 'eval_precision': 0.7465315913464979, 'eval_recall': 0.6418959807566055, 'eval_runtime': 13.326, 'eval_samples_per_second': 2884.67, 'eval_steps_per_second': 22.587, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [54:47<06:51, 5.84it/s]***** Running Evaluation ***** +{'loss': 0.2701, 'learning_rate': 2.5349922239502335e-06, 'epoch': 6.03} +{'loss': 0.2658, 'learning_rate': 2.4813642945245886e-06, 'epoch': 6.08} +{'loss': 0.2602, 'learning_rate': 2.4277363650989438e-06, 'epoch': 6.12} +{'loss': 0.2666, 'learning_rate': 2.374108435673299e-06, 'epoch': 6.16} +{'loss': 0.2625, 'learning_rate': 2.320480506247654e-06, 'epoch': 6.2} +{'loss': 0.2644, 'learning_rate': 2.266852576822009e-06, 'epoch': 6.24} +{'loss': 0.2625, 'learning_rate': 2.2132246473963644e-06, 'epoch': 6.28} +{'loss': 0.2638, 'learning_rate': 2.1595967179707195e-06, 'epoch': 6.33} +{'loss': 0.2642, 'learning_rate': 2.106505067839331e-06, 'epoch': 6.37} +{'loss': 0.2652, 'learning_rate': 2.052877138413686e-06, 'epoch': 6.41} +{'loss': 0.261, 'learning_rate': 1.999249208988041e-06, 'epoch': 6.45} +{'loss': 0.2595, 'learning_rate': 1.9456212795623963e-06, 'epoch': 6.49} +{'loss': 0.2624, 'learning_rate': 1.8919933501367512e-06, 'epoch': 6.53} +{'loss': 0.262, 'learning_rate': 1.8383654207111066e-06, 'epoch': 6.58} +{'loss': 0.2577, 'learning_rate': 1.7847374912854615e-06, 'epoch': 6.62} +{'loss': 0.2668, 'learning_rate': 1.7311095618598167e-06, 'epoch': 6.66} +{'loss': 0.2646, 'learning_rate': 1.677481632434172e-06, 'epoch': 6.7} +{'loss': 0.2627, 'learning_rate': 1.623853703008527e-06, 'epoch': 6.74} +{'loss': 0.2593, 'learning_rate': 1.5702257735828821e-06, 'epoch': 6.78} +{'loss': 0.28, 'learning_rate': 1.516597844157237e-06, 'epoch': 6.82} +{'loss': 0.2561, 'learning_rate': 1.4629699147315922e-06, 'epoch': 6.87} +{'loss': 0.2654, 'learning_rate': 1.4093419853059476e-06, 'epoch': 6.91} +{'loss': 0.2678, 'learning_rate': 1.3557140558803025e-06, 'epoch': 6.95} +{'loss': 0.2622, 'learning_rate': 1.3020861264546577e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [55:00<06:51, 5.84iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3768942356109619, 'eval_accuracy': 0.8600452641710673, 'eval_f1': 0.6799821461944016, 'eval_matthews_correlation': 0.37395988847338846, 'eval_precision': 0.7234059370881429, 'eval_recall': 0.6564931532368521, 'eval_runtime': 13.3086, 'eval_samples_per_second': 2888.433, 'eval_steps_per_second': 22.617, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [1:02:38<00:00, 5.77it/s]***** Running Evaluation ***** +{'loss': 0.2488, 'learning_rate': 1.2484581970290129e-06, 'epoch': 7.03} +{'loss': 0.2473, 'learning_rate': 1.194830267603368e-06, 'epoch': 7.07} +{'loss': 0.2447, 'learning_rate': 1.141202338177723e-06, 'epoch': 7.12} +{'loss': 0.2598, 'learning_rate': 1.0875744087520781e-06, 'epoch': 7.16} +{'loss': 0.2444, 'learning_rate': 1.0339464793264333e-06, 'epoch': 7.2} +{'loss': 0.2488, 'learning_rate': 9.808548291950447e-07, 'epoch': 7.24} +{'loss': 0.2452, 'learning_rate': 9.272268997693999e-07, 'epoch': 7.28} +{'loss': 0.2465, 'learning_rate': 8.735989703437551e-07, 'epoch': 7.32} +{'loss': 0.2502, 'learning_rate': 8.199710409181102e-07, 'epoch': 7.37} +{'loss': 0.2373, 'learning_rate': 7.663431114924654e-07, 'epoch': 7.41} +{'loss': 0.2481, 'learning_rate': 7.127151820668204e-07, 'epoch': 7.45} +{'loss': 0.2484, 'learning_rate': 6.590872526411756e-07, 'epoch': 7.49} +{'loss': 0.2519, 'learning_rate': 6.054593232155307e-07, 'epoch': 7.53} +{'loss': 0.2543, 'learning_rate': 5.518313937898858e-07, 'epoch': 7.57} +{'loss': 0.2607, 'learning_rate': 4.982034643642409e-07, 'epoch': 7.62} +{'loss': 0.2453, 'learning_rate': 4.4457553493859607e-07, 'epoch': 7.66} +{'loss': 0.2538, 'learning_rate': 3.9094760551295117e-07, 'epoch': 7.7} +{'loss': 0.2553, 'learning_rate': 3.3731967608730633e-07, 'epoch': 7.74} +{'loss': 0.2442, 'learning_rate': 2.8369174666166143e-07, 'epoch': 7.78} +{'loss': 0.2573, 'learning_rate': 2.3006381723601653e-07, 'epoch': 7.82} +{'loss': 0.2485, 'learning_rate': 1.7643588781037166e-07, 'epoch': 7.87} +{'loss': 0.2593, 'learning_rate': 1.228079583847268e-07, 'epoch': 7.91} +{'loss': 0.2499, 'learning_rate': 6.918002895908189e-08, 'epoch': 7.95} +{'loss': 0.2454, 'learning_rate': 1.5552099533437016e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [1:02:51<00:00, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.3912976384162903, 'eval_accuracy': 0.8592908613199448, 'eval_f1': 0.6755602480938058, 'eval_matthews_correlation': 0.36653062670190134, 'eval_precision': 0.7213841624644448, 'eval_recall': 0.6517099267795013, 'eval_runtime': 13.32, 'eval_samples_per_second': 2885.961, 'eval_steps_per_second': 22.598, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-7209 (score: 0.6895651152444551). +100%|██████████| 19224/19224 [1:02:53<00:00, 5.77it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 3773.2959, 'train_samples_per_second': 652.011, 'train_steps_per_second': 5.095, 'train_loss': 0.3030893008658353, 'epoch': 8.0} +100%|██████████| 19224/19224 [1:02:53<00:00, 5.09it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.97it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_205648-smymbkb0/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_205648-smymbkb0/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_205648-smymbkb0/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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0.7864312989962449, 'eval_recall': 0.6338154156126563, 'eval_runtime': 13.3112, 'eval_samples_per_second': 2887.874, 'eval_steps_per_second': 22.613, 'epoch': 1.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-2403/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-2403/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-2403/special_tokens_map.json + 20%|██ | 4806/24030 [15:27<56:03, 5.72it/s] ***** Running Evaluation ***** +{'loss': 0.3355, 'learning_rate': 9.236775494444207e-06, 'epoch': 1.04} +{'loss': 0.3434, 'learning_rate': 9.193873611051526e-06, 'epoch': 1.08} +{'loss': 0.337, 'learning_rate': 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'learning_rate': 8.550345360161311e-06, 'epoch': 1.71} +{'loss': 0.3309, 'learning_rate': 8.50744347676863e-06, 'epoch': 1.75} +{'loss': 0.3467, 'learning_rate': 8.46454159337595e-06, 'epoch': 1.79} +{'loss': 0.3373, 'learning_rate': 8.42163970998327e-06, 'epoch': 1.83} +{'loss': 0.3345, 'learning_rate': 8.378737826590588e-06, 'epoch': 1.87} +{'loss': 0.3341, 'learning_rate': 8.335835943197907e-06, 'epoch': 1.91} +{'loss': 0.3321, 'learning_rate': 8.292934059805227e-06, 'epoch': 1.96} +{'loss': 0.3246, 'learning_rate': 8.250032176412546e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [15:40<56:03, 5.72itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 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8.207130293019864e-06, 'epoch': 2.04} +{'loss': 0.3306, 'learning_rate': 8.164228409627184e-06, 'epoch': 2.08} +{'loss': 0.3212, 'learning_rate': 8.121326526234501e-06, 'epoch': 2.12} +{'loss': 0.3204, 'learning_rate': 8.078424642841821e-06, 'epoch': 2.16} +{'loss': 0.3218, 'learning_rate': 8.03552275944914e-06, 'epoch': 2.21} +{'loss': 0.3261, 'learning_rate': 7.99262087605646e-06, 'epoch': 2.25} +{'loss': 0.3222, 'learning_rate': 7.949718992663778e-06, 'epoch': 2.29} +{'loss': 0.3293, 'learning_rate': 7.906817109271098e-06, 'epoch': 2.33} +{'loss': 0.3259, 'learning_rate': 7.863915225878417e-06, 'epoch': 2.37} +{'loss': 0.3245, 'learning_rate': 7.821013342485737e-06, 'epoch': 2.41} +{'loss': 0.3294, 'learning_rate': 7.778111459093054e-06, 'epoch': 2.46} +{'loss': 0.3234, 'learning_rate': 7.735209575700374e-06, 'epoch': 2.5} +{'loss': 0.3256, 'learning_rate': 7.692307692307694e-06, 'epoch': 2.54} +{'loss': 0.3237, 'learning_rate': 7.649405808915013e-06, 'epoch': 2.58} +{'loss': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.342809796333313, 'eval_accuracy': 0.8689160011446112, 'eval_f1': 0.692971863497438, 'eval_matthews_correlation': 0.40571818201075355, 'eval_precision': 0.7502889572047888, 'eval_recall': 0.664417205070126, 'eval_runtime': 13.4048, 'eval_samples_per_second': 2867.694, 'eval_steps_per_second': 22.455, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [31:12<41:28, 5.79it/s]***** Running Evaluation ***** +{'loss': 0.3087, 'learning_rate': 7.1774850915955215e-06, 'epoch': 3.04} +{'loss': 0.3117, 'learning_rate': 7.134583208202841e-06, 'epoch': 3.08} +{'loss': 0.3031, 'learning_rate': 7.09168132481016e-06, 'epoch': 3.12} +{'loss': 0.3127, 'learning_rate': 7.048779441417479e-06, 'epoch': 3.16} +{'loss': 0.3087, 'learning_rate': 7.005877558024799e-06, 'epoch': 3.2} +{'loss': 0.301, 'learning_rate': 6.962975674632117e-06, 'epoch': 3.25} +{'loss': 0.3126, 'learning_rate': 6.920073791239435e-06, 'epoch': 3.29} +{'loss': 0.2951, 'learning_rate': 6.877171907846755e-06, 'epoch': 3.33} +{'loss': 0.3019, 'learning_rate': 6.834699043288001e-06, 'epoch': 3.37} +{'loss': 0.3079, 'learning_rate': 6.79179715989532e-06, 'epoch': 3.41} +{'loss': 0.3225, 'learning_rate': 6.74889527650264e-06, 'epoch': 3.45} +{'loss': 0.3213, 'learning_rate': 6.705993393109958e-06, 'epoch': 3.5} +{'loss': 0.3017, 'learning_rate': 6.663091509717276e-06, 'epoch': 3.54} +{'loss': 0.3045, 'learning_rate': 6.620189626324596e-06, 'epoch': 3.58} +{'loss': 0.3061, 'learning_rate': 6.5772877429319144e-06, 'epoch': 3.62} +{'loss': 0.3155, 'learning_rate': 6.534385859539234e-06, 'epoch': 3.66} +{'loss': 0.3195, 'learning_rate': 6.491483976146553e-06, 'epoch': 3.7} +{'loss': 0.3104, 'learning_rate': 6.448582092753872e-06, 'epoch': 3.75} +{'loss': 0.312, 'learning_rate': 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'learning_rate': 5.462267793556138e-06, 'epoch': 4.7} +{'loss': 0.2951, 'learning_rate': 5.4193659101634566e-06, 'epoch': 4.74} +{'loss': 0.2867, 'learning_rate': 5.376464026770776e-06, 'epoch': 4.79} +{'loss': 0.2989, 'learning_rate': 5.333562143378095e-06, 'epoch': 4.83} +{'loss': 0.2933, 'learning_rate': 5.290660259985414e-06, 'epoch': 4.87} +{'loss': 0.2938, 'learning_rate': 5.247758376592733e-06, 'epoch': 4.91} +{'loss': 0.2888, 'learning_rate': 5.204856493200053e-06, 'epoch': 4.95} +{'loss': 0.2919, 'learning_rate': 5.161954609807371e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 12015/24030 [39:16<36:28, 5.49iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015/config.json +{'eval_loss': 0.3489874303340912, 'eval_accuracy': 0.870164667932676, 'eval_f1': 0.6713730161766944, 'eval_matthews_correlation': 0.38362616881371175, 'eval_precision': 0.76569297368997, 'eval_recall': 0.6384765989054852, 'eval_runtime': 13.2783, 'eval_samples_per_second': 2895.026, 'eval_steps_per_second': 22.669, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [46:53<27:30, 5.82it/s]***** Running Evaluation ***** +{'loss': 0.267, 'learning_rate': 5.119052726414691e-06, 'epoch': 5.04} +{'loss': 0.2765, 'learning_rate': 5.076150843022009e-06, 'epoch': 5.08} +{'loss': 0.2693, 'learning_rate': 5.0332489596293275e-06, 'epoch': 5.12} +{'loss': 0.2674, 'learning_rate': 4.990347076236647e-06, 'epoch': 5.16} +{'loss': 0.2731, 'learning_rate': 4.9474451928439666e-06, 'epoch': 5.2} +{'loss': 0.2677, 'learning_rate': 4.904543309451285e-06, 'epoch': 5.24} +{'loss': 0.2636, 'learning_rate': 4.861641426058604e-06, 'epoch': 5.29} +{'loss': 0.2646, 'learning_rate': 4.8187395426659235e-06, 'epoch': 5.33} +{'loss': 0.2781, 'learning_rate': 4.775837659273242e-06, 'epoch': 5.37} +{'loss': 0.2699, 'learning_rate': 4.732935775880562e-06, 'epoch': 5.41} +{'loss': 0.2741, 'learning_rate': 4.6900338924878805e-06, 'epoch': 5.45} +{'loss': 0.2743, 'learning_rate': 4.6471320090952e-06, 'epoch': 5.49} +{'loss': 0.2701, 'learning_rate': 4.604659144536446e-06, 'epoch': 5.53} +{'loss': 0.2767, 'learning_rate': 4.561757261143764e-06, 'epoch': 5.58} +{'loss': 0.2608, 'learning_rate': 4.518855377751084e-06, 'epoch': 5.62} +{'loss': 0.2775, 'learning_rate': 4.475953494358403e-06, 'epoch': 5.66} +{'loss': 0.2755, 'learning_rate': 4.433051610965722e-06, 'epoch': 5.7} +{'loss': 0.27, 'learning_rate': 4.390149727573041e-06, 'epoch': 5.74} +{'loss': 0.2754, 'learning_rate': 4.34724784418036e-06, 'epoch': 5.78} +{'loss': 0.2656, 'learning_rate': 4.304345960787679e-06, 'epoch': 5.83} +{'loss': 0.2772, 'learning_rate': 4.261444077394998e-06, 'epoch': 5.87} +{'loss': 0.2691, 'learning_rate': 4.2185421940023165e-06, 'epoch': 5.91} +{'loss': 0.2712, 'learning_rate': 4.175640310609636e-06, 'epoch': 5.95} +{'loss': 0.2792, 'learning_rate': 4.132738427216955e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [47:07<27:30, 5.82iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35959097743034363, 'eval_accuracy': 0.8648578340834006, 'eval_f1': 0.6760849617613066, 'eval_matthews_correlation': 0.3765167235123387, 'eval_precision': 0.739904224228892, 'eval_recall': 0.6477306657897877, 'eval_runtime': 13.4837, 'eval_samples_per_second': 2850.916, 'eval_steps_per_second': 22.323, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [54:45<20:56, 5.74it/s]***** Running Evaluation ***** +{'loss': 0.2562, 'learning_rate': 4.089836543824274e-06, 'epoch': 6.03} +{'loss': 0.2513, 'learning_rate': 4.046934660431593e-06, 'epoch': 6.08} +{'loss': 0.2424, 'learning_rate': 4.004032777038913e-06, 'epoch': 6.12} +{'loss': 0.2496, 'learning_rate': 3.961130893646231e-06, 'epoch': 6.16} +{'loss': 0.2494, 'learning_rate': 3.91822901025355e-06, 'epoch': 6.2} +{'loss': 0.2529, 'learning_rate': 3.8753271268608696e-06, 'epoch': 6.24} +{'loss': 0.253, 'learning_rate': 3.832425243468188e-06, 'epoch': 6.28} +{'loss': 0.2513, 'learning_rate': 3.789523360075508e-06, 'epoch': 6.33} +{'loss': 0.2487, 'learning_rate': 3.7470504955167534e-06, 'epoch': 6.37} +{'loss': 0.2487, 'learning_rate': 3.7041486121240725e-06, 'epoch': 6.41} +{'loss': 0.2487, 'learning_rate': 3.661246728731392e-06, 'epoch': 6.45} +{'loss': 0.2459, 'learning_rate': 3.6183448453387104e-06, 'epoch': 6.49} +{'loss': 0.2405, 'learning_rate': 3.5754429619460295e-06, 'epoch': 6.53} +{'loss': 0.2463, 'learning_rate': 3.5325410785533486e-06, 'epoch': 6.58} +{'loss': 0.2437, 'learning_rate': 3.4896391951606677e-06, 'epoch': 6.62} +{'loss': 0.2553, 'learning_rate': 3.446737311767987e-06, 'epoch': 6.66} +{'loss': 0.2546, 'learning_rate': 3.403835428375306e-06, 'epoch': 6.7} +{'loss': 0.2461, 'learning_rate': 3.360933544982625e-06, 'epoch': 6.74} +{'loss': 0.2472, 'learning_rate': 3.318031661589944e-06, 'epoch': 6.78} +{'loss': 0.2667, 'learning_rate': 3.275129778197263e-06, 'epoch': 6.82} +{'loss': 0.2454, 'learning_rate': 3.232227894804582e-06, 'epoch': 6.87} +{'loss': 0.2507, 'learning_rate': 3.1893260114119012e-06, 'epoch': 6.91} +{'loss': 0.2588, 'learning_rate': 3.1464241280192204e-06, 'epoch': 6.95} +{'loss': 0.2512, 'learning_rate': 3.1035222446265395e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [54:58<20:56, 5.74iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3868589699268341, 'eval_accuracy': 0.8578861111833719, 'eval_f1': 0.6805845198263591, 'eval_matthews_correlation': 0.3721430323623432, 'eval_precision': 0.7174706233402299, 'eval_recall': 0.6592059129742475, 'eval_runtime': 13.6367, 'eval_samples_per_second': 2818.942, 'eval_steps_per_second': 22.073, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [1:02:37<13:47, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.2329, 'learning_rate': 3.0606203612338586e-06, 'epoch': 7.03} +{'loss': 0.2279, 'learning_rate': 3.0177184778411773e-06, 'epoch': 7.07} +{'loss': 0.2243, 'learning_rate': 2.9748165944484965e-06, 'epoch': 7.12} +{'loss': 0.2343, 'learning_rate': 2.9319147110558156e-06, 'epoch': 7.16} +{'loss': 0.226, 'learning_rate': 2.8894418464970616e-06, 'epoch': 7.2} +{'loss': 0.2299, 'learning_rate': 2.8465399631043807e-06, 'epoch': 7.24} +{'loss': 0.2268, 'learning_rate': 2.8036380797117e-06, 'epoch': 7.28} +{'loss': 0.2234, 'learning_rate': 2.760736196319019e-06, 'epoch': 7.32} +{'loss': 0.2289, 'learning_rate': 2.717834312926338e-06, 'epoch': 7.37} +{'loss': 0.2185, 'learning_rate': 2.6749324295336564e-06, 'epoch': 7.41} +{'loss': 0.2264, 'learning_rate': 2.6320305461409755e-06, 'epoch': 7.45} +{'loss': 0.2339, 'learning_rate': 2.5891286627482946e-06, 'epoch': 7.49} +{'loss': 0.232, 'learning_rate': 2.5462267793556138e-06, 'epoch': 7.53} +{'loss': 0.2328, 'learning_rate': 2.503324895962933e-06, 'epoch': 7.57} +{'loss': 0.2356, 'learning_rate': 2.460423012570252e-06, 'epoch': 7.62} +{'loss': 0.2311, 'learning_rate': 2.417521129177571e-06, 'epoch': 7.66} +{'loss': 0.2356, 'learning_rate': 2.3746192457848903e-06, 'epoch': 7.7} +{'loss': 0.2297, 'learning_rate': 2.3317173623922094e-06, 'epoch': 7.74} +{'loss': 0.2301, 'learning_rate': 2.288815478999528e-06, 'epoch': 7.78} +{'loss': 0.2341, 'learning_rate': 2.2459135956068473e-06, 'epoch': 7.82} +{'loss': 0.2345, 'learning_rate': 2.2030117122141664e-06, 'epoch': 7.87} +{'loss': 0.2371, 'learning_rate': 2.1601098288214855e-06, 'epoch': 7.91} +{'loss': 0.2319, 'learning_rate': 2.1172079454288042e-06, 'epoch': 7.95} +{'loss': 0.2306, 'learning_rate': 2.0743060620361234e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [1:02:50<13:47, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.4152064025402069, 'eval_accuracy': 0.8589266668400926, 'eval_f1': 0.6699398988823501, 'eval_matthews_correlation': 0.35801950659107634, 'eval_precision': 0.7205297968069078, 'eval_recall': 0.6453068575716643, 'eval_runtime': 13.2899, 'eval_samples_per_second': 2892.495, 'eval_steps_per_second': 22.649, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [1:10:28<06:54, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.2114, 'learning_rate': 2.0314041786434425e-06, 'epoch': 8.03} +{'loss': 0.2138, 'learning_rate': 1.9889313140846885e-06, 'epoch': 8.07} +{'loss': 0.2127, 'learning_rate': 1.9460294306920076e-06, 'epoch': 8.11} +{'loss': 0.2145, 'learning_rate': 1.9031275472993265e-06, 'epoch': 8.16} +{'loss': 0.2113, 'learning_rate': 1.8602256639066457e-06, 'epoch': 8.2} +{'loss': 0.2152, 'learning_rate': 1.8173237805139646e-06, 'epoch': 8.24} +{'loss': 0.207, 'learning_rate': 1.7744218971212837e-06, 'epoch': 8.28} +{'loss': 0.2174, 'learning_rate': 1.7315200137286028e-06, 'epoch': 8.32} +{'loss': 0.2075, 'learning_rate': 1.688618130335922e-06, 'epoch': 8.36} +{'loss': 0.2115, 'learning_rate': 1.6457162469432409e-06, 'epoch': 8.41} +{'loss': 0.2174, 'learning_rate': 1.60281436355056e-06, 'epoch': 8.45} +{'loss': 0.214, 'learning_rate': 1.5599124801578792e-06, 'epoch': 8.49} +{'loss': 0.213, 'learning_rate': 1.5170105967651983e-06, 'epoch': 8.53} +{'loss': 0.2121, 'learning_rate': 1.4741087133725172e-06, 'epoch': 8.57} +{'loss': 0.2191, 'learning_rate': 1.4312068299798363e-06, 'epoch': 8.61} +{'loss': 0.2163, 'learning_rate': 1.3883049465871555e-06, 'epoch': 8.66} +{'loss': 0.2062, 'learning_rate': 1.3454030631944742e-06, 'epoch': 8.7} +{'loss': 0.2172, 'learning_rate': 1.3025011798017933e-06, 'epoch': 8.74} +{'loss': 0.2132, 'learning_rate': 1.2595992964091124e-06, 'epoch': 8.78} +{'loss': 0.2095, 'learning_rate': 1.2166974130164316e-06, 'epoch': 8.82} +{'loss': 0.2065, 'learning_rate': 1.1737955296237507e-06, 'epoch': 8.86} +{'loss': 0.2133, 'learning_rate': 1.1308936462310696e-06, 'epoch': 8.91} +{'loss': 0.2168, 'learning_rate': 1.0884207816723156e-06, 'epoch': 8.95} +{'loss': 0.2234, 'learning_rate': 1.0455188982796345e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [1:10:42<06:54, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.44508305191993713, 'eval_accuracy': 0.8588486251658386, 'eval_f1': 0.6661522752634735, 'eval_matthews_correlation': 0.3526372527548518, 'eval_precision': 0.7204952917333032, 'eval_recall': 0.6409928428096535, 'eval_runtime': 13.3109, 'eval_samples_per_second': 2887.93, 'eval_steps_per_second': 22.613, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [1:18:20<00:00, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.1982, 'learning_rate': 1.0026170148869536e-06, 'epoch': 9.03} +{'loss': 0.2065, 'learning_rate': 9.597151314942726e-07, 'epoch': 9.07} +{'loss': 0.1965, 'learning_rate': 9.168132481015918e-07, 'epoch': 9.11} +{'loss': 0.2036, 'learning_rate': 8.739113647089108e-07, 'epoch': 9.16} +{'loss': 0.2033, 'learning_rate': 8.3100948131623e-07, 'epoch': 9.2} +{'loss': 0.2056, 'learning_rate': 7.881075979235489e-07, 'epoch': 9.24} +{'loss': 0.2045, 'learning_rate': 7.452057145308679e-07, 'epoch': 9.28} +{'loss': 0.2022, 'learning_rate': 7.02303831138187e-07, 'epoch': 9.32} +{'loss': 0.1965, 'learning_rate': 6.594019477455061e-07, 'epoch': 9.36} +{'loss': 0.2077, 'learning_rate': 6.165000643528252e-07, 'epoch': 9.4} +{'loss': 0.1915, 'learning_rate': 5.735981809601442e-07, 'epoch': 9.45} +{'loss': 0.2027, 'learning_rate': 5.306962975674632e-07, 'epoch': 9.49} +{'loss': 0.2047, 'learning_rate': 4.877944141747823e-07, 'epoch': 9.53} +{'loss': 0.1972, 'learning_rate': 4.4489253078210134e-07, 'epoch': 9.57} +{'loss': 0.2012, 'learning_rate': 4.019906473894204e-07, 'epoch': 9.61} +{'loss': 0.1956, 'learning_rate': 3.590887639967395e-07, 'epoch': 9.65} +{'loss': 0.1988, 'learning_rate': 3.1618688060405857e-07, 'epoch': 9.7} +{'loss': 0.2092, 'learning_rate': 2.732849972113776e-07, 'epoch': 9.74} +{'loss': 0.1999, 'learning_rate': 2.3038311381869664e-07, 'epoch': 9.78} +{'loss': 0.1981, 'learning_rate': 1.8791024925994252e-07, 'epoch': 9.82} +{'loss': 0.1969, 'learning_rate': 1.4500836586726157e-07, 'epoch': 9.86} +{'loss': 0.2013, 'learning_rate': 1.0210648247458065e-07, 'epoch': 9.9} +{'loss': 0.1993, 'learning_rate': 5.92045990818997e-08, 'epoch': 9.95} +{'loss': 0.193, 'learning_rate': 1.6302715689218757e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [1:18:33<00:00, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.45584559440612793, 'eval_accuracy': 0.8526833328997685, 'eval_f1': 0.6704967828458709, 'eval_matthews_correlation': 0.35086367024620124, 'eval_precision': 0.7037869440497239, 'eval_recall': 0.6510220829806906, 'eval_runtime': 13.3023, 'eval_samples_per_second': 2889.795, 'eval_steps_per_second': 22.628, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-7209 (score: 0.692971863497438). +100%|██████████| 24030/24030 [1:18:35<00:00, 5.80it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.03_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 4715.4322, 'train_samples_per_second': 652.176, 'train_steps_per_second': 5.096, 'train_loss': 0.27859540967905566, 'epoch': 10.0} +100%|██████████| 24030/24030 [1:18:35<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:22<00:00, 13.56it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_220122-h2bn8t0e/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_220122-h2bn8t0e/files/requirements.txt 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.06 +warmup_steps: + value: 0 +weight_decay: + value: 0.01 diff --git a/VASC/len2_5120/wandb/run-20260307_232134-tlj8onax/files/output.log b/VASC/len2_5120/wandb/run-20260307_232134-tlj8onax/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..f34e480ec4cd8edde8e67fc73b5f5f7172985675 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_232134-tlj8onax/files/output.log @@ -0,0 +1,232 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.weight', 'classifier.weight', 'bert.pooler.dense.bias', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [23:19<20:42, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.3207, 'learning_rate': 7.02331759149941e-06, 'epoch': 2.04} +{'loss': 0.3305, 'learning_rate': 6.9495277449822905e-06, 'epoch': 2.08} +{'loss': 0.3211, 'learning_rate': 6.875737898465171e-06, 'epoch': 2.12} +{'loss': 0.3204, 'learning_rate': 6.801948051948053e-06, 'epoch': 2.16} +{'loss': 0.321, 'learning_rate': 6.728158205430933e-06, 'epoch': 2.21} +{'loss': 0.3248, 'learning_rate': 6.654368358913814e-06, 'epoch': 2.25} +{'loss': 0.3229, 'learning_rate': 6.5805785123966945e-06, 'epoch': 2.29} +{'loss': 0.3291, 'learning_rate': 6.506788665879575e-06, 'epoch': 2.33} +{'loss': 0.3247, 'learning_rate': 6.432998819362456e-06, 'epoch': 2.37} +{'loss': 0.3246, 'learning_rate': 6.359208972845336e-06, 'epoch': 2.41} +{'loss': 0.3261, 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+ Num examples = 38441 + Batch size = 128 + 50%|█████ | 7209/14418 [23:32<20:42, 5.80itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3375459313392639, 'eval_accuracy': 0.8718295569834291, 'eval_f1': 0.6938437099246832, 'eval_matthews_correlation': 0.41250805811617514, 'eval_precision': 0.7615534387315988, 'eval_recall': 0.6626463972677832, 'eval_runtime': 13.2712, 'eval_samples_per_second': 2896.565, 'eval_steps_per_second': 22.681, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [31:10<13:55, 5.75it/s]***** Running Evaluation ***** +{'loss': 0.3084, 'learning_rate': 5.252361275088548e-06, 'epoch': 3.04} +{'loss': 0.3109, 'learning_rate': 5.1785714285714296e-06, 'epoch': 3.08} +{'loss': 0.3041, 'learning_rate': 5.10478158205431e-06, 'epoch': 3.12} +{'loss': 0.3124, 'learning_rate': 5.030991735537191e-06, 'epoch': 3.16} +{'loss': 0.3064, 'learning_rate': 4.957201889020071e-06, 'epoch': 3.2} +{'loss': 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'eval_recall': 0.6507226067109113, 'eval_runtime': 13.2893, 'eval_samples_per_second': 2892.636, 'eval_steps_per_second': 22.65, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-9612/special_tokens_map.json + 83%|████████▎ | 12015/14418 [39:01<06:56, 5.77it/s]***** Running Evaluation ***** +{'loss': 0.2995, 'learning_rate': 3.482142857142857e-06, 'epoch': 4.04} +{'loss': 0.2954, 'learning_rate': 3.4083530106257382e-06, 'epoch': 4.08} +{'loss': 0.3017, 'learning_rate': 3.334563164108619e-06, 'epoch': 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'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [47:05<00:00, 5.73iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3548549711704254, 'eval_accuracy': 0.8654301396945969, 'eval_f1': 0.6822236098115213, 'eval_matthews_correlation': 0.38548988468841316, 'eval_precision': 0.74050432538099, 'eval_recall': 0.6544696243629721, 'eval_runtime': 13.3117, 'eval_samples_per_second': 2887.767, 'eval_steps_per_second': 22.612, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-7209 (score: 0.6938437099246832). +100%|██████████| 14418/14418 [47:07<00:00, 5.73it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 2827.0732, 'train_samples_per_second': 652.68, 'train_steps_per_second': 5.1, 'train_loss': 0.31692984369066024, 'epoch': 6.0} +100%|██████████| 14418/14418 [47:07<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 14.00it/s] diff --git a/VASC/len2_5120/wandb/run-20260307_232134-tlj8onax/files/requirements.txt b/VASC/len2_5120/wandb/run-20260307_232134-tlj8onax/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260307_232134-tlj8onax/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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b/VASC/len2_5120/wandb/run-20260308_001017-hbhfi2gh/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['classifier.weight', 'classifier.bias', 'bert.pooler.dense.bias', 'bert.pooler.dense.