data:
  batch_size: 144
  count_cell_norm_method: null
  count_count_norm_method: shifted_log
  count_gene_norm_method: null
  dataset_name: hst_corpus_110m
  model_input_size: 2816
  n_neighs: 10
  n_segments: 11
  num_workers: 16
  pin_memory: true
  precomputed_n_nonzero_tokens: /fsx-shared/s3/hst_corpus_110m/hst_corpus_110m_32_None_None_None_None_None_shifted_log_knn_10_n_nonzero_tokens_train.pkl
  precomputed_split: /fsx-shared/s3/hst_corpus_110m/hst_corpus_110m_32_None_None_None_None_None_shifted_log_knn_10_precomputed_split_train.pkl
  random_state: 0
  rank_cell_norm_method: null
  rank_count_norm_method: null
  rank_gene_norm_method: null
  raw_data_folder_path: /lustre/scratch126/cellgen/lotfollahi/DATASETS/silver/hst_corpus_110m
  sample_subset: false
  sampling_strategy: null
  sep_gene_tokens_neb: false
  seq_len_cell: 256
  seq_len_neighborhood: 2560
  split: 0
  stratify: false
  test_batch_ids:
  - 49_batch0
  token_dict_folder_path: /fsx-shared/s3/token_dictionary_homo_sapiens.pkl
  tokenized_data_folder_path: /fsx-shared/s3/hst_corpus_110m/hst_corpus_110m_32_None_None_None_None_None_shifted_log_knn_10.dataset
  tokenizer_type: cell_graph
  use_sampler: true
  val_batch_ids:
  - 49_batch0
mask:
  block_masking: true
  cell_masking: false
  context_mask_size: 200
  n_contexts: 1
  n_targets: 1
  per_block_mask_ratio: 0.8
  sample_segments: true
  target_mask_size: 50
  targets_list: null
  restrict_special_attention: False
meta:
  add_cls: false
  api_version: v3
  cell_pos_enc: coord
  count_encoding: mlp
  enc_depth: 12
  enc_emb_dim: 384
  gt_type: combined
  mlp_ratio: 4
  n_value_bins: 100
  num_heads: 6
  pos_learnable: false
  pred_depth: 12
  pred_emb_dim: 192
  predict_gene: true
  seg_learnable: false
  special_tokens: []
  use_bfloat16: true
  use_flash_attention: true
  use_layer_norm: true
  restrict_special_attention: false
optimization:
  clip_grad: 2.0
  ema:
  - 0.9995
  - 1.0
  epochs: 5
  final_lr: 1.0e-06
  final_weight_decay: 0.4
  ipe_scale: 1.25
  lr: 6.0e-05
  start_lr: 1.0e-06
  warmup: 1
  weight_decay: 0.04
state:
  checkpoint_freq: 1
  checkpoint_freq_iter: 5000
  folder_path: null
  load_checkpoint: false
  log_freq: 20
  read_checkpoint: null
  read_timestamp: 'nichejepa-ep2.pth.tar'
  write_tag: nichejepa