Upload folder using huggingface_hub

.gitattributes

@@ -57,3 +57,23 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+archiveII_16s/lightning_logs/recycle/fit-0-\[Strategy\]DDPStrategy.training_step.1764232055478164722.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_16s/lightning_logs/recycle/fit-0-\[Strategy\]DDPStrategy.validation_step.1764232569909811481.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_16s/lightning_logs/recycle/fit-1-\[Strategy\]DDPStrategy.training_step.1764232055510431706.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_16s/lightning_logs/recycle/fit-1-\[Strategy\]DDPStrategy.validation_step.1764232575089305445.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_16s/lightning_logs/trm/fit-0-\[Strategy\]DDPStrategy.training_step.1764446103650290357.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_16s/lightning_logs/trm/fit-0-\[Strategy\]DDPStrategy.validation_step.1764446399758831684.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_16s/lightning_logs/trm/fit-1-\[Strategy\]DDPStrategy.training_step.1764446103655326473.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_16s/lightning_logs/trm/fit-1-\[Strategy\]DDPStrategy.validation_step.1764446405066586106.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_RNaseP/lightning_logs/trm/fit-0-\[Strategy\]DDPStrategy.training_step.1764385752161692485.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_RNaseP/lightning_logs/trm/fit-0-\[Strategy\]DDPStrategy.validation_step.1764386015000580213.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_RNaseP/lightning_logs/trm/fit-1-\[Strategy\]DDPStrategy.training_step.1764385752170859786.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_RNaseP/lightning_logs/trm/fit-1-\[Strategy\]DDPStrategy.validation_step.1764386011212177784.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_tRNA/lightning_logs/recycle/fit-0-\[Strategy\]DDPStrategy.training_step.1764137161739522933.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_tRNA/lightning_logs/recycle/fit-0-\[Strategy\]DDPStrategy.validation_step.1764137594100245783.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_tRNA/lightning_logs/recycle/fit-1-\[Strategy\]DDPStrategy.training_step.1764137161736889801.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_tRNA/lightning_logs/recycle/fit-1-\[Strategy\]DDPStrategy.validation_step.1764137584697726899.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_tmRNA/lightning_logs/trm/fit-0-\[Strategy\]DDPStrategy.training_step.1764316842086592337.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_tmRNA/lightning_logs/trm/fit-0-\[Strategy\]DDPStrategy.validation_step.1764317097928436432.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_tmRNA/lightning_logs/trm/fit-1-\[Strategy\]DDPStrategy.training_step.1764316842095403422.pt.trace.json filter=lfs diff=lfs merge=lfs -text
+archiveII_tmRNA/lightning_logs/trm/fit-1-\[Strategy\]DDPStrategy.validation_step.1764317097649390017.pt.trace.json filter=lfs diff=lfs merge=lfs -text

archiveII_16s/lightning_logs/recycle/checkpoints/ss-epoch=49-valF1=0.980.ckpt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ceda1adf58e2719c0724c18609dc5643c0ffdc49720cfdfe10fff162d60b46f3
+size 19293822882