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3405361771583557, 'eval_accuracy': 0.8704508207382743, 'eval_f1': 0.6948478046966576, 'eval_matthews_correlation': 0.4109546840825322, 'eval_precision': 0.7554982854718088, 'eval_recall': 0.6652493988927455, 'eval_runtime': 13.3133, 'eval_samples_per_second': 2887.404, 'eval_steps_per_second': 22.609, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [31:08<27:34, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.3039, 'learning_rate': 6.598782512451578e-06, 'epoch': 3.04} +{'loss': 0.3083, 'learning_rate': 6.543442169341451e-06, 'epoch': 3.08} +{'loss': 0.3013, 'learning_rate': 6.488101826231323e-06, 'epoch': 3.12} +{'loss': 0.309, 'learning_rate': 6.432761483121196e-06, 'epoch': 3.16} +{'loss': 0.3054, 'learning_rate': 6.377421140011068e-06, 'epoch': 3.2} +{'loss': 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0.6686009231032081, 'eval_runtime': 13.2812, 'eval_samples_per_second': 2894.396, 'eval_steps_per_second': 22.664, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [38:59<20:53, 5.75it/s]***** Running Evaluation ***** +{'loss': 0.2948, 'learning_rate': 5.271721084670725e-06, 'epoch': 4.04} +{'loss': 0.2865, 'learning_rate': 5.216380741560599e-06, 'epoch': 4.08} +{'loss': 0.2951, 'learning_rate': 5.161040398450471e-06, 'epoch': 4.12} +{'loss': 0.2869, 'learning_rate': 5.105700055340344e-06, 'epoch': 4.16} +{'loss': 0.2778, 'learning_rate': 5.050359712230216e-06, 'epoch': 4.2} +{'loss': 0.2982, 'learning_rate': 4.995019369120089e-06, 'epoch': 4.24} +{'loss': 0.2876, 'learning_rate': 4.939679026009961e-06, 'epoch': 4.29} +{'loss': 0.2861, 'learning_rate': 4.884338682899835e-06, 'epoch': 4.33} +{'loss': 0.2978, 'learning_rate': 4.828998339789707e-06, 'epoch': 4.37} +{'loss': 0.2875, 'learning_rate': 4.77365799667958e-06, 'epoch': 4.41} +{'loss': 0.291, 'learning_rate': 4.718317653569452e-06, 'epoch': 4.45} +{'loss': 0.2829, 'learning_rate': 4.662977310459325e-06, 'epoch': 4.49} +{'loss': 0.2841, 'learning_rate': 4.6076369673491975e-06, 'epoch': 4.54} +{'loss': 0.2874, 'learning_rate': 4.552296624239071e-06, 'epoch': 4.58} +{'loss': 0.2945, 'learning_rate': 4.496956281128943e-06, 'epoch': 4.62} +{'loss': 0.2758, 'learning_rate': 4.441615938018816e-06, 'epoch': 4.66} +{'loss': 0.293, 'learning_rate': 4.3862755949086885e-06, 'epoch': 4.7} +{'loss': 0.2874, 'learning_rate': 4.330935251798561e-06, 'epoch': 4.74} +{'loss': 0.2802, 'learning_rate': 4.2755949086884344e-06, 'epoch': 4.79} +{'loss': 0.2937, 'learning_rate': 4.220254565578307e-06, 'epoch': 4.83} +{'loss': 0.2866, 'learning_rate': 4.1649142224681795e-06, 'epoch': 4.87} +{'loss': 0.2916, 'learning_rate': 4.109573879358053e-06, 'epoch': 4.91} +{'loss': 0.2844, 'learning_rate': 4.0542335362479255e-06, 'epoch': 4.95} +{'loss': 0.2868, 'learning_rate': 3.998893193137798e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 62%|██████▎ | 12015/19224 [39:12<20:53, 5.75iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015/config.json +{'eval_loss': 0.3493526875972748, 'eval_accuracy': 0.8682656538591608, 'eval_f1': 0.6769979676605756, 'eval_matthews_correlation': 0.38487193769848504, 'eval_precision': 0.7535762290966379, 'eval_recall': 0.646037356257214, 'eval_runtime': 13.3124, 'eval_samples_per_second': 2887.618, 'eval_steps_per_second': 22.611, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [46:50<14:46, 5.42it/s]***** Running Evaluation ***** +{'loss': 0.2667, 'learning_rate': 3.9435528500276705e-06, 'epoch': 5.04} +{'loss': 0.2692, 'learning_rate': 3.888212506917543e-06, 'epoch': 5.08} +{'loss': 0.2657, 'learning_rate': 3.832872163807416e-06, 'epoch': 5.12} +{'loss': 0.259, 'learning_rate': 3.777531820697289e-06, 'epoch': 5.16} +{'loss': 0.2721, 'learning_rate': 3.7221914775871616e-06, 'epoch': 5.2} +{'loss': 0.2623, 'learning_rate': 3.666851134477034e-06, 'epoch': 5.24} +{'loss': 0.2605, 'learning_rate': 3.6115107913669066e-06, 'epoch': 5.29} +{'loss': 0.2591, 'learning_rate': 3.556170448256779e-06, 'epoch': 5.33} +{'loss': 0.2738, 'learning_rate': 3.500830105146652e-06, 'epoch': 5.37} +{'loss': 0.2649, 'learning_rate': 3.4454897620365247e-06, 'epoch': 5.41} +{'loss': 0.276, 'learning_rate': 3.3901494189263977e-06, 'epoch': 5.45} +{'loss': 0.2713, 'learning_rate': 3.3348090758162706e-06, 'epoch': 5.49} +{'loss': 0.2639, 'learning_rate': 3.280022136137244e-06, 'epoch': 5.53} +{'loss': 0.2743, 'learning_rate': 3.2246817930271166e-06, 'epoch': 5.58} +{'loss': 0.2598, 'learning_rate': 3.16934144991699e-06, 'epoch': 5.62} +{'loss': 0.272, 'learning_rate': 3.1140011068068626e-06, 'epoch': 5.66} +{'loss': 0.2748, 'learning_rate': 3.058660763696735e-06, 'epoch': 5.7} +{'loss': 0.2659, 'learning_rate': 3.003320420586608e-06, 'epoch': 5.74} +{'loss': 0.2696, 'learning_rate': 2.9479800774764806e-06, 'epoch': 5.78} +{'loss': 0.2593, 'learning_rate': 2.892639734366353e-06, 'epoch': 5.83} +{'loss': 0.2708, 'learning_rate': 2.8372993912562257e-06, 'epoch': 5.87} +{'loss': 0.2665, 'learning_rate': 2.781959048146099e-06, 'epoch': 5.91} +{'loss': 0.2649, 'learning_rate': 2.7266187050359716e-06, 'epoch': 5.95} +{'loss': 0.2708, 'learning_rate': 2.671278361925844e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [47:03<14:46, 5.42iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3664167523384094, 'eval_accuracy': 0.8632449728154835, 'eval_f1': 0.6797481266099321, 'eval_matthews_correlation': 0.378428883412296, 'eval_precision': 0.7333951800796098, 'eval_recall': 0.6533969336382928, 'eval_runtime': 13.2783, 'eval_samples_per_second': 2895.022, 'eval_steps_per_second': 22.669, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [54:41<07:02, 5.69it/s]***** Running Evaluation ***** +{'loss': 0.2478, 'learning_rate': 2.6159380188157167e-06, 'epoch': 6.03} +{'loss': 0.2509, 'learning_rate': 2.5605976757055893e-06, 'epoch': 6.08} +{'loss': 0.2395, 'learning_rate': 2.5052573325954622e-06, 'epoch': 6.12} +{'loss': 0.2509, 'learning_rate': 2.449916989485335e-06, 'epoch': 6.16} +{'loss': 0.2516, 'learning_rate': 2.3945766463752078e-06, 'epoch': 6.2} +{'loss': 0.246, 'learning_rate': 2.3392363032650807e-06, 'epoch': 6.24} +{'loss': 0.2485, 'learning_rate': 2.2838959601549533e-06, 'epoch': 6.28} +{'loss': 0.2506, 'learning_rate': 2.228555617044826e-06, 'epoch': 6.33} +{'loss': 0.2477, 'learning_rate': 2.1732152739346983e-06, 'epoch': 6.37} +{'loss': 0.2479, 'learning_rate': 2.1184283342556726e-06, 'epoch': 6.41} +{'loss': 0.2467, 'learning_rate': 2.063087991145545e-06, 'epoch': 6.45} +{'loss': 0.2447, 'learning_rate': 2.007747648035418e-06, 'epoch': 6.49} +{'loss': 0.2419, 'learning_rate': 1.9524073049252907e-06, 'epoch': 6.53} +{'loss': 0.2456, 'learning_rate': 1.8970669618151635e-06, 'epoch': 6.58} +{'loss': 0.2455, 'learning_rate': 1.8417266187050362e-06, 'epoch': 6.62} +{'loss': 0.2557, 'learning_rate': 1.7863862755949088e-06, 'epoch': 6.66} +{'loss': 0.2506, 'learning_rate': 1.7310459324847815e-06, 'epoch': 6.7} +{'loss': 0.2473, 'learning_rate': 1.6757055893746543e-06, 'epoch': 6.74} +{'loss': 0.2465, 'learning_rate': 1.620365246264527e-06, 'epoch': 6.78} +{'loss': 0.2627, 'learning_rate': 1.5650249031543996e-06, 'epoch': 6.82} +{'loss': 0.2438, 'learning_rate': 1.5096845600442725e-06, 'epoch': 6.87} +{'loss': 0.2507, 'learning_rate': 1.454344216934145e-06, 'epoch': 6.91} +{'loss': 0.2512, 'learning_rate': 1.3990038738240178e-06, 'epoch': 6.95} +{'loss': 0.2438, 'learning_rate': 1.3436635307138906e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [54:54<07:02, 5.69iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3879360556602478, 'eval_accuracy': 0.85502458312739, 'eval_f1': 0.6836849773139634, 'eval_matthews_correlation': 0.37410139815251625, 'eval_precision': 0.7107876645788869, 'eval_recall': 0.6659867720192074, 'eval_runtime': 13.3272, 'eval_samples_per_second': 2884.406, 'eval_steps_per_second': 22.585, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [1:02:32<00:00, 5.82it/s]***** Running Evaluation ***** +{'loss': 0.2323, 'learning_rate': 1.2883231876037633e-06, 'epoch': 7.03} +{'loss': 0.2284, 'learning_rate': 1.2329828444936359e-06, 'epoch': 7.07} +{'loss': 0.2269, 'learning_rate': 1.1776425013835086e-06, 'epoch': 7.12} +{'loss': 0.2421, 'learning_rate': 1.1223021582733814e-06, 'epoch': 7.16} +{'loss': 0.2271, 'learning_rate': 1.0669618151632542e-06, 'epoch': 7.2} +{'loss': 0.2317, 'learning_rate': 1.011621472053127e-06, 'epoch': 7.24} +{'loss': 0.231, 'learning_rate': 9.568345323741008e-07, 'epoch': 7.28} +{'loss': 0.2315, 'learning_rate': 9.014941892639735e-07, 'epoch': 7.32} +{'loss': 0.2349, 'learning_rate': 8.461538461538463e-07, 'epoch': 7.37} +{'loss': 0.2188, 'learning_rate': 7.908135030437189e-07, 'epoch': 7.41} +{'loss': 0.2312, 'learning_rate': 7.354731599335917e-07, 'epoch': 7.45} +{'loss': 0.2305, 'learning_rate': 6.801328168234643e-07, 'epoch': 7.49} +{'loss': 0.2356, 'learning_rate': 6.247924737133371e-07, 'epoch': 7.53} +{'loss': 0.2349, 'learning_rate': 5.694521306032098e-07, 'epoch': 7.57} +{'loss': 0.2404, 'learning_rate': 5.141117874930825e-07, 'epoch': 7.62} +{'loss': 0.2289, 'learning_rate': 4.587714443829552e-07, 'epoch': 7.66} +{'loss': 0.2405, 'learning_rate': 4.034311012728279e-07, 'epoch': 7.7} +{'loss': 0.2332, 'learning_rate': 3.480907581627006e-07, 'epoch': 7.74} +{'loss': 0.2278, 'learning_rate': 2.9275041505257337e-07, 'epoch': 7.78} +{'loss': 0.2392, 'learning_rate': 2.3741007194244607e-07, 'epoch': 7.82} +{'loss': 0.2309, 'learning_rate': 1.8206972883231878e-07, 'epoch': 7.87} +{'loss': 0.2368, 'learning_rate': 1.2672938572219148e-07, 'epoch': 7.91} +{'loss': 0.2337, 'learning_rate': 7.138904261206419e-08, 'epoch': 7.95} +{'loss': 0.2257, 'learning_rate': 1.6048699501936912e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [1:02:45<00:00, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.40158483386039734, 'eval_accuracy': 0.8578340834005359, 'eval_f1': 0.6792932014544275, 'eval_matthews_correlation': 0.3701288563929457, 'eval_precision': 0.717300750680554, 'eval_recall': 0.6576103279736729, 'eval_runtime': 13.3123, 'eval_samples_per_second': 2887.634, 'eval_steps_per_second': 22.611, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-7209 (score: 0.6948478046966576). +100%|██████████| 19224/19224 [1:02:47<00:00, 5.82it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 3767.2678, 'train_samples_per_second': 653.055, 'train_steps_per_second': 5.103, 'train_loss': 0.2948587938392852, 'epoch': 8.0} +100%|██████████| 19224/19224 [1:02:47<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.99it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_001017-hbhfi2gh/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_001017-hbhfi2gh/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_001017-hbhfi2gh/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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0.7833408582235938, 'eval_recall': 0.6376873114412593, 'eval_runtime': 13.2872, 'eval_samples_per_second': 2893.077, 'eval_steps_per_second': 22.653, 'epoch': 1.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-2403/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-2403/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-2403/special_tokens_map.json + 20%|██ | 4806/24030 [15:26<58:00, 5.52it/s] ***** Running Evaluation ***** +{'loss': 0.3379, 'learning_rate': 9.531609704267753e-06, 'epoch': 1.04} +{'loss': 0.3464, 'learning_rate': 9.487338409775103e-06, 'epoch': 1.08} +{'loss': 0.3388, 'learning_rate': 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'learning_rate': 8.823268992385337e-06, 'epoch': 1.71} +{'loss': 0.3328, 'learning_rate': 8.778997697892687e-06, 'epoch': 1.75} +{'loss': 0.3483, 'learning_rate': 8.734726403400036e-06, 'epoch': 1.79} +{'loss': 0.3399, 'learning_rate': 8.690455108907386e-06, 'epoch': 1.83} +{'loss': 0.336, 'learning_rate': 8.646183814414734e-06, 'epoch': 1.87} +{'loss': 0.3356, 'learning_rate': 8.601912519922083e-06, 'epoch': 1.91} +{'loss': 0.3344, 'learning_rate': 8.557641225429433e-06, 'epoch': 1.96} +{'loss': 0.3249, 'learning_rate': 8.51336993093678e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 20%|██ | 4806/24030 [15:40<58:00, 5.52itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-4806/config.json +{'eval_loss': 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8.46909863644413e-06, 'epoch': 2.04} +{'loss': 0.3325, 'learning_rate': 8.42482734195148e-06, 'epoch': 2.08} +{'loss': 0.3246, 'learning_rate': 8.38055604745883e-06, 'epoch': 2.12} +{'loss': 0.3231, 'learning_rate': 8.336284752966177e-06, 'epoch': 2.16} +{'loss': 0.3269, 'learning_rate': 8.292013458473527e-06, 'epoch': 2.21} +{'loss': 0.3276, 'learning_rate': 8.247742163980875e-06, 'epoch': 2.25} +{'loss': 0.325, 'learning_rate': 8.203470869488224e-06, 'epoch': 2.29} +{'loss': 0.3311, 'learning_rate': 8.159199574995574e-06, 'epoch': 2.33} +{'loss': 0.3274, 'learning_rate': 8.114928280502923e-06, 'epoch': 2.37} +{'loss': 0.327, 'learning_rate': 8.070656986010271e-06, 'epoch': 2.41} +{'loss': 0.3305, 'learning_rate': 8.02638569151762e-06, 'epoch': 2.46} +{'loss': 0.326, 'learning_rate': 7.982114397024969e-06, 'epoch': 2.5} +{'loss': 0.3289, 'learning_rate': 7.937843102532318e-06, 'epoch': 2.54} +{'loss': 0.3259, 'learning_rate': 7.893571808039668e-06, 'epoch': 2.58} +{'loss': 0.3332, 'learning_rate': 7.849300513547017e-06, 'epoch': 2.62} +{'loss': 0.3207, 'learning_rate': 7.805029219054365e-06, 'epoch': 2.66} +{'loss': 0.3191, 'learning_rate': 7.760757924561715e-06, 'epoch': 2.7} +{'loss': 0.3259, 'learning_rate': 7.716486630069064e-06, 'epoch': 2.75} +{'loss': 0.3289, 'learning_rate': 7.672215335576412e-06, 'epoch': 2.79} +{'loss': 0.3324, 'learning_rate': 7.6279440410837625e-06, 'epoch': 2.83} +{'loss': 0.3204, 'learning_rate': 7.583672746591111e-06, 'epoch': 2.87} +{'loss': 0.3249, 'learning_rate': 7.539401452098461e-06, 'epoch': 2.91} +{'loss': 0.3229, 'learning_rate': 7.495130157605809e-06, 'epoch': 2.95} +{'loss': 0.3289, 'learning_rate': 7.450858863113158e-06, 'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 30%|███ | 7209/24030 [23:31<48:21, 5.80itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.34084999561309814, 'eval_accuracy': 0.8707890013267084, 'eval_f1': 0.6911239932198271, 'eval_matthews_correlation': 0.40706531332233514, 'eval_precision': 0.7583819944132693, 'eval_recall': 0.6603267380206633, 'eval_runtime': 13.2892, 'eval_samples_per_second': 2892.653, 'eval_steps_per_second': 22.65, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [31:09<41:35, 5.78it/s]***** Running Evaluation ***** +{'loss': 0.3128, 'learning_rate': 7.406587568620507e-06, 'epoch': 3.04} +{'loss': 0.3132, 'learning_rate': 7.362316274127856e-06, 'epoch': 3.08} +{'loss': 0.3057, 'learning_rate': 7.318044979635205e-06, 'epoch': 3.12} +{'loss': 0.3148, 'learning_rate': 7.273773685142555e-06, 'epoch': 3.16} +{'loss': 0.3119, 'learning_rate': 7.2295023906499025e-06, 'epoch': 3.2} +{'loss': 0.3045, 'learning_rate': 7.185231096157252e-06, 'epoch': 3.25} +{'loss': 0.322, 'learning_rate': 7.140959801664601e-06, 'epoch': 3.29} +{'loss': 0.3008, 'learning_rate': 7.09668850717195e-06, 'epoch': 3.33} +{'loss': 0.3063, 'learning_rate': 7.052859925624226e-06, 'epoch': 3.37} +{'loss': 0.3128, 'learning_rate': 7.008588631131576e-06, 'epoch': 3.41} +{'loss': 0.3269, 'learning_rate': 6.9643173366389235e-06, 'epoch': 3.45} +{'loss': 0.3234, 'learning_rate': 6.920046042146273e-06, 'epoch': 3.5} +{'loss': 0.3038, 'learning_rate': 6.875774747653622e-06, 'epoch': 3.54} +{'loss': 0.3068, 'learning_rate': 6.831503453160971e-06, 'epoch': 3.58} +{'loss': 0.3085, 'learning_rate': 6.78723215866832e-06, 'epoch': 3.62} +{'loss': 0.3202, 'learning_rate': 6.7429608641756695e-06, 'epoch': 3.66} +{'loss': 0.3241, 'learning_rate': 6.698689569683018e-06, 'epoch': 3.7} +{'loss': 0.3147, 'learning_rate': 6.654418275190368e-06, 'epoch': 3.75} +{'loss': 0.3181, 'learning_rate': 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0.3047, 'learning_rate': 5.636621214804321e-06, 'epoch': 4.7} +{'loss': 0.3024, 'learning_rate': 5.5923499203116705e-06, 'epoch': 4.74} +{'loss': 0.2897, 'learning_rate': 5.548078625819019e-06, 'epoch': 4.79} +{'loss': 0.3035, 'learning_rate': 5.503807331326369e-06, 'epoch': 4.83} +{'loss': 0.2991, 'learning_rate': 5.459536036833717e-06, 'epoch': 4.87} +{'loss': 0.304, 'learning_rate': 5.415264742341066e-06, 'epoch': 4.91} +{'loss': 0.2935, 'learning_rate': 5.370993447848416e-06, 'epoch': 4.95} +{'loss': 0.2995, 'learning_rate': 5.326722153355764e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 12015/24030 [39:14<36:36, 5.47iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-12015/config.json +{'eval_loss': 0.3432164788246155, 'eval_accuracy': 0.8720636820061913, 'eval_f1': 0.6723125235964373, 'eval_matthews_correlation': 0.39018747626110445, 'eval_precision': 0.7756078442750192, 'eval_recall': 0.6381004476047214, 'eval_runtime': 13.2643, 'eval_samples_per_second': 2898.075, 'eval_steps_per_second': 22.692, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [46:52<27:51, 5.75it/s]***** Running Evaluation ***** +{'loss': 0.2773, 'learning_rate': 5.282450858863114e-06, 'epoch': 5.04} +{'loss': 0.2862, 'learning_rate': 5.238179564370463e-06, 'epoch': 5.08} +{'loss': 0.2759, 'learning_rate': 5.193908269877812e-06, 'epoch': 5.12} +{'loss': 0.2765, 'learning_rate': 5.149636975385161e-06, 'epoch': 5.16} +{'loss': 0.2786, 'learning_rate': 5.1053656808925104e-06, 'epoch': 5.2} +{'loss': 0.2773, 'learning_rate': 5.061094386399858e-06, 'epoch': 5.24} +{'loss': 0.2725, 'learning_rate': 5.016823091907208e-06, 'epoch': 5.29} +{'loss': 0.2721, 'learning_rate': 4.972551797414557e-06, 'epoch': 5.33} +{'loss': 0.2845, 'learning_rate': 4.928280502921906e-06, 'epoch': 5.37} +{'loss': 0.2849, 'learning_rate': 4.884009208429255e-06, 'epoch': 5.41} +{'loss': 0.2858, 'learning_rate': 4.839737913936604e-06, 'epoch': 5.45} +{'loss': 0.2841, 'learning_rate': 4.795466619443953e-06, 'epoch': 5.49} +{'loss': 0.28, 'learning_rate': 4.751638037896229e-06, 'epoch': 5.53} +{'loss': 0.2808, 'learning_rate': 4.7073667434035775e-06, 'epoch': 5.58} +{'loss': 0.2692, 'learning_rate': 4.663095448910926e-06, 'epoch': 5.62} +{'loss': 0.2889, 'learning_rate': 4.618824154418276e-06, 'epoch': 5.66} +{'loss': 0.2861, 'learning_rate': 4.5745528599256245e-06, 'epoch': 5.7} +{'loss': 0.2748, 'learning_rate': 4.530281565432973e-06, 'epoch': 5.74} +{'loss': 0.2808, 'learning_rate': 4.486010270940323e-06, 'epoch': 5.78} +{'loss': 0.2743, 'learning_rate': 4.4417389764476714e-06, 'epoch': 5.83} +{'loss': 0.2864, 'learning_rate': 4.39746768195502e-06, 'epoch': 5.87} +{'loss': 0.2796, 'learning_rate': 4.35319638746237e-06, 'epoch': 5.91} +{'loss': 0.2801, 'learning_rate': 4.308925092969719e-06, 'epoch': 5.95} +{'loss': 0.2828, 'learning_rate': 4.264653798477068e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [47:05<27:51, 5.75iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3546922206878662, 'eval_accuracy': 0.863895320100934, 'eval_f1': 0.6808294549799458, 'eval_matthews_correlation': 0.380972560528273, 'eval_precision': 0.7354100952748983, 'eval_recall': 0.6541353735339838, 'eval_runtime': 13.2922, 'eval_samples_per_second': 2891.994, 'eval_steps_per_second': 22.645, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [54:42<20:49, 5.77it/s]***** Running Evaluation ***** +{'loss': 0.2667, 'learning_rate': 4.2203825039844175e-06, 'epoch': 6.03} +{'loss': 0.2631, 'learning_rate': 4.176111209491766e-06, 'epoch': 6.08} +{'loss': 0.2535, 'learning_rate': 4.131839914999115e-06, 'epoch': 6.12} +{'loss': 0.263, 'learning_rate': 4.0875686205064644e-06, 'epoch': 6.16} +{'loss': 0.26, 'learning_rate': 4.043297326013813e-06, 'epoch': 6.2} +{'loss': 0.2605, 'learning_rate': 3.999026031521162e-06, 'epoch': 6.24} +{'loss': 0.2622, 'learning_rate': 3.954754737028511e-06, 'epoch': 6.28} +{'loss': 0.2587, 'learning_rate': 3.91048344253586e-06, 'epoch': 6.33} +{'loss': 0.2619, 'learning_rate': 3.866212148043209e-06, 'epoch': 6.37} +{'loss': 0.2585, 'learning_rate': 3.8223835664954845e-06, 'epoch': 6.41} +{'loss': 0.2602, 'learning_rate': 3.7781122720028337e-06, 'epoch': 6.45} +{'loss': 0.2555, 'learning_rate': 3.7338409775101824e-06, 'epoch': 6.49} +{'loss': 0.2521, 'learning_rate': 3.6895696830175315e-06, 'epoch': 6.53} +{'loss': 0.2588, 'learning_rate': 3.6452983885248806e-06, 'epoch': 6.58} +{'loss': 0.2536, 'learning_rate': 3.60102709403223e-06, 'epoch': 6.62} +{'loss': 0.2681, 'learning_rate': 3.556755799539579e-06, 'epoch': 6.66} +{'loss': 0.2622, 'learning_rate': 3.512484505046928e-06, 'epoch': 6.7} +{'loss': 0.2559, 'learning_rate': 3.468213210554277e-06, 'epoch': 6.74} +{'loss': 0.2615, 'learning_rate': 3.4239419160616263e-06, 'epoch': 6.78} +{'loss': 0.2751, 'learning_rate': 3.379670621568975e-06, 'epoch': 6.82} +{'loss': 0.2549, 'learning_rate': 3.335399327076324e-06, 'epoch': 6.87} +{'loss': 0.2624, 'learning_rate': 3.2911280325836732e-06, 'epoch': 6.91} +{'loss': 0.2656, 'learning_rate': 3.246856738091022e-06, 'epoch': 6.95} +{'loss': 0.2631, 'learning_rate': 3.202585443598371e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [54:56<20:49, 5.77iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3745085895061493, 'eval_accuracy': 0.8570276527665773, 'eval_f1': 0.6814531347184493, 'eval_matthews_correlation': 0.3725151146683302, 'eval_precision': 0.7153180296992021, 'eval_recall': 0.6611192416749965, 'eval_runtime': 13.32, 'eval_samples_per_second': 2885.957, 'eval_steps_per_second': 22.598, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [1:02:34<14:03, 5.70it/s]***** Running Evaluation ***** +{'loss': 0.2391, 'learning_rate': 3.15831414910572e-06, 'epoch': 7.03} +{'loss': 0.2373, 'learning_rate': 3.1140428546130693e-06, 'epoch': 7.07} +{'loss': 0.2287, 'learning_rate': 3.069771560120418e-06, 'epoch': 7.12} +{'loss': 0.2489, 'learning_rate': 3.025500265627767e-06, 'epoch': 7.16} +{'loss': 0.2365, 'learning_rate': 2.9812289711351163e-06, 'epoch': 7.2} +{'loss': 0.2405, 'learning_rate': 2.936957676642465e-06, 'epoch': 7.24} +{'loss': 0.2363, 'learning_rate': 2.892686382149814e-06, 'epoch': 7.28} +{'loss': 0.2388, 'learning_rate': 2.8488578006020903e-06, 'epoch': 7.32} +{'loss': 0.2419, 'learning_rate': 2.804586506109439e-06, 'epoch': 7.37} +{'loss': 0.2335, 'learning_rate': 2.760315211616788e-06, 'epoch': 7.41} +{'loss': 0.2441, 'learning_rate': 2.7160439171241372e-06, 'epoch': 7.45} +{'loss': 0.2372, 'learning_rate': 2.671772622631486e-06, 'epoch': 7.49} +{'loss': 0.244, 'learning_rate': 2.627501328138835e-06, 'epoch': 7.53} +{'loss': 0.2413, 'learning_rate': 2.583230033646184e-06, 'epoch': 7.57} +{'loss': 0.2515, 'learning_rate': 2.538958739153533e-06, 'epoch': 7.62} +{'loss': 0.2434, 'learning_rate': 2.494687444660882e-06, 'epoch': 7.66} +{'loss': 0.2492, 'learning_rate': 2.450416150168231e-06, 'epoch': 7.7} +{'loss': 0.2446, 'learning_rate': 2.4061448556755803e-06, 'epoch': 7.74} +{'loss': 0.2363, 'learning_rate': 2.361873561182929e-06, 'epoch': 7.78} +{'loss': 0.2467, 'learning_rate': 2.317602266690278e-06, 'epoch': 7.82} +{'loss': 0.2407, 'learning_rate': 2.273330972197627e-06, 'epoch': 7.87} +{'loss': 0.2476, 'learning_rate': 2.2290596777049763e-06, 'epoch': 7.91} +{'loss': 0.2517, 'learning_rate': 2.1847883832123255e-06, 'epoch': 7.95} +{'loss': 0.234, 'learning_rate': 2.1405170887196746e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [1:02:47<14:03, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.3975587785243988, 'eval_accuracy': 0.8558570276527666, 'eval_f1': 0.6751176896880727, 'eval_matthews_correlation': 0.3614816682819677, 'eval_precision': 0.7119883405934548, 'eval_recall': 0.6540992727926813, 'eval_runtime': 13.3055, 'eval_samples_per_second': 2889.109, 'eval_steps_per_second': 22.622, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [1:10:24<06:53, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.2263, 'learning_rate': 2.0962457942270233e-06, 'epoch': 8.03} +{'loss': 0.2258, 'learning_rate': 2.0519744997343724e-06, 'epoch': 8.07} +{'loss': 0.2257, 'learning_rate': 2.0077032052417215e-06, 'epoch': 8.11} +{'loss': 0.224, 'learning_rate': 1.963874623693997e-06, 'epoch': 8.16} +{'loss': 