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| lr: 2.881339661302105e-05 | |
| weight_decay: 1.1586679936312845e-05 | |
| log_only_loss_at_stages: [] | |
| bootstrap_metrics: true | |
| df_test_path: /data/yzhouc01/FILIP-MS/experiments/20250913_optimized_filip-model/result.pkl | |
| job_key: '' | |
| run_name: optimized_filip-model | |
| run_details: '' | |
| project_name: '' | |
| wandb_entity_name: mass-spec-ml | |
| no_wandb: true | |
| seed: 0 | |
| debug: false | |
| checkpoint_pth: null | |
| max_epochs: 2000 | |
| accelerator: gpu | |
| devices: | |
| - 1 | |
| log_every_n_steps: 250 | |
| val_check_interval: 1.0 | |
| candidates_pth: /r/hassounlab/spectra_data/msgym/molecules/MassSpecGym_retrieval_candidates_mass.json | |
| dataset_pth: /r/hassounlab/spectra_data/msgym/MassSpecGym.tsv | |
| subformula_dir_pth: /data/yzhouc01/MVP/data/MassSpecGym/data/subformulae_default | |
| split_pth: null | |
| fp_dir_pth: null | |
| cons_spec_dir_pth: null | |
| NL_spec_dir_pth: '' | |
| partial_checkpoint: '' | |
| batch_size: 64 | |
| contr_temp: 0.022772534845886608 | |
| early_stopping_patience: 300 | |
| loss_strategy: static | |
| num_workers: 50 | |
| spectra_view: SpecFormula | |
| formula_source: default | |
| max_mz: 1000 | |
| bin_width: 1 | |
| mask_peak_ratio: 0.0 | |
| element_list: | |
| - H | |
| - C | |
| - O | |
| - 'N' | |
| - P | |
| - S | |
| - Cl | |
| - F | |
| - Br | |
| - I | |
| - B | |
| - As | |
| - Si | |
| - Se | |
| add_intensities: true | |
| mask_precursor: false | |
| molecule_view: MolGraph | |
| atom_feature: full | |
| bond_feature: full | |
| use_contr: false | |
| contr_wt: 1 | |
| contr_wt_update: {} | |
| use_cons_spec: false | |
| cons_spec_wt: 3 | |
| cons_spec_wt_update: {} | |
| cons_loss_type: l2 | |
| pred_fp: false | |
| use_fp: false | |
| fp_loss_type: cosine | |
| fp_wt: 3 | |
| fp_wt_update: {} | |
| fp_size: 1024 | |
| fp_radius: 5 | |
| fp_dropout: 0.4 | |
| aug_cands: false | |
| aug_cands_wt: 0.1 | |
| aug_cands_update: {} | |
| aug_cands_size: 3 | |
| use_NL: false | |
| task: retrieval | |
| spec_enc: Transformer_Formula | |
| mol_enc: GNN | |
| model: filipContrastive | |
| contr_views: | |
| - - spec_enc | |
| - mol_enc | |
| final_embedding_dim: 512 | |
| fc_dropout: 0.4 | |
| hidden_dims: | |
| - 64 | |
| - 128 | |
| formula_dropout: 0.2 | |
| formula_dims: | |
| - 512 | |
| - 256 | |
| - 512 | |
| cross_attn_heads: 2 | |
| use_cls: false | |
| peak_dropout: 0.414425691950033 | |
| formula_attn_heads: 4 | |
| formula_transformer_layers: 2 | |
| attn_heads: | |
| - 12 | |
| - 12 | |
| - 12 | |
| gnn_channels: | |
| - 64 | |
| - 128 | |
| - 512 | |
| gnn_type: gcn | |
| num_gnn_layers: 3 | |
| gnn_hidden_dim: 512 | |
| gnn_dropout: 0.23234950970370824 | |
| experiment_dir: /data/yzhouc01/FILIP-MS/experiments/20250913_optimized_filip-model | |
| at_ks: | |
| - 1 | |
| - 5 | |
| - 20 | |
| myopic_mces_kwargs: null | |