archiveII_16s/lightning_logs/recycle/config.yaml

@@ -0,0 +1,194 @@
+# lightning.pytorch==2.5.2
+seed_everything: 0
+trainer:
+  accelerator: auto
+  strategy:
+    class_path: lightning.pytorch.strategies.DDPStrategy
+    init_args:
+      accelerator: null
+      parallel_devices: null
+      cluster_environment: null
+      checkpoint_io: null
+      precision_plugin: null
+      ddp_comm_state: null
+      ddp_comm_hook: null
+      ddp_comm_wrapper: null
+      model_averaging_period: null
+      process_group_backend: null
+      timeout: 0:30:00
+      start_method: popen
+      output_device: null
+      dim: 0
+      broadcast_buffers: true
+      init_sync: true
+      process_group: null
+      bucket_cap_mb: null
+      find_unused_parameters: true
+      check_reduction: false
+      gradient_as_bucket_view: false
+      static_graph: false
+      delay_all_reduce_named_params: null
+      param_to_hook_all_reduce: null
+      mixed_precision: null
+      device_mesh: null
+      skip_all_reduce_unused_params: false
+  devices: 0,1
+  num_nodes: 1
+  precision: 16-mixed
+  logger: null
+  callbacks:
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
+    init_args:
+      dirpath: null
+      filename: ss-epoch={epoch}-valF1={val/f1:.3f}
+      monitor: val/f1
+      verbose: true
+      save_last: true
+      save_top_k: 1
+      save_weights_only: false
+      mode: max
+      auto_insert_metric_name: false
+      every_n_train_steps: null
+      train_time_interval: null
+      every_n_epochs: 1
+      save_on_train_epoch_end: null
+      enable_version_counter: true
+  - class_path: lightning.pytorch.callbacks.LearningRateMonitor
+    init_args:
+      logging_interval: step
+      log_momentum: false
+      log_weight_decay: false
+  - class_path: modelgenerator.callbacks.FTScheduler
+    init_args:
+      ft_schedule_path: ft_schedules/layers_0_32.yaml
+  fast_dev_run: false
+  max_epochs: 60
+  min_epochs: null
+  max_steps: -1
+  min_steps: null
+  max_time: null
+  limit_train_batches: null
+  limit_val_batches: null
+  limit_test_batches: null
+  limit_predict_batches: null
+  overfit_batches: 0.0
+  val_check_interval: null
+  check_val_every_n_epoch: 1
+  num_sanity_val_steps: null
+  log_every_n_steps: 50
+  enable_checkpointing: null
+  enable_progress_bar: null
+  enable_model_summary: null
+  accumulate_grad_batches: 2
+  gradient_clip_val: null
+  gradient_clip_algorithm: null
+  deterministic: null
+  benchmark: null
+  inference_mode: true
+  use_distributed_sampler: true
+  profiler:
+    class_path: lightning.pytorch.profilers.PyTorchProfiler
+    init_args:
+      dirpath: null
+      filename: null
+      group_by_input_shapes: false
+      emit_nvtx: false
+      export_to_chrome: true
+      row_limit: 20
+      sort_by_key: null
+      record_module_names: true
+      table_kwargs: null
+      record_shapes: false
+    dict_kwargs:
+      profile_memory: true
+  detect_anomaly: false
+  barebones: false
+  plugins: null
+  sync_batchnorm: false
+  reload_dataloaders_every_n_epochs: 0
+  default_root_dir: logs/rna_ss/archiveII_16s
+  model_registry: null
+model:
+  class_path: modelgenerator.rna_ss.rna_ss_task.RNASSPairwiseTokenClassification
+  init_args:
+    backbone_fn:
+      class_path: modelgenerator.backbones.aido_rna_1b600m
+      init_args:
+        from_scratch: false
+        max_length: 1024
+        use_peft: false
+        frozen: false
+        save_peft_only: true
+        lora_r: 16
+        lora_alpha: 32
+        lora_dropout: 0.1
+        lora_target_modules:
+        - query
+        - value
+        config_overwrites:
+          hidden_dropout_prob: 0.1
+          attention_probs_dropout_prob: 0.1
+        model_init_args: null
+    adapter_fn:
+      class_path: modelgenerator.adapters.ResNet2DAdapter
+      init_args:
+        conv_channels: 64
+        kernel_size: 3
+        mode: latent_with_protenix
+    tune_threshold_every_n_epoch: 1
+    optimizer:
+      class_path: torch.optim.AdamW
+      init_args:
+        lr: 0.0001
+        betas:
+        - 0.9
+        - 0.999
+        eps: 1.0e-08
+        weight_decay: 0.01
+        amsgrad: false
+        maximize: false
+        foreach: null
+        capturable: false
+        differentiable: false
+        fused: null
+    lr_scheduler:
+      class_path: torch.optim.lr_scheduler.LinearLR
+      init_args:
+        start_factor: 1.0
+        end_factor: 0.1
+        total_iters: 7500
+        last_epoch: -1
+    use_legacy_adapter: false
+    strict_loading: true
+    reset_optimizer_states: false
+data:
+  class_path: modelgenerator.rna_ss.rna_ss_data.RNASSPairwiseTokenClassification
+  init_args:
+    num_workers: 4
+    pin_memory: true
+    persistent_workers: true
+    min_seq_len: 0
+    max_seq_len: 999999999
+    dataset: archiveII_16s
+    path: /home/e/e0517239/yiming/rna_ss_data/
+    config_name: null
+    train_split_name: train
+    test_split_name: test
+    valid_split_name: null
+    train_split_files: null
+    test_split_files: null
+    valid_split_files: null
+    test_split_size: 0.2
+    valid_split_size: 0.1
+    random_seed: 42
+    extra_reader_kwargs: null
+    batch_size: 128
+    shuffle: true
+    sampler: null
+    cv_num_folds: 1
+    cv_test_fold_id: 0
+    cv_enable_val_fold: true
+    cv_replace_val_fold_as_test_fold: false
+    cv_fold_id_col: null
+    cv_val_offset: 1
+ckpt_path: /home/e/e0517239/yiming/rna_ss_reasoning/experiments/AIDO.RNA/rna_secondary_structure_prediction/logs/rna_ss/archiveII_16s/lightning_logs/version_0/checkpoints/last.ckpt

archiveII_16s/lightning_logs/recycle/fit-0-[Strategy]DDPStrategy.training_step.1764232055478164722.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7646fd54f5ba59a68addae1aed0f4643abdc40aa09efe0f6ceacb4f419919413
+size 114180758

archiveII_16s/lightning_logs/recycle/fit-0-[Strategy]DDPStrategy.validation_step.1764232569909811481.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9b43121e05bac077e77714f62c59358c643eaaf01b0f6685c3b77cc86f3a466c
+size 15485900

archiveII_16s/lightning_logs/recycle/fit-1-[Strategy]DDPStrategy.training_step.1764232055510431706.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b6573a9f6fd1550a668417c94dd50b1824a81656fd238223773a413422a3d6ad
+size 114336161

archiveII_16s/lightning_logs/recycle/fit-1-[Strategy]DDPStrategy.validation_step.1764232575089305445.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7cee046b5d7bd5b776d34f097ab8ecd786a0995926484be59380dbb13e084988
+size 15477826

archiveII_16s/lightning_logs/recycle/hparams.yaml

@@ -0,0 +1,52 @@
+backbone_fn:
+  class_path: modelgenerator.backbones.aido_rna_1b600m
+  init_args:
+    from_scratch: false
+    max_length: 1024
+    use_peft: false
+    frozen: false
+    save_peft_only: true
+    lora_r: 16
+    lora_alpha: 32
+    lora_dropout: 0.1
+    lora_target_modules:
+    - query
+    - value
+    config_overwrites:
+      hidden_dropout_prob: 0.1
+      attention_probs_dropout_prob: 0.1
+    model_init_args: null
+adapter_fn:
+  class_path: modelgenerator.adapters.ResNet2DAdapter
+  init_args:
+    conv_channels: 64
+    kernel_size: 3
+    mode: latent_with_protenix
+tune_threshold_every_n_epoch: 1
+optimizer:
+  class_path: torch.optim.AdamW
+  init_args:
+    lr: 0.0001
+    betas:
+    - 0.9
+    - 0.999
+    eps: 1.0e-08
+    weight_decay: 0.01
+    amsgrad: false
+    maximize: false
+    foreach: null
+    capturable: false
+    differentiable: false
+    fused: null
+lr_scheduler:
+  class_path: torch.optim.lr_scheduler.LinearLR
+  init_args:
+    start_factor: 1.0
+    end_factor: 0.1
+    total_iters: 7500
+    last_epoch: -1
+batch_size: 128
+use_legacy_adapter: false
+strict_loading: true
+reset_optimizer_states: false
+_instantiator: lightning.pytorch.cli.instantiate_module

archiveII_16s/lightning_logs/trm/16s_probs_and_gts.pkl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ae30ec5034627087651059b9a1c49957bd13acb1e62e12d5be7220d93e9cdd2d
+size 10429322640