0.2197, 'learning_rate': 1.919603329201346e-06, 'epoch': 8.2} +{'loss': 0.2279, 'learning_rate': 1.8753320347086951e-06, 'epoch': 8.24} +{'loss': 0.2181, 'learning_rate': 1.831060740216044e-06, 'epoch': 8.28} +{'loss': 0.2265, 'learning_rate': 1.7867894457233932e-06, 'epoch': 8.32} +{'loss': 0.2201, 'learning_rate': 1.742518151230742e-06, 'epoch': 8.36} +{'loss': 0.2265, 'learning_rate': 1.698246856738091e-06, 'epoch': 8.41} +{'loss': 0.234, 'learning_rate': 1.6539755622454401e-06, 'epoch': 8.45} +{'loss': 0.225, 'learning_rate': 1.609704267752789e-06, 'epoch': 8.49} +{'loss': 0.2259, 'learning_rate': 1.5654329732601384e-06, 'epoch': 8.53} +{'loss': 0.2192, 'learning_rate': 1.5211616787674873e-06, 'epoch': 8.57} +{'loss': 0.228, 'learning_rate': 1.4768903842748364e-06, 'epoch': 8.61} +{'loss': 0.2247, 'learning_rate': 1.4326190897821853e-06, 'epoch': 8.66} +{'loss': 0.2237, 'learning_rate': 1.3883477952895345e-06, 'epoch': 8.7} +{'loss': 0.226, 'learning_rate': 1.3440765007968834e-06, 'epoch': 8.74} +{'loss': 0.2256, 'learning_rate': 1.2998052063042325e-06, 'epoch': 8.78} +{'loss': 0.2191, 'learning_rate': 1.2555339118115814e-06, 'epoch': 8.82} +{'loss': 0.2225, 'learning_rate': 1.2112626173189305e-06, 'epoch': 8.86} +{'loss': 0.2215, 'learning_rate': 1.1669913228262794e-06, 'epoch': 8.91} +{'loss': 0.2316, 'learning_rate': 1.1227200283336286e-06, 'epoch': 8.95} +{'loss': 0.2337, 'learning_rate': 1.0784487338409775e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [1:10:37<06:53, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.4247246980667114, 'eval_accuracy': 0.8561431804583648, 'eval_f1': 0.6705892523747684, 'eval_matthews_correlation': 0.35502514293199045, 'eval_precision': 0.7124904482076844, 'eval_recall': 0.6482923740537836, 'eval_runtime': 13.2765, 'eval_samples_per_second': 2895.413, 'eval_steps_per_second': 22.672, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [1:18:15<00:00, 5.71it/s]***** Running Evaluation ***** +{'loss': 0.2118, 'learning_rate': 1.034620152293253e-06, 'epoch': 9.03} +{'loss': 0.2173, 'learning_rate': 9.903488578006022e-07, 'epoch': 9.07} +{'loss': 0.2049, 'learning_rate': 9.460775633079512e-07, 'epoch': 9.11} +{'loss': 0.2116, 'learning_rate': 9.018062688153002e-07, 'epoch': 9.16} +{'loss': 0.22, 'learning_rate': 8.575349743226492e-07, 'epoch': 9.2} +{'loss': 0.2232, 'learning_rate': 8.132636798299982e-07, 'epoch': 9.24} +{'loss': 0.2139, 'learning_rate': 7.689923853373474e-07, 'epoch': 9.28} +{'loss': 0.2047, 'learning_rate': 7.247210908446964e-07, 'epoch': 9.32} +{'loss': 0.2115, 'learning_rate': 6.804497963520454e-07, 'epoch': 9.36} +{'loss': 0.2137, 'learning_rate': 6.361785018593944e-07, 'epoch': 9.4} +{'loss': 0.2085, 'learning_rate': 5.919072073667434e-07, 'epoch': 9.45} +{'loss': 0.2141, 'learning_rate': 5.476359128740925e-07, 'epoch': 9.49} +{'loss': 0.2138, 'learning_rate': 5.033646183814416e-07, 'epoch': 9.53} +{'loss': 0.2081, 'learning_rate': 4.5909332388879056e-07, 'epoch': 9.57} +{'loss': 0.2113, 'learning_rate': 4.1482202939613953e-07, 'epoch': 9.61} +{'loss': 0.2044, 'learning_rate': 3.705507349034886e-07, 'epoch': 9.65} +{'loss': 0.2102, 'learning_rate': 3.262794404108376e-07, 'epoch': 9.7} +{'loss': 0.214, 'learning_rate': 2.820081459181867e-07, 'epoch': 9.74} +{'loss': 0.213, 'learning_rate': 2.3773685142553572e-07, 'epoch': 9.78} +{'loss': 0.2085, 'learning_rate': 1.9346555693288474e-07, 'epoch': 9.82} +{'loss': 0.2155, 'learning_rate': 1.4919426244023376e-07, 'epoch': 9.86} +{'loss': 0.2116, 'learning_rate': 1.053656808925093e-07, 'epoch': 9.9} +{'loss': 0.2194, 'learning_rate': 6.109438639985834e-08, 'epoch': 9.95} +{'loss': 0.2117, 'learning_rate': 1.6823091907207366e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [1:18:28<00:00, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.4346405565738678, 'eval_accuracy': 0.8505241799120731, 'eval_f1': 0.6714741752883098, 'eval_matthews_correlation': 0.35035619461186235, 'eval_precision': 0.6991515540059257, 'eval_recall': 0.6540905162849655, 'eval_runtime': 13.3067, 'eval_samples_per_second': 2888.836, 'eval_steps_per_second': 22.62, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-7209 (score: 0.6911239932198271). +100%|██████████| 24030/24030 [1:18:30<00:00, 5.71it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.06_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 4710.4976, 'train_samples_per_second': 652.859, 'train_steps_per_second': 5.101, 'train_loss': 0.28602660663714274, 'epoch': 10.0} +100%|██████████| 24030/24030 [1:18:30<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.99it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_011443-7lxf0tob/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_011443-7lxf0tob/files/requirements.txt 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.1 +warmup_steps: + value: 0 +weight_decay: + value: 0.01 diff --git a/VASC/len2_5120/wandb/run-20260308_023449-5f4aqujg/files/output.log b/VASC/len2_5120/wandb/run-20260308_023449-5f4aqujg/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..fff8d9b7af07ed93a70d27ced1bfcf47074569bf --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_023449-5f4aqujg/files/output.log @@ -0,0 +1,232 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['classifier.weight', 'bert.pooler.dense.weight', 'bert.pooler.dense.bias', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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+{'loss': 0.3152, 'learning_rate': 6.179099876695438e-06, 'epoch': 2.66} +{'loss': 0.3123, 'learning_rate': 6.102034525277436e-06, 'epoch': 2.7} +{'loss': 0.3219, 'learning_rate': 6.024969173859433e-06, 'epoch': 2.75} +{'loss': 0.3233, 'learning_rate': 5.947903822441431e-06, 'epoch': 2.79} +{'loss': 0.3276, 'learning_rate': 5.870838471023428e-06, 'epoch': 2.83} +{'loss': 0.3132, 'learning_rate': 5.793773119605426e-06, 'epoch': 2.87} +{'loss': 0.3195, 'learning_rate': 5.716707768187424e-06, 'epoch': 2.91} +{'loss': 0.3176, 'learning_rate': 5.639642416769421e-06, 'epoch': 2.95} +{'loss': 0.3232, 'learning_rate': 5.562577065351419e-06, 'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 7209/14418 [23:31<20:43, 5.80itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3382365107536316, 'eval_accuracy': 0.8707369735438725, 'eval_f1': 0.6957198261967793, 'eval_matthews_correlation': 0.41259415335851407, 'eval_precision': 0.7562868187187328, 'eval_recall': 0.6660580284978055, 'eval_runtime': 13.3098, 'eval_samples_per_second': 2888.174, 'eval_steps_per_second': 22.615, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [31:08<13:46, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.3042, 'learning_rate': 5.485511713933416e-06, 'epoch': 3.04} +{'loss': 0.305, 'learning_rate': 5.408446362515414e-06, 'epoch': 3.08} +{'loss': 0.2984, 'learning_rate': 5.331381011097411e-06, 'epoch': 3.12} +{'loss': 0.3062, 'learning_rate': 5.2543156596794085e-06, 'epoch': 3.16} +{'loss': 0.3011, 'learning_rate': 5.1772503082614055e-06, 'epoch': 3.2} +{'loss': 0.2941, 'learning_rate': 5.100184956843403e-06, 'epoch': 3.25} +{'loss': 0.3114, 'learning_rate': 5.023119605425402e-06, 'epoch': 3.29} +{'loss': 0.2897, 'learning_rate': 4.946054254007398e-06, 'epoch': 3.33} +{'loss': 0.2969, 'learning_rate': 4.869759556103576e-06, 'epoch': 3.37} +{'loss': 0.3045, 'learning_rate': 4.792694204685574e-06, 'epoch': 3.41} +{'loss': 0.3169, 'learning_rate': 4.7156288532675715e-06, 'epoch': 3.45} +{'loss': 0.3147, 'learning_rate': 4.6385635018495685e-06, 'epoch': 3.5} +{'loss': 0.2967, 'learning_rate': 4.561498150431566e-06, 'epoch': 3.54} +{'loss': 0.2981, 'learning_rate': 4.484432799013564e-06, 'epoch': 3.58} +{'loss': 0.299, 'learning_rate': 4.407367447595561e-06, 'epoch': 3.62} +{'loss': 0.3095, 'learning_rate': 4.330302096177559e-06, 'epoch': 3.66} +{'loss': 0.3149, 'learning_rate': 4.253236744759556e-06, 'epoch': 3.7} +{'loss': 0.3033, 'learning_rate': 4.176171393341554e-06, 'epoch': 3.75} +{'loss': 0.3066, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-12015/config.json +{'eval_loss': 0.35111451148986816, 'eval_accuracy': 0.8713352930464868, 'eval_f1': 0.6816448625254484, 'eval_matthews_correlation': 0.39755171785861615, 'eval_precision': 0.7655923250992914, 'eval_recall': 0.6487687646030913, 'eval_runtime': 13.297, 'eval_samples_per_second': 2890.959, 'eval_steps_per_second': 22.637, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [46:51<00:00, 5.79it/s]***** Running Evaluation ***** +{'loss': 0.2627, 'learning_rate': 1.7886868064118373e-06, 'epoch': 5.04} +{'loss': 0.2749, 'learning_rate': 1.7116214549938347e-06, 'epoch': 5.08} +{'loss': 0.2671, 'learning_rate': 1.6345561035758326e-06, 'epoch': 5.12} +{'loss': 0.2645, 'learning_rate': 1.55749075215783e-06, 'epoch': 5.16} +{'loss': 0.2746, 'learning_rate': 1.4804254007398274e-06, 'epoch': 5.2} +{'loss': 0.2652, 'learning_rate': 1.4033600493218249e-06, 'epoch': 5.24} +{'loss': 0.2621, 'learning_rate': 1.3262946979038225e-06, 'epoch': 5.29} +{'loss': 0.2589, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-7209 (score: 0.6957198261967793). +100%|██████████| 14418/14418 [47:05<00:00, 5.79it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 2825.8789, 'train_samples_per_second': 652.956, 'train_steps_per_second': 5.102, 'train_loss': 0.31270061992444714, 'epoch': 6.0} +100%|██████████| 14418/14418 [47:06<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.99it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_023449-5f4aqujg/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_023449-5f4aqujg/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_023449-5f4aqujg/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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+push_to_hub_organization: + value: null +push_to_hub_token: + value: +ray_scope: + value: last +remove_invalid_values: + value: false +remove_unused_columns: + value: true +repetition_penalty: + value: 1 +report_to: + value: + - wandb +resume_from_checkpoint: + value: null +return_dict: + value: true +return_dict_in_generate: + value: false +run_name: + value: hg38_len2_3072_binary_VASC_lr1e-5_wd0.01_wr0.10_ep8_seed42 +save_model: + value: false +save_on_each_node: + value: false +save_safetensors: + value: true +save_steps: + value: 100 +save_strategy: + value: epoch +save_total_limit: + value: 1 +seed: + value: 42 +sep_token_id: + value: null +skip_memory_metrics: + value: true +split_batches: + value: false +suppress_tokens: + value: null +task_specific_params: + value: null +temperature: + value: 1 +tf_legacy_loss: + value: false +tf32: + value: null +tie_encoder_decoder: + value: false +tie_word_embeddings: + value: true +tokenizer_class: + value: null +top_k: + value: 50 +top_p: + value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.1 +warmup_steps: + value: 0 +weight_decay: + value: 0.01 diff --git a/VASC/len2_5120/wandb/run-20260308_032331-04xba6r6/files/output.log b/VASC/len2_5120/wandb/run-20260308_032331-04xba6r6/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..e48204e731f8651c14ad36607ae9a2652e5ab8b2 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_032331-04xba6r6/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.weight', 'classifier.weight', 'bert.pooler.dense.bias', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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+{'loss': 0.3209, 'learning_rate': 7.412288307034276e-06, 'epoch': 2.66} +{'loss': 0.318, 'learning_rate': 7.354488179873997e-06, 'epoch': 2.7} +{'loss': 0.327, 'learning_rate': 7.296688052713716e-06, 'epoch': 2.75} +{'loss': 0.3301, 'learning_rate': 7.238887925553437e-06, 'epoch': 2.79} +{'loss': 0.3312, 'learning_rate': 7.181087798393157e-06, 'epoch': 2.83} +{'loss': 0.3192, 'learning_rate': 7.123287671232877e-06, 'epoch': 2.87} +{'loss': 0.3257, 'learning_rate': 7.065487544072598e-06, 'epoch': 2.91} +{'loss': 0.324, 'learning_rate': 7.007687416912318e-06, 'epoch': 2.95} +{'loss': 0.3281, 'learning_rate': 6.9498872897520375e-06, 'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 38%|███▊ | 7209/19224 [23:31<34:49, 5.75itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33867359161376953, 'eval_accuracy': 0.8708930568923805, 'eval_f1': 0.690432575546204, 'eval_matthews_correlation': 0.4064603276624109, 'eval_precision': 0.7591251440831249, 'eval_recall': 0.6593920946460107, 'eval_runtime': 13.3134, 'eval_samples_per_second': 2887.396, 'eval_steps_per_second': 22.609, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [31:10<27:48, 5.76it/s]***** Running Evaluation ***** +{'loss': 0.3114, 'learning_rate': 6.892087162591759e-06, 'epoch': 3.04} +{'loss': 0.3141, 'learning_rate': 6.834287035431478e-06, 'epoch': 3.08} +{'loss': 0.3053, 'learning_rate': 6.776486908271199e-06, 'epoch': 3.12} +{'loss': 0.3135, 'learning_rate': 6.718686781110919e-06, 'epoch': 3.16} +{'loss': 0.3107, 'learning_rate': 6.660886653950639e-06, 'epoch': 3.2} +{'loss': 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+{'loss': 0.2928, 'learning_rate': 5.332639731807411e-06, 'epoch': 4.16} +{'loss': 0.2843, 'learning_rate': 5.274839604647131e-06, 'epoch': 4.2} +{'loss': 0.3036, 'learning_rate': 5.21703947748685e-06, 'epoch': 4.24} +{'loss': 0.2994, 'learning_rate': 5.159239350326571e-06, 'epoch': 4.29} +{'loss': 0.2946, 'learning_rate': 5.101439223166291e-06, 'epoch': 4.33} +{'loss': 0.3038, 'learning_rate': 5.043639096006011e-06, 'epoch': 4.37} +{'loss': 0.2926, 'learning_rate': 4.985838968845732e-06, 'epoch': 4.41} +{'loss': 0.2992, 'learning_rate': 4.928038841685452e-06, 'epoch': 4.45} +{'loss': 0.291, 'learning_rate': 4.870238714525172e-06, 'epoch': 4.49} +{'loss': 0.2953, 'learning_rate': 4.812438587364893e-06, 'epoch': 4.54} +{'loss': 0.2956, 'learning_rate': 4.754638460204613e-06, 'epoch': 4.58} +{'loss': 0.304, 'learning_rate': 4.6968383330443325e-06, 'epoch': 4.62} +{'loss': 0.2882, 'learning_rate': 4.639038205884053e-06, 'epoch': 4.66} +{'loss': 0.3017, 'learning_rate': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [46:52<14:13, 5.63it/s]***** Running Evaluation ***** +{'loss': 0.2712, 'learning_rate': 4.118837061441535e-06, 'epoch': 5.04} +{'loss': 0.2793, 'learning_rate': 4.061036934281256e-06, 'epoch': 5.08} +{'loss': 0.2714, 'learning_rate': 4.003236807120976e-06, 'epoch': 5.12} +{'loss': 0.2735, 'learning_rate': 3.9454366799606964e-06, 'epoch': 5.16} +{'loss': 0.281, 'learning_rate': 3.887636552800417e-06, 'epoch': 5.2} +{'loss': 0.2703, 'learning_rate': 3.829836425640136e-06, 'epoch': 5.24} +{'loss': 0.2689, 'learning_rate': 3.772036298479857e-06, 'epoch': 5.29} +{'loss': 0.2698, 'learning_rate': 3.7142361713195775e-06, 'epoch': 5.33} +{'loss': 0.2786, 'learning_rate': 3.6564360441592974e-06, 'epoch': 5.37} +{'loss': 0.2779, 'learning_rate': 3.5986359169990178e-06, 'epoch': 5.41} +{'loss': 0.2828, 'learning_rate': 3.540835789838738e-06, 'epoch': 5.45} +{'loss': 0.2801, 'learning_rate': 3.4830356626784585e-06, 'epoch': 5.49} +{'loss': 0.2809, 'learning_rate': 3.425813536789781e-06, 'epoch': 5.53} +{'loss': 0.278, 'learning_rate': 3.3680134096295014e-06, 'epoch': 5.58} +{'loss': 0.2658, 'learning_rate': 3.3102132824692217e-06, 'epoch': 5.62} +{'loss': 0.2815, 'learning_rate': 3.252413155308942e-06, 'epoch': 5.66} +{'loss': 0.2823, 'learning_rate': 3.194613028148662e-06, 'epoch': 5.7} +{'loss': 0.2748, 'learning_rate': 3.1368129009883824e-06, 'epoch': 5.74} +{'loss': 0.2767, 'learning_rate': 3.0790127738281028e-06, 'epoch': 5.78} +{'loss': 0.2702, 'learning_rate': 3.0212126466678227e-06, 'epoch': 5.83} +{'loss': 0.2815, 'learning_rate': 2.963412519507543e-06, 'epoch': 5.87} +{'loss': 0.2748, 'learning_rate': 2.9056123923472634e-06, 'epoch': 5.91} +{'loss': 0.2798, 'learning_rate': 2.8478122651869838e-06, 'epoch': 5.95} +{'loss': 0.2806, 'learning_rate': 2.7900121380267037e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [47:06<14:13, 5.63iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3548169732093811, 'eval_accuracy': 0.8674852371166203, 'eval_f1': 0.6778005823447515, 'eval_matthews_correlation': 0.38405261721484785, 'eval_precision': 0.7498756591062419, 'eval_recall': 0.6475698086371651, 'eval_runtime': 13.275, 'eval_samples_per_second': 2895.741, 'eval_steps_per_second': 22.674, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [54:43<06:59, 5.73it/s]***** Running Evaluation ***** +{'loss': 0.265, 'learning_rate': 2.732212010866424e-06, 'epoch': 6.03} +{'loss': 0.2625, 'learning_rate': 2.6744118837061445e-06, 'epoch': 6.08} +{'loss': 0.2519, 'learning_rate': 2.616611756545865e-06, 'epoch': 6.12} +{'loss': 0.2603, 'learning_rate': 2.5588116293855848e-06, 'epoch': 6.16} +{'loss': 0.2597, 'learning_rate': 2.501011502225305e-06, 'epoch': 6.2} +{'loss': 0.2586, 'learning_rate': 2.4432113750650255e-06, 'epoch': 6.24} +{'loss': 0.2605, 'learning_rate': 2.3854112479047454e-06, 'epoch': 6.28} +{'loss': 0.2569, 'learning_rate': 2.327611120744466e-06, 'epoch': 6.33} +{'loss': 0.26, 'learning_rate': 2.269810993584186e-06, 'epoch': 6.37} +{'loss': 0.2626, 'learning_rate': 2.212588867695509e-06, 'epoch': 6.41} +{'loss': 0.2569, 'learning_rate': 2.1547887405352294e-06, 'epoch': 6.45} +{'loss': 0.2546, 'learning_rate': 2.0969886133749494e-06, 'epoch': 6.49} +{'loss': 0.2506, 'learning_rate': 2.0391884862146698e-06, 'epoch': 6.53} +{'loss': 0.2564, 'learning_rate': 1.98138835905439e-06, 'epoch': 6.58} +{'loss': 0.2502, 'learning_rate': 1.9235882318941105e-06, 'epoch': 6.62} +{'loss': 0.2619, 'learning_rate': 1.8657881047338306e-06, 'epoch': 6.66} +{'loss': 0.2584, 'learning_rate': 1.807987977573551e-06, 'epoch': 6.7} +{'loss': 0.2603, 'learning_rate': 1.7501878504132711e-06, 'epoch': 6.74} +{'loss': 0.2539, 'learning_rate': 1.692387723252991e-06, 'epoch': 6.78} +{'loss': 0.2715, 'learning_rate': 1.6345875960927117e-06, 'epoch': 6.82} +{'loss': 0.2497, 'learning_rate': 1.5767874689324316e-06, 'epoch': 6.87} +{'loss': 0.2606, 'learning_rate': 1.518987341772152e-06, 'epoch': 6.91} +{'loss': 0.2628, 'learning_rate': 1.4611872146118721e-06, 'epoch': 6.95} +{'loss': 0.2617, 'learning_rate': 1.4033870874515925e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [54:57<06:59, 5.73iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.37750527262687683, 'eval_accuracy': 0.8581982778803882, 'eval_f1': 0.6820613612181302, 'eval_matthews_correlation': 0.3747472080831707, 'eval_precision': 0.7183219805505312, 'eval_recall': 0.6608123350795949, 'eval_runtime': 13.3771, 'eval_samples_per_second': 2873.642, 'eval_steps_per_second': 22.501, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [1:02:35<00:00, 5.40it/s]***** Running Evaluation ***** +{'loss': 0.2455, 'learning_rate': 1.3455869602913126e-06, 'epoch': 7.03} +{'loss': 0.2441, 'learning_rate': 1.287786833131033e-06, 'epoch': 7.07} +{'loss': 0.2338, 'learning_rate': 1.2299867059707532e-06, 'epoch': 7.12} +{'loss': 0.2488, 'learning_rate': 1.1721865788104735e-06, 'epoch': 7.16} +{'loss': 0.2391, 'learning_rate': 1.1143864516501937e-06, 'epoch': 7.2} +{'loss': 0.2407, 'learning_rate': 1.0571643257615168e-06, 'epoch': 7.24} +{'loss': 0.2427, 'learning_rate': 9.99364198601237e-07, 'epoch': 7.28} +{'loss': 0.2416, 'learning_rate': 9.415640714409572e-07, 'epoch': 7.32} +{'loss': 0.2415, 'learning_rate': 8.837639442806775e-07, 'epoch': 7.37} +{'loss': 0.2308, 'learning_rate': 8.259638171203977e-07, 'epoch': 7.41} +{'loss': 0.241, 'learning_rate': 7.68163689960118e-07, 'epoch': 7.45} +{'loss': 0.2472, 'learning_rate': 7.103635627998383e-07, 'epoch': 7.49} +{'loss': 0.2432, 'learning_rate': 6.525634356395584e-07, 'epoch': 7.53} +{'loss': 0.2488, 'learning_rate': 5.947633084792788e-07, 'epoch': 7.57} +{'loss': 0.2525, 'learning_rate': 5.36963181318999e-07, 'epoch': 7.62} +{'loss': 0.2402, 'learning_rate': 4.791630541587192e-07, 'epoch': 7.66} +{'loss': 0.2489, 'learning_rate': 4.2136292699843943e-07, 'epoch': 7.7} +{'loss': 0.2466, 'learning_rate': 3.635627998381597e-07, 'epoch': 7.74} +{'loss': 0.2339, 'learning_rate': 3.0576267267787995e-07, 'epoch': 7.78} +{'loss': 0.2488, 'learning_rate': 2.4796254551760015e-07, 'epoch': 7.82} +{'loss': 0.243, 'learning_rate': 1.901624183573204e-07, 'epoch': 7.87} +{'loss': 0.2474, 'learning_rate': 1.3236229119704064e-07, 'epoch': 7.91} +{'loss': 0.2458, 'learning_rate': 7.456216403676089e-08, 'epoch': 7.95} +{'loss': 0.2422, 'learning_rate': 1.676203687648113e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [1:02:48<00:00, 5.4Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.39215126633644104, 'eval_accuracy': 0.8580942223147161, 'eval_f1': 0.6779031747880262, 'eval_matthews_correlation': 0.36836415913376, 'eval_precision': 0.7179732103107833, 'eval_recall': 0.6556293931039209, 'eval_runtime': 13.295, 'eval_samples_per_second': 2891.388, 'eval_steps_per_second': 22.64, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-7209 (score: 0.690432575546204). +100%|██████████| 19224/19224 [1:02:50<00:00, 5.40it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 3770.0764, 'train_samples_per_second': 652.568, 'train_steps_per_second': 5.099, 'train_loss': 0.30145156904403936, 'epoch': 8.0} +100%|██████████| 19224/19224 [1:02:50<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.95it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_032331-04xba6r6/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_032331-04xba6r6/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_032331-04xba6r6/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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8.845424700605725e-06, 'epoch': 2.04} +{'loss': 0.3328, 'learning_rate': 8.799186202432147e-06, 'epoch': 2.08} +{'loss': 0.3241, 'learning_rate': 8.752947704258567e-06, 'epoch': 2.12} +{'loss': 0.3244, 'learning_rate': 8.706709206084987e-06, 'epoch': 2.16} +{'loss': 0.3255, 'learning_rate': 8.660470707911408e-06, 'epoch': 2.21} +{'loss': 0.3266, 'learning_rate': 8.614232209737828e-06, 'epoch': 2.25} +{'loss': 0.3246, 'learning_rate': 8.567993711564248e-06, 'epoch': 2.29} +{'loss': 0.331, 'learning_rate': 8.52175521339067e-06, 'epoch': 2.33} +{'loss': 0.3285, 'learning_rate': 8.47551671521709e-06, 'epoch': 2.37} +{'loss': 0.3284, 'learning_rate': 8.429278217043511e-06, 'epoch': 2.41} +{'loss': 0.3315, 'learning_rate': 8.383039718869931e-06, 'epoch': 2.46} +{'loss': 0.3269, 'learning_rate': 8.336801220696353e-06, 'epoch': 2.5} +{'loss': 0.3278, 'learning_rate': 8.290562722522774e-06, 'epoch': 2.54} +{'loss': 0.3263, 'learning_rate': 8.244324224349194e-06, 'epoch': 2.58} +{'loss': 0.3341, 'learning_rate': 8.198085726175614e-06, 'epoch': 2.62} +{'loss': 0.32, 'learning_rate': 8.151847228002036e-06, 'epoch': 2.66} +{'loss': 0.3192, 'learning_rate': 8.105608729828456e-06, 'epoch': 2.7} +{'loss': 0.3274, 'learning_rate': 8.059370231654875e-06, 'epoch': 2.75} +{'loss': 0.3311, 'learning_rate': 8.013131733481297e-06, 'epoch': 2.79} +{'loss': 0.3331, 'learning_rate': 7.966893235307717e-06, 'epoch': 2.83} +{'loss': 0.3192, 'learning_rate': 7.920654737134139e-06, 'epoch': 2.87} +{'loss': 0.3248, 'learning_rate': 7.87441623896056e-06, 'epoch': 2.91} +{'loss': 0.3245, 'learning_rate': 7.82817774078698e-06, 'epoch': 2.95} +{'loss': 0.3303, 'learning_rate': 7.781939242613402e-06, 'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 30%|███ | 7209/24030 [23:31<48:57, 5.73itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33942896127700806, 'eval_accuracy': 0.8711271819151427, 'eval_f1': 0.6953640759646235, 'eval_matthews_correlation': 0.41291022169287667, 'eval_precision': 0.7579805142734204, 'eval_recall': 0.6652206675944541, 'eval_runtime': 13.2939, 'eval_samples_per_second': 2891.628, 'eval_steps_per_second': 22.642, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [31:10<41:18, 5.82it/s]***** Running Evaluation ***** +{'loss': 0.3098, 'learning_rate': 7.735700744439821e-06, 'epoch': 3.04} +{'loss': 0.3136, 'learning_rate': 7.689462246266241e-06, 'epoch': 3.08} +{'loss': 0.3054, 'learning_rate': 7.643223748092663e-06, 'epoch': 3.12} +{'loss': 0.3123, 'learning_rate': 7.596985249919083e-06, 'epoch': 3.16} +{'loss': 0.3113, 'learning_rate': 7.550746751745504e-06, 'epoch': 3.2} +{'loss': 0.3017, 'learning_rate': 7.504508253571925e-06, 'epoch': 3.25} +{'loss': 0.3175, 'learning_rate': 7.458269755398345e-06, 'epoch': 3.29} +{'loss': 0.3007, 'learning_rate': 7.412031257224766e-06, 'epoch': 3.33} +{'loss': 0.3023, 'learning_rate': 7.3662551440329225e-06, 'epoch': 3.37} +{'loss': 0.3128, 'learning_rate': 7.320016645859343e-06, 'epoch': 3.41} +{'loss': 0.3263, 'learning_rate': 7.273778147685764e-06, 'epoch': 3.45} +{'loss': 0.3237, 'learning_rate': 7.227539649512184e-06, 'epoch': 3.5} +{'loss': 0.3056, 'learning_rate': 7.1813011513386055e-06, 'epoch': 3.54} +{'loss': 0.3074, 'learning_rate': 7.135062653165026e-06, 'epoch': 3.58} +{'loss': 0.3078, 'learning_rate': 7.088824154991446e-06, 'epoch': 3.62} +{'loss': 0.3179, 'learning_rate': 7.042585656817868e-06, 'epoch': 3.66} +{'loss': 0.3216, 'learning_rate': 6.9963471586442876e-06, 'epoch': 3.7} +{'loss': 0.311, 'learning_rate': 6.950108660470708e-06, 'epoch': 3.75} +{'loss': 0.3179, 'learning_rate': 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0.2994, 'learning_rate': 5.8870855874601196e-06, 'epoch': 4.7} +{'loss': 0.2977, 'learning_rate': 5.840847089286541e-06, 'epoch': 4.74} +{'loss': 0.2843, 'learning_rate': 5.794608591112961e-06, 'epoch': 4.79} +{'loss': 0.2983, 'learning_rate': 5.748370092939382e-06, 'epoch': 4.83} +{'loss': 0.2955, 'learning_rate': 5.7021315947658025e-06, 'epoch': 4.87} +{'loss': 0.2991, 'learning_rate': 5.655893096592223e-06, 'epoch': 4.91} +{'loss': 0.2897, 'learning_rate': 5.609654598418643e-06, 'epoch': 