3D_Swin_transformer_classification

Introduction

The model is modified by Swin_UNTER. The model has been augmented with a classification head, which can classify the type you want. Noticed that the model is for 3D medical image. Please modify your dataloader (data_utils.py) to customize the dataset.

Installation and dependencies

1. Clone the repository
2. Install required packages
   please download Pytorch on the official website and download dependencies by following command:

pip install -r requirements.txt

Training

Depending on the classification task — binary or two-class(multiple classes) — different loss functions and evaluation metrics are used:

For two-class(multiple classes) classification model is defined as below:

model = SwinTransformerForClassification(
    img_size=(64,64,64),
    num_classes = 2,
    in_channels=1,
    out_channels=786, 
    feature_size=48,
    drop_rate=0.0,
    attn_drop_rate=0.0,
    dropout_path_rate=0.0,
)

The above model is used for CT images (1-channel input) with input image size (64, 64, 64) and for 2 classes for the classification output and feature size of 48. out_channels means the number of output channels from the feature map.

• Loss function: CrossEntropyLoss(). This loss is used for multi-class classification problems (in this case, two classes). It is combined with a softmax activation function, which transforms the output into a probability distribution.
• Evaluation Metric: The predicted class is the one with the highest probability, determined by finding the maximum value in the predictions.

For binary classification model is defined as below:

model = SwinTransformerForClassification(
    img_size=(64,64,64),
    num_classes = 1,
    in_channels=1,
    out_channels=786, 
    feature_size=48,
    drop_rate=0.0,
    attn_drop_rate=0.0,
    dropout_path_rate=0.0,
)

The above model is used for CT images (1-channel input) with input image size (64, 64, 64). Noticed that the class (num_classes) will be set as 1 because it predicts the positive or not.

• Loss function: BCEWithLogitsLoss(). This loss function combines a sigmoid activation with binary cross-entropy loss, outputting a single probability score.
• Evaluation Metric: A prediction value greater than 0.5 is classified as positive (commonly labeled as 1), and less than 0.5 as negative (commonly labeled as 0).

Usage

For Training:

python main.py --batch_size=<batch_size> --logdir=<model_name> --optim_lr=1e-4 --lrschedule=warmup_cosine --roi_x=64 --roi_y=64 --roi_z=64 --val_every 1 --save_checkpoint

For evaluation:
Please modify the dataloader to customize the dataset.

python evaluation.py