changed folder hierarchy

9ca1a12e · Ycblue · d7fe105e · 9ca1a12e · 9ca1a12e · 9ca1a12e
Commit 9ca1a12e authored Jul 14, 2022 by Ycblue
--- a/DeepGraft/AttMIL_simple_no_other.yaml
+++ b/DeepGraft/AttMIL_simple_no_other.yaml
@@ -16,7 +16,7 @@ General:
 Data:
    dataset_name: custom
    data_shuffle: False
-    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    data_dir: '/home/ylan/data/DeepGraft/224_128um/'
    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_no_other.json'
    fold: 1
    nfold: 3

--- a/DeepGraft/AttMIL_simple_no_viral.yaml
+++ b/DeepGraft/AttMIL_simple_no_viral.yaml
@@ -6,7 +6,7 @@ General:
    precision: 16 
    multi_gpu_mode: dp
    gpus: [3]
-    epochs: &epoch 500 
+    epochs: &epoch 200 
    grad_acc: 2
    frozen_bn: False
    patience: 50
@@ -16,7 +16,7 @@ General:
 Data:
    dataset_name: custom
    data_shuffle: False
-    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    data_dir: '/home/ylan/data/DeepGraft/224_128um/'
    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_no_viral.json'
    fold: 1
    nfold: 4
@@ -41,7 +41,7 @@ Optimizer:
    opt_eps: null 
    opt_betas: null
    momentum: null 
-    weight_decay: 0.00001
+    weight_decay: 0.01

 Loss:
    base_loss: CrossEntropyLoss

--- a/DeepGraft/AttMIL_simple_tcmr_viral.yaml
+++ b/DeepGraft/AttMIL_simple_tcmr_viral.yaml
@@ -6,7 +6,7 @@ General:
    precision: 16 
    multi_gpu_mode: dp
    gpus: [3]
-    epochs: &epoch 300 
+    epochs: &epoch 200 
    grad_acc: 2
    frozen_bn: False
    patience: 20
@@ -16,7 +16,7 @@ General:
 Data:
    dataset_name: custom
    data_shuffle: False
-    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    data_dir: '/home/ylan/data/DeepGraft/224_128um/'
    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_tcmr_viral.json'
    fold: 1
    nfold: 3
@@ -34,6 +34,7 @@ Model:
    name: AttMIL
    n_classes: 2
    backbone: simple
+    in_features: 512


 Optimizer:
@@ -42,7 +43,7 @@ Optimizer:
    opt_eps: null 
    opt_betas: null
    momentum: null 
-    weight_decay: 0.00001
+    weight_decay: 0.01

 Loss:
    base_loss: CrossEntropyLoss

--- a/DeepGraft/DTFDMIL_resnet50_tcmr_viral.yaml
+++ b/DeepGraft/DTFDMIL_resnet50_tcmr_viral.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: 50
+    server: test #train #test
+    log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/data/DeepGraft/224_128um/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_tcmr_viral.json'
+    fold: 1
+    nfold: 3
+    cross_val: False
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+Model:
+    name: DTFDMIL
+    n_classes: 2
+    backbone: resnet50
+    in_features: 512
+    out_features: 512
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.01
+
+Loss:
+    base_loss: CrossEntropyLoss
+
--- a/DeepGraft/TransMIL_efficientnet_no_viral.yaml
+++ b/DeepGraft/TransMIL_efficientnet_no_viral.yaml
@@ -11,15 +11,16 @@ General:
    frozen_bn: False
    patience: 20
    server: test #train #test
-    log_path: logs/
+    log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/

 Data:
    dataset_name: custom
    data_shuffle: False
-    data_dir: '/home/ylan/DeepGraft/dataset/hdf5/256_256um_split/'
+    data_dir: '/home/ylan/data/DeepGraft/256_256um/'
    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_no_viral.json'
    fold: 1
    nfold: 4
+    cross_val: False

    train_dataloader:
        batch_size: 1 

--- a/DeepGraft/TransMIL_efficientnet_tcmr_viral.yaml
+++ b/DeepGraft/TransMIL_efficientnet_tcmr_viral.yaml
@@ -6,21 +6,21 @@ General:
    precision: 16 
    multi_gpu_mode: dp
    gpus: [0]
-    epochs: &epoch 500 
+    epochs: &epoch 200 
    grad_acc: 2
    frozen_bn: False
-    patience: 200
+    patience: 20
    server: train #train #test
-    log_path: logs/
+    log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/