4.95} +{'loss': 0.2956, 'learning_rate': 5.563416100245065e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 12015/24030 [39:13<34:55, 5.73iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/config.json +{'eval_loss': 0.3444816768169403, 'eval_accuracy': 0.8695403345386437, 'eval_f1': 0.6769146076791848, 'eval_matthews_correlation': 0.3878512380577438, 'eval_precision': 0.7594704361189578, 'eval_recall': 0.6449380757139116, 'eval_runtime': 13.2837, 'eval_samples_per_second': 2893.857, 'eval_steps_per_second': 22.659, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [46:51<27:43, 5.78it/s]***** Running Evaluation ***** +{'loss': 0.2678, 'learning_rate': 5.5171776020714855e-06, 'epoch': 5.04} +{'loss': 0.2773, 'learning_rate': 5.470939103897905e-06, 'epoch': 5.08} +{'loss': 0.2702, 'learning_rate': 5.424700605724327e-06, 'epoch': 5.12} +{'loss': 0.2677, 'learning_rate': 5.378462107550747e-06, 'epoch': 5.16} +{'loss': 0.2771, 'learning_rate': 5.332223609377168e-06, 'epoch': 5.2} +{'loss': 0.2678, 'learning_rate': 5.285985111203588e-06, 'epoch': 5.24} +{'loss': 0.2641, 'learning_rate': 5.239746613030009e-06, 'epoch': 5.29} +{'loss': 0.2686, 'learning_rate': 5.193508114856431e-06, 'epoch': 5.33} +{'loss': 0.2793, 'learning_rate': 5.147269616682851e-06, 'epoch': 5.37} +{'loss': 0.2733, 'learning_rate': 5.101031118509271e-06, 'epoch': 5.41} +{'loss': 0.2798, 'learning_rate': 5.054792620335692e-06, 'epoch': 5.45} +{'loss': 0.2722, 'learning_rate': 5.008554122162113e-06, 'epoch': 5.49} +{'loss': 0.2746, 'learning_rate': 4.9627780089702695e-06, 'epoch': 5.53} +{'loss': 0.2776, 'learning_rate': 4.916539510796689e-06, 'epoch': 5.58} +{'loss': 0.2659, 'learning_rate': 4.87030101262311e-06, 'epoch': 5.62} +{'loss': 0.2794, 'learning_rate': 4.824062514449531e-06, 'epoch': 5.66} +{'loss': 0.2782, 'learning_rate': 4.777824016275952e-06, 'epoch': 5.7} +{'loss': 0.2684, 'learning_rate': 4.731585518102372e-06, 'epoch': 5.74} +{'loss': 0.2709, 'learning_rate': 4.685347019928793e-06, 'epoch': 5.78} +{'loss': 0.2664, 'learning_rate': 4.639108521755214e-06, 'epoch': 5.83} +{'loss': 0.2823, 'learning_rate': 4.5928700235816345e-06, 'epoch': 5.87} +{'loss': 0.2739, 'learning_rate': 4.546631525408055e-06, 'epoch': 5.91} +{'loss': 0.2756, 'learning_rate': 4.500393027234476e-06, 'epoch': 5.95} +{'loss': 0.2778, 'learning_rate': 4.454154529060897e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [47:04<27:43, 5.78iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35841867327690125, 'eval_accuracy': 0.8632189589240654, 'eval_f1': 0.6838464835434064, 'eval_matthews_correlation': 0.3840155727369281, 'eval_precision': 0.7326988636368055, 'eval_recall': 0.6584321876348285, 'eval_runtime': 13.3302, 'eval_samples_per_second': 2883.753, 'eval_steps_per_second': 22.58, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [54:42<20:37, 5.83it/s]***** Running Evaluation ***** +{'loss': 0.2527, 'learning_rate': 4.407916030887317e-06, 'epoch': 6.03} +{'loss': 0.2507, 'learning_rate': 4.361677532713738e-06, 'epoch': 6.08} +{'loss': 0.2422, 'learning_rate': 4.315439034540159e-06, 'epoch': 6.12} +{'loss': 0.2514, 'learning_rate': 4.269200536366579e-06, 'epoch': 6.16} +{'loss': 0.2555, 'learning_rate': 4.222962038193e-06, 'epoch': 6.2} +{'loss': 0.2478, 'learning_rate': 4.17672354001942e-06, 'epoch': 6.24} +{'loss': 0.2526, 'learning_rate': 4.130485041845841e-06, 'epoch': 6.28} +{'loss': 0.2497, 'learning_rate': 4.084246543672262e-06, 'epoch': 6.33} +{'loss': 0.2516, 'learning_rate': 4.0384704304804185e-06, 'epoch': 6.37} +{'loss': 0.2502, 'learning_rate': 3.992231932306839e-06, 'epoch': 6.41} +{'loss': 0.253, 'learning_rate': 3.945993434133259e-06, 'epoch': 6.45} +{'loss': 0.2504, 'learning_rate': 3.899754935959681e-06, 'epoch': 6.49} +{'loss': 0.2463, 'learning_rate': 3.8535164377861015e-06, 'epoch': 6.53} +{'loss': 0.2465, 'learning_rate': 3.8072779396125214e-06, 'epoch': 6.58} +{'loss': 0.2459, 'learning_rate': 3.761039441438942e-06, 'epoch': 6.62} +{'loss': 0.2612, 'learning_rate': 3.7148009432653633e-06, 'epoch': 6.66} +{'loss': 0.2534, 'learning_rate': 3.668562445091784e-06, 'epoch': 6.7} +{'loss': 0.2456, 'learning_rate': 3.6223239469182043e-06, 'epoch': 6.74} +{'loss': 0.2471, 'learning_rate': 3.576085448744625e-06, 'epoch': 6.78} +{'loss': 0.2647, 'learning_rate': 3.529846950571046e-06, 'epoch': 6.82} +{'loss': 0.2446, 'learning_rate': 3.483608452397466e-06, 'epoch': 6.87} +{'loss': 0.2537, 'learning_rate': 3.437369954223887e-06, 'epoch': 6.91} +{'loss': 0.2488, 'learning_rate': 3.3911314560503076e-06, 'epoch': 6.95} +{'loss': 0.2463, 'learning_rate': 3.3448929578767288e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [54:55<20:37, 5.83iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.38773176074028015, 'eval_accuracy': 0.8542181524934315, 'eval_f1': 0.6798091917316378, 'eval_matthews_correlation': 0.3671298445248152, 'eval_precision': 0.7085156958891463, 'eval_recall': 0.6615997325358072, 'eval_runtime': 13.296, 'eval_samples_per_second': 2891.175, 'eval_steps_per_second': 22.638, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [1:02:33<13:47, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.2273, 'learning_rate': 3.298654459703149e-06, 'epoch': 7.03} +{'loss': 0.2286, 'learning_rate': 3.25241596152957e-06, 'epoch': 7.07} +{'loss': 0.2216, 'learning_rate': 3.2061774633559906e-06, 'epoch': 7.12} +{'loss': 0.2366, 'learning_rate': 3.1599389651824113e-06, 'epoch': 7.16} +{'loss': 0.2222, 'learning_rate': 3.1141628519905676e-06, 'epoch': 7.2} +{'loss': 0.2271, 'learning_rate': 3.0679243538169883e-06, 'epoch': 7.24} +{'loss': 0.2263, 'learning_rate': 3.021685855643409e-06, 'epoch': 7.28} +{'loss': 0.2298, 'learning_rate': 2.9754473574698293e-06, 'epoch': 7.32} +{'loss': 0.2251, 'learning_rate': 2.9292088592962505e-06, 'epoch': 7.37} +{'loss': 0.2126, 'learning_rate': 2.8829703611226713e-06, 'epoch': 7.41} +{'loss': 0.2316, 'learning_rate': 2.8367318629490916e-06, 'epoch': 7.45} +{'loss': 0.2296, 'learning_rate': 2.7904933647755123e-06, 'epoch': 7.49} +{'loss': 0.2333, 'learning_rate': 2.744254866601933e-06, 'epoch': 7.53} +{'loss': 0.2316, 'learning_rate': 2.698016368428354e-06, 'epoch': 7.57} +{'loss': 0.2418, 'learning_rate': 2.651777870254774e-06, 'epoch': 7.62} +{'loss': 0.2285, 'learning_rate': 2.605539372081195e-06, 'epoch': 7.66} +{'loss': 0.2389, 'learning_rate': 2.559300873907616e-06, 'epoch': 7.7} +{'loss': 0.2286, 'learning_rate': 2.513062375734036e-06, 'epoch': 7.74} +{'loss': 0.2246, 'learning_rate': 2.466823877560457e-06, 'epoch': 7.78} +{'loss': 0.235, 'learning_rate': 2.420585379386878e-06, 'epoch': 7.82} +{'loss': 0.2245, 'learning_rate': 2.374346881213298e-06, 'epoch': 7.87} +{'loss': 0.2342, 'learning_rate': 2.3281083830397193e-06, 'epoch': 7.91} +{'loss': 0.2323, 'learning_rate': 2.2818698848661396e-06, 'epoch': 7.95} +{'loss': 0.2245, 'learning_rate': 2.2356313866925604e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [1:02:46<13:47, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.4040641784667969, 'eval_accuracy': 0.8554408053900783, 'eval_f1': 0.6691288286826669, 'eval_matthews_correlation': 0.3519564378463615, 'eval_precision': 0.7105307235245361, 'eval_recall': 0.6470965045715323, 'eval_runtime': 13.2759, 'eval_samples_per_second': 2895.541, 'eval_steps_per_second': 22.673, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [1:10:23<06:53, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.2112, 'learning_rate': 2.189392888518981e-06, 'epoch': 8.03} +{'loss': 0.2134, 'learning_rate': 2.1436167753271373e-06, 'epoch': 8.07} +{'loss': 0.2131, 'learning_rate': 2.0973782771535585e-06, 'epoch': 8.11} +{'loss': 0.2159, 'learning_rate': 2.051139778979979e-06, 'epoch': 8.16} +{'loss': 0.2045, 'learning_rate': 2.0049012808063996e-06, 'epoch': 8.2} +{'loss': 0.214, 'learning_rate': 1.9586627826328203e-06, 'epoch': 8.24} +{'loss': 0.2029, 'learning_rate': 1.912424284459241e-06, 'epoch': 8.28} +{'loss': 0.2107, 'learning_rate': 1.8661857862856616e-06, 'epoch': 8.32} +{'loss': 0.2014, 'learning_rate': 1.8199472881120823e-06, 'epoch': 8.36} +{'loss': 0.2142, 'learning_rate': 1.773708789938503e-06, 'epoch': 8.41} +{'loss': 0.2175, 'learning_rate': 1.7274702917649236e-06, 'epoch': 8.45} +{'loss': 0.2064, 'learning_rate': 1.6812317935913443e-06, 'epoch': 8.49} +{'loss': 0.2138, 'learning_rate': 1.634993295417765e-06, 'epoch': 8.53} +{'loss': 0.208, 'learning_rate': 1.5887547972441856e-06, 'epoch': 8.57} +{'loss': 0.2085, 'learning_rate': 1.5425162990706063e-06, 'epoch': 8.61} +{'loss': 0.2088, 'learning_rate': 1.4962778008970269e-06, 'epoch': 8.66} +{'loss': 0.2042, 'learning_rate': 1.4500393027234478e-06, 'epoch': 8.7} +{'loss': 0.2103, 'learning_rate': 1.4038008045498683e-06, 'epoch': 8.74} +{'loss': 0.2109, 'learning_rate': 1.357562306376289e-06, 'epoch': 8.78} +{'loss': 0.207, 'learning_rate': 1.3113238082027096e-06, 'epoch': 8.82} +{'loss': 0.2044, 'learning_rate': 1.2650853100291306e-06, 'epoch': 8.86} +{'loss': 0.2105, 'learning_rate': 1.218846811855551e-06, 'epoch': 8.91} +{'loss': 0.2127, 'learning_rate': 1.1730706986637075e-06, 'epoch': 8.95} +{'loss': 0.2193, 'learning_rate': 1.126832200490128e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [1:10:36<06:53, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.4291970431804657, 'eval_accuracy': 0.8530735412710387, 'eval_f1': 0.6648180661734737, 'eval_matthews_correlation': 0.342552358504452, 'eval_precision': 0.7040269824937243, 'eval_recall': 0.6437825978735091, 'eval_runtime': 13.2936, 'eval_samples_per_second': 2891.682, 'eval_steps_per_second': 22.642, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [1:18:14<00:00, 5.82it/s]***** Running Evaluation ***** +{'loss': 0.1996, 'learning_rate': 1.0805937023165488e-06, 'epoch': 9.03} +{'loss': 0.1935, 'learning_rate': 1.0343552041429696e-06, 'epoch': 9.07} +{'loss': 0.1925, 'learning_rate': 9.881167059693903e-07, 'epoch': 9.11} +{'loss': 0.1998, 'learning_rate': 9.418782077958109e-07, 'epoch': 9.16} +{'loss': 0.1943, 'learning_rate': 8.956397096222315e-07, 'epoch': 9.2} +{'loss': 0.2014, 'learning_rate': 8.494012114486522e-07, 'epoch': 9.24} +{'loss': 0.2023, 'learning_rate': 8.031627132750728e-07, 'epoch': 9.28} +{'loss': 0.1902, 'learning_rate': 7.569242151014936e-07, 'epoch': 9.32} +{'loss': 0.1941, 'learning_rate': 7.106857169279142e-07, 'epoch': 9.36} +{'loss': 0.2025, 'learning_rate': 6.64447218754335e-07, 'epoch': 9.4} +{'loss': 0.1931, 'learning_rate': 6.182087205807556e-07, 'epoch': 9.45} +{'loss': 0.192, 'learning_rate': 5.719702224071762e-07, 'epoch': 9.49} +{'loss': 0.1961, 'learning_rate': 5.25731724233597e-07, 'epoch': 9.53} +{'loss': 0.1928, 'learning_rate': 4.794932260600176e-07, 'epoch': 9.57} +{'loss': 0.1975, 'learning_rate': 4.3325472788643834e-07, 'epoch': 9.61} +{'loss': 0.1938, 'learning_rate': 3.870162297128589e-07, 'epoch': 9.65} +{'loss': 0.1914, 'learning_rate': 3.407777315392796e-07, 'epoch': 9.7} +{'loss': 0.2027, 'learning_rate': 2.945392333657003e-07, 'epoch': 9.74} +{'loss': 0.193, 'learning_rate': 2.48300735192121e-07, 'epoch': 9.78} +{'loss': 0.1947, 'learning_rate': 2.0206223701854164e-07, 'epoch': 9.82} +{'loss': 0.1967, 'learning_rate': 1.5582373884496233e-07, 'epoch': 9.86} +{'loss': 0.1958, 'learning_rate': 1.1004762565311879e-07, 'epoch': 9.9} +{'loss': 0.2031, 'learning_rate': 6.380912747953947e-08, 'epoch': 9.95} +{'loss': 0.1917, 'learning_rate': 1.7570629305960146e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [1:18:27<00:00, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.4470909833908081, 'eval_accuracy': 0.8495096381467704, 'eval_f1': 0.6701072085185786, 'eval_matthews_correlation': 0.34725383606996946, 'eval_precision': 0.6967660765895511, 'eval_recall': 0.6532088619585159, 'eval_runtime': 13.3162, 'eval_samples_per_second': 2886.795, 'eval_steps_per_second': 22.604, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-7209 (score: 0.6953640759646235). +100%|██████████| 24030/24030 [1:18:29<00:00, 5.82it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.01_wr0.10_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 4709.3175, 'train_samples_per_second': 653.022, 'train_steps_per_second': 5.103, 'train_loss': 0.27989991059464014, 'epoch': 10.0} +100%|██████████| 24030/24030 [1:18:29<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.98it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_042802-k45d89yt/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_042802-k45d89yt/files/requirements.txt 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.03 +warmup_steps: + value: 0 +weight_decay: + value: 0.05 diff --git a/VASC/len2_5120/wandb/run-20260308_054809-euenapke/files/output.log b/VASC/len2_5120/wandb/run-20260308_054809-euenapke/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..7b4c1b03c4cb1d35602a0178e97652307694d1a4 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_054809-euenapke/files/output.log @@ -0,0 +1,232 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['classifier.bias', 'classifier.weight', 'bert.pooler.dense.weight', 'bert.pooler.dense.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [23:17<20:57, 5.73it/s]***** Running Evaluation ***** +{'loss': 0.3203, 'learning_rate': 6.80586342509832e-06, 'epoch': 2.04} +{'loss': 0.3297, 'learning_rate': 6.7343582409724705e-06, 'epoch': 2.08} +{'loss': 0.3221, 'learning_rate': 6.662853056846622e-06, 'epoch': 2.12} +{'loss': 0.3212, 'learning_rate': 6.5913478727207724e-06, 'epoch': 2.16} +{'loss': 0.322, 'learning_rate': 6.519842688594924e-06, 'epoch': 2.21} +{'loss': 0.3252, 'learning_rate': 6.448337504469074e-06, 'epoch': 2.25} +{'loss': 0.3227, 'learning_rate': 6.376832320343226e-06, 'epoch': 2.29} +{'loss': 0.3297, 'learning_rate': 6.305327136217376e-06, 'epoch': 2.33} +{'loss': 0.3254, 'learning_rate': 6.2338219520915265e-06, 'epoch': 2.37} +{'loss': 0.3238, 'learning_rate': 6.162316767965678e-06, 'epoch': 2.41} +{'loss': 0.325, 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'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 7209/14418 [23:30<20:57, 5.73itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.34060487151145935, 'eval_accuracy': 0.8697224317785698, 'eval_f1': 0.6923882234559753, 'eval_matthews_correlation': 0.4064758717278056, 'eval_precision': 0.7535644107587868, 'eval_recall': 0.6629000633433274, 'eval_runtime': 13.3376, 'eval_samples_per_second': 2882.155, 'eval_steps_per_second': 22.568, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [31:08<13:55, 5.75it/s]***** Running Evaluation ***** +{'loss': 0.3095, 'learning_rate': 5.0897390060779406e-06, 'epoch': 3.04} +{'loss': 0.3113, 'learning_rate': 5.018233821952092e-06, 'epoch': 3.08} +{'loss': 0.3048, 'learning_rate': 4.946728637826243e-06, 'epoch': 3.12} +{'loss': 0.3124, 'learning_rate': 4.8752234537003935e-06, 'epoch': 3.16} +{'loss': 0.309, 'learning_rate': 4.8037182695745445e-06, 'epoch': 3.2} +{'loss': 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'eval_recall': 0.6422648843795804, 'eval_runtime': 13.2959, 'eval_samples_per_second': 2891.191, 'eval_steps_per_second': 22.639, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-9612/special_tokens_map.json + 83%|████████▎ | 12015/14418 [38:59<06:56, 5.77it/s]***** Running Evaluation ***** +{'loss': 0.2995, 'learning_rate': 3.375044690740079e-06, 'epoch': 4.04} +{'loss': 0.296, 'learning_rate': 3.30353950661423e-06, 'epoch': 4.08} +{'loss': 0.3034, 'learning_rate': 3.2320343224883805e-06, 'epoch': 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'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [47:03<00:00, 5.76iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3542402684688568, 'eval_accuracy': 0.8649618896490726, 'eval_f1': 0.6744106098012982, 'eval_matthews_correlation': 0.3746117891527172, 'eval_precision': 0.7407447915671816, 'eval_recall': 0.6457290017144967, 'eval_runtime': 13.303, 'eval_samples_per_second': 2889.649, 'eval_steps_per_second': 22.626, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-7209 (score: 0.6923882234559753). +100%|██████████| 14418/14418 [47:05<00:00, 5.76it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 2825.3578, 'train_samples_per_second': 653.076, 'train_steps_per_second': 5.103, 'train_loss': 0.3168913098045685, 'epoch': 6.0} +100%|██████████| 14418/14418 [47:05<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 14.01it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_054809-euenapke/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_054809-euenapke/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_054809-euenapke/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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b/VASC/len2_5120/wandb/run-20260308_063652-7l50puhg/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.weight', 'bert.pooler.dense.weight', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33802223205566406, 'eval_accuracy': 0.8706329179782003, 'eval_f1': 0.6907508794608819, 'eval_matthews_correlation': 0.40629024585925605, 'eval_precision': 0.7578900255071478, 'eval_recall': 0.6600214699616209, 'eval_runtime': 13.2961, 'eval_samples_per_second': 2891.156, 'eval_steps_per_second': 22.638, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [31:07<27:35, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.3086, 'learning_rate': 6.394594304713896e-06, 'epoch': 3.04} +{'loss': 0.3094, 'learning_rate': 6.340966375288251e-06, 'epoch': 3.08} +{'loss': 0.3017, 'learning_rate': 6.287338445862605e-06, 'epoch': 3.12} +{'loss': 0.3103, 'learning_rate': 6.23371051643696e-06, 'epoch': 3.16} +{'loss': 0.3049, 'learning_rate': 6.1800825870113155e-06, 'epoch': 3.2} +{'loss': 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'epoch': 3.79} +{'loss': 0.3119, 'learning_rate': 5.3761999249209e-06, 'epoch': 3.83} +{'loss': 0.3125, 'learning_rate': 5.323108274789511e-06, 'epoch': 3.87} +{'loss': 0.3036, 'learning_rate': 5.269480345363865e-06, 'epoch': 3.91} +{'loss': 0.3066, 'learning_rate': 5.2158524159382205e-06, 'epoch': 3.95} +{'loss': 0.3111, 'learning_rate': 5.162224486512576e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 9612/19224 [31:21<27:35, 5.81itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-9612/config.json +{'eval_loss': 0.3400851786136627, 'eval_accuracy': 0.8669649592882599, 'eval_f1': 0.6863452393921506, 'eval_matthews_correlation': 0.3936226420027935, 'eval_precision': 0.7450383260569506, 'eval_recall': 0.6580760720072512, 'eval_runtime': 13.2957, 'eval_samples_per_second': 2891.226, 'eval_steps_per_second': 22.639, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [38:58<20:43, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.2959, 'learning_rate': 5.108596557086931e-06, 'epoch': 4.04} +{'loss': 0.2903, 'learning_rate': 5.054968627661287e-06, 'epoch': 4.08} +{'loss': 0.2992, 'learning_rate': 5.001340698235642e-06, 'epoch': 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0.34993991255760193, 'eval_accuracy': 0.8690200567102833, 'eval_f1': 0.6695583278391447, 'eval_matthews_correlation': 0.3785592370893873, 'eval_precision': 0.7607933133097118, 'eval_recall': 0.6373761218865215, 'eval_runtime': 13.3577, 'eval_samples_per_second': 2877.807, 'eval_steps_per_second': 22.534, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [46:49<14:09, 5.66it/s]***** Running Evaluation ***** +{'loss': 0.2683, 'learning_rate': 3.821526250871454e-06, 'epoch': 5.04} +{'loss': 0.2787, 'learning_rate': 3.7678983214458092e-06, 'epoch': 5.08} +{'loss': 0.2689, 'learning_rate': 3.7142703920201644e-06, 'epoch': 5.12} +{'loss': 0.2662, 'learning_rate': 3.6606424625945195e-06, 'epoch': 5.16} +{'loss': 0.278, 'learning_rate': 3.6070145331688743e-06, 'epoch': 5.2} +{'loss': 0.2704, 'learning_rate': 3.55338660374323e-06, 'epoch': 5.24} +{'loss': 0.2666, 'learning_rate': 3.499758674317585e-06, 'epoch': 5.29} +{'loss': 0.2651, 'learning_rate': 3.44613074489194e-06, 'epoch': 5.33} +{'loss': 0.2766, 'learning_rate': 3.3925028154662953e-06, 'epoch': 5.37} +{'loss': 0.2716, 'learning_rate': 3.33887488604065e-06, 'epoch': 5.41} +{'loss': 0.2817, 'learning_rate': 3.285246956615005e-06, 'epoch': 5.45} +{'loss': 0.2739, 'learning_rate': 3.2316190271893603e-06, 'epoch': 5.49} +{'loss': 0.2727, 'learning_rate': 3.178527377057972e-06, 'epoch': 5.53} +{'loss': 0.2754, 'learning_rate': 3.1248994476323276e-06, 'epoch': 5.58} +{'loss': 0.2615, 'learning_rate': 3.071271518206682e-06, 'epoch': 5.62} +{'loss': 0.2805, 'learning_rate': 3.0176435887810375e-06, 'epoch': 5.66} +{'loss': 0.2788, 'learning_rate': 2.9640156593553926e-06, 'epoch': 5.7} +{'loss': 0.2697, 'learning_rate': 2.910387729929748e-06, 'epoch': 5.74} +{'loss': 0.2723, 'learning_rate': 2.8567598005041025e-06, 'epoch': 5.78} +{'loss': 0.2684, 'learning_rate': 2.8031318710784577e-06, 'epoch': 5.83} +{'loss': 0.2795, 'learning_rate': 2.749503941652813e-06, 'epoch': 5.87} +{'loss': 0.2696, 'learning_rate': 2.6958760122271684e-06, 'epoch': 5.91} +{'loss': 0.2707, 'learning_rate': 2.6422480828015236e-06, 'epoch': 5.95} +{'loss': 0.2752, 'learning_rate': 2.5886201533758783e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [47:03<14:09, 5.66iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3621392250061035, 'eval_accuracy': 0.8646497229520564, 'eval_f1': 0.6739082642049807, 'eval_matthews_correlation': 0.3733568949430185, 'eval_precision': 0.7396707198878882, 'eval_recall': 0.6454030044499154, 'eval_runtime': 13.3689, 'eval_samples_per_second': 2875.407, 'eval_steps_per_second': 22.515, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [54:40<06:58, 5.75it/s]***** Running Evaluation ***** +{'loss': 0.2612, 'learning_rate': 2.5349922239502335e-06, 'epoch': 6.03} +{'loss': 0.2569, 'learning_rate': 2.4813642945245886e-06, 'epoch': 6.08} +{'loss': 0.2483, 'learning_rate': 2.4277363650989438e-06, 'epoch': 6.12} +{'loss': 0.2589, 'learning_rate': 2.374108435673299e-06, 'epoch': 6.16} +{'loss': 0.2577, 'learning_rate': 2.320480506247654e-06, 'epoch': 6.2} +{'loss': 0.2577, 'learning_rate': 2.266852576822009e-06, 'epoch': 6.24} +{'loss': 0.2611, 'learning_rate': 2.2132246473963644e-06, 'epoch': 6.28} +{'loss': 0.2531, 'learning_rate': 2.1595967179707195e-06, 'epoch': 6.33} +{'loss': 0.2545, 'learning_rate': 2.1059687885450743e-06, 'epoch': 6.37} +{'loss': 0.2539, 'learning_rate': 2.052877138413686e-06, 'epoch': 6.41} +{'loss': 0.2544, 'learning_rate': 1.999249208988041e-06, 'epoch': 6.45} +{'loss': 0.2537, 'learning_rate': 1.9456212795623963e-06, 'epoch': 6.49} +{'loss': 0.2492, 'learning_rate': 1.8919933501367512e-06, 'epoch': 6.53} +{'loss': 0.253, 'learning_rate': 1.8383654207111066e-06, 'epoch': 6.58} +{'loss': 0.2497, 'learning_rate': 1.7847374912854615e-06, 'epoch': 6.62} +{'loss': 0.261, 'learning_rate': 1.7311095618598167e-06, 'epoch': 6.66} +{'loss': 0.2564, 'learning_rate': 1.677481632434172e-06, 'epoch': 6.7} +{'loss': 0.253, 'learning_rate': 1.623853703008527e-06, 'epoch': 6.74} +{'loss': 0.2519, 'learning_rate': 1.5702257735828821e-06, 'epoch': 6.78} +{'loss': 0.2619, 'learning_rate': 1.516597844157237e-06, 'epoch': 6.82} +{'loss': 0.2435, 'learning_rate': 1.4629699147315922e-06, 'epoch': 6.87} +{'loss': 0.2579, 'learning_rate': 1.4093419853059476e-06, 'epoch': 6.91} +{'loss': 0.2594, 'learning_rate': 1.3557140558803025e-06, 'epoch': 6.95} +{'loss': 0.2533, 'learning_rate': 1.3020861264546577e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [54:54<06:58, 5.75iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.38136914372444153, 'eval_accuracy': 0.8557269581956765, 'eval_f1': 0.6777226547865204, 'eval_matthews_correlation': 0.3653406551977632, 'eval_precision': 0.7118519738061999, 'eval_recall': 0.6575083204823376, 'eval_runtime': 13.3189, 'eval_samples_per_second': 2886.198, 'eval_steps_per_second': 22.599, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [1:02:32<00:00, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.2405, 'learning_rate': 1.2484581970290129e-06, 'epoch': 7.03} +{'loss': 0.2425, 'learning_rate': 1.194830267603368e-06, 'epoch': 7.07} +{'loss': 0.2336, 'learning_rate': 1.141202338177723e-06, 'epoch': 7.12} +{'loss': 0.2465, 'learning_rate': 1.0875744087520781e-06, 'epoch': 7.16} +{'loss': 0.2339, 'learning_rate': 1.0339464793264333e-06, 'epoch': 7.2} +{'loss': 0.2426, 'learning_rate': 9.808548291950447e-07, 'epoch': 7.24} +{'loss': 0.241, 'learning_rate': 9.272268997693999e-07, 'epoch': 7.28} +{'loss': 0.2405, 'learning_rate': 8.735989703437551e-07, 'epoch': 7.32} +{'loss': 0.2415, 'learning_rate': 8.199710409181102e-07, 'epoch': 7.37} +{'loss': 0.2313, 'learning_rate': 7.663431114924654e-07, 'epoch': 7.41} +{'loss': 0.2453, 'learning_rate': 7.127151820668204e-07, 'epoch': 7.45} +{'loss': 0.2405, 'learning_rate': 6.590872526411756e-07, 'epoch': 7.49} +{'loss': 0.2433, 'learning_rate': 6.054593232155307e-07, 'epoch': 7.53} +{'loss': 0.2454, 'learning_rate': 5.518313937898858e-07, 'epoch': 7.57} +{'loss': 0.2529, 'learning_rate': 4.982034643642409e-07, 'epoch': 7.62} +{'loss': 0.2421, 'learning_rate': 4.4457553493859607e-07, 'epoch': 7.66} +{'loss': 0.2457, 'learning_rate': 3.9094760551295117e-07, 'epoch': 7.7} +{'loss': 0.2428, 'learning_rate': 3.3731967608730633e-07, 'epoch': 7.74} +{'loss': 0.2379, 'learning_rate': 2.8369174666166143e-07, 'epoch': 7.78} +{'loss': 0.2449, 'learning_rate': 2.3006381723601653e-07, 'epoch': 7.82} +{'loss': 0.2392, 'learning_rate': 1.7643588781037166e-07, 'epoch': 7.87} +{'loss': 0.242, 'learning_rate': 1.228079583847268e-07, 'epoch': 7.91} +{'loss': 0.2434, 'learning_rate': 6.918002895908189e-08, 'epoch': 7.95} +{'loss': 0.2331, 'learning_rate': 