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igcraft-model/hydra/config.yaml

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+trainer:
+  _target_: pytorch_lightning.Trainer
+  accelerator: auto
+  devices: auto
+  precision: 16-mixed
+  gradient_clip_val: 1.0
+  enable_progress_bar: false
+  log_every_n_steps: 5
+  val_check_interval: null
+  limit_val_batches: null
+  strategy:
+    _target_: pytorch_lightning.strategies.DDPStrategy
+    find_unused_parameters: true
+  logger:
+    _target_: pytorch_lightning.loggers.WandbLogger
+  callbacks:
+  - _target_: pytorch_lightning.callbacks.ModelCheckpoint
+    monitor: val_loss
+    mode: min
+    save_top_k: 3
+    dirpath: ${hydra:run.dir}/checkpoints
+    save_last: true
+  max_epochs: 250
+  accumulate_grad_batches: 4
+model:
+  network:
+    backbone_heavy:
+      _target_: igcraft.model.network.SequenceTransformer
+      cfg:
+        _target_: igcraft.model.network.SequenceTransformerConfig
+        num_layers: 12
+        embed_dim: 768
+        num_heads: 24
+        dropout_p: 0.1
+        output_dim: 21
+        use_entropy_encoding: true
+        fourier_n_min: -1
+        fourier_n_max: 16
+    backbone_light:
+      _target_: igcraft.model.network.SequenceTransformer
+      cfg:
+        _target_: igcraft.model.network.SequenceTransformerConfig
+        num_layers: 12
+        embed_dim: 768
+        num_heads: 24
+        dropout_p: 0.1
+        output_dim: 21
+        use_entropy_encoding: true
+        fourier_n_min: -1
+        fourier_n_max: 16
+    _target_: igcraft.model.network.PairedSequenceTransformer
+    cfg:
+      _target_: igcraft.model.network.PairedSequenceTransformerConfig
+      embed_dim: 256
+      num_heads: 8
+      dropout_p: 0.1
+      gate_bias_value: 0.0
+      freeze_heavy: false
+      freeze_light: false
+      freeze_all: true
+    structure_encoder:
+      _target_: igcraft.nn.geometric.PairedStructureEncoder
+      input_vh_dim: ${model.network.backbone_heavy.cfg.embed_dim}
+      input_vl_dim: ${model.network.backbone_light.cfg.embed_dim}
+      embed_dim: 512
+      num_heads: 64
+      num_layers: 4
+      dropout_p: 0.1
+      gate_bias_value: -5.0
+  bfn:
+    schedule:
+      _target_: igcraft.bfn.schedule.DiscreteBFNAccuracySchedule
+      variables_shape: ${model.bfn.variables_shape}
+      beta_1: 1.0
+    _target_: igcraft.bfn.bfn.DiscreteBFN
+    variables_shape:
+    - 291
+    num_classes: 21
+  datamodule:
+    _target_: igcraft.model.datamodule.PairedStructureDatamodule
+    cfg:
+      _target_: igcraft.model.config.PairedStructureDatamoduleConfig
+      batch_size: 64
+      num_workers: 4
+      vh_colnames:
+      - fwr1_aa_heavy
+      - cdr1_aa_heavy
+      - fwr2_aa_heavy
+      - cdr2_aa_heavy
+      - fwr3_aa_heavy
+      - cdr3_aa_heavy
+      - fwr4_aa_heavy
+      vl_colnames:
+      - fwr1_aa_light
+      - cdr1_aa_light
+      - fwr2_aa_light
+      - cdr2_aa_light
+      - fwr3_aa_light
+      - cdr3_aa_light
+      - fwr4_aa_light
+      train_dataset: /spinning2/shared/databases/paired_oas/train_structures.hdf5
+      val_dataset: /spinning2/shared/databases/paired_oas/val_structures.hdf5
+      test_dataset: /spinning2/shared/databases/paired_oas/test_structures.hdf5
+      max_epitope_length: 128
+      vh_key: vh
+      vl_key: vl
+      epitope_key: epitope
+    vh_tokenizer:
+      _target_: igcraft.model.datamodule.IMGTTokenizer
+      region_lengths:
+        fwr1: 30
+        cdr1: 15
+        fwr2: 20
+        cdr2: 15
+        fwr3: 42
+        cdr3: 30
+        fwr4: 12
+    vl_tokenizer:
+      _target_: igcraft.model.datamodule.IMGTTokenizer
+      region_lengths:
+        fwr1: 26
+        cdr1: 12
+        fwr2: 18
+        cdr2: 8
+        fwr3: 38
+        cdr3: 14
+        fwr4: 11
+  cfg:
+    _target_: igcraft.model.config.PairedSequenceModelConfig
+    max_lr: 0.0001
+    min_lr: 1.0e-05
+    use_lr_schedule: false
+    warmup_steps: 10000
+    transition_steps: 40000
+    ema_decay: 0.999
+    num_eval_time_bins: 10
+    out_dir: ${hydra:run.dir}
+    vh_ckpt_path: null
+    vl_ckpt_path: null
+  _target_: igcraft.model.PairedSequenceBFN
+wandb:
+  entity: sormanni-lab
+  project: IgCraft
+  run_name: finetune_paired_bfn
+  tags: null
+checkpoint:
+  config_path: /spinning1/sharedby/mg989/igcraft/train_paired_bfn-2024-12-29-09-53-54/.hydra/config.yaml
+  checkpoint_path: /spinning1/sharedby/mg989/igcraft/train_paired_bfn-2024-12-29-09-53-54/checkpoints/epoch=61-step=179955.ckpt
+  reset_optimizer: true

igcraft-model/hydra/hydra.yaml

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+hydra:
+  run:
+    dir: ${wandb.run_name}-${now:%Y-%m-%d-%H-%M-%S}
+  sweep:
+    dir: multirun/${now:%Y-%m-%d}/${now:%H-%M-%S}
+    subdir: ${hydra.job.num}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][%(name)s][%(levelname)s] - %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: RUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.mode=RUN
+    task: []
+  job:
+    name: train
+    chdir: null
+    override_dirname: ''
+    id: ???
+    num: ???
+    config_name: finetune_paired_bfn
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /spinning1/sharedby/mg989/igcraft
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /spinning1/sharedby/mg989/igcraft/config
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /spinning1/sharedby/mg989/igcraft/finetune_paired_bfn-2025-02-05-16-00-22
+    choices:
+      model: paired_bfn
+      model/cfg: paired
+      model/datamodule: paired
+      model/datamodule/vl_tokenizer: defaults
+      model/datamodule/vh_tokenizer: defaults
+      model/bfn: discrete
+      model/bfn/schedule: default
+      model/network: paired
+      trainer: defaults
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false

igcraft-model/hydra/overrides.yaml

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+[]