archiveII_16s/lightning_logs/trm/checkpoints/ss-epoch=57-valF1=0.980.ckpt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0181f817a90741018855eadaf728f65940bf5ecf813e6da68270c6ec5137d6b5
+size 19293822882

archiveII_16s/lightning_logs/trm/config.yaml

@@ -0,0 +1,194 @@
+# lightning.pytorch==2.5.2
+seed_everything: 0
+trainer:
+  accelerator: auto
+  strategy:
+    class_path: lightning.pytorch.strategies.DDPStrategy
+    init_args:
+      accelerator: null
+      parallel_devices: null
+      cluster_environment: null
+      checkpoint_io: null
+      precision_plugin: null
+      ddp_comm_state: null
+      ddp_comm_hook: null
+      ddp_comm_wrapper: null
+      model_averaging_period: null
+      process_group_backend: null
+      timeout: 0:30:00
+      start_method: popen
+      output_device: null
+      dim: 0
+      broadcast_buffers: true
+      init_sync: true
+      process_group: null
+      bucket_cap_mb: null
+      find_unused_parameters: true
+      check_reduction: false
+      gradient_as_bucket_view: false
+      static_graph: false
+      delay_all_reduce_named_params: null
+      param_to_hook_all_reduce: null
+      mixed_precision: null
+      device_mesh: null
+      skip_all_reduce_unused_params: false
+  devices: 0,1
+  num_nodes: 1
+  precision: 16-mixed
+  logger: null
+  callbacks:
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
+    init_args:
+      dirpath: null
+      filename: ss-epoch={epoch}-valF1={val/f1:.3f}
+      monitor: val/f1
+      verbose: true
+      save_last: true
+      save_top_k: 1
+      save_weights_only: false
+      mode: max
+      auto_insert_metric_name: false
+      every_n_train_steps: null
+      train_time_interval: null
+      every_n_epochs: 1
+      save_on_train_epoch_end: null
+      enable_version_counter: true
+  - class_path: lightning.pytorch.callbacks.LearningRateMonitor
+    init_args:
+      logging_interval: step
+      log_momentum: false
+      log_weight_decay: false
+  - class_path: modelgenerator.callbacks.FTScheduler
+    init_args:
+      ft_schedule_path: ft_schedules/layers_0_32.yaml
+  fast_dev_run: false
+  max_epochs: 60
+  min_epochs: null
+  max_steps: -1
+  min_steps: null
+  max_time: null
+  limit_train_batches: null
+  limit_val_batches: null
+  limit_test_batches: null
+  limit_predict_batches: null
+  overfit_batches: 0.0
+  val_check_interval: null
+  check_val_every_n_epoch: 1
+  num_sanity_val_steps: null
+  log_every_n_steps: 50
+  enable_checkpointing: null
+  enable_progress_bar: null
+  enable_model_summary: null
+  accumulate_grad_batches: 2
+  gradient_clip_val: null
+  gradient_clip_algorithm: null
+  deterministic: null
+  benchmark: null
+  inference_mode: true
+  use_distributed_sampler: true
+  profiler:
+    class_path: lightning.pytorch.profilers.PyTorchProfiler
+    init_args:
+      dirpath: null
+      filename: null
+      group_by_input_shapes: false
+      emit_nvtx: false
+      export_to_chrome: true
+      row_limit: 20
+      sort_by_key: null
+      record_module_names: true
+      table_kwargs: null
+      record_shapes: false
+    dict_kwargs:
+      profile_memory: true
+  detect_anomaly: false
+  barebones: false
+  plugins: null
+  sync_batchnorm: false
+  reload_dataloaders_every_n_epochs: 0
+  default_root_dir: logs/rna_ss/archiveII_16s
+  model_registry: null
+model:
+  class_path: modelgenerator.rna_ss.rna_ss_task.RNASSPairwiseTokenClassification
+  init_args:
+    backbone_fn:
+      class_path: modelgenerator.backbones.aido_rna_1b600m
+      init_args:
+        from_scratch: false
+        max_length: 1024
+        use_peft: false
+        frozen: false
+        save_peft_only: true
+        lora_r: 16
+        lora_alpha: 32
+        lora_dropout: 0.1
+        lora_target_modules:
+        - query
+        - value
+        config_overwrites:
+          hidden_dropout_prob: 0.1
+          attention_probs_dropout_prob: 0.1
+        model_init_args: null
+    adapter_fn:
+      class_path: modelgenerator.adapters.ResNet2DAdapter
+      init_args:
+        conv_channels: 64
+        kernel_size: 3
+        mode: latent_with_protenix_with_trm
+    tune_threshold_every_n_epoch: 1
+    optimizer:
+      class_path: torch.optim.AdamW
+      init_args:
+        lr: 0.0001
+        betas:
+        - 0.9
+        - 0.999
+        eps: 1.0e-08
+        weight_decay: 0.01
+        amsgrad: false
+        maximize: false
+        foreach: null
+        capturable: false
+        differentiable: false
+        fused: null
+    lr_scheduler:
+      class_path: torch.optim.lr_scheduler.LinearLR
+      init_args:
+        start_factor: 1.0
+        end_factor: 0.1
+        total_iters: 7500
+        last_epoch: -1
+    use_legacy_adapter: false
+    strict_loading: true
+    reset_optimizer_states: false
+data:
+  class_path: modelgenerator.rna_ss.rna_ss_data.RNASSPairwiseTokenClassification
+  init_args:
+    num_workers: 4
+    pin_memory: true
+    persistent_workers: true
+    min_seq_len: 0
+    max_seq_len: 999999999
+    dataset: archiveII_16s
+    path: /home/e/e0517239/yiming/rna_ss_data/
+    config_name: null
+    train_split_name: train
+    test_split_name: test
+    valid_split_name: null
+    train_split_files: null
+    test_split_files: null
+    valid_split_files: null
+    test_split_size: 0.2
+    valid_split_size: 0.1
+    random_seed: 42
+    extra_reader_kwargs: null
+    batch_size: 128
+    shuffle: true
+    sampler: null
+    cv_num_folds: 1
+    cv_test_fold_id: 0
+    cv_enable_val_fold: true
+    cv_replace_val_fold_as_test_fold: false
+    cv_fold_id_col: null
+    cv_val_offset: 1
+ckpt_path: null