1.5552099533437016e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [1:02:45<00:00, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.3935122489929199, 'eval_accuracy': 0.8580942223147161, 'eval_f1': 0.6768750641688646, 'eval_matthews_correlation': 0.36683806563654203, 'eval_precision': 0.7179641495408745, 'eval_recall': 0.6543489682631548, 'eval_runtime': 13.3018, 'eval_samples_per_second': 2889.917, 'eval_steps_per_second': 22.629, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-7209 (score: 0.6907508794608819). +100%|██████████| 19224/19224 [1:02:47<00:00, 5.81it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 3767.0961, 'train_samples_per_second': 653.084, 'train_steps_per_second': 5.103, 'train_loss': 0.2977647630066064, 'epoch': 8.0} +100%|██████████| 19224/19224 [1:02:47<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.98it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_063652-7l50puhg/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_063652-7l50puhg/files/requirements.txt new 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b/VASC/len2_5120/wandb/run-20260308_074117-tmcjsfu5/files/output.log @@ -0,0 +1,368 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.weight', 'bert.pooler.dense.weight', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 10 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 24,030 + Number of trainable parameters = 88,402,178 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 10%|█ | 2403/24030 [07:36<1:03:12, 5.70it/s]***** Running Evaluation ***** +{'loss': 0.5412, 'learning_rate': 1.3869625520110958e-06, 'epoch': 0.04} +{'loss': 0.3785, 'learning_rate': 2.7739251040221917e-06, 'epoch': 0.08} +{'loss': 0.3604, 'learning_rate': 4.160887656033287e-06, 'epoch': 0.12} +{'loss': 0.355, 'learning_rate': 5.547850208044383e-06, 'epoch': 0.17} +{'loss': 0.3603, 'learning_rate': 6.93481276005548e-06, 'epoch': 0.21} +{'loss': 0.3566, 'learning_rate': 8.321775312066574e-06, 'epoch': 0.25} +{'loss': 0.3574, 'learning_rate': 9.708737864077671e-06, 'epoch': 0.29} +{'loss': 0.3475, 'learning_rate': 9.966107512119783e-06, 'epoch': 0.33} +{'loss': 0.3586, 'learning_rate': 9.923205628727102e-06, 'epoch': 0.37} +{'loss': 0.3542, 'learning_rate': 9.88030374533442e-06, 'epoch': 0.42} +{'loss': 0.3514, 'learning_rate': 9.83740186194174e-06, 'epoch': 0.46} +{'loss': 0.3548, 'learning_rate': 9.79449997854906e-06, 'epoch': 0.5} +{'loss': 0.3496, 'learning_rate': 9.751598095156379e-06, 'epoch': 0.54} +{'loss': 0.3476, 'learning_rate': 9.708696211763697e-06, 'epoch': 0.58} +{'loss': 0.3568, 'learning_rate': 9.665794328371016e-06, 'epoch': 0.62} +{'loss': 0.3432, 'learning_rate': 9.622892444978336e-06, 'epoch': 0.67} +{'loss': 0.3452, 'learning_rate': 9.579990561585655e-06, 'epoch': 0.71} +{'loss': 0.3394, 'learning_rate': 9.537088678192973e-06, 'epoch': 0.75} +{'loss': 0.3511, 'learning_rate': 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8.207130293019864e-06, 'epoch': 2.04} +{'loss': 0.3289, 'learning_rate': 8.164228409627184e-06, 'epoch': 2.08} +{'loss': 0.3213, 'learning_rate': 8.121326526234501e-06, 'epoch': 2.12} +{'loss': 0.319, 'learning_rate': 8.078424642841821e-06, 'epoch': 2.16} +{'loss': 0.3196, 'learning_rate': 8.03552275944914e-06, 'epoch': 2.21} +{'loss': 0.3223, 'learning_rate': 7.99262087605646e-06, 'epoch': 2.25} +{'loss': 0.3213, 'learning_rate': 7.949718992663778e-06, 'epoch': 2.29} +{'loss': 0.3278, 'learning_rate': 7.906817109271098e-06, 'epoch': 2.33} +{'loss': 0.3242, 'learning_rate': 7.863915225878417e-06, 'epoch': 2.37} +{'loss': 0.3238, 'learning_rate': 7.821013342485737e-06, 'epoch': 2.41} +{'loss': 0.326, 'learning_rate': 7.778111459093054e-06, 'epoch': 2.46} +{'loss': 0.3213, 'learning_rate': 7.735209575700374e-06, 'epoch': 2.5} +{'loss': 0.3231, 'learning_rate': 7.692307692307694e-06, 'epoch': 2.54} +{'loss': 0.324, 'learning_rate': 7.649405808915013e-06, 'epoch': 2.58} +{'loss': 0.3291, 'learning_rate': 7.60650392552233e-06, 'epoch': 2.62} +{'loss': 0.3157, 'learning_rate': 7.56360204212965e-06, 'epoch': 2.66} +{'loss': 0.3147, 'learning_rate': 7.520700158736968e-06, 'epoch': 2.7} +{'loss': 0.3243, 'learning_rate': 7.477798275344288e-06, 'epoch': 2.75} +{'loss': 0.3264, 'learning_rate': 7.434896391951607e-06, 'epoch': 2.79} +{'loss': 0.3282, 'learning_rate': 7.391994508558926e-06, 'epoch': 2.83} +{'loss': 0.314, 'learning_rate': 7.349092625166245e-06, 'epoch': 2.87} +{'loss': 0.3209, 'learning_rate': 7.3061907417735645e-06, 'epoch': 2.91} +{'loss': 0.321, 'learning_rate': 7.263288858380883e-06, 'epoch': 2.95} +{'loss': 0.3255, 'learning_rate': 7.220386974988203e-06, 'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 30%|███ | 7209/24030 [23:32<50:31, 5.55itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3399583697319031, 'eval_accuracy': 0.8704768346296923, 'eval_f1': 0.6933396044042176, 'eval_matthews_correlation': 0.409128092543836, 'eval_precision': 0.7561859052600988, 'eval_recall': 0.6633440722847488, 'eval_runtime': 13.5121, 'eval_samples_per_second': 2844.931, 'eval_steps_per_second': 22.276, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [31:10<41:38, 5.77it/s]***** Running Evaluation ***** +{'loss': 0.305, 'learning_rate': 7.1774850915955215e-06, 'epoch': 3.04} +{'loss': 0.3075, 'learning_rate': 7.134583208202841e-06, 'epoch': 3.08} +{'loss': 0.3008, 'learning_rate': 7.09168132481016e-06, 'epoch': 3.12} +{'loss': 0.3074, 'learning_rate': 7.048779441417479e-06, 'epoch': 3.16} +{'loss': 0.3062, 'learning_rate': 7.005877558024799e-06, 'epoch': 3.2} +{'loss': 0.2963, 'learning_rate': 6.962975674632117e-06, 'epoch': 3.25} +{'loss': 0.3116, 'learning_rate': 6.920073791239435e-06, 'epoch': 3.29} +{'loss': 0.2952, 'learning_rate': 6.877171907846755e-06, 'epoch': 3.33} +{'loss': 0.2974, 'learning_rate': 6.834699043288001e-06, 'epoch': 3.37} +{'loss': 0.306, 'learning_rate': 6.79179715989532e-06, 'epoch': 3.41} +{'loss': 0.3212, 'learning_rate': 6.74889527650264e-06, 'epoch': 3.45} +{'loss': 0.3189, 'learning_rate': 6.705993393109958e-06, 'epoch': 3.5} +{'loss': 0.3016, 'learning_rate': 6.663091509717276e-06, 'epoch': 3.54} +{'loss': 0.3012, 'learning_rate': 6.620189626324596e-06, 'epoch': 3.58} +{'loss': 0.3017, 'learning_rate': 6.5772877429319144e-06, 'epoch': 3.62} +{'loss': 0.3137, 'learning_rate': 6.534385859539234e-06, 'epoch': 3.66} +{'loss': 0.3173, 'learning_rate': 6.491483976146553e-06, 'epoch': 3.7} +{'loss': 0.3064, 'learning_rate': 6.448582092753872e-06, 'epoch': 3.75} +{'loss': 0.3118, 'learning_rate': 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+{'eval_loss': 0.35087865591049194, 'eval_accuracy': 0.8690200567102833, 'eval_f1': 0.6821184195160425, 'eval_matthews_correlation': 0.3925519908372963, 'eval_precision': 0.7547102870614182, 'eval_recall': 0.6512473909948202, 'eval_runtime': 13.5631, 'eval_samples_per_second': 2834.234, 'eval_steps_per_second': 22.193, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [46:52<27:36, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.2594, 'learning_rate': 5.119052726414691e-06, 'epoch': 5.04} +{'loss': 0.2675, 'learning_rate': 5.076150843022009e-06, 'epoch': 5.08} +{'loss': 0.262, 'learning_rate': 5.0332489596293275e-06, 'epoch': 5.12} +{'loss': 0.256, 'learning_rate': 4.990347076236647e-06, 'epoch': 5.16} +{'loss': 0.2714, 'learning_rate': 4.9474451928439666e-06, 'epoch': 5.2} +{'loss': 0.2623, 'learning_rate': 4.904543309451285e-06, 'epoch': 5.24} +{'loss': 0.2576, 'learning_rate': 4.861641426058604e-06, 'epoch': 5.29} +{'loss': 0.258, 'learning_rate': 4.8187395426659235e-06, 'epoch': 5.33} +{'loss': 0.2714, 'learning_rate': 4.775837659273242e-06, 'epoch': 5.37} +{'loss': 0.2624, 'learning_rate': 4.732935775880562e-06, 'epoch': 5.41} +{'loss': 0.272, 'learning_rate': 4.6900338924878805e-06, 'epoch': 5.45} +{'loss': 0.2688, 'learning_rate': 4.6471320090952e-06, 'epoch': 5.49} +{'loss': 0.2641, 'learning_rate': 4.604659144536446e-06, 'epoch': 5.53} +{'loss': 0.2708, 'learning_rate': 4.561757261143764e-06, 'epoch': 5.58} +{'loss': 0.2578, 'learning_rate': 4.518855377751084e-06, 'epoch': 5.62} +{'loss': 0.2727, 'learning_rate': 4.475953494358403e-06, 'epoch': 5.66} +{'loss': 0.2741, 'learning_rate': 4.433051610965722e-06, 'epoch': 5.7} +{'loss': 0.2601, 'learning_rate': 4.390149727573041e-06, 'epoch': 5.74} +{'loss': 0.2642, 'learning_rate': 4.34724784418036e-06, 'epoch': 5.78} +{'loss': 0.2603, 'learning_rate': 4.304345960787679e-06, 'epoch': 5.83} +{'loss': 0.2735, 'learning_rate': 4.261444077394998e-06, 'epoch': 5.87} +{'loss': 0.2627, 'learning_rate': 4.2185421940023165e-06, 'epoch': 5.91} +{'loss': 0.2636, 'learning_rate': 4.175640310609636e-06, 'epoch': 5.95} +{'loss': 0.2675, 'learning_rate': 4.132738427216955e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [47:06<27:36, 5.80iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.36878931522369385, 'eval_accuracy': 0.8594729585598709, 'eval_f1': 0.6840685423151865, 'eval_matthews_correlation': 0.3792733016598204, 'eval_precision': 0.7217105136234988, 'eval_recall': 0.6622027695044486, 'eval_runtime': 13.3341, 'eval_samples_per_second': 2882.915, 'eval_steps_per_second': 22.574, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [54:44<20:47, 5.78it/s]***** Running Evaluation ***** +{'loss': 0.2463, 'learning_rate': 4.089836543824274e-06, 'epoch': 6.03} +{'loss': 0.2456, 'learning_rate': 4.046934660431593e-06, 'epoch': 6.08} +{'loss': 0.2361, 'learning_rate': 4.004032777038913e-06, 'epoch': 6.12} +{'loss': 0.2426, 'learning_rate': 3.961130893646231e-06, 'epoch': 6.16} +{'loss': 0.2454, 'learning_rate': 3.91822901025355e-06, 'epoch': 6.2} +{'loss': 0.2403, 'learning_rate': 3.8753271268608696e-06, 'epoch': 6.24} +{'loss': 0.2412, 'learning_rate': 3.832425243468188e-06, 'epoch': 6.28} +{'loss': 0.244, 'learning_rate': 3.789523360075508e-06, 'epoch': 6.33} +{'loss': 0.2409, 'learning_rate': 3.7470504955167534e-06, 'epoch': 6.37} +{'loss': 0.2399, 'learning_rate': 3.7041486121240725e-06, 'epoch': 6.41} +{'loss': 0.2428, 'learning_rate': 3.661246728731392e-06, 'epoch': 6.45} +{'loss': 0.2437, 'learning_rate': 3.6183448453387104e-06, 'epoch': 6.49} +{'loss': 0.2381, 'learning_rate': 3.5754429619460295e-06, 'epoch': 6.53} +{'loss': 0.2422, 'learning_rate': 3.5325410785533486e-06, 'epoch': 6.58} +{'loss': 0.2381, 'learning_rate': 3.4896391951606677e-06, 'epoch': 6.62} +{'loss': 0.2505, 'learning_rate': 3.446737311767987e-06, 'epoch': 6.66} +{'loss': 0.242, 'learning_rate': 3.403835428375306e-06, 'epoch': 6.7} +{'loss': 0.2409, 'learning_rate': 3.360933544982625e-06, 'epoch': 6.74} +{'loss': 0.2422, 'learning_rate': 3.318031661589944e-06, 'epoch': 6.78} +{'loss': 0.2582, 'learning_rate': 3.275129778197263e-06, 'epoch': 6.82} +{'loss': 0.2325, 'learning_rate': 3.232227894804582e-06, 'epoch': 6.87} +{'loss': 0.2399, 'learning_rate': 3.1893260114119012e-06, 'epoch': 6.91} +{'loss': 0.2436, 'learning_rate': 3.1464241280192204e-06, 'epoch': 6.95} +{'loss': 0.2415, 'learning_rate': 3.1035222446265395e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [54:57<20:47, 5.78iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.4002498388290405, 'eval_accuracy': 0.8497957909523686, 'eval_f1': 0.6828777774691686, 'eval_matthews_correlation': 0.3689878664143939, 'eval_precision': 0.7001130200953625, 'eval_recall': 0.6700939367865273, 'eval_runtime': 13.3317, 'eval_samples_per_second': 2883.431, 'eval_steps_per_second': 22.578, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [1:02:35<13:54, 5.76it/s]***** Running Evaluation ***** +{'loss': 0.2238, 'learning_rate': 3.0606203612338586e-06, 'epoch': 7.03} +{'loss': 0.2161, 'learning_rate': 3.0177184778411773e-06, 'epoch': 7.07} +{'loss': 0.2163, 'learning_rate': 2.9748165944484965e-06, 'epoch': 7.12} +{'loss': 0.2284, 'learning_rate': 2.9319147110558156e-06, 'epoch': 7.16} +{'loss': 0.2145, 'learning_rate': 2.8894418464970616e-06, 'epoch': 7.2} +{'loss': 0.2188, 'learning_rate': 2.8465399631043807e-06, 'epoch': 7.24} +{'loss': 0.2154, 'learning_rate': 2.8036380797117e-06, 'epoch': 7.28} +{'loss': 0.2194, 'learning_rate': 2.760736196319019e-06, 'epoch': 7.32} +{'loss': 0.2227, 'learning_rate': 2.717834312926338e-06, 'epoch': 7.37} +{'loss': 0.2067, 'learning_rate': 2.6749324295336564e-06, 'epoch': 7.41} +{'loss': 0.2174, 'learning_rate': 2.6320305461409755e-06, 'epoch': 7.45} +{'loss': 0.2196, 'learning_rate': 2.5891286627482946e-06, 'epoch': 7.49} +{'loss': 0.2283, 'learning_rate': 2.5462267793556138e-06, 'epoch': 7.53} +{'loss': 0.2257, 'learning_rate': 2.503324895962933e-06, 'epoch': 7.57} +{'loss': 0.2332, 'learning_rate': 2.460423012570252e-06, 'epoch': 7.62} +{'loss': 0.2235, 'learning_rate': 2.417521129177571e-06, 'epoch': 7.66} +{'loss': 0.2286, 'learning_rate': 2.3746192457848903e-06, 'epoch': 7.7} +{'loss': 0.2222, 'learning_rate': 2.3317173623922094e-06, 'epoch': 7.74} +{'loss': 0.2212, 'learning_rate': 2.288815478999528e-06, 'epoch': 7.78} +{'loss': 0.2236, 'learning_rate': 2.2459135956068473e-06, 'epoch': 7.82} +{'loss': 0.2196, 'learning_rate': 2.2030117122141664e-06, 'epoch': 7.87} +{'loss': 0.2236, 'learning_rate': 2.1601098288214855e-06, 'epoch': 7.91} +{'loss': 0.2215, 'learning_rate': 2.1172079454288042e-06, 'epoch': 7.95} +{'loss': 0.2135, 'learning_rate': 2.0743060620361234e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [1:02:48<13:54, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.4245302975177765, 'eval_accuracy': 0.8551286386930621, 'eval_f1': 0.6791799245818857, 'eval_matthews_correlation': 0.3669993001218785, 'eval_precision': 0.7105423072004731, 'eval_recall': 0.6599304292814907, 'eval_runtime': 13.3336, 'eval_samples_per_second': 2883.01, 'eval_steps_per_second': 22.574, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [1:10:26<06:56, 5.77it/s]***** Running Evaluation ***** +{'loss': 0.2008, 'learning_rate': 2.0314041786434425e-06, 'epoch': 8.03} +{'loss': 0.2006, 'learning_rate': 1.9889313140846885e-06, 'epoch': 8.07} +{'loss': 0.2047, 'learning_rate': 1.9460294306920076e-06, 'epoch': 8.11} +{'loss': 0.2071, 'learning_rate': 1.9031275472993265e-06, 'epoch': 8.16} +{'loss': 0.1996, 'learning_rate': 1.8602256639066457e-06, 'epoch': 8.2} +{'loss': 0.2017, 'learning_rate': 1.8173237805139646e-06, 'epoch': 8.24} +{'loss': 0.1974, 'learning_rate': 1.7744218971212837e-06, 'epoch': 8.28} +{'loss': 0.2026, 'learning_rate': 1.7315200137286028e-06, 'epoch': 8.32} +{'loss': 0.1989, 'learning_rate': 1.688618130335922e-06, 'epoch': 8.36} +{'loss': 0.2049, 'learning_rate': 1.6457162469432409e-06, 'epoch': 8.41} +{'loss': 0.2015, 'learning_rate': 1.60281436355056e-06, 'epoch': 8.45} +{'loss': 0.2037, 'learning_rate': 1.5599124801578792e-06, 'epoch': 8.49} +{'loss': 0.2017, 'learning_rate': 1.5170105967651983e-06, 'epoch': 8.53} +{'loss': 0.2012, 'learning_rate': 1.4741087133725172e-06, 'epoch': 8.57} +{'loss': 0.2074, 'learning_rate': 1.4312068299798363e-06, 'epoch': 8.61} +{'loss': 0.2032, 'learning_rate': 1.3883049465871555e-06, 'epoch': 8.66} +{'loss': 0.2043, 'learning_rate': 1.3454030631944742e-06, 'epoch': 8.7} +{'loss': 0.2074, 'learning_rate': 1.3025011798017933e-06, 'epoch': 8.74} +{'loss': 0.2054, 'learning_rate': 1.2595992964091124e-06, 'epoch': 8.78} +{'loss': 0.199, 'learning_rate': 1.2166974130164316e-06, 'epoch': 8.82} +{'loss': 0.2003, 'learning_rate': 1.1737955296237507e-06, 'epoch': 8.86} +{'loss': 0.2013, 'learning_rate': 1.1308936462310696e-06, 'epoch': 8.91} +{'loss': 0.2018, 'learning_rate': 1.0879917628383887e-06, 'epoch': 8.95} +{'loss': 0.213, 'learning_rate': 1.0450898794457077e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [1:10:39<06:56, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.448630690574646, 'eval_accuracy': 0.8536198329908171, 'eval_f1': 0.6699598253734579, 'eval_matthews_correlation': 0.35103985270984306, 'eval_precision': 0.7059562557959944, 'eval_recall': 0.6495814945196544, 'eval_runtime': 13.3153, 'eval_samples_per_second': 2886.986, 'eval_steps_per_second': 22.606, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [1:18:17<00:00, 5.79it/s]***** Running Evaluation ***** +{'loss': 0.1901, 'learning_rate': 1.0026170148869536e-06, 'epoch': 9.03} +{'loss': 0.1889, 'learning_rate': 9.597151314942726e-07, 'epoch': 9.07} +{'loss': 0.1848, 'learning_rate': 9.168132481015918e-07, 'epoch': 9.11} +{'loss': 0.1888, 'learning_rate': 8.739113647089108e-07, 'epoch': 9.16} +{'loss': 0.1901, 'learning_rate': 8.3100948131623e-07, 'epoch': 9.2} +{'loss': 0.1934, 'learning_rate': 7.881075979235489e-07, 'epoch': 9.24} +{'loss': 0.1968, 'learning_rate': 7.452057145308679e-07, 'epoch': 9.28} +{'loss': 0.1865, 'learning_rate': 7.02303831138187e-07, 'epoch': 9.32} +{'loss': 0.187, 'learning_rate': 6.594019477455061e-07, 'epoch': 9.36} +{'loss': 0.1909, 'learning_rate': 6.165000643528252e-07, 'epoch': 9.4} +{'loss': 0.1854, 'learning_rate': 5.735981809601442e-07, 'epoch': 9.45} +{'loss': 0.1918, 'learning_rate': 5.306962975674632e-07, 'epoch': 9.49} +{'loss': 0.1869, 'learning_rate': 4.877944141747823e-07, 'epoch': 9.53} +{'loss': 0.1852, 'learning_rate': 4.4489253078210134e-07, 'epoch': 9.57} +{'loss': 0.1928, 'learning_rate': 4.019906473894204e-07, 'epoch': 9.61} +{'loss': 0.1828, 'learning_rate': 3.590887639967395e-07, 'epoch': 9.65} +{'loss': 0.1867, 'learning_rate': 3.1618688060405857e-07, 'epoch': 9.7} +{'loss': 0.1948, 'learning_rate': 2.732849972113776e-07, 'epoch': 9.74} +{'loss': 0.1889, 'learning_rate': 2.3038311381869664e-07, 'epoch': 9.78} +{'loss': 0.1834, 'learning_rate': 1.8748123042601572e-07, 'epoch': 9.82} +{'loss': 0.1916, 'learning_rate': 1.4457934703333477e-07, 'epoch': 9.86} +{'loss': 0.188, 'learning_rate': 1.0210648247458065e-07, 'epoch': 9.9} +{'loss': 0.191, 'learning_rate': 5.92045990818997e-08, 'epoch': 9.95} +{'loss': 0.1869, 'learning_rate': 1.6302715689218757e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [1:18:30<00:00, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.4654063880443573, 'eval_accuracy': 0.8488072630784839, 'eval_f1': 0.6748055579102887, 'eval_matthews_correlation': 0.35452501247336865, 'eval_precision': 0.6964119285587363, 'eval_recall': 0.6599800803743643, 'eval_runtime': 13.3063, 'eval_samples_per_second': 2888.924, 'eval_steps_per_second': 22.621, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-7209 (score: 0.6933396044042176). +100%|██████████| 24030/24030 [1:18:32<00:00, 5.79it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.03_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 4712.4134, 'train_samples_per_second': 652.593, 'train_steps_per_second': 5.099, 'train_loss': 0.2729448675662837, 'epoch': 10.0} +100%|██████████| 24030/24030 [1:18:32<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.93it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_074117-tmcjsfu5/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_074117-tmcjsfu5/files/requirements.txt 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.06 +warmup_steps: + value: 0 +weight_decay: + value: 0.05 diff --git a/VASC/len2_5120/wandb/run-20260308_090125-5rtg1dnc/files/output.log b/VASC/len2_5120/wandb/run-20260308_090125-5rtg1dnc/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..8f07e4111d30d01c615234b1c7eaf50cdefe2249 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_090125-5rtg1dnc/files/output.log @@ -0,0 +1,232 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['classifier.weight', 'bert.pooler.dense.weight', 'classifier.bias', 'bert.pooler.dense.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33800190687179565, 'eval_accuracy': 0.8707890013267084, 'eval_f1': 0.6911239932198271, 'eval_matthews_correlation': 0.40706531332233514, 'eval_precision': 0.7583819944132693, 'eval_recall': 0.6603267380206633, 'eval_runtime': 13.331, 'eval_samples_per_second': 2883.587, 'eval_steps_per_second': 22.579, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [31:08<13:54, 5.76it/s]***** Running Evaluation ***** +{'loss': 0.3052, 'learning_rate': 5.252361275088548e-06, 'epoch': 3.04} +{'loss': 0.306, 'learning_rate': 5.1785714285714296e-06, 'epoch': 3.08} +{'loss': 0.2983, 'learning_rate': 5.10478158205431e-06, 'epoch': 3.12} +{'loss': 0.3076, 'learning_rate': 5.030991735537191e-06, 'epoch': 3.16} +{'loss': 0.3032, 'learning_rate': 4.957201889020071e-06, 'epoch': 3.2} +{'loss': 0.2967, 'learning_rate': 4.883412042502952e-06, 'epoch': 3.25} +{'loss': 0.3127, 'learning_rate': 4.809622195985833e-06, 'epoch': 3.29} +{'loss': 0.2926, 'learning_rate': 4.735832349468713e-06, 'epoch': 3.33} +{'loss': 0.2962, 'learning_rate': 4.662780401416766e-06, 'epoch': 3.37} +{'loss': 0.3028, 'learning_rate': 4.588990554899646e-06, 'epoch': 3.41} +{'loss': 0.3191, 'learning_rate': 4.515200708382527e-06, 'epoch': 3.45} +{'loss': 0.3177, 'learning_rate': 4.4414108618654075e-06, 'epoch': 3.5} +{'loss': 0.2974, 'learning_rate': 4.367621015348288e-06, 'epoch': 3.54} +{'loss': 0.3008, 'learning_rate': 4.293831168831169e-06, 'epoch': 3.58} +{'loss': 0.3022, 'learning_rate': 4.22004132231405e-06, 'epoch': 3.62} +{'loss': 0.3101, 'learning_rate': 4.146251475796931e-06, 'epoch': 3.66} +{'loss': 0.3154, 'learning_rate': 4.072461629279811e-06, 'epoch': 3.7} +{'loss': 0.3053, 'learning_rate': 3.998671782762692e-06, 'epoch': 3.75} +{'loss': 0.3085, 'learning_rate': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015/config.json +{'eval_loss': 0.34796157479286194, 'eval_accuracy': 0.8678234177050544, 'eval_f1': 0.6814322980524714, 'eval_matthews_correlation': 0.38914676538017834, 'eval_precision': 0.7499461152690842, 'eval_recall': 0.6514678522236934, 'eval_runtime': 13.3527, 'eval_samples_per_second': 2878.891, 'eval_steps_per_second': 22.542, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [46:52<00:00, 5.69it/s]***** Running Evaluation ***** +{'loss': 0.2701, 'learning_rate': 1.7119244391971665e-06, 'epoch': 5.04} +{'loss': 0.2794, 'learning_rate': 1.6381345926800473e-06, 'epoch': 5.08} +{'loss': 0.2709, 'learning_rate': 1.564344746162928e-06, 'epoch': 5.12} +{'loss': 0.2702, 'learning_rate': 1.4905548996458088e-06, 'epoch': 5.16} +{'loss': 0.2808, 'learning_rate': 1.4167650531286898e-06, 'epoch': 5.2} +{'loss': 0.2696, 'learning_rate': 1.3429752066115702e-06, 'epoch': 5.24} +{'loss': 0.2689, 'learning_rate': 1.2691853600944513e-06, 'epoch': 5.29} +{'loss': 0.2638, 'learning_rate': 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0.2676, 'learning_rate': 1.6307556080283354e-07, 'epoch': 5.91} +{'loss': 0.2718, 'learning_rate': 8.928571428571429e-08, 'epoch': 5.95} +{'loss': 0.2749, 'learning_rate': 1.5495867768595042e-08, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [47:05<00:00, 5.69iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3586041331291199, 'eval_accuracy': 0.8660544730886294, 'eval_f1': 0.6844629034547001, 'eval_matthews_correlation': 0.389533265269852, 'eval_precision': 0.7422113635859356, 'eval_recall': 0.6566154478730284, 'eval_runtime': 13.322, 'eval_samples_per_second': 2885.52, 'eval_steps_per_second': 22.594, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-7209 (score: 0.6911239932198271). +100%|██████████| 14418/14418 [47:07<00:00, 5.69it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 2827.175, 'train_samples_per_second': 652.656, 'train_steps_per_second': 5.1, 'train_loss': 0.3137895978924173, 'epoch': 6.0} +100%|██████████| 14418/14418 [47:07<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.99it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_090125-5rtg1dnc/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_090125-5rtg1dnc/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_090125-5rtg1dnc/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 +nvidia-nccl-cu12==2.27.3 +debugpy==1.8.16 +ipython==8.18.1 +anyio==4.12.0 +prompt_toolkit==3.0.51 +mkl_fft==1.3.11 +httpcore==1.0.9 +Jinja2==3.1.6 +ply==3.11 +zipp==3.23.0 +setproctitle==1.3.6 +docker-pycreds==0.4.0 +nvidia-cuda-nvrtc-cu12==12.8.93 +urllib3==2.5.0 +kiwisolver==1.4.4 +nvidia-curand-cu12==10.3.9.90 +llvmlite==0.43.0 +six==1.17.0 +frozenlist==1.8.0 +wcwidth==0.2.13 +numexpr==2.10.1 +click==8.1.8 +multiprocess==0.70.18 +threadpoolctl==3.6.0 +typing_extensions==4.15.0 +decorator==5.2.1 +sip==6.7.12 +pure_eval==0.2.3 +async-timeout==5.0.1 +Pygments==2.19.2 +mkl-service==2.4.0 +transformers==4.35.2 +numba==0.60.0 +pyzmq==27.0.2 +mkl_random==1.2.8 +ptyprocess==0.7.0 +nvidia-cuda-cupti-cu12==12.8.90 +charset-normalizer==3.4.4 +nvidia-cublas-cu12==12.8.4.1 +PyQt5_sip==12.13.0 +Bottleneck==1.4.2 +networkx==3.2.1 +PySocks==1.7.1 +pysam==0.9.1 +tornado==6.5.2 +pandas==2.3.3 +smmap==5.0.2 +PyQt5==5.15.10 +nvidia-cufft-cu12==11.3.3.83 +safetensors==0.7.0 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+nvidia-cuda-runtime-cu12==12.8.90 +filelock==3.17.0 +aiohappyeyeballs==2.6.1 +setuptools==80.9.0 diff --git a/VASC/len2_5120/wandb/run-20260308_090125-5rtg1dnc/files/wandb-metadata.json b/VASC/len2_5120/wandb/run-20260308_090125-5rtg1dnc/files/wandb-metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..5beccf97eae7c1de428ff93aa8ac49fd56ec203b --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_090125-5rtg1dnc/files/wandb-metadata.json @@ -0,0 +1,144 @@ +{ + "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", + "python": "CPython 3.9.18", + "startedAt": "2026-03-08T09:01:25.124416Z", + "args": [ + "--model_name_or_path", + "/home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000", + "--tokenizer_path", + "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_3072/merge_tokenizer_unigram_len2.json", + "--trust_remote_code", + "True", + "--data_path", + "/home/n5huang/dna_token/Finetune-screen/finetune_data/super_binary/VASC", + 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b/VASC/len2_5120/wandb/run-20260308_095008-6v62tslb/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.weight', 'classifier.bias', 'bert.pooler.dense.bias', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.33878323435783386, 'eval_accuracy': 0.8713092791550688, 'eval_f1': 0.6920170698037325, 'eval_matthews_correlation': 0.4092314267018049, 'eval_precision': 0.760180482348027, 'eval_recall': 0.6609174899372161, 'eval_runtime': 13.3852, 'eval_samples_per_second': 2871.895, 'eval_steps_per_second': 22.487, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [31:09<27:51, 5.75it/s]***** Running Evaluation ***** +{'loss': 0.308, 'learning_rate': 6.598782512451578e-06, 'epoch': 3.04} +{'loss': 0.3105, 'learning_rate': 6.543442169341451e-06, 'epoch': 3.08} +{'loss': 0.3022, 'learning_rate': 6.488101826231323e-06, 'epoch': 3.12} +{'loss': 0.3103, 'learning_rate': 6.432761483121196e-06, 'epoch': 3.16} +{'loss': 0.3087, 'learning_rate': 6.377421140011068e-06, 'epoch': 3.2} +{'loss': 0.2987, 'learning_rate': 6.322080796900941e-06, 'epoch': 3.25} +{'loss': 0.316, 'learning_rate': 6.266740453790814e-06, 'epoch': 3.29} +{'loss': 0.2974, 'learning_rate': 6.211400110680687e-06, 'epoch': 3.33} +{'loss': 0.2996, 'learning_rate': 6.156613171001661e-06, 'epoch': 3.37} +{'loss': 0.3074, 'learning_rate': 6.101272827891534e-06, 'epoch': 3.41} +{'loss': 0.322, 'learning_rate': 6.045932484781406e-06, 'epoch': 3.45} +{'loss': 0.3209, 'learning_rate': 5.990592141671279e-06, 'epoch': 3.5} +{'loss': 0.3011, 'learning_rate': 5.935251798561151e-06, 'epoch': 3.54} +{'loss': 0.3053, 'learning_rate': 5.879911455451024e-06, 'epoch': 3.58} +{'loss': 0.3036, 'learning_rate': 5.824571112340896e-06, 'epoch': 3.62} +{'loss': 0.3157, 'learning_rate': 5.769230769230769e-06, 'epoch': 3.66} +{'loss': 0.3192, 'learning_rate': 5.713890426120643e-06, 'epoch': 3.7} +{'loss': 0.3098, 'learning_rate': 5.658550083010516e-06, 'epoch': 3.75} +{'loss': 0.3122, 'learning_rate': 5.603209739900388e-06, 'epoch': 3.79} +{'loss': 0.3135, 'learning_rate': 5.547869396790261e-06, 'epoch': 3.83} +{'loss': 0.3143, 'learning_rate': 5.493082457111234e-06, 'epoch': 3.87} +{'loss': 0.3012, 'learning_rate': 5.437742114001108e-06, 'epoch': 3.91} +{'loss': 0.3049, 'learning_rate': 5.38240177089098e-06, 'epoch': 3.95} +{'loss': 0.3131, 'learning_rate': 5.327061427780853e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 9612/19224 [31:22<27:51, 5.75itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/config.json +{'eval_loss': 0.34052377939224243, 'eval_accuracy': 0.8687078900132671, 'eval_f1': 0.6831993122901399, 'eval_matthews_correlation': 0.39315342210899323, 'eval_precision': 0.752943487735267, 'eval_recall': 0.652770896278012, 'eval_runtime': 13.3009, 'eval_samples_per_second': 2890.107, 'eval_steps_per_second': 22.63, 'epoch': 4.