train_both_mh_MF_hr.yml

run_name:
data:
  num_entries: -1
  primary_dset: ["nist","mb_na"]
  secondary_dset: []
  ce_key: "nce"
  inst_type: ["FT"]
  frag_mode: ["HCD"]
  pos_prec_type: ['[M+H]+']
  fp_types:   ["morgan","rdkit","maccs"]
  preproc_ce: "normalize"
  spectrum_normalization: "l1"
  gf_algos_v: "algos2"
  mz_bin_res: 0.1
model:
  embed_types: ["gf_v2"]
  ff_layer_type: "neims"
  ff_h_dim: 1000
  ff_num_layers: 4
  ff_skip: True
  dropout: 0.4
  output_normalization: "l1"
  bidirectional_prediction: True
  gf_model_name: "graphormer_base"
  gf_pretrain_name: "pcqm4mv2_graphormer_base"
  fix_num_pt_layers: 0
  reinit_num_pt_layers: -1
  reinit_layernorm: True
  model_seed: 6666
run:
  loss: "cos"
  sim: "cos"
  lr: 0.001
  batch_size: 100
  clip_grad_norm: 5.0
  scheduler: "polynomial"
  scheduler_peak_lr: 0.0002
  weight_decay: 0.001
  pt_weight_decay: 0.0
  dp: False
  dp_num_gpus: 0
  flag: True
  num_epochs: 20
  num_workers: 8
  cuda_deterministic: False
  do_test: True
  do_casmi: False
  do_pcasmi: False
  do_casmi22: False
  save_state: True
  save_media: False
  log_auxiliary: True
  train_seed: 5585
  split_seed: 420
  split_key: "inchikey_s"
  log_tqdm: False
  grad_acc_interval: 4 # for 12GB
  test_sets: ["train","val"]
  save_test_sims: True
  test_frac: 0.