updated param file

hparams.yaml → params.yaml

@@ -1,118 +1,97 @@
-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
+# FLARE — FILIP contrastive retrieval (SpecFormula + GNN).
+# Paths below are relative to the repository root unless absolute.
+# Override file location: FLARE_PARAMS=/path/to/custom.yaml
+
+# --- Run / logging ---
+run_name: flare_filip
 job_key: ''
-run_name: optimized_filip-model
 run_details: ''
 project_name: ''
-wandb_entity_name: mass-spec-ml
+wandb_entity_name: ''
 no_wandb: true
 seed: 0
 debug: false
-checkpoint_pth: null
+bootstrap_metrics: true
+log_only_loss_at_stages: []
+
+# --- Training ---
+lr: 2.881339661302105e-05
+weight_decay: 1.1586679936312845e-05
 max_epochs: 2000
 accelerator: gpu
-devices:
-- 1
+devices: [1]
+batch_size: 64
+num_workers: 50
 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
+contr_temp: 0.022772534845886608
 loss_strategy: static
-num_workers: 50
-spectra_view: SpecFormula
+checkpoint_pth: null
+
+# --- Data (set to your local copies) ---
+dataset_pth: data/MassSpecGym.tsv
+candidates_pth: data/MassSpecGym_retrieval_candidates_mass.json
+subformula_dir_pth: data/subformulae_default
+split_pth: null
 formula_source: default
+
+# --- Views / featurizers ---
+spectra_view: SpecFormula
+molecule_view: MolGraph
 max_mz: 1000
 bin_width: 1
 mask_peak_ratio: 0.0
+mask_precursor: false
 element_list:
-- H
-- C
-- O
-- 'N'
-- P
-- S
-- Cl
-- F
-- Br
-- I
-- B
-- As
-- Si
-- Se
+  - 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 & model ---
 task: retrieval
 spec_enc: Transformer_Formula
 mol_enc: GNN
 model: filipContrastive
 contr_views:
-- - spec_enc
-  - mol_enc
+  - [spec_enc, mol_enc]
+
 final_embedding_dim: 512
 fc_dropout: 0.4
-hidden_dims:
-- 64
-- 128
+hidden_dims: [64, 128]
+
 formula_dropout: 0.2
-formula_dims:
-- 512
-- 256
-- 512
+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
+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
+
+# --- Evaluation (retrieval base class) ---
+at_ks: [1, 5, 20]
 myopic_mces_kwargs: null
+
+# --- Outputs (optional; train/test override as needed) ---
+df_test_path: ''