 Data:
    dataset_name: custom
    data_shuffle: False
-    data_dir: '/home/ylan/data/DeepGraft/256_256um/'
+    data_dir: '/home/ylan/data/DeepGraft/224_128um/'
    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_tcmr_viral.json'
    fold: 1
    nfold: 3
-    cross_val: True
+    cross_val: False

    train_dataloader:
        batch_size: 1 
@@ -35,6 +35,7 @@ Model:
    n_classes: 2
    backbone: efficientnet
    in_features: 512
+    out_features: 512


 Optimizer:
@@ -43,7 +44,7 @@ Optimizer:
    opt_eps: null 
    opt_betas: null
    momentum: null 
-    weight_decay: 0.00001
+    weight_decay: 0.01

 Loss:
    base_loss: CrossEntropyLoss

--- a/DeepGraft/TransMIL_resnet18_tcmr_viral.yaml
+++ b/DeepGraft/TransMIL_resnet18_tcmr_viral.yaml
@@ -5,21 +5,22 @@ General:
    amp_level: O2
    precision: 16 
    multi_gpu_mode: dp
-    gpus: [3]
-    epochs: &epoch 500 
+    gpus: [0]
+    epochs: &epoch 200 
    grad_acc: 2
    frozen_bn: False
    patience: 50
    server: test #train #test
-    log_path: logs/
+    log_path: /home/ylan/workspace/TransMIL-DeepGraft/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'
+    data_dir: '/home/ylan/data/DeepGraft/224_128um/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_bt_PAS_tcmr_viral.json'
    fold: 1
-    nfold: 4
+    nfold: 3
+    cross_val: False

    train_dataloader:
        batch_size: 1 
@@ -33,6 +34,8 @@ Model:
    name: TransMIL
    n_classes: 2
    backbone: resnet18
+    in_features: 512
+    out_features: 512


 Optimizer:
@@ -41,7 +44,7 @@ Optimizer:
    opt_eps: null 
    opt_betas: null
    momentum: null 
-    weight_decay: 0.00001
+    weight_decay: 0.01

 Loss:
    base_loss: CrossEntropyLoss

--- a/DeepGraft/TransMIL_resnet50_tcmr_viral.yaml
+++ b/DeepGraft/TransMIL_resnet50_tcmr_viral.yaml
@@ -6,21 +6,21 @@ General:
    precision: 16 
    multi_gpu_mode: dp
    gpus: [0]
-    epochs: &epoch 200 
+    epochs: &epoch 500 
    grad_acc: 2
    frozen_bn: False
    patience: 50
    server: test #train #test
-    log_path: logs/
+    log_path: /home/ylan/workspace/TransMIL-DeepGraft/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_bt_PAS_tcmr_viral.json'
+    data_dir: '/home/ylan/data/DeepGraft/224_128um/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_tcmr_viral.json'
    fold: 1
    nfold: 3
-    cross_val: True
+    cross_val: False

    train_dataloader:
        batch_size: 1 
@@ -34,6 +34,8 @@ Model:
    name: TransMIL
    n_classes: 2
    backbone: resnet50
+    in_features: 512
+    out_features: 512


 Optimizer:
@@ -42,8 +44,9 @@ Optimizer:
    opt_eps: null 
    opt_betas: null
    momentum: null 
-    weight_decay: 0.00001
+    weight_decay: 0.01

 Loss:
    base_loss: CrossEntropyLoss
+    loss_weight: [1., 1.]