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612/special_tokens_map.json + 62%|██████▎ | 12015/19224 [39:00<20:41, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.2959, 'learning_rate': 5.271721084670725e-06, 'epoch': 4.04} +{'loss': 0.2899, 'learning_rate': 5.216380741560599e-06, 'epoch': 4.08} +{'loss': 0.2957, 'learning_rate': 5.161040398450471e-06, 'epoch': 4.12} +{'loss': 0.2921, 'learning_rate': 5.105700055340344e-06, 'epoch': 4.16} +{'loss': 0.2796, 'learning_rate': 5.050359712230216e-06, 'epoch': 4.2} +{'loss': 0.2981, 'learning_rate': 4.995019369120089e-06, 'epoch': 4.24} +{'loss': 0.2934, 'learning_rate': 4.939679026009961e-06, 'epoch': 4.29} +{'loss': 0.2911, 'learning_rate': 4.884338682899835e-06, 'epoch': 4.33} +{'loss': 0.3003, 'learning_rate': 4.828998339789707e-06, 'epoch': 4.37} +{'loss': 0.2897, 'learning_rate': 4.77365799667958e-06, 'epoch': 4.41} +{'loss': 0.295, 'learning_rate': 4.718317653569452e-06, 'epoch': 4.45} +{'loss': 0.286, 'learning_rate': 4.662977310459325e-06, 'epoch': 4.49} +{'loss': 0.2919, 'learning_rate': 4.6076369673491975e-06, 'epoch': 4.54} +{'loss': 0.2866, 'learning_rate': 4.552296624239071e-06, 'epoch': 4.58} +{'loss': 0.2994, 'learning_rate': 4.496956281128943e-06, 'epoch': 4.62} +{'loss': 0.2785, 'learning_rate': 4.441615938018816e-06, 'epoch': 4.66} +{'loss': 0.2935, 'learning_rate': 4.3862755949086885e-06, 'epoch': 4.7} +{'loss': 0.2911, 'learning_rate': 4.330935251798561e-06, 'epoch': 4.74} +{'loss': 0.2825, 'learning_rate': 4.2755949086884344e-06, 'epoch': 4.79} +{'loss': 0.2963, 'learning_rate': 4.220254565578307e-06, 'epoch': 4.83} +{'loss': 0.2928, 'learning_rate': 4.1649142224681795e-06, 'epoch': 4.87} +{'loss': 0.2942, 'learning_rate': 4.109573879358053e-06, 'epoch': 4.91} +{'loss': 0.287, 'learning_rate': 4.0542335362479255e-06, 'epoch': 4.95} +{'loss': 0.2877, 'learning_rate': 3.998893193137798e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 62%|██████▎ | 12015/19224 [39:14<20:41, 5.81iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015/config.json +{'eval_loss': 0.3485703766345978, 'eval_accuracy': 0.8706589318696184, 'eval_f1': 0.6749847420474482, 'eval_matthews_correlation': 0.3887220408801068, 'eval_precision': 0.7660885294405697, 'eval_recall': 0.6419685634172971, 'eval_runtime': 13.5777, 'eval_samples_per_second': 2831.177, 'eval_steps_per_second': 22.169, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [46:52<14:19, 5.59it/s]***** Running Evaluation ***** +{'loss': 0.2674, 'learning_rate': 3.9435528500276705e-06, 'epoch': 5.04} +{'loss': 0.2754, 'learning_rate': 3.888212506917543e-06, 'epoch': 5.08} +{'loss': 0.268, 'learning_rate': 3.832872163807416e-06, 'epoch': 5.12} +{'loss': 0.2671, 'learning_rate': 3.777531820697289e-06, 'epoch': 5.16} +{'loss': 0.2735, 'learning_rate': 3.7221914775871616e-06, 'epoch': 5.2} +{'loss': 0.263, 'learning_rate': 3.666851134477034e-06, 'epoch': 5.24} +{'loss': 0.2632, 'learning_rate': 3.6115107913669066e-06, 'epoch': 5.29} +{'loss': 0.2608, 'learning_rate': 3.556170448256779e-06, 'epoch': 5.33} +{'loss': 0.2761, 'learning_rate': 3.500830105146652e-06, 'epoch': 5.37} +{'loss': 0.2741, 'learning_rate': 3.4454897620365247e-06, 'epoch': 5.41} +{'loss': 0.2793, 'learning_rate': 3.3901494189263977e-06, 'epoch': 5.45} +{'loss': 0.2727, 'learning_rate': 3.3348090758162706e-06, 'epoch': 5.49} +{'loss': 0.2695, 'learning_rate': 3.280022136137244e-06, 'epoch': 5.53} +{'loss': 0.2719, 'learning_rate': 3.2246817930271166e-06, 'epoch': 5.58} +{'loss': 0.2594, 'learning_rate': 3.16934144991699e-06, 'epoch': 5.62} +{'loss': 0.2751, 'learning_rate': 3.1140011068068626e-06, 'epoch': 5.66} +{'loss': 0.2738, 'learning_rate': 3.058660763696735e-06, 'epoch': 5.7} +{'loss': 0.2704, 'learning_rate': 3.003320420586608e-06, 'epoch': 5.74} +{'loss': 0.2735, 'learning_rate': 2.9479800774764806e-06, 'epoch': 5.78} +{'loss': 0.2661, 'learning_rate': 2.892639734366353e-06, 'epoch': 5.83} +{'loss': 0.2767, 'learning_rate': 2.8372993912562257e-06, 'epoch': 5.87} +{'loss': 0.267, 'learning_rate': 2.781959048146099e-06, 'epoch': 5.91} +{'loss': 0.2703, 'learning_rate': 2.7266187050359716e-06, 'epoch': 5.95} +{'loss': 0.2772, 'learning_rate': 2.671278361925844e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [47:05<14:19, 5.59iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3610495328903198, 'eval_accuracy': 0.864025389558024, 'eval_f1': 0.6804550992150599, 'eval_matthews_correlation': 0.3806916781901651, 'eval_precision': 0.7359258578784209, 'eval_recall': 0.6535717143793631, 'eval_runtime': 13.3152, 'eval_samples_per_second': 2887.004, 'eval_steps_per_second': 22.606, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [54:44<08:21, 4.79it/s]***** Running Evaluation ***** +{'loss': 0.2573, 'learning_rate': 2.6159380188157167e-06, 'epoch': 6.03} +{'loss': 0.2533, 'learning_rate': 2.5605976757055893e-06, 'epoch': 6.08} +{'loss': 0.2474, 'learning_rate': 2.5052573325954622e-06, 'epoch': 6.12} +{'loss': 0.251, 'learning_rate': 2.449916989485335e-06, 'epoch': 6.16} +{'loss': 0.254, 'learning_rate': 2.3945766463752078e-06, 'epoch': 6.2} +{'loss': 0.2503, 'learning_rate': 2.3392363032650807e-06, 'epoch': 6.24} +{'loss': 0.2543, 'learning_rate': 2.2838959601549533e-06, 'epoch': 6.28} +{'loss': 0.2528, 'learning_rate': 2.228555617044826e-06, 'epoch': 6.33} +{'loss': 0.2503, 'learning_rate': 2.1732152739346983e-06, 'epoch': 6.37} +{'loss': 0.2532, 'learning_rate': 2.1178749308245713e-06, 'epoch': 6.41} +{'loss': 0.2484, 'learning_rate': 2.063087991145545e-06, 'epoch': 6.45} +{'loss': 0.2471, 'learning_rate': 2.007747648035418e-06, 'epoch': 6.49} +{'loss': 0.2447, 'learning_rate': 1.9524073049252907e-06, 'epoch': 6.53} +{'loss': 0.2487, 'learning_rate': 1.8970669618151635e-06, 'epoch': 6.58} +{'loss': 0.2463, 'learning_rate': 1.8417266187050362e-06, 'epoch': 6.62} +{'loss': 0.2587, 'learning_rate': 1.7863862755949088e-06, 'epoch': 6.66} +{'loss': 0.2551, 'learning_rate': 1.7310459324847815e-06, 'epoch': 6.7} +{'loss': 0.25, 'learning_rate': 1.6757055893746543e-06, 'epoch': 6.74} +{'loss': 0.2439, 'learning_rate': 1.620365246264527e-06, 'epoch': 6.78} +{'loss': 0.264, 'learning_rate': 1.5650249031543996e-06, 'epoch': 6.82} +{'loss': 0.2426, 'learning_rate': 1.5096845600442725e-06, 'epoch': 6.87} +{'loss': 0.253, 'learning_rate': 1.454344216934145e-06, 'epoch': 6.91} +{'loss': 0.2515, 'learning_rate': 1.3990038738240178e-06, 'epoch': 6.95} +{'loss': 0.2517, 'learning_rate': 1.3436635307138906e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [54:57<08:21, 4.79iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3849492073059082, 'eval_accuracy': 0.8579901667490439, 'eval_f1': 0.6767528318767724, 'eval_matthews_correlation': 0.3665243084068005, 'eval_precision': 0.7176778290149889, 'eval_recall': 0.6542877256505449, 'eval_runtime': 13.3164, 'eval_samples_per_second': 2886.748, 'eval_steps_per_second': 22.604, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [1:02:35<00:00, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.2349, 'learning_rate': 1.2883231876037633e-06, 'epoch': 7.03} +{'loss': 0.2352, 'learning_rate': 1.2329828444936359e-06, 'epoch': 7.07} +{'loss': 0.23, 'learning_rate': 1.1776425013835086e-06, 'epoch': 7.12} +{'loss': 0.2427, 'learning_rate': 1.1223021582733814e-06, 'epoch': 7.16} +{'loss': 0.2352, 'learning_rate': 1.0669618151632542e-06, 'epoch': 7.2} +{'loss': 0.2366, 'learning_rate': 1.011621472053127e-06, 'epoch': 7.24} +{'loss': 0.2338, 'learning_rate': 9.568345323741008e-07, 'epoch': 7.28} +{'loss': 0.2326, 'learning_rate': 9.014941892639735e-07, 'epoch': 7.32} +{'loss': 0.2392, 'learning_rate': 8.461538461538463e-07, 'epoch': 7.37} +{'loss': 0.2227, 'learning_rate': 7.908135030437189e-07, 'epoch': 7.41} +{'loss': 0.2349, 'learning_rate': 7.354731599335917e-07, 'epoch': 7.45} +{'loss': 0.2379, 'learning_rate': 6.801328168234643e-07, 'epoch': 7.49} +{'loss': 0.2377, 'learning_rate': 6.247924737133371e-07, 'epoch': 7.53} +{'loss': 0.2394, 'learning_rate': 5.694521306032098e-07, 'epoch': 7.57} +{'loss': 0.2461, 'learning_rate': 5.141117874930825e-07, 'epoch': 7.62} +{'loss': 0.236, 'learning_rate': 4.587714443829552e-07, 'epoch': 7.66} +{'loss': 0.2421, 'learning_rate': 4.034311012728279e-07, 'epoch': 7.7} +{'loss': 0.2387, 'learning_rate': 3.480907581627006e-07, 'epoch': 7.74} +{'loss': 0.2275, 'learning_rate': 2.9275041505257337e-07, 'epoch': 7.78} +{'loss': 0.2425, 'learning_rate': 2.3741007194244607e-07, 'epoch': 7.82} +{'loss': 0.234, 'learning_rate': 1.8206972883231878e-07, 'epoch': 7.87} +{'loss': 0.2445, 'learning_rate': 1.2672938572219148e-07, 'epoch': 7.91} +{'loss': 0.2389, 'learning_rate': 7.138904261206419e-08, 'epoch': 7.95} +{'loss': 0.2292, 'learning_rate': 1.6048699501936912e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [1:02:49<00:00, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.39941489696502686, 'eval_accuracy': 0.8573918472464296, 'eval_f1': 0.6755922652527833, 'eval_matthews_correlation': 0.36404392067732994, 'eval_precision': 0.7160314893702067, 'eval_recall': 0.6533665029210312, 'eval_runtime': 13.2941, 'eval_samples_per_second': 2891.593, 'eval_steps_per_second': 22.642, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-7209 (score: 0.6920170698037325). +100%|██████████| 19224/19224 [1:02:50<00:00, 5.80it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 3770.6, 'train_samples_per_second': 652.478, 'train_steps_per_second': 5.098, 'train_loss': 0.2973411852649684, 'epoch': 8.0} +100%|██████████| 19224/19224 [1:02:50<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.94it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_095008-6v62tslb/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_095008-6v62tslb/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_095008-6v62tslb/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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b/VASC/len2_5120/wandb/run-20260308_105437-mmqslv3t/files/output.log @@ -0,0 +1,368 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.weight', 'classifier.weight', 'classifier.bias', 'bert.pooler.dense.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 10 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 24,030 + Number of trainable parameters = 88,402,178 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 10%|█ | 2403/24030 [07:35<1:02:23, 5.78it/s]***** Running Evaluation ***** +{'loss': 0.5247, 'learning_rate': 6.934812760055479e-07, 'epoch': 0.04} +{'loss': 0.397, 'learning_rate': 1.3869625520110958e-06, 'epoch': 0.08} +{'loss': 0.3671, 'learning_rate': 2.0804438280166435e-06, 'epoch': 0.12} +{'loss': 0.3575, 'learning_rate': 2.7739251040221917e-06, 'epoch': 0.17} +{'loss': 0.3602, 'learning_rate': 3.46740638002774e-06, 'epoch': 0.21} +{'loss': 0.357, 'learning_rate': 4.160887656033287e-06, 'epoch': 0.25} +{'loss': 0.3585, 'learning_rate': 4.854368932038836e-06, 'epoch': 0.29} +{'loss': 0.3497, 'learning_rate': 5.547850208044383e-06, 'epoch': 0.33} +{'loss': 0.359, 'learning_rate': 6.24133148404993e-06, 'epoch': 0.37} +{'loss': 0.3563, 'learning_rate': 6.93481276005548e-06, 'epoch': 0.42} +{'loss': 0.355, 'learning_rate': 7.628294036061027e-06, 'epoch': 0.46} +{'loss': 0.3584, 'learning_rate': 8.321775312066574e-06, 'epoch': 0.5} +{'loss': 0.3529, 'learning_rate': 9.015256588072124e-06, 'epoch': 0.54} +{'loss': 0.351, 'learning_rate': 9.708737864077671e-06, 'epoch': 0.58} +{'loss': 0.3594, 'learning_rate': 9.974322649194264e-06, 'epoch': 0.62} +{'loss': 0.3463, 'learning_rate': 9.930051354701612e-06, 'epoch': 0.67} +{'loss': 0.3483, 'learning_rate': 9.885780060208962e-06, 'epoch': 0.71} +{'loss': 0.3439, 'learning_rate': 9.84150876571631e-06, 'epoch': 0.75} +{'loss': 0.3533, 'learning_rate': 9.797237471223659e-06, 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+{'loss': 0.3312, 'learning_rate': 9.398795820789802e-06, 'epoch': 1.17} +{'loss': 0.3329, 'learning_rate': 9.35452452629715e-06, 'epoch': 1.21} +{'loss': 0.3406, 'learning_rate': 9.310253231804499e-06, 'epoch': 1.25} +{'loss': 0.3345, 'learning_rate': 9.265981937311847e-06, 'epoch': 1.29} +{'loss': 0.3417, 'learning_rate': 9.221710642819196e-06, 'epoch': 1.33} +{'loss': 0.3371, 'learning_rate': 9.177439348326546e-06, 'epoch': 1.37} +{'loss': 0.3447, 'learning_rate': 9.133168053833896e-06, 'epoch': 1.41} +{'loss': 0.3399, 'learning_rate': 9.088896759341243e-06, 'epoch': 1.46} +{'loss': 0.3382, 'learning_rate': 9.044625464848593e-06, 'epoch': 1.5} +{'loss': 0.3305, 'learning_rate': 9.000354170355941e-06, 'epoch': 1.54} +{'loss': 0.3455, 'learning_rate': 8.95608287586329e-06, 'epoch': 1.58} +{'loss': 0.3296, 'learning_rate': 8.91181158137064e-06, 'epoch': 1.62} +{'loss': 0.3323, 'learning_rate': 8.86754028687799e-06, 'epoch': 1.66} +{'loss': 0.3349, 'learning_rate': 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8.46909863644413e-06, 'epoch': 2.04} +{'loss': 0.3331, 'learning_rate': 8.42482734195148e-06, 'epoch': 2.08} +{'loss': 0.3246, 'learning_rate': 8.38055604745883e-06, 'epoch': 2.12} +{'loss': 0.3238, 'learning_rate': 8.336284752966177e-06, 'epoch': 2.16} +{'loss': 0.326, 'learning_rate': 8.292013458473527e-06, 'epoch': 2.21} +{'loss': 0.3277, 'learning_rate': 8.247742163980875e-06, 'epoch': 2.25} +{'loss': 0.3252, 'learning_rate': 8.203470869488224e-06, 'epoch': 2.29} +{'loss': 0.3314, 'learning_rate': 8.159199574995574e-06, 'epoch': 2.33} +{'loss': 0.3274, 'learning_rate': 8.114928280502923e-06, 'epoch': 2.37} +{'loss': 0.3259, 'learning_rate': 8.070656986010271e-06, 'epoch': 2.41} +{'loss': 0.3303, 'learning_rate': 8.02638569151762e-06, 'epoch': 2.46} +{'loss': 0.3279, 'learning_rate': 7.982114397024969e-06, 'epoch': 2.5} +{'loss': 0.3285, 'learning_rate': 7.937843102532318e-06, 'epoch': 2.54} +{'loss': 0.326, 'learning_rate': 7.893571808039668e-06, 'epoch': 2.58} +{'loss': 0.3343, 'learning_rate': 7.849300513547017e-06, 'epoch': 2.62} +{'loss': 0.3221, 'learning_rate': 7.805029219054365e-06, 'epoch': 2.66} +{'loss': 0.318, 'learning_rate': 7.760757924561715e-06, 'epoch': 2.7} +{'loss': 0.3265, 'learning_rate': 7.716486630069064e-06, 'epoch': 2.75} +{'loss': 0.3305, 'learning_rate': 7.672215335576412e-06, 'epoch': 2.79} +{'loss': 0.3334, 'learning_rate': 7.6279440410837625e-06, 'epoch': 2.83} +{'loss': 0.3187, 'learning_rate': 7.583672746591111e-06, 'epoch': 2.87} +{'loss': 0.3245, 'learning_rate': 7.539401452098461e-06, 'epoch': 2.91} +{'loss': 0.3238, 'learning_rate': 7.495130157605809e-06, 'epoch': 2.95} +{'loss': 0.3292, 'learning_rate': 7.450858863113158e-06, 'epoch': 3.0} + Num examples = 38441 + Batch size = 128 + 30%|███ | 7209/24030 [23:29<50:11, 5.58itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.34000787138938904, 'eval_accuracy': 0.8718035430920111, 'eval_f1': 0.6901031281887009, 'eval_matthews_correlation': 0.40808356030703696, 'eval_precision': 0.7632510492253939, 'eval_recall': 0.6581495996719496, 'eval_runtime': 13.3022, 'eval_samples_per_second': 2889.817, 'eval_steps_per_second': 22.628, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [31:08<42:24, 5.67it/s]***** Running Evaluation ***** +{'loss': 0.3111, 'learning_rate': 7.406587568620507e-06, 'epoch': 3.04} +{'loss': 0.3145, 'learning_rate': 7.362316274127856e-06, 'epoch': 3.08} +{'loss': 0.3061, 'learning_rate': 7.318044979635205e-06, 'epoch': 3.12} +{'loss': 0.3164, 'learning_rate': 7.273773685142555e-06, 'epoch': 3.16} +{'loss': 0.3117, 'learning_rate': 7.2295023906499025e-06, 'epoch': 3.2} +{'loss': 0.302, 'learning_rate': 7.185231096157252e-06, 'epoch': 3.25} +{'loss': 0.3196, 'learning_rate': 7.140959801664601e-06, 'epoch': 3.29} +{'loss': 0.2996, 'learning_rate': 7.09668850717195e-06, 'epoch': 3.33} +{'loss': 0.304, 'learning_rate': 7.052859925624226e-06, 'epoch': 3.37} +{'loss': 0.3093, 'learning_rate': 7.008588631131576e-06, 'epoch': 3.41} +{'loss': 0.325, 'learning_rate': 6.9643173366389235e-06, 'epoch': 3.45} +{'loss': 0.3247, 'learning_rate': 6.920046042146273e-06, 'epoch': 3.5} +{'loss': 0.3069, 'learning_rate': 6.875774747653622e-06, 'epoch': 3.54} +{'loss': 0.3073, 'learning_rate': 6.831503453160971e-06, 'epoch': 3.58} +{'loss': 0.3088, 'learning_rate': 6.78723215866832e-06, 'epoch': 3.62} +{'loss': 0.3195, 'learning_rate': 6.7429608641756695e-06, 'epoch': 3.66} +{'loss': 0.3223, 'learning_rate': 6.698689569683018e-06, 'epoch': 3.7} +{'loss': 0.3146, 'learning_rate': 6.654418275190368e-06, 'epoch': 3.75} +{'loss': 0.3163, 'learning_rate': 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+{'eval_loss': 0.3473089635372162, 'eval_accuracy': 0.8721677375718634, 'eval_f1': 0.6724427142676288, 'eval_matthews_correlation': 0.39063430182254166, 'eval_precision': 0.776116985686027, 'eval_recall': 0.6381616902173313, 'eval_runtime': 13.2793, 'eval_samples_per_second': 2894.805, 'eval_steps_per_second': 22.667, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [46:50<27:32, 5.82it/s]***** Running Evaluation ***** +{'loss': 0.2728, 'learning_rate': 5.282450858863114e-06, 'epoch': 5.04} +{'loss': 0.2796, 'learning_rate': 5.238179564370463e-06, 'epoch': 5.08} +{'loss': 0.2736, 'learning_rate': 5.193908269877812e-06, 'epoch': 5.12} +{'loss': 0.2719, 'learning_rate': 5.149636975385161e-06, 'epoch': 5.16} +{'loss': 0.2784, 'learning_rate': 5.1053656808925104e-06, 'epoch': 5.2} +{'loss': 0.2695, 'learning_rate': 5.061094386399858e-06, 'epoch': 5.24} +{'loss': 0.2727, 'learning_rate': 5.016823091907208e-06, 'epoch': 5.29} +{'loss': 0.2676, 'learning_rate': 4.972551797414557e-06, 'epoch': 5.33} +{'loss': 0.2836, 'learning_rate': 4.928280502921906e-06, 'epoch': 5.37} +{'loss': 0.2777, 'learning_rate': 4.884009208429255e-06, 'epoch': 5.41} +{'loss': 0.285, 'learning_rate': 4.839737913936604e-06, 'epoch': 5.45} +{'loss': 0.2767, 'learning_rate': 4.795466619443953e-06, 'epoch': 5.49} +{'loss': 0.2771, 'learning_rate': 4.751638037896229e-06, 'epoch': 5.53} +{'loss': 0.2801, 'learning_rate': 4.7073667434035775e-06, 'epoch': 5.58} +{'loss': 0.2652, 'learning_rate': 4.663095448910926e-06, 'epoch': 5.62} +{'loss': 0.2817, 'learning_rate': 4.618824154418276e-06, 'epoch': 5.66} +{'loss': 0.2799, 'learning_rate': 4.5745528599256245e-06, 'epoch': 5.7} +{'loss': 0.2701, 'learning_rate': 4.530281565432973e-06, 'epoch': 5.74} +{'loss': 0.2765, 'learning_rate': 4.486010270940323e-06, 'epoch': 5.78} +{'loss': 0.2679, 'learning_rate': 4.4417389764476714e-06, 'epoch': 5.83} +{'loss': 0.2824, 'learning_rate': 4.39746768195502e-06, 'epoch': 5.87} +{'loss': 0.2719, 'learning_rate': 4.35319638746237e-06, 'epoch': 5.91} +{'loss': 0.276, 'learning_rate': 4.308925092969719e-06, 'epoch': 5.95} +{'loss': 0.279, 'learning_rate': 4.264653798477068e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [47:03<27:32, 5.82iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35823291540145874, 'eval_accuracy': 0.8649098618662365, 'eval_f1': 0.6779859110269594, 'eval_matthews_correlation': 0.3790439833977837, 'eval_precision': 0.7396244479236405, 'eval_recall': 0.6498953284973693, 'eval_runtime': 13.3147, 'eval_samples_per_second': 2887.105, 'eval_steps_per_second': 22.607, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [54:40<21:30, 5.59it/s]***** Running Evaluation ***** +{'loss': 0.2589, 'learning_rate': 4.2203825039844175e-06, 'epoch': 6.03} +{'loss': 0.2581, 'learning_rate': 4.176111209491766e-06, 'epoch': 6.08} +{'loss': 0.2474, 'learning_rate': 4.131839914999115e-06, 'epoch': 6.12} +{'loss': 0.2574, 'learning_rate': 4.0875686205064644e-06, 'epoch': 6.16} +{'loss': 0.2534, 'learning_rate': 4.043297326013813e-06, 'epoch': 6.2} +{'loss': 0.2508, 'learning_rate': 3.999026031521162e-06, 'epoch': 6.24} +{'loss': 0.258, 'learning_rate': 3.954754737028511e-06, 'epoch': 6.28} +{'loss': 0.2488, 'learning_rate': 3.91048344253586e-06, 'epoch': 6.33} +{'loss': 0.2528, 'learning_rate': 3.866654860988136e-06, 'epoch': 6.37} +{'loss': 0.253, 'learning_rate': 3.8223835664954845e-06, 'epoch': 6.41} +{'loss': 0.249, 'learning_rate': 3.7781122720028337e-06, 'epoch': 6.45} +{'loss': 0.2534, 'learning_rate': 3.7338409775101824e-06, 'epoch': 6.49} +{'loss': 0.251, 'learning_rate': 3.6895696830175315e-06, 'epoch': 6.53} +{'loss': 0.252, 'learning_rate': 3.6452983885248806e-06, 'epoch': 6.58} +{'loss': 0.2502, 'learning_rate': 3.60102709403223e-06, 'epoch': 6.62} +{'loss': 0.2614, 'learning_rate': 3.556755799539579e-06, 'epoch': 6.66} +{'loss': 0.2558, 'learning_rate': 3.512484505046928e-06, 'epoch': 6.7} +{'loss': 0.25, 'learning_rate': 3.468213210554277e-06, 'epoch': 6.74} +{'loss': 0.2527, 'learning_rate': 3.4239419160616263e-06, 'epoch': 6.78} +{'loss': 0.264, 'learning_rate': 3.379670621568975e-06, 'epoch': 6.82} +{'loss': 0.2449, 'learning_rate': 3.335399327076324e-06, 'epoch': 6.87} +{'loss': 0.2534, 'learning_rate': 3.2911280325836732e-06, 'epoch': 6.91} +{'loss': 0.2563, 'learning_rate': 3.246856738091022e-06, 'epoch': 6.95} +{'loss': 0.2533, 'learning_rate': 3.202585443598371e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [54:54<21:30, 5.59iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3831358253955841, 'eval_accuracy': 0.8548684997788819, 'eval_f1': 0.6790965466563835, 'eval_matthews_correlation': 0.3666106402041201, 'eval_precision': 0.709924088356288, 'eval_recall': 0.6600618616034697, 'eval_runtime': 13.316, 'eval_samples_per_second': 2886.819, 'eval_steps_per_second': 22.604, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [1:02:31<13:51, 5.78it/s]***** Running Evaluation ***** +{'loss': 0.2315, 'learning_rate': 3.15831414910572e-06, 'epoch': 7.03} +{'loss': 0.2307, 'learning_rate': 3.1140428546130693e-06, 'epoch': 7.07} +{'loss': 0.2234, 'learning_rate': 3.069771560120418e-06, 'epoch': 7.12} +{'loss': 0.2378, 'learning_rate': 3.025500265627767e-06, 'epoch': 7.16} +{'loss': 0.2244, 'learning_rate': 2.9816716840800425e-06, 'epoch': 7.2} +{'loss': 0.232, 'learning_rate': 2.937400389587392e-06, 'epoch': 7.24} +{'loss': 0.2276, 'learning_rate': 2.893129095094741e-06, 'epoch': 7.28} +{'loss': 0.2305, 'learning_rate': 2.8488578006020903e-06, 'epoch': 7.32} +{'loss': 0.2308, 'learning_rate': 2.804586506109439e-06, 'epoch': 7.37} +{'loss': 0.221, 'learning_rate': 2.760315211616788e-06, 'epoch': 7.41} +{'loss': 0.2345, 'learning_rate': 2.7160439171241372e-06, 'epoch': 7.45} +{'loss': 0.234, 'learning_rate': 2.671772622631486e-06, 'epoch': 7.49} +{'loss': 0.2349, 'learning_rate': 2.627501328138835e-06, 'epoch': 7.53} +{'loss': 0.2372, 'learning_rate': 2.583230033646184e-06, 'epoch': 7.57} +{'loss': 0.2441, 'learning_rate': 2.538958739153533e-06, 'epoch': 7.62} +{'loss': 0.233, 'learning_rate': 2.494687444660882e-06, 'epoch': 7.66} +{'loss': 0.2407, 'learning_rate': 2.450416150168231e-06, 'epoch': 7.7} +{'loss': 0.2397, 'learning_rate': 2.4061448556755803e-06, 