template.yml

entity_name: "wandb_entity_name"
project_name: "wandb_project_name"
run_name: "template"

data:
  proc_dp: "data/proc"
  cfm_dp: "data/cfm"
  checkpoint_dp: "checkpoints"
  primary_dset: ["nist"]
  secondary_dset: []
  inst_type: ["FT"]
  frag_mode: ["HCD"]
  ion_mode: "P"
  pos_prec_type: ['[M+H]+', '[M+H-H2O]+', '[M+H-2H2O]+', '[M+2H]2+', '[M+H-NH3]+']
  neg_prec_type: ['[M-H]-', '[M-H-H2O]-']
  res: [1,2,3,4,5,6,7]
  mz_bin_res: 1.
  mz_max: 1000.
  transform: "log10over3"
  atom_feature_mode: "medium"
  bond_feature_mode: "full"
  spec_meta_node: True
  spec_meta_global: True
  self_loop: True
  preproc_ce: "normalize"
  subsample_size: 0
  ints_thresh: 0.
  subsample_seed: 42069
  spectrum_normalization: "l1"
  num_entries: -1
  selfies_encoding: True
  max_seq_len: 500
  num_canonicals: 1
  subsample_long_seq: True
  ce_key: "nce"
  fp_types: ["morgan"]
  max_node: 128
  multi_hop_max_dist: 20
  spatial_pos_max: 1024
  casmi_num_entries: -1
  pcasmi_num_entries: -1
  casmi22_num_entries: -1
  casmi_nces: [20,35,50]
  casmi22_nces: [35,45,65]
  convert_ce: False
  casmi_dp: "casmi_2016"
  pcasmi_dp: "nist20_outlier"
  casmi22_dp: "casmi_2022"
  gf_algos_v: "algos2"
  casmi_fp: False
  process_spec_old: False

model:
  embed_types: ["fp"]
  gnn_num_layers: 3
  gnn_h_dim: 196
  gnn_pool_type: "max"
  ff_layer_type: "neims"
  ff_skip: False
  ff_num_layers: 3
  ff_h_dim: 1000
  gate_prediction: True
  gt_gate_prediction: False
  gt_gate_val: 0.8
  bidirectional_prediction: False
  mass_tau: 1 
  gat_num_heads: 4
  dropout: 0.15
  output_activation: "relu"
  output_normalization: "l1"
  model_seed: 6666
  conv_num_layers: 3
  conv_kernel_size: 5
  conv_num_kernels: 32
  conv_stride: 1
  conv_pool_type: "max"
  conv_pool_size: 4
  fix_num_pt_layers: 0
  reinit_num_pt_layers: 0
  cfm_postprocessing: False
  tf_h_dim: 256
  tf_num_layers: 4
  tf_num_heads: 6
  spectrum_attention: False
  gf_model_name: "graphormer_base"
  gf_pretrain_name: "pcqm4mv2_graphormer_base"
  reinit_layernorm: False
  cfm_model: False
  cfm_rb: True
  esp_model: False
  esp_new_reverse: False
  prec_mass_offset: 0
  embed_dim: -1
  embed_agg: "concat"
  embed_linear: False
  checkpoint_name:

run:
  learning_rate: 0.001
  num_epochs: 500
  num_decay_epochs: -1
  val_frac: 0.10
  test_frac: 0.20
  sec_frac: 1.00
  optimizer: "adamw"
  batch_size: 32
  batch_loss_agg: "mean"
  split_key: "scaffold"
  split_seed: 420
  loss: "cos"
  sim: "cos"
  weight_decay: 0.001
  pt_weight_decay: -1.
  clip_grad_norm: 1000000.0
  early_stop_thresh: 10
  scheduler: "plateau"
  scheduler_period: 5
  scheduler_ratio: 0.1
  scheduler_peak_lr: 0.0002
  scheduler_end_lr: 0.000000001 #1e-9
  scheduler_warmup_frac: 0.1
  scheduler_power: 1.0
  match_seed: 69
  train_seed: 112233
  device: "cuda:0"
  non_blocking: False
  log_interval: 10
  do_test: True
  num_workers: 6
  num_track: 5
  pred_viz: True
  track_plot_title: True
  do_casmi: False
  do_pcasmi: False
  do_casmi22: False
  casmi_batch_size: -1
  casmi_num_workers: -1
  casmi_pred_all: True
  pcasmi_pred_all: False
  casmi22_pred_all: False
  log_pcasmi_um: False
  match_num_cands: 50
  match_num_reps: 1
  match_exact: True
  match_max_num_cands: 1000
  match_batch_size: 50
  match_num_workers: 6
  pin_memory: True
  match_remove_mol_dups: False
  match_type: "formula"
  stop_key: "mol_loss_obj_mean"
  cuda_deterministic: False
  parallel_strategy: "fd"
  save_state: True
  save_media: True
  save_split: True
  casmi_save_sim: False
  amp: False
  dp: False
  dp_num_gpus: 2
  flag: False
  flag_m: 3
  flag_step_size: 0.001
  flag_mag: 0.001
  filter_spec: False
  log_auxiliary: False
  log_tqdm: True
  use_val_info: True
  grad_acc_interval: 1
  test_sets: ["test"]
  save_test_sims: False
  ignore_casmi_in_split: False
  lda_topic_loss: False
  lda_topic_loss_weight: 0.01
  print_stats: False