| { |
| "seed": 42, |
| "wandb": true, |
| "truncation_seq_length": 512, |
| "batch_size": 16, |
| "foldseek_path": "/fs/gpfs41/lv11/fileset01/pool/pool-chen/softwares/micromamba/envs/foldseek/bin/foldseek", |
| "datamodule": { |
| "batch_size": 64, |
| "num_workers": 32, |
| "_target_": "foldmae.data.TEDLightningDataset", |
| "root": "./datasets/afdb_FS_plddt80", |
| "dataset_name": "ted" |
| }, |
| "trainer": { |
| "_target_": "pytorch_lightning.Trainer", |
| "accelerator": "auto", |
| "max_steps": 18300, |
| "strategy": "ddp_find_unused_parameters_true", |
| "devices": "auto", |
| "default_root_dir": "${logs.path}", |
| "num_sanity_val_steps": 0, |
| "accumulate_grad_batches": 16 |
| }, |
| "model": { |
| "name": "SaProt_650M_AF2", |
| "path": "cache/torch/hub/checkpoints/${model.name}", |
| "num_classes": 965, |
| "avg_pool": false |
| }, |
| "train": { |
| "optimizer": { |
| "_target_": "torch.optim.AdamW", |
| "lr": 0.0016, |
| "weight_decay": 0.1, |
| "betas": [ |
| 0.9, |
| 0.95 |
| ] |
| }, |
| "lr_scheduler": { |
| "_target_": "foldmae.lr_schedulers.get_cosine_schedule_with_warmup", |
| "warmup_steps": 1830, |
| "max_steps": "${trainer.max_steps}" |
| }, |
| "loss": { |
| "_target_": "torch.nn.CrossEntropyLoss" |
| }, |
| "llrd": 0.8, |
| "ckpt_path": "logs/saprot/finetune/ted/42/runs/2026-01-20_22-15-11/model.ckpt" |
| }, |
| "logs": { |
| "prefix": "logs/saprot/finetune/${datamodule.dataset_name}/${seed}", |
| "path": "${logs.prefix}/runs/${now:%Y-%m-%d}_${now:%H-%M-%S}" |
| }, |
| "_model_class": "saprot" |
| } |
