| logging: | |
| log_dir: /data/ziweicui/cellvit-unireplknet-n/2024-04-30T135715_CellViT-unireplknet-fold1 | |
| mode: online | |
| project: Cell-Segmentation | |
| notes: CellViT-256 | |
| log_comment: CellViT-unireplknet-fold1 | |
| tags: | |
| - Fold-1 | |
| - ViT256 | |
| wandb_dir: /home/ziweicui/cell_unireplknet/results | |
| level: Debug | |
| group: CellViT256 | |
| run_id: iuq2auqz | |
| wandb_file: iuq2auqz | |
| random_seed: 19 | |
| gpu: 0 | |
| data: | |
| dataset: PanNuke | |
| dataset_path: /data/ziweicui/cellvit-png | |
| train_folds: | |
| - 0 | |
| val_folds: | |
| - 1 | |
| test_folds: | |
| - 2 | |
| num_nuclei_classes: 6 | |
| num_tissue_classes: 19 | |
| model: | |
| backbone: default | |
| pretrained_encoder: /data/ziweicui/cellvit-unireplknet-n/unireplknet_n_in1k_224_acc81.64.pth | |
| shared_skip_connections: true | |
| loss: | |
| nuclei_binary_map: | |
| focaltverskyloss: | |
| loss_fn: FocalTverskyLoss | |
| weight: 1 | |
| dice: | |
| loss_fn: dice_loss | |
| weight: 1 | |
| hv_map: | |
| mse: | |
| loss_fn: mse_loss_maps | |
| weight: 2.5 | |
| msge: | |
| loss_fn: msge_loss_maps | |
| weight: 8 | |
| nuclei_type_map: | |
| bce: | |
| loss_fn: xentropy_loss | |
| weight: 0.5 | |
| dice: | |
| loss_fn: dice_loss | |
| weight: 0.2 | |
| mcfocaltverskyloss: | |
| loss_fn: MCFocalTverskyLoss | |
| weight: 0.5 | |
| args: | |
| num_classes: 6 | |
| tissue_types: | |
| ce: | |
| loss_fn: CrossEntropyLoss | |
| weight: 0.1 | |
| training: | |
| drop_rate: 0 | |
| attn_drop_rate: 0.1 | |
| drop_path_rate: 0.1 | |
| batch_size: 16 | |
| world_size: 2 | |
| rank: 0 | |
| epochs: 100 | |
| optimizer: AdamW | |
| early_stopping_patience: 70 | |
| scheduler: | |
| scheduler_type: cosine | |
| hyperparameters: | |
| eta_min: 1e-5 | |
| optimizer_hyperparameter: | |
| betas: | |
| - 0.85 | |
| - 0.95 | |
| lr: 0.001 | |
| weight_decay: 0.1 | |
| opt_eps: 8.0e-08 | |
| layer_decay: 0.999999 | |
| unfreeze_epoch: 0 | |
| sampling_gamma: 0.85 | |
| sampling_strategy: cell+tissue | |
| mixed_precision: false | |
| transformations: | |
| randomrotate90: | |
| p: 0.5 | |
| horizontalflip: | |
| p: 0.5 | |
| verticalflip: | |
| p: 0.5 | |
| downscale: | |
| p: 0.15 | |
| scale: 0.5 | |
| blur: | |
| p: 0.2 | |
| blur_limit: 10 | |
| gaussnoise: | |
| p: 0.25 | |
| var_limit: 50 | |
| colorjitter: | |
| p: 0.2 | |
| scale_setting: 0.25 | |
| scale_color: 0.1 | |
| superpixels: | |
| p: 0.1 | |
| zoomblur: | |
| p: 0.1 | |
| randomsizedcrop: | |
| p: 0.1 | |
| elastictransform: | |
| p: 0.2 | |
| normalize: | |
| mean: | |
| - 0.5 | |
| - 0.5 | |
| - 0.5 | |
| std: | |
| - 0.5 | |
| - 0.5 | |
| - 0.5 | |
| eval_checkpoint: latest_checkpoint.pth | |
| dataset_config: | |
| tissue_types: | |
| Adrenal_gland: 0 | |
| Bile-duct: 1 | |
| Bladder: 2 | |
| Breast: 3 | |
| Cervix: 4 | |
| Colon: 5 | |
| Esophagus: 6 | |
| HeadNeck: 7 | |
| Kidney: 8 | |
| Liver: 9 | |
| Lung: 10 | |
| Ovarian: 11 | |
| Pancreatic: 12 | |
| Prostate: 13 | |
| Skin: 14 | |
| Stomach: 15 | |
| Testis: 16 | |
| Thyroid: 17 | |
| Uterus: 18 | |
| nuclei_types: | |
| Background: 0 | |
| Neoplastic: 1 | |
| Inflammatory: 2 | |
| Connective: 3 | |
| Dead: 4 | |
| Epithelial: 5 | |
| run_sweep: false | |
| agent: null | |