config.yaml

# lightning.pytorch==2.0.9.post0
seed_everything: 42
trainer:
  accelerator: auto
  strategy: auto
  devices: auto
  num_nodes: 1
  precision: 16
  logger: false
  callbacks:
  - class_path: scprint.trainer.TrainingMode
    init_args:
      do_denoise: true
      noise:
      - 0.3
      do_cce: true
      cce_sim: 0.5
      do_ecs: true
      ecs_threshold: 0.3
      ecs_scale: 1.0
      do_mvc: false
      do_adv_cls: false
      do_next_tp: false
      class_scale: 1.0
      mask_ratio:
      - 0.15
      - 0.3
      log_grad: false
  - class_path: lightning.pytorch.callbacks.StochasticWeightAveraging
    init_args:
      swa_lrs: 0.01
      swa_epoch_start: 0.8
      annealing_epochs: 10
      annealing_strategy: cos
      avg_fn: null
      device: cpu
  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
    init_args:
      dirpath: null
      filename: null
      monitor: val_loss
      verbose: false
      save_last: null
      save_top_k: -1
      save_weights_only: false
      mode: min
      auto_insert_metric_name: true
      every_n_train_steps: null
      train_time_interval: null
      every_n_epochs: null
      save_on_train_epoch_end: null
  - class_path: lightning.pytorch.callbacks.EarlyStopping
    init_args:
      monitor: val_loss
      min_delta: 0.0
      patience: 10
      verbose: false
      mode: min
      strict: true
      check_finite: true
      stopping_threshold: null
      divergence_threshold: null
      check_on_train_epoch_end: null
      log_rank_zero_only: false
  - class_path: lightning.pytorch.callbacks.LearningRateMonitor
    init_args:
      logging_interval: step
      log_momentum: false
  fast_dev_run: false
  max_epochs: null
  min_epochs: null
  max_steps: -1
  min_steps: null
  max_time: '{''hours'': 12}'
  limit_train_batches: null
  limit_val_batches: null
  limit_test_batches: null
  limit_predict_batches: null
  overfit_batches: 0.0
  val_check_interval: null
  check_val_every_n_epoch: 1
  num_sanity_val_steps: null
  log_every_n_steps: null
  enable_checkpointing: null
  enable_progress_bar: null
  enable_model_summary: null
  accumulate_grad_batches: 1
  gradient_clip_val: 10
  gradient_clip_algorithm: null
  deterministic: null
  benchmark: null
  inference_mode: true
  use_distributed_sampler: true
  profiler: simple
  detect_anomaly: false
  barebones: false
  plugins: null
  sync_batchnorm: false
  reload_dataloaders_every_n_epochs: 0
  default_root_dir: null
model:
  d_model: 128
  nhead: 4
  d_hid: 128
  edge_dim: 12
  nlayers: 4
  layers_cls: []
  dropout: 0.2
  transformer: flash
  expr_emb_style: continuous
  domain_spec_batchnorm: None
  n_input_bins: 0
  mvc_decoder: inner product
  pred_embedding:
  - cell_type_ontology_term_id
  - disease_ontology_term_id
  - self_reported_ethnicity_ontology_term_id
  - sex_ontology_term_id
  cell_emb_style: cls
  lr: 0.001
  residual_in_fp32: true
  num_heads_kv: null
  checkpointing: false
  fused_dropout_add_ln: false
  return_residual: false
  prenorm: true
  mlp_ratio: 4.0
  fused_mlp: false
  fused_bias_fc: false
  sequence_parallel: false
  drop_path_rate: 0.02
  weight_init: ''
data:
  mdataset: null
  collection_name: preprocessed dataset
  organisms:
  - NCBITaxon:9606
  weight_scaler: 30
  label_to_weight:
  - cell_type_ontology_term_id
  - disease_ontology_term_id
  - assay_ontology_term_id
  - self_reported_ethnicity_ontology_term_id
  - sex_ontology_term_id
  - organism_ontology_term_id
  label_to_pred:
  - cell_type_ontology_term_id
  - disease_ontology_term_id
  - assay_ontology_term_id
  - self_reported_ethnicity_ontology_term_id
  - sex_ontology_term_id
  - organism_ontology_term_id
  validation_split: 0.2
  test_split: 0.0
  use_default_col: true
  all_clss:
  - cell_type_ontology_term_id
  - disease_ontology_term_id
  - assay_ontology_term_id
  - self_reported_ethnicity_ontology_term_id
  - sex_ontology_term_id
  - organism_ontology_term_id
  - heat_diff
  - total_counts
  - nnz
  - dpt_group
  hierarchical_labels:
  - cell_type_ontology_term_id
  - disease_ontology_term_id
  - assay_ontology_term_id
  - self_reported_ethnicity_ontology_term_id
  how: most expr
  organism_name: organism_ontology_term_id
  max_len: 1000
  add_zero_genes: 100
  do_gene_pos: true
  gene_embeddings: ./data/temp/embeddings.parquet
  gene_position_tolerance: 10000
  batch_size: 64
  shuffle: null
  batch_sampler: null
  num_workers: 8
  pin_memory: false
  drop_last: false
  timeout: 0.0
  worker_init_fn: null
  multiprocessing_context: null
  generator: null
  prefetch_factor: null
  persistent_workers: false
  pin_memory_device: ''
set_float32_matmul_precision: true
project: scprint_test
ckpt_path: null