--- a/DeepGraft/TransformerMIL_resnet50_tcmr_viral.yaml
+++ b/DeepGraft/TransformerMIL_resnet50_tcmr_viral.yaml
+General:
+    comment: 
+    seed: 2021
+    fp16: True
+    amp_level: O2
+    precision: 16 
+    multi_gpu_mode: dp
+    gpus: [0]
+    epochs: &epoch 500 
+    grad_acc: 2
+    frozen_bn: False
+    patience: 50
+    server: test #train #test
+    log_path: /home/ylan/workspace/TransMIL-DeepGraft/logs/
+
+Data:
+    dataset_name: custom
+    data_shuffle: False
+    data_dir: '/home/ylan/data/DeepGraft/224_128um/'
+    label_file: '/home/ylan/DeepGraft/training_tables/split_PAS_tcmr_viral.json'
+    fold: 1
+    nfold: 3
+    cross_val: False
+
+    train_dataloader:
+        batch_size: 1 
+        num_workers: 8
+
+    test_dataloader:
+        batch_size: 1
+        num_workers: 8
+
+Model:
+    name: TransformerMIL
+    n_classes: 2
+    backbone: resnet50
+    in_features: 512
+    out_features: 512
+
+
+Optimizer:
+    opt: lookahead_radam
+    lr: 0.0002
+    opt_eps: null 
+    opt_betas: null
+    momentum: null 
+    weight_decay: 0.01
+
+Loss:
+    base_loss: CrossEntropyLoss
+    
+
--- a/README.md
+++ b/README.md
@@ -13,3 +13,26 @@ python train.py --stage='test' --config='Camelyon/TransMIL.yaml'  --gpus=0 --fol

 ### Changes Made: 

+### Baseline: 
+
+lr = 0.0002
+wd = 0.01
+
+| task        | main | backbone | train_auc | val_auc | epochs | version |  
+|---|---|---|---|---|
+| tcmr_viral | TransMIL | resnet50 |  0.997 | 0.871 | 200 | 4 |
+|            |          | resnet18 |  0.999 | 0.687 | 200 | 0 |
+|            |          | efficientnet | 0.99 | 0.76 | 200 | 107 |
+|            | DTFD     | resnet50 | 0.989 | 0.621 | 200 | 44 |
+|            | AttMIL   | simple | 0.513 | 0.518 | 200 | 50 |
+
+
+159	28639			0.9222221970558167	0.19437336921691895	0.5906432867050171	0.56540447473526	0.7159091234207153	0.8709122538566589	0.30908203125
+
+### Ablation
+
+image drop out: 
+tcmr_viral TCMR efficientnet: version 0
+
+wd incerease: 
+tcmr_viral TCMR efficientnet: version 110
\ No newline at end of file
--- a/MyBackbone/__init__.py
+++ b/MyBackbone/__init__.py
--- a/MyBackbone/backbone_factory.py
+++ b/MyBackbone/backbone_factory.py
@@ -25,7 +25,6 @@ def init_backbone(**kargs):
        resnet18 = models.resnet18(pretrained=True)
        modules = list(resnet18.children())[:-1]
        # model_ft.fc = nn.Linear(512, out_features)
-
        res18 = nn.Sequential(
            *modules,
        )

--- a/MyLoss/ND_Crossentropy.py
+++ b/MyLoss/ND_Crossentropy.py
--- a/MyLoss/__init__.py
+++ b/MyLoss/__init__.py
--- a/MyLoss/__pycache__/ND_Crossentropy.cpython-39.pyc
+++ b/MyLoss/__pycache__/ND_Crossentropy.cpython-39.pyc
--- a/MyLoss/__pycache__/__init__.cpython-39.pyc
+++ b/MyLoss/__pycache__/__init__.cpython-39.pyc
--- a/MyLoss/__pycache__/boundary_loss.cpython-39.pyc
+++ b/MyLoss/__pycache__/boundary_loss.cpython-39.pyc
--- a/MyLoss/__pycache__/dice_loss.cpython-39.pyc
+++ b/MyLoss/__pycache__/dice_loss.cpython-39.pyc
--- a/MyLoss/__pycache__/focal_loss.cpython-39.pyc
+++ b/MyLoss/__pycache__/focal_loss.cpython-39.pyc
--- a/MyLoss/__pycache__/hausdorff.cpython-39.pyc
+++ b/MyLoss/__pycache__/hausdorff.cpython-39.pyc