archiveII_16s/lightning_logs/trm/fit-0-[Strategy]DDPStrategy.training_step.1764446103650290357.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:40e00737f46c0331e7b6db051d44db081555fbec8f03cb9c468e71865d598c2e
+size 72917271

archiveII_16s/lightning_logs/trm/fit-0-[Strategy]DDPStrategy.validation_step.1764446399758831684.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e7cbc103aaadb814332baeca6c687a2918bd5f15ab35bccd4c1aff41f479bfd2
+size 19093866

archiveII_16s/lightning_logs/trm/fit-1-[Strategy]DDPStrategy.training_step.1764446103655326473.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b4d889cb58e415db4571fe726a0fa1f745a1752bd7d967f40a8e990363309b08
+size 73127601

archiveII_16s/lightning_logs/trm/fit-1-[Strategy]DDPStrategy.validation_step.1764446405066586106.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:063ec73d97d4492c8b94c898eafda36fe930f3b74bb7f849cff177e670f920a4
+size 19057402

archiveII_16s/lightning_logs/trm/hparams.yaml

@@ -0,0 +1,52 @@
+backbone_fn:
+  class_path: modelgenerator.backbones.aido_rna_1b600m
+  init_args:
+    from_scratch: false
+    max_length: 1024
+    use_peft: false
+    frozen: false
+    save_peft_only: true
+    lora_r: 16
+    lora_alpha: 32
+    lora_dropout: 0.1
+    lora_target_modules:
+    - query
+    - value
+    config_overwrites:
+      hidden_dropout_prob: 0.1
+      attention_probs_dropout_prob: 0.1
+    model_init_args: null
+adapter_fn:
+  class_path: modelgenerator.adapters.ResNet2DAdapter
+  init_args:
+    conv_channels: 64
+    kernel_size: 3
+    mode: latent_with_protenix_with_trm
+tune_threshold_every_n_epoch: 1
+optimizer:
+  class_path: torch.optim.AdamW
+  init_args:
+    lr: 0.0001
+    betas:
+    - 0.9
+    - 0.999
+    eps: 1.0e-08
+    weight_decay: 0.01
+    amsgrad: false
+    maximize: false
+    foreach: null
+    capturable: false
+    differentiable: false
+    fused: null
+lr_scheduler:
+  class_path: torch.optim.lr_scheduler.LinearLR
+  init_args:
+    start_factor: 1.0
+    end_factor: 0.1
+    total_iters: 7500
+    last_epoch: -1
+batch_size: 128
+use_legacy_adapter: false
+strict_loading: true
+reset_optimizer_states: false
+_instantiator: lightning.pytorch.cli.instantiate_module

archiveII_RNaseP/lightning_logs/trm/checkpoints/ss-epoch=42-valF1=0.974.ckpt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e84d637cc631c92cf2169d536d2701cc5f0fff3c23ae3212555855235dc7f358
+size 19293822882

