First Commit

.gitignore

+logs/*
\ No newline at end of file

Camelyon/TransMIL.yaml

@@ -29,9 +29,13 @@ Data:
         batch_size: 1
         num_workers: 8
 
+        
+
+
 Model:
     name: TransMIL
     n_classes: 2
+    backbone: resnet18
 
 
 Optimizer:

DeepGraft/TransMIL.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16 
+    multi_gpu_mode: dp
+    gpus: [0]
+    epochs: &epoch 200 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 200
+    server: test #train #test
+    log_path: logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_bin.json'
+    fold: 0
+    nfold: 4
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+        
+
+Model:
+    name: TransMIL
+    n_classes: 6
+    backbone: resnet18
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.00001
+
+Loss:
+    base_loss: CrossEntropyLoss
+

DeepGraft/TransMIL_dino.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16 
+    multi_gpu_mode: dp
+    gpus: [0]
+    epochs: &epoch 1000 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 200
+    server: test #train #test
+    log_path: logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_bin.json'
+    fold: 0
+    nfold: 4
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+        
+
+Model:
+    name: TransMIL
+    n_classes: 2
+    backbone: dino
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.00001
+
+Loss:
+    base_loss: CrossEntropyLoss
+

DeepGraft/TransMIL_resnet18_all.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16 
+    multi_gpu_mode: dp
+    gpus: [3]
+    epochs: &epoch 500 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 200
+    server: test #train #test
+    log_path: logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_all.json'
+    fold: 1
+    nfold: 4
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+Model:
+    name: TransMIL
+    n_classes: 6
+    backbone: resnet18
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.00001
+
+Loss:
+    base_loss: CrossEntropyLoss
+

DeepGraft/TransMIL_resnet18_no_other.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16 
+    multi_gpu_mode: dp
+    gpus: [4]
+    epochs: &epoch 500 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 200
+    server: test #train #test
+    log_path: logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_no_other.json'
+    fold: 1
+    nfold: 4
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+Model:
+    name: TransMIL
+    n_classes: 5
+    backbone: resnet18
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.00001
+
+Loss:
+    base_loss: CrossEntropyLoss
+

DeepGraft/TransMIL_resnet18_no_viral.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16 
+    multi_gpu_mode: dp
+    gpus: [3]
+    epochs: &epoch 500 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 200
+    server: test #train #test
+    log_path: logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_no_viral.json'
+    fold: 1
+    nfold: 4
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+Model:
+    name: TransMIL
+    n_classes: 4
+    backbone: resnet18
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.00001
+
+Loss:
+    base_loss: CrossEntropyLoss
+

DeepGraft/TransMIL_resnet18_tcmr_viral.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16 
+    multi_gpu_mode: dp
+    gpus: [3]
+    epochs: &epoch 500 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 200
+    server: test #train #test
+    log_path: logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_tcmr_viral.json'
+    fold: 1
+    nfold: 4
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+Model:
+    name: TransMIL
+    n_classes: 2
+    backbone: resnet18
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.00001
+
+Loss:
+    base_loss: CrossEntropyLoss
+

DeepGraft/TransMIL_resnet50.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 32 
+    multi_gpu_mode: dp
+    gpus: [1]
+    epochs: &epoch 200 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 200
+    server: test #train #test
+    log_path: logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_bin.json'
+    fold: 0
+    nfold: 4
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+        
+
+Model:
+    name: TransMIL
+    n_classes: 2
+    backbone: resnet50
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.00001
+
+Loss:
+    base_loss: CrossEntropyLoss
+

DeepGraft/TransMIL_resnet50_all.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16 
+    multi_gpu_mode: dp
+    gpus: [1]
+    epochs: &epoch 1000 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 200
+    server: train #train #test
+    log_path: logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_all.json'
+    fold: 1
+    nfold: 4
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+        
+
+Model:
+    name: TransMIL
+    n_classes: 6
+    backbone: resnet50
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0001
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.00001
+
+Loss:
+    base_loss: CrossEntropyLoss
+

DeepGraft/TransMIL_simple.yaml

+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16 
+    multi_gpu_mode: dp
+    gpus: [1]
+    epochs: &epoch 200 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 200
+    server: test #train #test
+    log_path: logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_bin.json'
+    fold: 0
+    nfold: 4
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+        
+
+Model:
+    name: TransMIL
+    n_classes: 2
+    backbone: simple
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.00001
+
+Loss:
+    base_loss: CrossEntropyLoss
+

MyLoss/loss_factory.py

@@ -34,8 +34,6 @@ def create_loss(args, w1=1.0, w2=0.5):
         loss = L.BinaryDiceLoss()
     elif conf_loss == "dice_log":
         loss = L.BinaryDiceLogLoss()
-    elif conf_loss == "dice_log":
-        loss = L.BinaryDiceLogLoss()
     elif conf_loss == "bce+lovasz":
         loss = L.JointLoss(BCEWithLogitsLoss(), L.BinaryLovaszLoss(), w1, w2)
     elif conf_loss == "lovasz":
@@ -62,6 +60,7 @@ def make_parse():
 if __name__ == '__main__':
     args = make_parse()
     myloss = create_loss(args)
+    print(myloss)
     data = torch.randn(2, 3)
     label = torch.empty(2, dtype=torch.long).random_(3)
     loss = myloss(data, label)
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