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