archiveII_RNaseP/lightning_logs/trm/config.yaml

@@ -0,0 +1,194 @@
+# lightning.pytorch==2.5.2
+seed_everything: 0
+trainer:
+  accelerator: auto
+  strategy:
+    class_path: lightning.pytorch.strategies.DDPStrategy
+    init_args:
+      accelerator: null
+      parallel_devices: null
+      cluster_environment: null
+      checkpoint_io: null
+      precision_plugin: null
+      ddp_comm_state: null
+      ddp_comm_hook: null
+      ddp_comm_wrapper: null
+      model_averaging_period: null
+      process_group_backend: null
+      timeout: 0:30:00
+      start_method: popen
+      output_device: null
+      dim: 0
+      broadcast_buffers: true
+      init_sync: true
+      process_group: null
+      bucket_cap_mb: null
+      find_unused_parameters: true
+      check_reduction: false
+      gradient_as_bucket_view: false
+      static_graph: false
+      delay_all_reduce_named_params: null
+      param_to_hook_all_reduce: null
+      mixed_precision: null
+      device_mesh: null
+      skip_all_reduce_unused_params: false
+  devices: 0,1
+  num_nodes: 1
+  precision: 16-mixed
+  logger: null
+  callbacks:
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
+    init_args:
+      dirpath: null
+      filename: ss-epoch={epoch}-valF1={val/f1:.3f}
+      monitor: val/f1
+      verbose: true
+      save_last: true
+      save_top_k: 1
+      save_weights_only: false
+      mode: max
+      auto_insert_metric_name: false
+      every_n_train_steps: null
+      train_time_interval: null
+      every_n_epochs: 1
+      save_on_train_epoch_end: null
+      enable_version_counter: true
+  - class_path: lightning.pytorch.callbacks.LearningRateMonitor
+    init_args:
+      logging_interval: step
+      log_momentum: false
+      log_weight_decay: false
+  - class_path: modelgenerator.callbacks.FTScheduler
+    init_args:
+      ft_schedule_path: ft_schedules/layers_0_32.yaml
+  fast_dev_run: false
+  max_epochs: 60
+  min_epochs: null
+  max_steps: -1
+  min_steps: null
+  max_time: null
+  limit_train_batches: null
+  limit_val_batches: null
+  limit_test_batches: null
+  limit_predict_batches: null
+  overfit_batches: 0.0
+  val_check_interval: null
+  check_val_every_n_epoch: 1
+  num_sanity_val_steps: null
+  log_every_n_steps: 50
+  enable_checkpointing: null
+  enable_progress_bar: null
+  enable_model_summary: null
+  accumulate_grad_batches: 2
+  gradient_clip_val: null
+  gradient_clip_algorithm: null
+  deterministic: null
+  benchmark: null
+  inference_mode: true
+  use_distributed_sampler: true
+  profiler:
+    class_path: lightning.pytorch.profilers.PyTorchProfiler
+    init_args:
+      dirpath: null
+      filename: null
+      group_by_input_shapes: false
+      emit_nvtx: false
+      export_to_chrome: true
+      row_limit: 20
+      sort_by_key: null
+      record_module_names: true
+      table_kwargs: null
+      record_shapes: false
+    dict_kwargs:
+      profile_memory: true
+  detect_anomaly: false
+  barebones: false
+  plugins: null
+  sync_batchnorm: false
+  reload_dataloaders_every_n_epochs: 0
+  default_root_dir: logs/rna_ss/archiveII_RNaseP
+  model_registry: null
+model:
+  class_path: modelgenerator.rna_ss.rna_ss_task.RNASSPairwiseTokenClassification
+  init_args:
+    backbone_fn:
+      class_path: modelgenerator.backbones.aido_rna_1b600m
+      init_args:
+        from_scratch: false
+        max_length: 1024
+        use_peft: false
+        frozen: false
+        save_peft_only: true
+        lora_r: 16
+        lora_alpha: 32
+        lora_dropout: 0.1
+        lora_target_modules:
+        - query
+        - value
+        config_overwrites:
+          hidden_dropout_prob: 0.1
+          attention_probs_dropout_prob: 0.1
+        model_init_args: null
+    adapter_fn:
+      class_path: modelgenerator.adapters.ResNet2DAdapter
+      init_args:
+        conv_channels: 64
+        kernel_size: 3
+        mode: latent_with_protenix_with_trm
+    tune_threshold_every_n_epoch: 1
+    optimizer:
+      class_path: torch.optim.AdamW
+      init_args:
+        lr: 0.0001
+        betas:
+        - 0.9
+        - 0.999
+        eps: 1.0e-08
+        weight_decay: 0.01
+        amsgrad: false
+        maximize: false
+        foreach: null
+        capturable: false
+        differentiable: false
+        fused: null
+    lr_scheduler:
+      class_path: torch.optim.lr_scheduler.LinearLR
+      init_args:
+        start_factor: 1.0
+        end_factor: 0.1
+        total_iters: 7500
+        last_epoch: -1
+    use_legacy_adapter: false
+    strict_loading: true
+    reset_optimizer_states: false
+data:
+  class_path: modelgenerator.rna_ss.rna_ss_data.RNASSPairwiseTokenClassification
+  init_args:
+    num_workers: 4
+    pin_memory: true
+    persistent_workers: true
+    min_seq_len: 0
+    max_seq_len: 999999999
+    dataset: archiveII_RNaseP
+    path: /home/e/e0517239/yiming/rna_ss_data/
+    config_name: null
+    train_split_name: train
+    test_split_name: test
+    valid_split_name: null
+    train_split_files: null
+    test_split_files: null
+    valid_split_files: null
+    test_split_size: 0.2
+    valid_split_size: 0.1
+    random_seed: 42
+    extra_reader_kwargs: null
+    batch_size: 128
+    shuffle: true
+    sampler: null
+    cv_num_folds: 1
+    cv_test_fold_id: 0
+    cv_enable_val_fold: true
+    cv_replace_val_fold_as_test_fold: false
+    cv_fold_id_col: null
+    cv_val_offset: 1
+ckpt_path: null

archiveII_RNaseP/lightning_logs/trm/fit-0-[Strategy]DDPStrategy.training_step.1764385752161692485.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1495f5c2e15fa11570bf32ec21f18219eb44faa7ad014d17e804777f85e217df
+size 72318726

archiveII_RNaseP/lightning_logs/trm/fit-0-[Strategy]DDPStrategy.validation_step.1764386015000580213.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:96244e883273e47aa907657169f3270cfe24e0d80614a36166c66395b790a3f4
+size 19044574

archiveII_RNaseP/lightning_logs/trm/fit-1-[Strategy]DDPStrategy.training_step.1764385752170859786.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:57d92dc0fc249d901ca2df8cd67a2464e9205224cd11b7d797763fbbc5afc86b
+size 72370389

archiveII_RNaseP/lightning_logs/trm/fit-1-[Strategy]DDPStrategy.validation_step.1764386011212177784.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a6d44da622df008a1294f39e181a33545e95494ac2ef4b318ff21a28d4e6959f
+size 18884896

archiveII_RNaseP/lightning_logs/trm/hparams.yaml

@@ -0,0 +1,52 @@
+backbone_fn:
+  class_path: modelgenerator.backbones.aido_rna_1b600m
+  init_args:
+    from_scratch: false
+    max_length: 1024
+    use_peft: false
+    frozen: false
+    save_peft_only: true
+    lora_r: 16
+    lora_alpha: 32
+    lora_dropout: 0.1
+    lora_target_modules:
+    - query
+    - value
+    config_overwrites:
+      hidden_dropout_prob: 0.1
+      attention_probs_dropout_prob: 0.1
+    model_init_args: null
+adapter_fn:
+  class_path: modelgenerator.adapters.ResNet2DAdapter
+  init_args:
+    conv_channels: 64
+    kernel_size: 3
+    mode: latent_with_protenix_with_trm
+tune_threshold_every_n_epoch: 1
+optimizer:
+  class_path: torch.optim.AdamW
+  init_args:
+    lr: 0.0001
+    betas:
+    - 0.9
+    - 0.999
+    eps: 1.0e-08
+    weight_decay: 0.01
+    amsgrad: false
+    maximize: false
+    foreach: null
+    capturable: false
+    differentiable: false
+    fused: null
+lr_scheduler:
+  class_path: torch.optim.lr_scheduler.LinearLR
+  init_args:
+    start_factor: 1.0
+    end_factor: 0.1
+    total_iters: 7500
+    last_epoch: -1
+batch_size: 128
+use_legacy_adapter: false
+strict_loading: true
+reset_optimizer_states: false
+_instantiator: lightning.pytorch.cli.instantiate_module

archiveII_RNaseP/lightning_logs/trm/probs_and_gts.pkl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:493900753029de6b7de5f7bb6562ca801f5110d72feaefa7bacbfc877ba0d47b
+size 40345002780