'epoch': 7.74} +{'loss': 0.2285, 'learning_rate': 2.361873561182929e-06, 'epoch': 7.78} +{'loss': 0.2385, 'learning_rate': 2.317602266690278e-06, 'epoch': 7.82} +{'loss': 0.2313, 'learning_rate': 2.273330972197627e-06, 'epoch': 7.87} +{'loss': 0.2424, 'learning_rate': 2.2290596777049763e-06, 'epoch': 7.91} +{'loss': 0.2392, 'learning_rate': 2.1847883832123255e-06, 'epoch': 7.95} +{'loss': 0.2215, 'learning_rate': 2.1405170887196746e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [1:02:44<13:51, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.4076765775680542, 'eval_accuracy': 0.8588486251658386, 'eval_f1': 0.6697877248907552, 'eval_matthews_correlation': 0.3576860903697786, 'eval_precision': 0.7202967206784638, 'eval_recall': 0.6451897908988311, 'eval_runtime': 13.2943, 'eval_samples_per_second': 2891.533, 'eval_steps_per_second': 22.641, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [1:10:22<06:55, 5.79it/s]***** Running Evaluation ***** +{'loss': 0.2111, 'learning_rate': 2.0962457942270233e-06, 'epoch': 8.03} +{'loss': 0.2187, 'learning_rate': 2.0519744997343724e-06, 'epoch': 8.07} +{'loss': 0.2177, 'learning_rate': 2.008145918186648e-06, 'epoch': 8.11} +{'loss': 0.2131, 'learning_rate': 1.963874623693997e-06, 'epoch': 8.16} +{'loss': 0.2048, 'learning_rate': 1.919603329201346e-06, 'epoch': 8.2} +{'loss': 0.2173, 'learning_rate': 1.8753320347086951e-06, 'epoch': 8.24} +{'loss': 0.2115, 'learning_rate': 1.831060740216044e-06, 'epoch': 8.28} +{'loss': 0.2167, 'learning_rate': 1.7867894457233932e-06, 'epoch': 8.32} +{'loss': 0.2087, 'learning_rate': 1.742518151230742e-06, 'epoch': 8.36} +{'loss': 0.2201, 'learning_rate': 1.698246856738091e-06, 'epoch': 8.41} +{'loss': 0.2202, 'learning_rate': 1.6539755622454401e-06, 'epoch': 8.45} +{'loss': 0.2116, 'learning_rate': 1.609704267752789e-06, 'epoch': 8.49} +{'loss': 0.2134, 'learning_rate': 1.5654329732601384e-06, 'epoch': 8.53} +{'loss': 0.2125, 'learning_rate': 1.5211616787674873e-06, 'epoch': 8.57} +{'loss': 0.2264, 'learning_rate': 1.4768903842748364e-06, 'epoch': 8.61} +{'loss': 0.216, 'learning_rate': 1.4326190897821853e-06, 'epoch': 8.66} +{'loss': 0.2148, 'learning_rate': 1.3883477952895345e-06, 'epoch': 8.7} +{'loss': 0.2204, 'learning_rate': 1.3440765007968834e-06, 'epoch': 8.74} +{'loss': 0.2156, 'learning_rate': 1.2998052063042325e-06, 'epoch': 8.78} +{'loss': 0.2161, 'learning_rate': 1.2555339118115814e-06, 'epoch': 8.82} +{'loss': 0.2086, 'learning_rate': 1.2112626173189305e-06, 'epoch': 8.86} +{'loss': 0.2091, 'learning_rate': 1.1669913228262794e-06, 'epoch': 8.91} +{'loss': 0.2158, 'learning_rate': 1.123162741278555e-06, 'epoch': 8.95} +{'loss': 0.2283, 'learning_rate': 1.0788914467859041e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [1:10:36<06:55, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.4327849745750427, 'eval_accuracy': 0.8581202362061341, 'eval_f1': 0.6677776966604696, 'eval_matthews_correlation': 0.3537454317282757, 'eval_precision': 0.7181441982999018, 'eval_recall': 0.6434095330564202, 'eval_runtime': 13.3403, 'eval_samples_per_second': 2881.562, 'eval_steps_per_second': 22.563, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [1:18:14<00:00, 5.85it/s]***** Running Evaluation ***** +{'loss': 0.1971, 'learning_rate': 1.034620152293253e-06, 'epoch': 9.03} +{'loss': 0.2075, 'learning_rate': 9.903488578006022e-07, 'epoch': 9.07} +{'loss': 0.1969, 'learning_rate': 9.460775633079512e-07, 'epoch': 9.11} +{'loss': 0.2034, 'learning_rate': 9.018062688153002e-07, 'epoch': 9.16} +{'loss': 0.2055, 'learning_rate': 8.575349743226492e-07, 'epoch': 9.2} +{'loss': 0.2105, 'learning_rate': 8.132636798299982e-07, 'epoch': 9.24} +{'loss': 0.2101, 'learning_rate': 7.689923853373474e-07, 'epoch': 9.28} +{'loss': 0.1984, 'learning_rate': 7.247210908446964e-07, 'epoch': 9.32} +{'loss': 0.2029, 'learning_rate': 6.804497963520454e-07, 'epoch': 9.36} +{'loss': 0.2039, 'learning_rate': 6.361785018593944e-07, 'epoch': 9.4} +{'loss': 0.1961, 'learning_rate': 5.919072073667434e-07, 'epoch': 9.45} +{'loss': 0.2017, 'learning_rate': 5.476359128740925e-07, 'epoch': 9.49} +{'loss': 0.2068, 'learning_rate': 5.033646183814416e-07, 'epoch': 9.53} +{'loss': 0.2004, 'learning_rate': 4.5909332388879056e-07, 'epoch': 9.57} +{'loss': 0.2022, 'learning_rate': 4.1482202939613953e-07, 'epoch': 9.61} +{'loss': 0.1964, 'learning_rate': 3.705507349034886e-07, 'epoch': 9.65} +{'loss': 0.198, 'learning_rate': 3.262794404108376e-07, 'epoch': 9.7} +{'loss': 0.2031, 'learning_rate': 2.820081459181867e-07, 'epoch': 9.74} +{'loss': 0.2031, 'learning_rate': 2.381795643704622e-07, 'epoch': 9.78} +{'loss': 0.2003, 'learning_rate': 1.9390826987781125e-07, 'epoch': 9.82} +{'loss': 0.1996, 'learning_rate': 1.4963697538516027e-07, 'epoch': 9.86} +{'loss': 0.2039, 'learning_rate': 1.053656808925093e-07, 'epoch': 9.9} +{'loss': 0.2024, 'learning_rate': 6.109438639985834e-08, 'epoch': 9.95} +{'loss': 0.2003, 'learning_rate': 1.6823091907207366e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [1:18:27<00:00, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.4448564946651459, 'eval_accuracy': 0.8523711662027522, 'eval_f1': 0.67206550119288, 'eval_matthews_correlation': 0.35302086557408324, 'eval_precision': 0.7032921564158344, 'eval_recall': 0.6532569353976414, 'eval_runtime': 13.3075, 'eval_samples_per_second': 2888.677, 'eval_steps_per_second': 22.619, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-7209 (score: 0.6901031281887009). +100%|██████████| 24030/24030 [1:18:28<00:00, 5.85it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.06_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 4708.9415, 'train_samples_per_second': 653.075, 'train_steps_per_second': 5.103, 'train_loss': 0.2812733152137912, 'epoch': 10.0} +100%|██████████| 24030/24030 [1:18:29<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.88it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_105437-mmqslv3t/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_105437-mmqslv3t/files/requirements.txt 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+ value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.1 +warmup_steps: + value: 0 +weight_decay: + value: 0.05 diff --git a/VASC/len2_5120/wandb/run-20260308_121442-b8pjz8t5/files/output.log b/VASC/len2_5120/wandb/run-20260308_121442-b8pjz8t5/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..866babca73b4514aba65bc639b8a02ae8c3f9b50 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_121442-b8pjz8t5/files/output.log @@ -0,0 +1,232 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.bias', 'bert.pooler.dense.weight', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-2403] due to args.save_total_limit + 50%|█████ | 7209/14418 [23:16<21:37, 5.55it/s]***** Running Evaluation ***** +{'loss': 0.3189, 'learning_rate': 7.335080147965476e-06, 'epoch': 2.04} +{'loss': 0.3274, 'learning_rate': 7.258014796547473e-06, 'epoch': 2.08} +{'loss': 0.3197, 'learning_rate': 7.1809494451294705e-06, 'epoch': 2.12} +{'loss': 0.3194, 'learning_rate': 7.103884093711468e-06, 'epoch': 2.16} +{'loss': 0.3195, 'learning_rate': 7.026818742293465e-06, 'epoch': 2.21} +{'loss': 0.3218, 'learning_rate': 6.949753390875463e-06, 'epoch': 2.25} +{'loss': 0.3203, 'learning_rate': 6.87268803945746e-06, 'epoch': 2.29} +{'loss': 0.3266, 'learning_rate': 6.795622688039458e-06, 'epoch': 2.33} +{'loss': 0.3233, 'learning_rate': 6.718557336621455e-06, 'epoch': 2.37} +{'loss': 0.3209, 'learning_rate': 6.641491985203453e-06, 'epoch': 2.41} +{'loss': 0.3249, 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Num examples = 38441 + Batch size = 128 + 50%|█████ | 7209/14418 [23:29<21:37, 5.55itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3381330966949463, 'eval_accuracy': 0.8705548763039463, 'eval_f1': 0.69164584883306, 'eval_matthews_correlation': 0.40720987457801944, 'eval_precision': 0.7571890355284667, 'eval_recall': 0.6611848281295536, 'eval_runtime': 13.3239, 'eval_samples_per_second': 2885.125, 'eval_steps_per_second': 22.591, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-4806] due to args.save_total_limit + 67%|██████▋ | 9612/14418 [31:07<14:34, 5.49it/s]***** Running Evaluation ***** +{'loss': 0.3045, 'learning_rate': 5.485511713933416e-06, 'epoch': 3.04} +{'loss': 0.3096, 'learning_rate': 5.408446362515414e-06, 'epoch': 3.08} +{'loss': 0.2994, 'learning_rate': 5.331381011097411e-06, 'epoch': 3.12} +{'loss': 0.3066, 'learning_rate': 5.2543156596794085e-06, 'epoch': 3.16} +{'loss': 0.3041, 'learning_rate': 5.1772503082614055e-06, 'epoch': 3.2} +{'loss': 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[/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-9612] due to args.save_total_limit +100%|██████████| 14418/14418 [46:49<00:00, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.2666, 'learning_rate': 1.7886868064118373e-06, 'epoch': 5.04} +{'loss': 0.2782, 'learning_rate': 1.7116214549938347e-06, 'epoch': 5.08} +{'loss': 0.2678, 'learning_rate': 1.6345561035758326e-06, 'epoch': 5.12} +{'loss': 0.263, 'learning_rate': 1.55749075215783e-06, 'epoch': 5.16} +{'loss': 0.2723, 'learning_rate': 1.4804254007398274e-06, 'epoch': 5.2} +{'loss': 0.2679, 'learning_rate': 1.4033600493218249e-06, 'epoch': 5.24} +{'loss': 0.2616, 'learning_rate': 1.3262946979038225e-06, 'epoch': 5.29} +{'loss': 0.2638, 'learning_rate': 1.24922934648582e-06, 'epoch': 5.33} +{'loss': 0.277, 'learning_rate': 1.1721639950678176e-06, 'epoch': 5.37} +{'loss': 0.2706, 'learning_rate': 1.095098643649815e-06, 'epoch': 5.41} +{'loss': 0.2761, 'learning_rate': 1.0180332922318127e-06, 'epoch': 5.45} +{'loss': 0.2708, 'learning_rate': 9.409679408138102e-07, 'epoch': 5.49} +{'loss': 0.2693, 'learning_rate': 8.639025893958077e-07, 'epoch': 5.53} +{'loss': 0.2729, 'learning_rate': 7.868372379778052e-07, 'epoch': 5.58} +{'loss': 0.2602, 'learning_rate': 7.097718865598027e-07, 'epoch': 5.62} +{'loss': 0.2779, 'learning_rate': 6.327065351418003e-07, 'epoch': 5.66} +{'loss': 0.276, 'learning_rate': 5.556411837237978e-07, 'epoch': 5.7} +{'loss': 0.2658, 'learning_rate': 4.785758323057954e-07, 'epoch': 5.74} +{'loss': 0.2721, 'learning_rate': 4.0151048088779286e-07, 'epoch': 5.78} +{'loss': 0.2646, 'learning_rate': 3.244451294697904e-07, 'epoch': 5.83} +{'loss': 0.2753, 'learning_rate': 2.4815043156596797e-07, 'epoch': 5.87} +{'loss': 0.2643, 'learning_rate': 1.7108508014796548e-07, 'epoch': 5.91} +{'loss': 0.2674, 'learning_rate': 9.401972872996301e-08, 'epoch': 5.95} +{'loss': 0.2734, 'learning_rate': 1.6954377311960542e-08, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 14418/14418 [47:02<00:00, 5.80iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3609361946582794, 'eval_accuracy': 0.8654561535860149, 'eval_f1': 0.6862849867521869, 'eval_matthews_correlation': 0.3909141440591744, 'eval_precision': 0.7396806122134608, 'eval_recall': 0.6593932302390609, 'eval_runtime': 13.415, 'eval_samples_per_second': 2865.529, 'eval_steps_per_second': 22.438, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-12015] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-7209 (score: 0.69164584883306). +100%|██████████| 14418/14418 [47:04<00:00, 5.80it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep6_seed42/checkpoint-14418] due to args.save_total_limit +{'train_runtime': 2824.2411, 'train_samples_per_second': 653.334, 'train_steps_per_second': 5.105, 'train_loss': 0.3137001875849467, 'epoch': 6.0} +100%|██████████| 14418/14418 [47:04<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.99it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_121442-b8pjz8t5/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_121442-b8pjz8t5/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_121442-b8pjz8t5/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 +packaging==25.0 +nvidia-nccl-cu12==2.27.3 +debugpy==1.8.16 +ipython==8.18.1 +anyio==4.12.0 +prompt_toolkit==3.0.51 +mkl_fft==1.3.11 +httpcore==1.0.9 +Jinja2==3.1.6 +ply==3.11 +zipp==3.23.0 +setproctitle==1.3.6 +docker-pycreds==0.4.0 +nvidia-cuda-nvrtc-cu12==12.8.93 +urllib3==2.5.0 +kiwisolver==1.4.4 +nvidia-curand-cu12==10.3.9.90 +llvmlite==0.43.0 +six==1.17.0 +frozenlist==1.8.0 +wcwidth==0.2.13 +numexpr==2.10.1 +click==8.1.8 +multiprocess==0.70.18 +threadpoolctl==3.6.0 +typing_extensions==4.15.0 +decorator==5.2.1 +sip==6.7.12 +pure_eval==0.2.3 +async-timeout==5.0.1 +Pygments==2.19.2 +mkl-service==2.4.0 +transformers==4.35.2 +numba==0.60.0 +pyzmq==27.0.2 +mkl_random==1.2.8 +ptyprocess==0.7.0 +nvidia-cuda-cupti-cu12==12.8.90 +charset-normalizer==3.4.4 +nvidia-cublas-cu12==12.8.4.1 +PyQt5_sip==12.13.0 +Bottleneck==1.4.2 +networkx==3.2.1 +PySocks==1.7.1 +pysam==0.9.1 +tornado==6.5.2 +pandas==2.3.3 +smmap==5.0.2 +PyQt5==5.15.10 +nvidia-cufft-cu12==11.3.3.83 +safetensors==0.7.0 +requests==2.32.5 +pytz==2025.2 +fsspec==2025.7.0 +certifi==2025.10.5 +sentry-sdk==2.35.0 +parso==0.8.4 +aiosignal==1.4.0 +traitlets==5.14.3 +hf-xet==1.1.8 +nvidia-cudnn-cu12==9.10.2.21 +accelerate==0.25.0 +eval_type_backport==0.2.2 +datasets==4.4.1 +huggingface_hub==0.34.4 +wandb==0.23.1 +tomli==2.2.1 +comm==0.2.3 +executing==2.2.0 +PyYAML==6.0.2 +scipy==1.13.1 +pexpect==4.9.0 +matplotlib==3.9.2 +annotated-types==0.7.0 +asttokens==3.0.0 +tokenizers==0.15.2 +nvidia-cufile-cu12==1.13.1.3 +appdirs==1.4.4 +h11==0.16.0 +numpy==2.0.2 +jupyter_client==8.6.3 +joblib==1.5.1 +joblib==1.5.3 +jedi==0.19.2 +MarkupSafe==3.0.3 +nvidia-nvjitlink-cu12==12.8.93 +pyarrow==21.0.0 +torch==2.8.0 +protobuf==3.20.3 +propcache==0.4.1 +multidict==6.7.0 +nvidia-cusolver-cu12==11.7.3.90 +umap-learn==0.5.9.post2 +ipykernel==6.30.1 +triton==3.4.0 +sympy==1.14.0 +scikit-learn==1.6.1 +brotlicffi==1.0.9.2 +xxhash==3.6.0 +seaborn==0.13.2 +pynndescent==0.5.13 +regex==2025.11.3 +typing-inspection==0.4.1 +evaluate==0.4.6 +nvidia-cuda-runtime-cu12==12.8.90 +filelock==3.17.0 +aiohappyeyeballs==2.6.1 +setuptools==80.9.0 diff --git a/VASC/len2_5120/wandb/run-20260308_121442-b8pjz8t5/files/wandb-metadata.json b/VASC/len2_5120/wandb/run-20260308_121442-b8pjz8t5/files/wandb-metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..a8cef8cd46ea952139760c627f90ed305bb9b5de --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_121442-b8pjz8t5/files/wandb-metadata.json @@ -0,0 +1,144 @@ +{ + "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", + "python": "CPython 3.9.18", + "startedAt": "2026-03-08T12:14:42.719343Z", + "args": [ + "--model_name_or_path", + "/home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000", + "--tokenizer_path", + "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_3072/merge_tokenizer_unigram_len2.json", + "--trust_remote_code", + "True", + "--data_path", + "/home/n5huang/dna_token/Finetune-screen/finetune_data/super_binary/VASC", + 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+push_to_hub_organization: + value: null +push_to_hub_token: + value: +ray_scope: + value: last +remove_invalid_values: + value: false +remove_unused_columns: + value: true +repetition_penalty: + value: 1 +report_to: + value: + - wandb +resume_from_checkpoint: + value: null +return_dict: + value: true +return_dict_in_generate: + value: false +run_name: + value: hg38_len2_3072_binary_VASC_lr1e-5_wd0.05_wr0.10_ep8_seed42 +save_model: + value: false +save_on_each_node: + value: false +save_safetensors: + value: true +save_steps: + value: 100 +save_strategy: + value: epoch +save_total_limit: + value: 1 +seed: + value: 42 +sep_token_id: + value: null +skip_memory_metrics: + value: true +split_batches: + value: false +suppress_tokens: + value: null +task_specific_params: + value: null +temperature: + value: 1 +tf_legacy_loss: + value: false +tf32: + value: null +tie_encoder_decoder: + value: false +tie_word_embeddings: + value: true +tokenizer_class: + value: null +top_k: + value: 50 +top_p: + value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.1 +warmup_steps: + value: 0 +weight_decay: + value: 0.05 diff --git a/VASC/len2_5120/wandb/run-20260308_130322-gcnv0gtv/files/output.log b/VASC/len2_5120/wandb/run-20260308_130322-gcnv0gtv/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..22c9912a5860d3108d5b2ff3f6cc885433e960c0 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_130322-gcnv0gtv/files/output.log @@ -0,0 +1,300 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['classifier.weight', 'bert.pooler.dense.bias', 'bert.pooler.dense.weight', 'classifier.bias'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. 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+{'loss': 0.3333, 'learning_rate': 8.68389110456043e-06, 'epoch': 1.75} +{'loss': 0.3489, 'learning_rate': 8.62609097740015e-06, 'epoch': 1.79} +{'loss': 0.3402, 'learning_rate': 8.568290850239872e-06, 'epoch': 1.83} +{'loss': 0.3346, 'learning_rate': 8.510490723079593e-06, 'epoch': 1.87} +{'loss': 0.3359, 'learning_rate': 8.452690595919312e-06, 'epoch': 1.91} +{'loss': 0.3331, 'learning_rate': 8.394890468759032e-06, 'epoch': 1.96} +{'loss': 0.3262, 'learning_rate': 8.337090341598753e-06, 'epoch': 2.0} + Num examples = 38441 + Batch size = 128 + 25%|██▌ | 4806/19224 [15:39<43:59, 5.46itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-4806 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-4806/config.json +{'eval_loss': 0.3376946449279785, 'eval_accuracy': 0.8736245154912723, 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'learning_rate': 8.221490087278192e-06, 'epoch': 2.08} +{'loss': 0.3242, 'learning_rate': 8.163689960117913e-06, 'epoch': 2.12} +{'loss': 0.3217, 'learning_rate': 8.105889832957633e-06, 'epoch': 2.16} +{'loss': 0.3232, 'learning_rate': 8.048089705797354e-06, 'epoch': 2.21} +{'loss': 0.3272, 'learning_rate': 7.990289578637073e-06, 'epoch': 2.25} +{'loss': 0.324, 'learning_rate': 7.932489451476793e-06, 'epoch': 2.29} +{'loss': 0.3312, 'learning_rate': 7.874689324316514e-06, 'epoch': 2.33} +{'loss': 0.3273, 'learning_rate': 7.816889197156234e-06, 'epoch': 2.37} +{'loss': 0.327, 'learning_rate': 7.759089069995955e-06, 'epoch': 2.41} +{'loss': 0.3295, 'learning_rate': 7.701288942835674e-06, 'epoch': 2.46} +{'loss': 0.3262, 'learning_rate': 7.643488815675396e-06, 'epoch': 2.5} +{'loss': 0.3257, 'learning_rate': 7.585688688515115e-06, 'epoch': 2.54} +{'loss': 0.3261, 'learning_rate': 7.5278885613548355e-06, 'epoch': 2.58} +{'loss': 0.3346, 'learning_rate': 7.470088434194556e-06, 'epoch': 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/config.json +{'eval_loss': 0.3396933972835541, 'eval_accuracy': 0.8707369735438725, 'eval_f1': 0.6932660297409283, 'eval_matthews_correlation': 0.40955524087376305, 'eval_precision': 0.7572642357502788, 'eval_recall': 0.6629992358226422, 'eval_runtime': 13.2867, 'eval_samples_per_second': 2893.198, 'eval_steps_per_second': 22.654, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-4806] due to args.save_total_limit + 50%|█████ | 9612/19224 [31:09<28:27, 5.63it/s]***** Running Evaluation ***** +{'loss': 0.3095, 'learning_rate': 6.892087162591759e-06, 'epoch': 3.04} +{'loss': 0.3134, 'learning_rate': 6.834287035431478e-06, 'epoch': 3.08} +{'loss': 0.3042, 'learning_rate': 6.776486908271199e-06, 'epoch': 3.12} +{'loss': 0.3139, 'learning_rate': 6.718686781110919e-06, 'epoch': 3.16} +{'loss': 0.3107, 'learning_rate': 6.660886653950639e-06, 'epoch': 3.2} +{'loss': 0.303, 'learning_rate': 6.60308652679036e-06, 'epoch': 3.25} +{'loss': 0.3192, 'learning_rate': 6.54528639963008e-06, 'epoch': 3.29} +{'loss': 0.2999, 'learning_rate': 6.4874862724697995e-06, 'epoch': 3.33} +{'loss': 0.3023, 'learning_rate': 6.430264146581123e-06, 'epoch': 3.37} +{'loss': 0.3113, 'learning_rate': 6.372464019420843e-06, 'epoch': 3.41} +{'loss': 0.3256, 'learning_rate': 6.314663892260563e-06, 'epoch': 3.45} +{'loss': 0.3258, 'learning_rate': 6.2568637651002835e-06, 'epoch': 3.5} +{'loss': 0.3047, 'learning_rate': 6.199063637940004e-06, 'epoch': 3.54} +{'loss': 0.3053, 'learning_rate': 6.141263510779725e-06, 'epoch': 3.58} +{'loss': 0.3065, 'learning_rate': 6.083463383619445e-06, 'epoch': 3.62} +{'loss': 0.318, 'learning_rate': 6.025663256459164e-06, 'epoch': 3.66} +{'loss': 0.3226, 'learning_rate': 5.967863129298885e-06, 'epoch': 3.7} +{'loss': 0.3114, 'learning_rate': 5.910063002138605e-06, 'epoch': 3.75} +{'loss': 0.3156, 'learning_rate': 5.852262874978325e-06, 'epoch': 3.79} +{'loss': 0.3153, 'learning_rate': 5.794462747818046e-06, 'epoch': 3.83} +{'loss': 0.3175, 'learning_rate': 5.7372406219293685e-06, 'epoch': 3.87} +{'loss': 0.3046, 'learning_rate': 5.679440494769088e-06, 'epoch': 3.91} +{'loss': 0.3081, 'learning_rate': 5.621640367608809e-06, 'epoch': 3.95} +{'loss': 0.3139, 'learning_rate': 5.56384024044853e-06, 'epoch': 4.0} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 9612/19224 [31:22<28:27, 5.63itSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-9612 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-9612/config.json +{'eval_loss': 0.3391009569168091, 'eval_accuracy': 0.8684477510990869, 'eval_f1': 0.6903310849420633, 'eval_matthews_correlation': 0.40146976916919236, 'eval_precision': 0.7493768007001089, 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+{'loss': 0.2925, 'learning_rate': 5.332639731807411e-06, 'epoch': 4.16} +{'loss': 0.285, 'learning_rate': 5.274839604647131e-06, 'epoch': 4.2} +{'loss': 0.2998, 'learning_rate': 5.21703947748685e-06, 'epoch': 4.24} +{'loss': 0.2951, 'learning_rate': 5.159239350326571e-06, 'epoch': 4.29} +{'loss': 0.293, 'learning_rate': 5.101439223166291e-06, 'epoch': 4.33} +{'loss': 0.3042, 'learning_rate': 5.043639096006011e-06, 'epoch': 4.37} +{'loss': 0.2949, 'learning_rate': 4.985838968845732e-06, 'epoch': 4.41} +{'loss': 0.2998, 'learning_rate': 4.928038841685452e-06, 'epoch': 4.45} +{'loss': 0.2916, 'learning_rate': 4.870238714525172e-06, 'epoch': 4.49} +{'loss': 0.295, 'learning_rate': 4.812438587364893e-06, 'epoch': 4.54} +{'loss': 0.2934, 'learning_rate': 4.754638460204613e-06, 'epoch': 4.58} +{'loss': 0.301, 'learning_rate': 4.6968383330443325e-06, 'epoch': 4.62} +{'loss': 0.2842, 'learning_rate': 4.639038205884053e-06, 'epoch': 4.66} +{'loss': 0.2984, 'learning_rate': 4.581238078723773e-06, 'epoch': 4.7} +{'loss': 0.2973, 'learning_rate': 4.5234379515634945e-06, 'epoch': 4.74} +{'loss': 0.2875, 'learning_rate': 4.465637824403214e-06, 'epoch': 4.79} +{'loss': 0.2997, 'learning_rate': 4.407837697242934e-06, 'epoch': 4.83} +{'loss': 0.2933, 'learning_rate': 4.350037570082655e-06, 'epoch': 4.87} +{'loss': 0.2977, 'learning_rate': 4.292237442922374e-06, 'epoch': 4.91} +{'loss': 0.2919, 'learning_rate': 4.234437315762095e-06, 'epoch': 4.95} +{'loss': 0.296, 'learning_rate': 4.176637188601815e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 62%|██████▎ | 12015/19224 [39:13<20:54, 5.75iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-12015/config.json +{'eval_loss': 0.34544411301612854, 'eval_accuracy': 0.8726099737259697, 'eval_f1': 0.6786151204425603, 'eval_matthews_correlation': 0.3979070463366854, 'eval_precision': 0.7741222161194342, 'eval_recall': 0.6443972872444979, 'eval_runtime': 13.2931, 'eval_samples_per_second': 2891.799, 'eval_steps_per_second': 22.643, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-9612] due to args.save_total_limit + 75%|███████▌ | 14418/19224 [46:51<14:26, 5.54it/s]***** Running Evaluation ***** +{'loss': 0.2695, 'learning_rate': 4.118837061441535e-06, 'epoch': 5.04} +{'loss': 0.2827, 'learning_rate': 4.061036934281256e-06, 'epoch': 5.08} +{'loss': 0.2725, 'learning_rate': 4.003236807120976e-06, 'epoch': 5.12} +{'loss': 0.2713, 'learning_rate': 3.9454366799606964e-06, 'epoch': 5.16} +{'loss': 0.2781, 'learning_rate': 3.887636552800417e-06, 'epoch': 5.2} +{'loss': 0.2723, 'learning_rate': 3.829836425640136e-06, 'epoch': 5.24} +{'loss': 0.2687, 'learning_rate': 3.772036298479857e-06, 'epoch': 5.29} +{'loss': 0.2721, 'learning_rate': 3.7142361713195775e-06, 'epoch': 5.33} +{'loss': 0.2796, 'learning_rate': 3.6564360441592974e-06, 'epoch': 5.37} +{'loss': 0.28, 'learning_rate': 3.5986359169990178e-06, 'epoch': 5.41} +{'loss': 0.2839, 'learning_rate': 3.540835789838738e-06, 'epoch': 5.45} +{'loss': 0.2777, 'learning_rate': 3.4830356626784585e-06, 'epoch': 5.49} +{'loss': 0.2771, 'learning_rate': 3.425813536789781e-06, 'epoch': 5.53} +{'loss': 0.2804, 'learning_rate': 3.3680134096295014e-06, 'epoch': 5.58} +{'loss': 0.2683, 'learning_rate': 3.3102132824692217e-06, 'epoch': 5.62} +{'loss': 0.2814, 'learning_rate': 3.252413155308942e-06, 'epoch': 5.66} +{'loss': 0.2812, 'learning_rate': 3.194613028148662e-06, 'epoch': 5.7} +{'loss': 0.2692, 'learning_rate': 3.1368129009883824e-06, 'epoch': 5.74} +{'loss': 0.2764, 'learning_rate': 3.0790127738281028e-06, 'epoch': 5.78} +{'loss': 0.2733, 'learning_rate': 3.0212126466678227e-06, 'epoch': 5.83} +{'loss': 0.2823, 'learning_rate': 2.963412519507543e-06, 'epoch': 5.87} +{'loss': 0.2711, 'learning_rate': 2.9056123923472634e-06, 'epoch': 5.91} +{'loss': 0.2725, 'learning_rate': 2.8478122651869838e-06, 'epoch': 5.95} +{'loss': 0.2807, 'learning_rate': 2.7900121380267037e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 75%|███████▌ | 14418/19224 [47:04<14:26, 5.54iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/config.json +{'eval_loss': 0.35580945014953613, 'eval_accuracy': 0.8681355844020707, 'eval_f1': 0.6790391032663143, 'eval_matthews_correlation': 0.38695812266252855, 'eval_precision': 0.7521658239266813, 'eval_recall': 0.648450517959608, 'eval_runtime': 13.313, 'eval_samples_per_second': 2887.479, 'eval_steps_per_second': 22.609, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-12015] due to args.save_total_limit + 88%|████████▊ | 16821/19224 [54:43<06:55, 5.78it/s]***** Running