# Training configuration for the OmicsFM checkpoint in this folder.
# Extracted verbatim from best_model.ckpt.

checkpoint: bulk_transcriptomics
training_run: bulk_trans
epoch: 53
val_loss: 2.6126632893882027
vocabulary_size: 20272
config:
  data:
    train_path: data/bulk_trans/protein_mapped/train.h5ad
    valid_path: data/bulk_trans/protein_mapped/valid.h5ad
    test_path: data/bulk_trans/protein_mapped/test.h5ad
    num_bins: 10
    detect_groups: false
    cache_build_workers: 1
  transfer:
    checkpoint_path: C:\Users\sander\OneDrive\Bureaublad\Projects\prot_GPT\code\protgpt\model\bulk_trans\best_model.ckpt
    freeze_transformer: false
    freeze_epochs: 0
  device: cuda
  model:
    d_model: 256
    n_heads: 8
    n_layers: 6
    d_ff: 1024
    dropout: 0.1
    input_features: 1024
    feature_context_ratio: 0.85
    use_esmc: false
    fasta_path: fasta/human_proteome_canonical_31032022.fasta
    esmc_model: esmc_600m
    esmc_cache: data/esmc_human_cache.pt
    absent_species:
      enabled: false
      input_absent: 50
      absent_context_ratio: 0.5
    protein_groups:
      enabled: false
      max_group_size: 20
      input_groups: 256
      group_context_ratio: 0.2
      encoder: mean
      attention:
        n_heads: 4
        n_encoder_layers: 1
  training:
    batch_size: 64
    learning_rate: 0.0001
    weight_decay: 1.0e-05
    max_epochs: 200
    val_frequency: 0.25
    early_stopping_patience: 5000
    early_stopping_delta: 0.001
    gradient_clip: 1.0
    num_workers: 0
  output:
    save_dir: model
    experiment_name: bulk_trans