archiveII_tRNA/lightning_logs/recycle/checkpoints/ss-epoch=41-valF1=0.974.ckpt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:362f2353ffc8bad946dd3052ae1cc8df94d50159f0779c79c8e3ac23afc64442
+size 19293823597

archiveII_tRNA/lightning_logs/recycle/config.yaml

@@ -0,0 +1,194 @@
+# lightning.pytorch==2.5.2
+seed_everything: 0
+trainer:
+  accelerator: auto
+  strategy:
+    class_path: lightning.pytorch.strategies.DDPStrategy
+    init_args:
+      accelerator: null
+      parallel_devices: null
+      cluster_environment: null
+      checkpoint_io: null
+      precision_plugin: null
+      ddp_comm_state: null
+      ddp_comm_hook: null
+      ddp_comm_wrapper: null
+      model_averaging_period: null
+      process_group_backend: null
+      timeout: 0:30:00
+      start_method: popen
+      output_device: null
+      dim: 0
+      broadcast_buffers: true
+      init_sync: true
+      process_group: null
+      bucket_cap_mb: null
+      find_unused_parameters: true
+      check_reduction: false
+      gradient_as_bucket_view: false
+      static_graph: false
+      delay_all_reduce_named_params: null
+      param_to_hook_all_reduce: null
+      mixed_precision: null
+      device_mesh: null
+      skip_all_reduce_unused_params: false
+  devices: 0,1
+  num_nodes: 1
+  precision: 16-mixed
+  logger: null
+  callbacks:
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
+    init_args:
+      dirpath: null
+      filename: ss-epoch={epoch}-valF1={val/f1:.3f}
+      monitor: val/f1
+      verbose: true
+      save_last: true
+      save_top_k: 1
+      save_weights_only: false
+      mode: max
+      auto_insert_metric_name: false
+      every_n_train_steps: null
+      train_time_interval: null
+      every_n_epochs: 1
+      save_on_train_epoch_end: null
+      enable_version_counter: true
+  - class_path: lightning.pytorch.callbacks.LearningRateMonitor
+    init_args:
+      logging_interval: step
+      log_momentum: false
+      log_weight_decay: false
+  - class_path: modelgenerator.callbacks.FTScheduler
+    init_args:
+      ft_schedule_path: ft_schedules/layers_0_32.yaml
+  fast_dev_run: false
+  max_epochs: 60
+  min_epochs: null
+  max_steps: -1
+  min_steps: null
+  max_time: null
+  limit_train_batches: null
+  limit_val_batches: null
+  limit_test_batches: null
+  limit_predict_batches: null
+  overfit_batches: 0.0
+  val_check_interval: null
+  check_val_every_n_epoch: 1
+  num_sanity_val_steps: null
+  log_every_n_steps: 50
+  enable_checkpointing: null
+  enable_progress_bar: null
+  enable_model_summary: null
+  accumulate_grad_batches: 2
+  gradient_clip_val: null
+  gradient_clip_algorithm: null
+  deterministic: null
+  benchmark: null
+  inference_mode: true
+  use_distributed_sampler: true
+  profiler:
+    class_path: lightning.pytorch.profilers.PyTorchProfiler
+    init_args:
+      dirpath: null
+      filename: null
+      group_by_input_shapes: false
+      emit_nvtx: false
+      export_to_chrome: true
+      row_limit: 20
+      sort_by_key: null
+      record_module_names: true
+      table_kwargs: null
+      record_shapes: false
+    dict_kwargs:
+      profile_memory: true
+  detect_anomaly: false
+  barebones: false
+  plugins: null
+  sync_batchnorm: false
+  reload_dataloaders_every_n_epochs: 0
+  default_root_dir: logs/rna_ss/archiveII_tRNA
+  model_registry: null
+model:
+  class_path: modelgenerator.rna_ss.rna_ss_task.RNASSPairwiseTokenClassification
+  init_args:
+    backbone_fn:
+      class_path: modelgenerator.backbones.aido_rna_1b600m
+      init_args:
+        from_scratch: false
+        max_length: 1024
+        use_peft: false
+        frozen: false
+        save_peft_only: true
+        lora_r: 16
+        lora_alpha: 32
+        lora_dropout: 0.1
+        lora_target_modules:
+        - query
+        - value
+        config_overwrites:
+          hidden_dropout_prob: 0.1
+          attention_probs_dropout_prob: 0.1
+        model_init_args: null
+    adapter_fn:
+      class_path: modelgenerator.adapters.ResNet2DAdapter
+      init_args:
+        conv_channels: 64
+        kernel_size: 3
+        mode: latent_with_protenix
+    tune_threshold_every_n_epoch: 1
+    optimizer:
+      class_path: torch.optim.AdamW
+      init_args:
+        lr: 0.0001
+        betas:
+        - 0.9
+        - 0.999
+        eps: 1.0e-08
+        weight_decay: 0.01
+        amsgrad: false
+        maximize: false
+        foreach: null
+        capturable: false
+        differentiable: false
+        fused: null
+    lr_scheduler:
+      class_path: torch.optim.lr_scheduler.LinearLR
+      init_args:
+        start_factor: 1.0
+        end_factor: 0.1
+        total_iters: 7500
+        last_epoch: -1
+    use_legacy_adapter: false
+    strict_loading: true
+    reset_optimizer_states: false
+data:
+  class_path: modelgenerator.rna_ss.rna_ss_data.RNASSPairwiseTokenClassification
+  init_args:
+    num_workers: 8
+    pin_memory: true
+    persistent_workers: true
+    min_seq_len: 0
+    max_seq_len: 999999999
+    dataset: archiveII_tRNA
+    path: /home/e/e0517239/yiming/rna_ss_data/
+    config_name: null
+    train_split_name: train
+    test_split_name: test
+    valid_split_name: null
+    train_split_files: null
+    test_split_files: null
+    valid_split_files: null
+    test_split_size: 0.2
+    valid_split_size: 0.1
+    random_seed: 42
+    extra_reader_kwargs: null
+    batch_size: 128
+    shuffle: true
+    sampler: null
+    cv_num_folds: 1
+    cv_test_fold_id: 0
+    cv_enable_val_fold: true
+    cv_replace_val_fold_as_test_fold: false
+    cv_fold_id_col: null
+    cv_val_offset: 1
+ckpt_path: /home/e/e0517239/yiming/rna_ss_reasoning/experiments/AIDO.RNA/rna_secondary_structure_prediction/logs/rna_ss/archiveII_tRNA/lightning_logs/version_0/checkpoints/last.ckpt

