|
{ |
|
"data_source": "/scratch/ssd004/datasets/cellxgene/scb_strict/human", |
|
"save_dir": "/scratch/ssd004/datasets/cellxgene/save/cellxgene_census_human-Dec18-13-52-2023", |
|
"load_model": "/scratch/ssd004/datasets/cellxgene/save/scGPT_human", |
|
"n_hvg": null, |
|
"valid_size_or_ratio": 0.003, |
|
"dist_backend": "nccl", |
|
"grad_accu_steps": 1, |
|
"pad_token": "<pad>", |
|
"input_style": "binned", |
|
"input_emb_style": "continuous", |
|
"n_bins": 51, |
|
"max_seq_len": 1200, |
|
"training_tasks": "both", |
|
"dist_url": "tcp://gpu183.cluster.local:54165", |
|
"mask_ratio": [ |
|
0.25, |
|
0.5, |
|
0.75 |
|
], |
|
"trunc_by_sample": true, |
|
"vocab_path": "/scratch/ssd004/datasets/cellxgene/scFormer/scformer/tokenizer/default_census_vocab.json", |
|
"rank": 0, |
|
"batch_size": 24, |
|
"eval_batch_size": 48, |
|
"epochs": 10, |
|
"lr": 0.0001, |
|
"scheduler_interval": 100, |
|
"scheduler_factor": 0.99, |
|
"warmup_ratio_or_step": 10000.0, |
|
"no_cls": false, |
|
"no_cce": true, |
|
"fp16": true, |
|
"fast_transformer": true, |
|
"annotation_source": "/scratch/ssd004/datasets/cellxgene/tabula_sapiens/parquet/", |
|
"annotation_valid_size_or_ratio": 0.1, |
|
"nlayers": 12, |
|
"nheads": 8, |
|
"embsize": 512, |
|
"d_hid": 512, |
|
"dropout": 0.2, |
|
"n_layers_cls": 3, |
|
"annote_max_seq_len": 5000, |
|
"log_interval": 500, |
|
"save_interval": 1000, |
|
"mask_value": -1, |
|
"pad_value": -2, |
|
"USE_CLS": true, |
|
"USE_CCE": false, |
|
"MVC": true, |
|
"USE_GENERATIVE_TRAINING": true, |
|
"world_size": 8, |
|
"distributed": true, |
|
"local_rank": 0, |
|
"gpu": 0 |
|
} |