Evaluation ***** +{'loss': 0.2627, 'learning_rate': 2.732212010866424e-06, 'epoch': 6.03} +{'loss': 0.261, 'learning_rate': 2.6744118837061445e-06, 'epoch': 6.08} +{'loss': 0.2547, 'learning_rate': 2.616611756545865e-06, 'epoch': 6.12} +{'loss': 0.2617, 'learning_rate': 2.5588116293855848e-06, 'epoch': 6.16} +{'loss': 0.2599, 'learning_rate': 2.501011502225305e-06, 'epoch': 6.2} +{'loss': 0.2569, 'learning_rate': 2.4432113750650255e-06, 'epoch': 6.24} +{'loss': 0.2604, 'learning_rate': 2.3854112479047454e-06, 'epoch': 6.28} +{'loss': 0.2586, 'learning_rate': 2.327611120744466e-06, 'epoch': 6.33} +{'loss': 0.2571, 'learning_rate': 2.269810993584186e-06, 'epoch': 6.37} +{'loss': 0.2562, 'learning_rate': 2.212588867695509e-06, 'epoch': 6.41} +{'loss': 0.2556, 'learning_rate': 2.1547887405352294e-06, 'epoch': 6.45} +{'loss': 0.2575, 'learning_rate': 2.0969886133749494e-06, 'epoch': 6.49} +{'loss': 0.252, 'learning_rate': 2.0391884862146698e-06, 'epoch': 6.53} +{'loss': 0.2536, 'learning_rate': 1.98138835905439e-06, 'epoch': 6.58} +{'loss': 0.2507, 'learning_rate': 1.9235882318941105e-06, 'epoch': 6.62} +{'loss': 0.263, 'learning_rate': 1.8657881047338306e-06, 'epoch': 6.66} +{'loss': 0.2601, 'learning_rate': 1.807987977573551e-06, 'epoch': 6.7} +{'loss': 0.2554, 'learning_rate': 1.7501878504132711e-06, 'epoch': 6.74} +{'loss': 0.2553, 'learning_rate': 1.692387723252991e-06, 'epoch': 6.78} +{'loss': 0.27, 'learning_rate': 1.6345875960927117e-06, 'epoch': 6.82} +{'loss': 0.2511, 'learning_rate': 1.5767874689324316e-06, 'epoch': 6.87} +{'loss': 0.2613, 'learning_rate': 1.518987341772152e-06, 'epoch': 6.91} +{'loss': 0.2604, 'learning_rate': 1.4611872146118721e-06, 'epoch': 6.95} +{'loss': 0.2564, 'learning_rate': 1.4033870874515925e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 88%|████████▊ | 16821/19224 [54:56<06:55, 5.78iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/config.json +{'eval_loss': 0.37344297766685486, 'eval_accuracy': 0.8599932363882313, 'eval_f1': 0.689395904465144, 'eval_matthews_correlation': 0.38797302731676697, 'eval_precision': 0.7230662711726488, 'eval_recall': 0.6686977026312003, 'eval_runtime': 13.3034, 'eval_samples_per_second': 2889.564, 'eval_steps_per_second': 22.626, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-14418] due to args.save_total_limit +100%|██████████| 19224/19224 [1:02:33<00:00, 5.79it/s]***** Running Evaluation ***** +{'loss': 0.2409, 'learning_rate': 1.3455869602913126e-06, 'epoch': 7.03} +{'loss': 0.2452, 'learning_rate': 1.287786833131033e-06, 'epoch': 7.07} +{'loss': 0.2358, 'learning_rate': 1.2299867059707532e-06, 'epoch': 7.12} +{'loss': 0.2481, 'learning_rate': 1.1721865788104735e-06, 'epoch': 7.16} +{'loss': 0.2384, 'learning_rate': 1.1143864516501937e-06, 'epoch': 7.2} +{'loss': 0.2398, 'learning_rate': 1.056586324489914e-06, 'epoch': 7.24} +{'loss': 0.2411, 'learning_rate': 9.99364198601237e-07, 'epoch': 7.28} +{'loss': 0.2436, 'learning_rate': 9.415640714409572e-07, 'epoch': 7.32} +{'loss': 0.2433, 'learning_rate': 8.837639442806775e-07, 'epoch': 7.37} +{'loss': 0.227, 'learning_rate': 8.259638171203977e-07, 'epoch': 7.41} +{'loss': 0.2411, 'learning_rate': 7.68163689960118e-07, 'epoch': 7.45} +{'loss': 0.2406, 'learning_rate': 7.103635627998383e-07, 'epoch': 7.49} +{'loss': 0.2442, 'learning_rate': 6.525634356395584e-07, 'epoch': 7.53} +{'loss': 0.2447, 'learning_rate': 5.947633084792788e-07, 'epoch': 7.57} +{'loss': 0.255, 'learning_rate': 5.36963181318999e-07, 'epoch': 7.62} +{'loss': 0.242, 'learning_rate': 4.791630541587192e-07, 'epoch': 7.66} +{'loss': 0.246, 'learning_rate': 4.2136292699843943e-07, 'epoch': 7.7} +{'loss': 0.2425, 'learning_rate': 3.635627998381597e-07, 'epoch': 7.74} +{'loss': 0.2402, 'learning_rate': 3.0576267267787995e-07, 'epoch': 7.78} +{'loss': 0.2469, 'learning_rate': 2.4796254551760015e-07, 'epoch': 7.82} +{'loss': 0.2411, 'learning_rate': 1.901624183573204e-07, 'epoch': 7.87} +{'loss': 0.2468, 'learning_rate': 1.3236229119704064e-07, 'epoch': 7.91} +{'loss': 0.2461, 'learning_rate': 7.456216403676089e-08, 'epoch': 7.95} +{'loss': 0.2369, 'learning_rate': 1.676203687648113e-08, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 19224/19224 [1:02:47<00:00, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/config.json +{'eval_loss': 0.3864426612854004, 'eval_accuracy': 0.8620483338102547, 'eval_f1': 0.6889089352974422, 'eval_matthews_correlation': 0.3896454841459382, 'eval_precision': 0.7286571195427378, 'eval_recall': 0.665994834994571, 'eval_runtime': 13.348, 'eval_samples_per_second': 2879.914, 'eval_steps_per_second': 22.55, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-16821] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-7209 (score: 0.6932660297409283). +100%|██████████| 19224/19224 [1:02:48<00:00, 5.79it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep8_seed42/checkpoint-19224] due to args.save_total_limit +{'train_runtime': 3768.6272, 'train_samples_per_second': 652.819, 'train_steps_per_second': 5.101, 'train_loss': 0.3016456620821197, 'epoch': 8.0} +100%|██████████| 19224/19224 [1:02:48<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.97it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_130322-gcnv0gtv/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_130322-gcnv0gtv/files/requirements.txt new 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+top_p: + value: 1 +torch_compile: + value: false +torch_compile_backend: + value: null +torch_compile_mode: + value: null +torch_dtype: + value: float32 +torchdynamo: + value: null +torchscript: + value: false +tpu_metrics_debug: + value: false +tpu_num_cores: + value: null +transformers_version: + value: 4.35.2 +type_vocab_size: + value: 2 +typical_p: + value: 1 +use_bfloat16: + value: false +use_cache: + value: true +use_cpu: + value: false +use_ipex: + value: false +use_legacy_prediction_loop: + value: false +use_mps_device: + value: false +vocab_file: + value: null +vocab_size: + value: 3072 +warmup_ratio: + value: 0.1 +warmup_steps: + value: 0 +weight_decay: + value: 0.05 diff --git a/VASC/len2_5120/wandb/run-20260308_140747-7mhn07ym/files/output.log b/VASC/len2_5120/wandb/run-20260308_140747-7mhn07ym/files/output.log new file mode 100644 index 0000000000000000000000000000000000000000..9aa5cee3d324fcf7be451a2f47f5bb3d9e4a3120 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_140747-7mhn07ym/files/output.log @@ -0,0 +1,368 @@ +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +WARNING:root:Perform single sequence classification... +Some weights of BertForSequenceClassification were not initialized from the model checkpoint at /home/n5huang/dna_token/pretrain/models/len2_3072/checkpoint-100000 and are newly initialized: ['bert.pooler.dense.bias', 'classifier.bias', 'bert.pooler.dense.weight', 'classifier.weight'] +You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference. +/home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/accelerate/accelerator.py:439: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead. + self.scaler = torch.cuda.amp.GradScaler(**kwargs) +Using auto half precision backend +***** Running training ***** + Num examples = 307,529 + Num Epochs = 10 + Instantaneous batch size per device = 128 + Total train batch size (w. parallel, distributed & accumulation) = 128 + Gradient Accumulation steps = 1 + Total optimization steps = 24,030 + Number of trainable parameters = 88,402,178 +Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true" + 10%|█ | 2403/24030 [07:34<1:02:11, 5.80it/s]***** Running Evaluation ***** +{'loss': 0.6158, 'learning_rate': 4.161464835622139e-07, 'epoch': 0.04} +{'loss': 0.4201, 'learning_rate': 8.322929671244278e-07, 'epoch': 0.08} +{'loss': 0.3717, 'learning_rate': 1.2484394506866417e-06, 'epoch': 0.12} +{'loss': 0.359, 'learning_rate': 1.6645859342488557e-06, 'epoch': 0.17} +{'loss': 0.3636, 'learning_rate': 2.0807324178110696e-06, 'epoch': 0.21} 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/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/config.json +{'eval_loss': 0.34122735261917114, 'eval_accuracy': 0.8704508207382743, 'eval_f1': 0.695017905278726, 'eval_matthews_correlation': 0.4111680421209115, 'eval_precision': 0.755433782945095, 'eval_recall': 0.6654628030328731, 'eval_runtime': 13.4061, 'eval_samples_per_second': 2867.43, 'eval_steps_per_second': 22.452, 'epoch': 3.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-2403] due to args.save_total_limit +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-4806] due to args.save_total_limit + 40%|████ | 9612/24030 [31:06<41:40, 5.77it/s]***** Running Evaluation ***** +{'loss': 0.3083, 'learning_rate': 7.735700744439821e-06, 'epoch': 3.04} +{'loss': 0.3122, 'learning_rate': 7.689462246266241e-06, 'epoch': 3.08} +{'loss': 0.3036, 'learning_rate': 7.643223748092663e-06, 'epoch': 3.12} +{'loss': 0.312, 'learning_rate': 7.596985249919083e-06, 'epoch': 3.16} +{'loss': 0.3071, 'learning_rate': 7.550746751745504e-06, 'epoch': 3.2} +{'loss': 0.3005, 'learning_rate': 7.504508253571925e-06, 'epoch': 3.25} +{'loss': 0.3159, 'learning_rate': 7.458269755398345e-06, 'epoch': 3.29} +{'loss': 0.2983, 'learning_rate': 7.412031257224766e-06, 'epoch': 3.33} +{'loss': 0.3022, 'learning_rate': 7.3662551440329225e-06, 'epoch': 3.37} +{'loss': 0.3106, 'learning_rate': 7.320016645859343e-06, 'epoch': 3.41} +{'loss': 0.3242, 'learning_rate': 7.273778147685764e-06, 'epoch': 3.45} +{'loss': 0.3228, 'learning_rate': 7.227539649512184e-06, 'epoch': 3.5} +{'loss': 0.3047, 'learning_rate': 7.1813011513386055e-06, 'epoch': 3.54} +{'loss': 0.3028, 'learning_rate': 7.135062653165026e-06, 'epoch': 3.58} +{'loss': 0.307, 'learning_rate': 7.088824154991446e-06, 'epoch': 3.62} +{'loss': 0.3176, 'learning_rate': 7.042585656817868e-06, 'epoch': 3.66} +{'loss': 0.3216, 'learning_rate': 6.9963471586442876e-06, 'epoch': 3.7} +{'loss': 0.3115, 'learning_rate': 6.950108660470708e-06, 'epoch': 3.75} +{'loss': 0.3155, 'learning_rate': 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'learning_rate': 5.8870855874601196e-06, 'epoch': 4.7} +{'loss': 0.2936, 'learning_rate': 5.840847089286541e-06, 'epoch': 4.74} +{'loss': 0.2857, 'learning_rate': 5.794608591112961e-06, 'epoch': 4.79} +{'loss': 0.2977, 'learning_rate': 5.748370092939382e-06, 'epoch': 4.83} +{'loss': 0.2944, 'learning_rate': 5.7021315947658025e-06, 'epoch': 4.87} +{'loss': 0.2966, 'learning_rate': 5.655893096592223e-06, 'epoch': 4.91} +{'loss': 0.2876, 'learning_rate': 5.609654598418643e-06, 'epoch': 4.95} +{'loss': 0.2909, 'learning_rate': 5.563416100245065e-06, 'epoch': 4.99} + Num examples = 38441 + Batch size = 128 + 50%|█████ | 12015/24030 [39:10<34:59, 5.72iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015/config.json +{'eval_loss': 0.3474220633506775, 'eval_accuracy': 0.8682136260763248, 'eval_f1': 0.6811178601187744, 'eval_matthews_correlation': 0.38959846933502823, 'eval_precision': 0.7516816806896645, 'eval_recall': 0.6507727607470939, 'eval_runtime': 13.3095, 'eval_samples_per_second': 2888.232, 'eval_steps_per_second': 22.615, 'epoch': 5.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-9612] due to args.save_total_limit + 60%|██████ | 14418/24030 [46:47<27:32, 5.82it/s]***** Running Evaluation ***** +{'loss': 0.2677, 'learning_rate': 5.5171776020714855e-06, 'epoch': 5.04} +{'loss': 0.2744, 'learning_rate': 5.470939103897905e-06, 'epoch': 5.08} +{'loss': 0.2672, 'learning_rate': 5.424700605724327e-06, 'epoch': 5.12} +{'loss': 0.2652, 'learning_rate': 5.378462107550747e-06, 'epoch': 5.16} +{'loss': 0.2755, 'learning_rate': 5.332223609377168e-06, 'epoch': 5.2} +{'loss': 0.2658, 'learning_rate': 5.285985111203588e-06, 'epoch': 5.24} +{'loss': 0.26, 'learning_rate': 5.239746613030009e-06, 'epoch': 5.29} +{'loss': 0.2625, 'learning_rate': 5.193508114856431e-06, 'epoch': 5.33} +{'loss': 0.2792, 'learning_rate': 5.147269616682851e-06, 'epoch': 5.37} +{'loss': 0.2696, 'learning_rate': 5.101031118509271e-06, 'epoch': 5.41} +{'loss': 0.2774, 'learning_rate': 5.054792620335692e-06, 'epoch': 5.45} +{'loss': 0.2715, 'learning_rate': 5.008554122162113e-06, 'epoch': 5.49} +{'loss': 0.2726, 'learning_rate': 4.9627780089702695e-06, 'epoch': 5.53} +{'loss': 0.2767, 'learning_rate': 4.916539510796689e-06, 'epoch': 5.58} +{'loss': 0.2629, 'learning_rate': 4.87030101262311e-06, 'epoch': 5.62} +{'loss': 0.277, 'learning_rate': 4.824062514449531e-06, 'epoch': 5.66} +{'loss': 0.2744, 'learning_rate': 4.777824016275952e-06, 'epoch': 5.7} +{'loss': 0.2669, 'learning_rate': 4.731585518102372e-06, 'epoch': 5.74} +{'loss': 0.2694, 'learning_rate': 4.685347019928793e-06, 'epoch': 5.78} +{'loss': 0.2651, 'learning_rate': 4.639108521755214e-06, 'epoch': 5.83} +{'loss': 0.2755, 'learning_rate': 4.5928700235816345e-06, 'epoch': 5.87} +{'loss': 0.2683, 'learning_rate': 4.546631525408055e-06, 'epoch': 5.91} +{'loss': 0.2692, 'learning_rate': 4.500393027234476e-06, 'epoch': 5.95} +{'loss': 0.2764, 'learning_rate': 4.454154529060897e-06, 'epoch': 5.99} + Num examples = 38441 + Batch size = 128 + 60%|██████ | 14418/24030 [47:01<27:32, 5.82iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/config.json +{'eval_loss': 0.3610430955886841, 'eval_accuracy': 0.8625946255300331, 'eval_f1': 0.6849676483475847, 'eval_matthews_correlation': 0.3846715772942777, 'eval_precision': 0.7306125144045535, 'eval_recall': 0.6604121775005738, 'eval_runtime': 13.3169, 'eval_samples_per_second': 2886.631, 'eval_steps_per_second': 22.603, 'epoch': 6.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-12015] due to args.save_total_limit + 70%|███████ | 16821/24030 [54:38<20:40, 5.81it/s]***** Running Evaluation ***** +{'loss': 0.2519, 'learning_rate': 4.407916030887317e-06, 'epoch': 6.03} +{'loss': 0.2502, 'learning_rate': 4.361677532713738e-06, 'epoch': 6.08} +{'loss': 0.2374, 'learning_rate': 4.315439034540159e-06, 'epoch': 6.12} +{'loss': 0.2503, 'learning_rate': 4.269200536366579e-06, 'epoch': 6.16} +{'loss': 0.2517, 'learning_rate': 4.222962038193e-06, 'epoch': 6.2} +{'loss': 0.246, 'learning_rate': 4.17672354001942e-06, 'epoch': 6.24} +{'loss': 0.2494, 'learning_rate': 4.130485041845841e-06, 'epoch': 6.28} +{'loss': 0.2442, 'learning_rate': 4.084246543672262e-06, 'epoch': 6.33} +{'loss': 0.2484, 'learning_rate': 4.038008045498683e-06, 'epoch': 6.37} +{'loss': 0.2474, 'learning_rate': 3.992231932306839e-06, 'epoch': 6.41} +{'loss': 0.2498, 'learning_rate': 3.945993434133259e-06, 'epoch': 6.45} +{'loss': 0.2465, 'learning_rate': 3.899754935959681e-06, 'epoch': 6.49} +{'loss': 0.2442, 'learning_rate': 3.8535164377861015e-06, 'epoch': 6.53} +{'loss': 0.2457, 'learning_rate': 3.8072779396125214e-06, 'epoch': 6.58} +{'loss': 0.2416, 'learning_rate': 3.761039441438942e-06, 'epoch': 6.62} +{'loss': 0.2528, 'learning_rate': 3.7148009432653633e-06, 'epoch': 6.66} +{'loss': 0.2478, 'learning_rate': 3.668562445091784e-06, 'epoch': 6.7} +{'loss': 0.2442, 'learning_rate': 3.6223239469182043e-06, 'epoch': 6.74} +{'loss': 0.2471, 'learning_rate': 3.576085448744625e-06, 'epoch': 6.78} +{'loss': 0.2655, 'learning_rate': 3.529846950571046e-06, 'epoch': 6.82} +{'loss': 0.2399, 'learning_rate': 3.483608452397466e-06, 'epoch': 6.87} +{'loss': 0.2481, 'learning_rate': 3.437369954223887e-06, 'epoch': 6.91} +{'loss': 0.2536, 'learning_rate': 3.3911314560503076e-06, 'epoch': 6.95} +{'loss': 0.2401, 'learning_rate': 3.3448929578767288e-06, 'epoch': 6.99} + Num examples = 38441 + Batch size = 128 + 70%|███████ | 16821/24030 [54:52<20:40, 5.81iSaving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/config.json +{'eval_loss': 0.3881157338619232, 'eval_accuracy': 0.8546083608647017, 'eval_f1': 0.6877683493437349, 'eval_matthews_correlation': 0.3804766938966969, 'eval_precision': 0.7104086054663982, 'eval_recall': 0.6720016563458464, 'eval_runtime': 13.3195, 'eval_samples_per_second': 2886.079, 'eval_steps_per_second': 22.599, 'epoch': 7.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-14418] due to args.save_total_limit + 80%|████████ | 19224/24030 [1:02:31<13:45, 5.82it/s]***** Running Evaluation ***** +{'loss': 0.2262, 'learning_rate': 3.298654459703149e-06, 'epoch': 7.03} +{'loss': 0.2236, 'learning_rate': 3.25241596152957e-06, 'epoch': 7.07} +{'loss': 0.2162, 'learning_rate': 3.2061774633559906e-06, 'epoch': 7.12} +{'loss': 0.2285, 'learning_rate': 3.1599389651824113e-06, 'epoch': 7.16} +{'loss': 0.2181, 'learning_rate': 3.1137004670088316e-06, 'epoch': 7.2} +{'loss': 0.2237, 'learning_rate': 3.0679243538169883e-06, 'epoch': 7.24} +{'loss': 0.2242, 'learning_rate': 3.021685855643409e-06, 'epoch': 7.28} +{'loss': 0.2272, 'learning_rate': 2.9754473574698293e-06, 'epoch': 7.32} +{'loss': 0.2259, 'learning_rate': 2.9292088592962505e-06, 'epoch': 7.37} +{'loss': 0.2104, 'learning_rate': 2.8829703611226713e-06, 'epoch': 7.41} +{'loss': 0.2231, 'learning_rate': 2.8367318629490916e-06, 'epoch': 7.45} +{'loss': 0.2236, 'learning_rate': 2.7904933647755123e-06, 'epoch': 7.49} +{'loss': 0.2292, 'learning_rate': 2.744254866601933e-06, 'epoch': 7.53} +{'loss': 0.2325, 'learning_rate': 2.698016368428354e-06, 'epoch': 7.57} +{'loss': 0.2397, 'learning_rate': 2.651777870254774e-06, 'epoch': 7.62} +{'loss': 0.2282, 'learning_rate': 2.605539372081195e-06, 'epoch': 7.66} +{'loss': 0.2354, 'learning_rate': 2.559300873907616e-06, 'epoch': 7.7} +{'loss': 0.227, 'learning_rate': 2.513062375734036e-06, 'epoch': 7.74} +{'loss': 0.2237, 'learning_rate': 2.466823877560457e-06, 'epoch': 7.78} +{'loss': 0.2295, 'learning_rate': 2.420585379386878e-06, 'epoch': 7.82} +{'loss': 0.2232, 'learning_rate': 2.374346881213298e-06, 'epoch': 7.87} +{'loss': 0.2329, 'learning_rate': 2.3281083830397193e-06, 'epoch': 7.91} +{'loss': 0.2294, 'learning_rate': 2.2818698848661396e-06, 'epoch': 7.95} +{'loss': 0.2173, 'learning_rate': 2.2356313866925604e-06, 'epoch': 7.99} + Num examples = 38441 + Batch size = 128 + 80%|████████ | 19224/24030 [1:02:44<13:45, 5.8Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/config.json +{'eval_loss': 0.411857932806015, 'eval_accuracy': 0.8553367498244062, 'eval_f1': 0.6804039621157125, 'eval_matthews_correlation': 0.36913839527969744, 'eval_precision': 0.7111515750879447, 'eval_recall': 0.6613333393474765, 'eval_runtime': 13.278, 'eval_samples_per_second': 2895.085, 'eval_steps_per_second': 22.669, 'epoch': 8.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-16821] due to args.save_total_limit + 90%|█████████ | 21627/24030 [1:10:22<06:56, 5.77it/s]***** Running Evaluation ***** +{'loss': 0.2077, 'learning_rate': 2.189392888518981e-06, 'epoch': 8.03} +{'loss': 0.2097, 'learning_rate': 2.1431543903454014e-06, 'epoch': 8.07} +{'loss': 0.206, 'learning_rate': 2.0973782771535585e-06, 'epoch': 8.11} +{'loss': 0.2077, 'learning_rate': 2.051139778979979e-06, 'epoch': 8.16} +{'loss': 0.2036, 'learning_rate': 2.0049012808063996e-06, 'epoch': 8.2} +{'loss': 0.2082, 'learning_rate': 1.9586627826328203e-06, 'epoch': 8.24} +{'loss': 0.2056, 'learning_rate': 1.912424284459241e-06, 'epoch': 8.28} +{'loss': 0.2072, 'learning_rate': 1.8661857862856616e-06, 'epoch': 8.32} +{'loss': 0.2036, 'learning_rate': 1.8199472881120823e-06, 'epoch': 8.36} +{'loss': 0.2132, 'learning_rate': 1.773708789938503e-06, 'epoch': 8.41} +{'loss': 0.2133, 'learning_rate': 1.7274702917649236e-06, 'epoch': 8.45} +{'loss': 0.2042, 'learning_rate': 1.6812317935913443e-06, 'epoch': 8.49} +{'loss': 0.2042, 'learning_rate': 1.634993295417765e-06, 'epoch': 8.53} +{'loss': 0.2023, 'learning_rate': 1.5887547972441856e-06, 'epoch': 8.57} +{'loss': 0.2146, 'learning_rate': 1.5425162990706063e-06, 'epoch': 8.61} +{'loss': 0.2043, 'learning_rate': 1.4962778008970269e-06, 'epoch': 8.66} +{'loss': 0.2087, 'learning_rate': 1.4500393027234478e-06, 'epoch': 8.7} +{'loss': 0.2105, 'learning_rate': 1.4038008045498683e-06, 'epoch': 8.74} +{'loss': 0.2056, 'learning_rate': 1.357562306376289e-06, 'epoch': 8.78} +{'loss': 0.2054, 'learning_rate': 1.3113238082027096e-06, 'epoch': 8.82} +{'loss': 0.2055, 'learning_rate': 1.2650853100291306e-06, 'epoch': 8.86} +{'loss': 0.2074, 'learning_rate': 1.218846811855551e-06, 'epoch': 8.91} +{'loss': 0.2081, 'learning_rate': 1.1726083136819716e-06, 'epoch': 8.95} +{'loss': 0.2132, 'learning_rate': 1.126832200490128e-06, 'epoch': 8.99} + Num examples = 38441 + Batch size = 128 + 90%|█████████ | 21627/24030 [1:10:35<06:56, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/config.json +{'eval_loss': 0.4375973343849182, 'eval_accuracy': 0.8530995551624567, 'eval_f1': 0.6791094254856543, 'eval_matthews_correlation': 0.36500459114138, 'eval_precision': 0.7059503690496023, 'eval_recall': 0.661723856297386, 'eval_runtime': 13.292, 'eval_samples_per_second': 2892.037, 'eval_steps_per_second': 22.645, 'epoch': 9.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-19224] due to args.save_total_limit +100%|██████████| 24030/24030 [1:18:13<00:00, 5.75it/s]***** Running Evaluation ***** +{'loss': 0.1959, 'learning_rate': 1.0805937023165488e-06, 'epoch': 9.03} +{'loss': 0.1978, 'learning_rate': 1.0343552041429696e-06, 'epoch': 9.07} +{'loss': 0.1832, 'learning_rate': 9.881167059693903e-07, 'epoch': 9.11} +{'loss': 0.1937, 'learning_rate': 9.418782077958109e-07, 'epoch': 9.16} +{'loss': 0.1906, 'learning_rate': 8.956397096222315e-07, 'epoch': 9.2} +{'loss': 0.1998, 'learning_rate': 8.494012114486522e-07, 'epoch': 9.24} +{'loss': 0.2021, 'learning_rate': 8.031627132750728e-07, 'epoch': 9.28} +{'loss': 0.1907, 'learning_rate': 7.569242151014936e-07, 'epoch': 9.32} +{'loss': 0.1888, 'learning_rate': 7.106857169279142e-07, 'epoch': 9.36} +{'loss': 0.2044, 'learning_rate': 6.64447218754335e-07, 'epoch': 9.4} +{'loss': 0.1891, 'learning_rate': 6.182087205807556e-07, 'epoch': 9.45} +{'loss': 0.1934, 'learning_rate': 5.719702224071762e-07, 'epoch': 9.49} +{'loss': 0.1961, 'learning_rate': 5.25731724233597e-07, 'epoch': 9.53} +{'loss': 0.1945, 'learning_rate': 4.794932260600176e-07, 'epoch': 9.57} +{'loss': 0.1967, 'learning_rate': 4.3325472788643834e-07, 'epoch': 9.61} +{'loss': 0.1893, 'learning_rate': 3.870162297128589e-07, 'epoch': 9.65} +{'loss': 0.195, 'learning_rate': 3.407777315392796e-07, 'epoch': 9.7} +{'loss': 0.1956, 'learning_rate': 2.945392333657003e-07, 'epoch': 9.74} +{'loss': 0.1896, 'learning_rate': 2.48300735192121e-07, 'epoch': 9.78} +{'loss': 0.1852, 'learning_rate': 2.0206223701854164e-07, 'epoch': 9.82} +{'loss': 0.1962, 'learning_rate': 1.5628612382669814e-07, 'epoch': 9.86} +{'loss': 0.1875, 'learning_rate': 1.1004762565311879e-07, 'epoch': 9.9} +{'loss': 0.1934, 'learning_rate': 6.380912747953947e-08, 'epoch': 9.95} +{'loss': 0.1864, 'learning_rate': 1.7570629305960146e-08, 'epoch': 9.99} + Num examples = 38441 + Batch size = 128 +100%|██████████| 24030/24030 [1:18:26<00:00, 5.7Saving model checkpoint to /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030 +Configuration saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030/config.json +{'eval_loss': 0.45599719882011414, 'eval_accuracy': 0.850472152129237, 'eval_f1': 0.6793308543383826, 'eval_matthews_correlation': 0.36333381649081975, 'eval_precision': 0.7006049597625444, 'eval_recall': 0.6645166978449165, 'eval_runtime': 13.3017, 'eval_samples_per_second': 2889.939, 'eval_steps_per_second': 22.629, 'epoch': 10.0} +Model weights saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030/pytorch_model.bin +tokenizer config file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030/tokenizer_config.json +Special tokens file saved in /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030/special_tokens_map.json +Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-21627] due to args.save_total_limit + + +Training completed. Do not forget to share your model on huggingface.co/models =) + + +Loading best model from /home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-7209 (score: 0.695017905278726). +100%|██████████| 24030/24030 [1:18:28<00:00, 5.75it/s]Deleting older checkpoint [/home/n5huang/dna_token/Finetune-species/super_binary_out_tune_1gpu_3072/VASC/len2_3072/lr1e-5_wd0.05_wr0.10_ep10_seed42/checkpoint-24030] due to args.save_total_limit +{'train_runtime': 4708.2775, 'train_samples_per_second': 653.167, 'train_steps_per_second': 5.104, 'train_loss': 0.2777588570063381, 'epoch': 10.0} +100%|██████████| 24030/24030 [1:18:28<00:00, 5.10it/s] +***** Running Evaluation ***** + Num examples = 38441 + Batch size = 128 +100%|██████████| 301/301 [00:21<00:00, 13.95it/s] diff --git a/VASC/len2_5120/wandb/run-20260308_140747-7mhn07ym/files/requirements.txt b/VASC/len2_5120/wandb/run-20260308_140747-7mhn07ym/files/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1de7237af3385ead30af1186a070d573708d520 --- /dev/null +++ b/VASC/len2_5120/wandb/run-20260308_140747-7mhn07ym/files/requirements.txt @@ -0,0 +1,148 @@ +fonttools==4.60.1 +mpmath==1.3.0 +httpx==0.28.1 +yarl==1.22.0 +attrs==25.4.0 +pydantic_core==2.33.2 +nvidia-cusparse-cu12==12.5.8.93 +GitPython==3.1.45 +PyQt6_sip==13.10.2 +nvidia-nvtx-cu12==12.8.90 +nest_asyncio==1.6.0 +cffi==2.0.0 +tqdm==4.67.1 +tzdata==2025.2 +dill==0.4.0 +cycler==0.11.0 +aiohttp==3.13.2 +pydantic==2.11.7 +pickleshare==0.7.5 +nvidia-cusparselt-cu12==0.7.1 +contourpy==1.2.1 +platformdirs==4.3.8 +importlib_metadata==8.7.0 +biopython==1.85 +idna==3.11 +stack_data==0.6.3 +pycparser==2.23 +python-dateutil==2.9.0.post0 +wheel==0.45.1 +psutil==7.0.0 +importlib_resources==6.5.2 +pyparsing==3.2.0 +exceptiongroup==1.3.0 +exceptiongroup==1.3.1 +gitdb==4.0.12 +pip==25.3 +pillow==11.3.0 +jupyter_core==5.8.1 +transformers==4.29.2 +matplotlib-inline==0.1.7 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