archiveII_tRNA/lightning_logs/recycle/fit-0-[Strategy]DDPStrategy.training_step.1764137161739522933.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:320684f3a9fe874af746084b975ec5c49ba378954d6df57bdcabff2b8fb1299d
+size 113348150

archiveII_tRNA/lightning_logs/recycle/fit-0-[Strategy]DDPStrategy.validation_step.1764137594100245783.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:15e9f2ec479a0f9ee5159e28620090c23188d76e22b686dc5ce7b3668b702cf8
+size 15376786

archiveII_tRNA/lightning_logs/recycle/fit-1-[Strategy]DDPStrategy.training_step.1764137161736889801.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f06fe39d733ecd93163a54d2d0e19d0669d7eeee1c1385367fa1de0dc899c398
+size 113891025

archiveII_tRNA/lightning_logs/recycle/fit-1-[Strategy]DDPStrategy.validation_step.1764137584697726899.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8f6e5f9aa671f4f9a84917316d3c9d25eac438fc6509f86e346a0275bb18171f
+size 15385866

archiveII_tRNA/lightning_logs/recycle/hparams.yaml

@@ -0,0 +1,52 @@
+backbone_fn:
+  class_path: modelgenerator.backbones.aido_rna_1b600m
+  init_args:
+    from_scratch: false
+    max_length: 1024
+    use_peft: false
+    frozen: false
+    save_peft_only: true
+    lora_r: 16
+    lora_alpha: 32
+    lora_dropout: 0.1
+    lora_target_modules:
+    - query
+    - value
+    config_overwrites:
+      hidden_dropout_prob: 0.1
+      attention_probs_dropout_prob: 0.1
+    model_init_args: null
+adapter_fn:
+  class_path: modelgenerator.adapters.ResNet2DAdapter
+  init_args:
+    conv_channels: 64
+    kernel_size: 3
+    mode: latent_with_protenix
+tune_threshold_every_n_epoch: 1
+optimizer:
+  class_path: torch.optim.AdamW
+  init_args:
+    lr: 0.0001
+    betas:
+    - 0.9
+    - 0.999
+    eps: 1.0e-08
+    weight_decay: 0.01
+    amsgrad: false
+    maximize: false
+    foreach: null
+    capturable: false
+    differentiable: false
+    fused: null
+lr_scheduler:
+  class_path: torch.optim.lr_scheduler.LinearLR
+  init_args:
+    start_factor: 1.0
+    end_factor: 0.1
+    total_iters: 7500
+    last_epoch: -1
+batch_size: 128
+use_legacy_adapter: false
+strict_loading: true
+reset_optimizer_states: false
+_instantiator: lightning.pytorch.cli.instantiate_module

archiveII_tmRNA/lightning_logs/trm/checkpoints/ss-epoch=54-valF1=0.975.ckpt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:575983b9d54d01ef9d2e63b96d04d2f048a8b6613bd38b7872bdec00fe98659e
+size 19293822882

