pretrained/args.json

{
  "data_source": "/scratch/hdd001/home/haotian/spatial_data/parquets_August_16_sample_zero_coordinates/combined_all_counts",
  "save_dir": "/scratch/hdd001/home/haotian/spatial_data/spatial_pretrain_save/spatial-continual-Nov29-05-56-2024",
  "load_model": "/scratch/ssd004/scratch/chloexq/scGPT_models/scGPT_human_model",
  "n_hvg": null,
  "valid_size_or_ratio": 0.003,
  "grad_accu_steps": 16,
  "pad_token": "<pad>",
  "input_style": "binned",
  "binning_style": "quantile",
  "input_emb_style": "continuous",
  "n_bins": 51,
  "max_seq_len": 600,
  "training_tasks": "both",
  "mask_ratio": [
    0.25,
    0.5,
    0.75
  ],
  "trunc_by_sample": true,
  "vocab_path": "/scratch/ssd004/scratch/chloexq/scGPT_models/scGPT_human_model/vocab.json",
  "batch_size": 16,
  "local_rank": 0,
  "eval_batch_size": 32,
  "epochs": 6,
  "lr": 5e-05,
  "scheduler_interval": 100,
  "scheduler_factor": 0.99,
  "warmup_ratio_or_step": 10000.0,
  "no_cls": true,
  "no_cce": true,
  "no_impute": false,
  "no_decmoe": false,
  "impute_k": 6,
  "no_batch": false,
  "fp16": true,
  "fast_transformer": true,
  "nlayers": 12,
  "nheads": 8,
  "embsize": 512,
  "d_hid": 512,
  "dropout": 0.2,
  "n_layers_cls": 3,
  "log_interval": 3000,
  "save_interval": 9000,
  "mask_value": -1,
  "pad_value": -2
}