| task_name: train |
| tags: |
| - finetune_altumage_small_age |
| - finetuning |
| - small |
| - altumage |
| - age |
| train: true |
| test: true |
| trainer_ckpt_path: null |
| model_ckpt_path: dependencies/model/weights/small.ckpt |
| strict_load: false |
| seed: 42 |
| data: |
| batch_size: 8 |
| dna_llm: nucleotide-transformer-v2-500m-multi-species |
| max_length: 20000 |
| sorting_strategy: sorted_chromosome |
| dna_context_len: 2001 |
| num_workers: 8 |
| pin_memory: false |
| _target_: cpgpt.data.cpgpt_datamodule.CpGPTDataModule |
| train_dir: ${paths.data_dir}/altumage/processed/train |
| val_dir: ${paths.data_dir}/altumage/processed/val |
| test_dir: ${paths.data_dir}/altumage/processed/test |
| dependencies_dir: ${paths.dependencies_dir}/human |
| model: |
| optimizer: |
| _target_: schedulefree.AdamWScheduleFree |
| _partial_: true |
| lr: 0.0001 |
| weight_decay: 0.1 |
| betas: |
| - 0.9 |
| - 0.95 |
| warmup_steps: ${trainer.min_steps} |
| scheduler: |
| _target_: torch.optim.lr_scheduler.ConstantLR |
| _partial_: true |
| factor: 1.0 |
| total_iters: 1 |
| net: |
| _target_: cpgpt.model.components.model.CpGPT |
| d_embedding: 128 |
| d_hidden: 128 |
| d_dna_embedding: 1024 |
| n_attention_heads: 8 |
| n_layers: 8 |
| n_mlp_blocks: 3 |
| dropout: 0.01 |
| architecture: transformer |
| activation: swiglu |
| positional_encoding: rotary |
| sample_embedding_method: cls |
| use_power_norm: false |
| fft: false |
| use_condition_decoder: true |
| condition_size: 1 |
| use_noise_decoder: false |
| mlp_block_bias: false |
| mlp_block_norm_type: rmsnorm |
| mlp_block_pre_norm: false |
| mlp_block_post_norm: false |
| transformer_block_bias: false |
| transformer_block_norm_type: rmsnorm |
| transformer_block_norm_first: true |
| transformer_block_dropout: 0.0 |
| training: |
| generative_splits: 10 |
| binarize_input: false |
| contrastive_threshold: 0.5 |
| diffusion: false |
| reconstruct_mode: all |
| diffusion_params: |
| num_timesteps: 1000 |
| loss_weights: |
| m_mae: 10.0 |
| m_mae_unc: 1.0 |
| betas_mae: 0.0 |
| betas_kld: 0.0 |
| betas_beta: 0.0 |
| betas_wd: 1.0 |
| contrastive: 1.0 |
| sample_kld: 1.0 |
| diffusion_mse: 0.0 |
| condition_loss: 0.1 |
| condition_decoder_loss: mae |
| _target_: cpgpt.model.cpgpt_module.CpGPTLitModule |
| compile: true |
| callbacks: |
| model_checkpoint: |
| _target_: lightning.pytorch.callbacks.ModelCheckpoint |
| dirpath: ${paths.output_dir}/checkpoints |
| filename: ${tags[0]} |
| monitor: val/condition_loss |
| verbose: false |
| save_last: true |
| save_top_k: 1 |
| mode: min |
| auto_insert_metric_name: false |
| save_weights_only: false |
| every_n_train_steps: null |
| train_time_interval: null |
| every_n_epochs: null |
| save_on_train_epoch_end: null |
| model_summary: |
| _target_: lightning.pytorch.callbacks.RichModelSummary |
| max_depth: 2 |
| rich_progress_bar: |
| _target_: lightning.pytorch.callbacks.RichProgressBar |
| logger: |
| wandb: |
| _target_: lightning.pytorch.loggers.wandb.WandbLogger |
| save_dir: ${paths.output_dir} |
| offline: false |
| id: null |
| anonymous: null |
| project: CpGPT |
| log_model: true |
| prefix: '' |
| entity: lucascamillo |
| group: '' |
| tags: ${tags} |
| job_type: '' |
| trainer: |
| _target_: lightning.pytorch.trainer.Trainer |
| default_root_dir: ${paths.output_dir} |
| min_steps: 2000 |
| max_steps: 100000 |
| accelerator: auto |
| devices: 1 |
| precision: 16-mixed |
| val_check_interval: 1000 |
| check_val_every_n_epoch: null |
| log_every_n_steps: 1 |
| detect_anomaly: false |
| deterministic: false |
| accumulate_grad_batches: 1 |
| paths: |
| root_dir: ${oc.env:PROJECT_ROOT} |
| data_dir: ${paths.root_dir}/data/ |
| dependencies_dir: ${paths.root_dir}/dependencies/ |
| log_dir: ${paths.root_dir}/logs/ |
| output_dir: ${hydra:runtime.output_dir} |
| work_dir: ${hydra:runtime.cwd} |
| extras: |
| ignore_warnings: true |
| enforce_tags: true |
| print_config: true |
|
|