archiveII_tmRNA/lightning_logs/trm/config.yaml

@@ -0,0 +1,194 @@
+# lightning.pytorch==2.5.2
+seed_everything: 0
+trainer:
+  accelerator: auto
+  strategy:
+    class_path: lightning.pytorch.strategies.DDPStrategy
+    init_args:
+      accelerator: null
+      parallel_devices: null
+      cluster_environment: null
+      checkpoint_io: null
+      precision_plugin: null
+      ddp_comm_state: null
+      ddp_comm_hook: null
+      ddp_comm_wrapper: null
+      model_averaging_period: null
+      process_group_backend: null
+      timeout: 0:30:00
+      start_method: popen
+      output_device: null
+      dim: 0
+      broadcast_buffers: true
+      init_sync: true
+      process_group: null
+      bucket_cap_mb: null
+      find_unused_parameters: true
+      check_reduction: false
+      gradient_as_bucket_view: false
+      static_graph: false
+      delay_all_reduce_named_params: null
+      param_to_hook_all_reduce: null
+      mixed_precision: null
+      device_mesh: null
+      skip_all_reduce_unused_params: false
+  devices: 0,1
+  num_nodes: 1
+  precision: 16-mixed
+  logger: null
+  callbacks:
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
+    init_args:
+      dirpath: null
+      filename: ss-epoch={epoch}-valF1={val/f1:.3f}
+      monitor: val/f1
+      verbose: true
+      save_last: true
+      save_top_k: 1
+      save_weights_only: false
+      mode: max
+      auto_insert_metric_name: false
+      every_n_train_steps: null
+      train_time_interval: null
+      every_n_epochs: 1
+      save_on_train_epoch_end: null
+      enable_version_counter: true
+  - class_path: lightning.pytorch.callbacks.LearningRateMonitor
+    init_args:
+      logging_interval: step
+      log_momentum: false
+      log_weight_decay: false
+  - class_path: modelgenerator.callbacks.FTScheduler
+    init_args:
+      ft_schedule_path: ft_schedules/layers_0_32.yaml
+  fast_dev_run: false
+  max_epochs: 60
+  min_epochs: null
+  max_steps: -1
+  min_steps: null
+  max_time: null
+  limit_train_batches: null
+  limit_val_batches: null
+  limit_test_batches: null
+  limit_predict_batches: null
+  overfit_batches: 0.0
+  val_check_interval: null
+  check_val_every_n_epoch: 1
+  num_sanity_val_steps: null
+  log_every_n_steps: 50
+  enable_checkpointing: null
+  enable_progress_bar: null
+  enable_model_summary: null
+  accumulate_grad_batches: 2
+  gradient_clip_val: null
+  gradient_clip_algorithm: null
+  deterministic: null
+  benchmark: null
+  inference_mode: true
+  use_distributed_sampler: true
+  profiler:
+    class_path: lightning.pytorch.profilers.PyTorchProfiler
+    init_args:
+      dirpath: null
+      filename: null
+      group_by_input_shapes: false
+      emit_nvtx: false
+      export_to_chrome: true
+      row_limit: 20
+      sort_by_key: null
+      record_module_names: true
+      table_kwargs: null
+      record_shapes: false
+    dict_kwargs:
+      profile_memory: true
+  detect_anomaly: false
+  barebones: false
+  plugins: null
+  sync_batchnorm: false
+  reload_dataloaders_every_n_epochs: 0
+  default_root_dir: logs/rna_ss/archiveII_tmRNA
+  model_registry: null
+model:
+  class_path: modelgenerator.rna_ss.rna_ss_task.RNASSPairwiseTokenClassification
+  init_args:
+    backbone_fn:
+      class_path: modelgenerator.backbones.aido_rna_1b600m
+      init_args:
+        from_scratch: false
+        max_length: 1024
+        use_peft: false
+        frozen: false
+        save_peft_only: true
+        lora_r: 16
+        lora_alpha: 32
+        lora_dropout: 0.1
+        lora_target_modules:
+        - query
+        - value
+        config_overwrites:
+          hidden_dropout_prob: 0.1
+          attention_probs_dropout_prob: 0.1
+        model_init_args: null
+    adapter_fn:
+      class_path: modelgenerator.adapters.ResNet2DAdapter
+      init_args:
+        conv_channels: 64
+        kernel_size: 3
+        mode: latent_with_protenix_with_trm
+    tune_threshold_every_n_epoch: 1
+    optimizer:
+      class_path: torch.optim.AdamW
+      init_args:
+        lr: 0.0001
+        betas:
+        - 0.9
+        - 0.999
+        eps: 1.0e-08
+        weight_decay: 0.01
+        amsgrad: false
+        maximize: false
+        foreach: null
+        capturable: false
+        differentiable: false
+        fused: null
+    lr_scheduler:
+      class_path: torch.optim.lr_scheduler.LinearLR
+      init_args:
+        start_factor: 1.0
+        end_factor: 0.1
+        total_iters: 7500
+        last_epoch: -1
+    use_legacy_adapter: false
+    strict_loading: true
+    reset_optimizer_states: false
+data:
+  class_path: modelgenerator.rna_ss.rna_ss_data.RNASSPairwiseTokenClassification
+  init_args:
+    num_workers: 4
+    pin_memory: true
+    persistent_workers: true
+    min_seq_len: 0
+    max_seq_len: 999999999
+    dataset: archiveII_tmRNA
+    path: /home/e/e0517239/yiming/rna_ss_data/
+    config_name: null
+    train_split_name: train
+    test_split_name: test
+    valid_split_name: null
+    train_split_files: null
+    test_split_files: null
+    valid_split_files: null
+    test_split_size: 0.2
+    valid_split_size: 0.1
+    random_seed: 42
+    extra_reader_kwargs: null
+    batch_size: 128
+    shuffle: true
+    sampler: null
+    cv_num_folds: 1
+    cv_test_fold_id: 0
+    cv_enable_val_fold: true
+    cv_replace_val_fold_as_test_fold: false
+    cv_fold_id_col: null
+    cv_val_offset: 1
+ckpt_path: null

archiveII_tmRNA/lightning_logs/trm/fit-0-[Strategy]DDPStrategy.training_step.1764316842086592337.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ac09d53deaa50f6848cc05945571b83db863752df2ed7810ca325c907dab8349
+size 73145024

archiveII_tmRNA/lightning_logs/trm/fit-0-[Strategy]DDPStrategy.validation_step.1764317097928436432.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9bcf148091ba479094d227772d542fe45b36cc2bf0157283baba8098381a63b9
+size 18938535

archiveII_tmRNA/lightning_logs/trm/fit-1-[Strategy]DDPStrategy.training_step.1764316842095403422.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:87660d23f8fea544bd5e83320e522c4237362d6a48251afaa72c5ba9442c0011
+size 74015386

archiveII_tmRNA/lightning_logs/trm/fit-1-[Strategy]DDPStrategy.validation_step.1764317097649390017.pt.trace.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:14c82d066898f94511cc09fffa904e9b16ec678d5a165847c43bcb1f74097cf8
+size 18905907

archiveII_tmRNA/lightning_logs/trm/hparams.yaml

@@ -0,0 +1,52 @@
+backbone_fn:
+  class_path: modelgenerator.backbones.aido_rna_1b600m
+  init_args:
+    from_scratch: false
+    max_length: 1024
+    use_peft: false
+    frozen: false
+    save_peft_only: true
+    lora_r: 16
+    lora_alpha: 32
+    lora_dropout: 0.1
+    lora_target_modules:
+    - query
+    - value
+    config_overwrites:
+      hidden_dropout_prob: 0.1
+      attention_probs_dropout_prob: 0.1
+    model_init_args: null
+adapter_fn:
+  class_path: modelgenerator.adapters.ResNet2DAdapter
+  init_args:
+    conv_channels: 64
+    kernel_size: 3
+    mode: latent_with_protenix_with_trm
+tune_threshold_every_n_epoch: 1
+optimizer:
+  class_path: torch.optim.AdamW
+  init_args:
+    lr: 0.0001
+    betas:
+    - 0.9
+    - 0.999
+    eps: 1.0e-08
+    weight_decay: 0.01
+    amsgrad: false
+    maximize: false
+    foreach: null
+    capturable: false
+    differentiable: false
+    fused: null
+lr_scheduler:
+  class_path: torch.optim.lr_scheduler.LinearLR
+  init_args:
+    start_factor: 1.0
+    end_factor: 0.1
+    total_iters: 7500
+    last_epoch: -1
+batch_size: 128
+use_legacy_adapter: false
+strict_loading: true
+reset_optimizer_states: false
+_instantiator: lightning.pytorch.cli.instantiate_module