nn:
  model: GeometricTransformer
  dataset: GeometricTransformerDataset
  dtype: float32
  device: cuda
  data_in_memory: false
  load_model: null
  batch_size: 128
  num_workers: 4
  collate_fn: geometric_transformer_collate_fn
  model_args:
    dim_model: 1536
    unified_transformer_args:
      n_layers: 48
      geom_layer_indices:
      - 0
      mha_layer_indices:
      - 0
      - 1
      - 2
      - 3
      - 4
      - 5
      - 6
      - 7
      - 8
      - 9
      - 10
      - 11
      - 12
      - 13
      - 14
      - 15
      - 16
      - 17
      - 18
      - 19
      - 20
      - 21
      - 22
      - 23
      - 24
      - 25
      - 26
      - 27
      - 28
      - 29
      - 30
      - 31
      - 32
      - 33
      - 34
      - 35
      - 36
      - 37
      - 38
      - 39
      - 40
      - 41
      - 42
      - 43
      - 44
      - 45
      - 46
      - 47
      bias: false
      mha_args:
        num_heads: 24
        bias: false
        qk_layernorm: true
      gha_args:
        num_heads: 256
        num_vector_messages: 1
        mask_and_zero_frameless: true
        bias: false
      scaling_factor: 1.1547005383792515
      ffn_type: swiglu
      norm_type: layer_norm
      expansion_ratio: 2.66666666667
    struc_token_info:
      mask: 4096
      eos: 4097
      bos: 4098
      pad: 4099
      total: 5001
      max_non_special_token: 4095
    residue_token_info:
      mask: 32
      eos: 2
      bos: 0
      pad: 1
      total: 33
      max_non_special_token: null
    sasa_token_info:
      mask: 0
      eos: 0
      bos: 0
      pad: 0
      total: null
      max_non_special_token: null
    sec_struct_token_info:
      mask: 0
      eos: 0
      bos: 0
      pad: 0
      total: null
      max_non_special_token: null
    res_annot_token_info:
      mask: 0
      eos: 0
      bos: 0
      pad: 0
      total: null
      max_non_special_token: null
  dataset_split_args:
    train: 0.8
    val: 0.2
    test: 0.0
train:
  lightning_model: TransformerModel
  resume_training_path: null
  lightning_model_args:
    eval_type: sft
    beta: null
    gamma: null
    sampling_temperature: null
    optimizer: Adam
    optimizer_args:
      lr: 0.0004
      betas:
      - 0.9
      - 0.95
      weight_decay: 0.01
    lr_scheduler: LinearWarmupCosineAnnealingLR
    lr_scheduler_args:
      warmup_epochs: 250000
      max_epochs: 2500000
      eta_min: 4.0e-05
    interval: step
    monitor: val/CELoss
    sync_dist: true
    on_step: true
  trainer_args:
    eval_type: era
    accelerator: cuda
    devices: 1
    strategy: auto
    log_every_n_steps: 500
    max_epochs: 10000
    enable_progress_bar: false
    gradient_clip_val: 1.0
  logger:
    loggertype: TensorBoard
  seed_args:
    seed: 42
    workers: true
global_args:
  dataset_filename: /scratch/group_scratch/era/directed_evolution/datasets/gb1/gb1_tokenized.h5
  keys_to_test:
  - nn.model
  - nn.model_args