| # Training configuration for the OmicsFM checkpoint in this folder. | |
| # Extracted verbatim from best_model.ckpt. | |
| checkpoint: bulk_transcriptomics_esmc | |
| training_run: bulk_trans_esmc | |
| epoch: 128 | |
| val_loss: 3.8213612177252925 | |
| 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: null | |
| 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: true | |
| 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_esmc | |