model

app_utils/model_utils.py

@@ -24,7 +24,7 @@ def load_model_components():
 
     # load model
 
-    checkpoint_pth = "experiments/20250913_optimized_filip-model/epoch=1993-train_loss=0.10.ckpt"
+    checkpoint_pth = "epoch=1993-train_loss=0.10.ckpt"
     params['checkpoint_pth'] = checkpoint_pth
     model = get_model(params['model'], params)
 

app_utils/upload_model.py

@@ -0,0 +1,10 @@
+from huggingface_hub import HfApi
+
+api = HfApi()
+api.upload_file(
+    path_or_fileobj="experiments/20250913_optimized_filip-model/epoch=1993-train_loss=0.10.ckpt",
+    path_in_repo="epoch=1993-train_loss=0.10.ckpt",
+    repo_id="yzhouchen001/flare",
+    repo_type="space", # automatically uses your saved token
+    use_auth_token=True
+)

experiments/20250913_optimized_filip-model/lightning_logs/version_0/hparams.yaml

@@ -0,0 +1,118 @@
+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