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2024-04-24T011302_CellViT-unireplknet-fold1-final/checkpoints/latest_checkpoint.pth

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2024-04-24T011302_CellViT-unireplknet-fold1-final/checkpoints/model_best.pth

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2024-04-24T011302_CellViT-unireplknet-fold1-final/config.yaml

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+logging:
+  log_dir: /data3/ziweicui/cell-unreplknet-small/2024-04-24T011302_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: przm46zv
+  wandb_file: przm46zv
+random_seed: 19
+gpu: 0
+data:
+  dataset: PanNuke
+  dataset_path: /data3/ziweicui/PanNuke/cellvit-png
+  train_folds:
+  - 2
+  val_folds:
+  - 1
+  test_folds:
+  - 0
+  num_nuclei_classes: 6
+  num_tissue_classes: 19
+model:
+  backbone: default
+  pretrained_encoder: /data3/ziweicui/cell-unreplknet-small/unireplknet_s_in1k_224_acc83.91.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

2024-04-24T013604_CellViT-unireplknet-fold1-final/checkpoints/latest_checkpoint.pth

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+size 1515916420

2024-04-24T013604_CellViT-unireplknet-fold1-final/checkpoints/model_best.pth

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2024-04-24T013604_CellViT-unireplknet-fold1-final/config.yaml

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+logging:
+  log_dir: /data3/ziweicui/cell-unreplknet-small/2024-04-24T013604_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: xii8r2nj
+  wandb_file: xii8r2nj
+random_seed: 19
+gpu: 0
+data:
+  dataset: PanNuke
+  dataset_path: /data3/ziweicui/PanNuke/cellvit-png
+  train_folds:
+  - 2
+  val_folds:
+  - 1
+  test_folds:
+  - 0
+  num_nuclei_classes: 6
+  num_tissue_classes: 19
+model:
+  backbone: default
+  pretrained_encoder: /data3/ziweicui/cell-unreplknet-small/unireplknet_s_in1k_224_acc83.91.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