| { | |
| "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 | |
| } |