Self-supervised U-Net for segmenting flat and sessile polyps

TY - CHAP

T1 - Self-supervised U-Net for segmenting flat and sessile polyps

AU - Bhattacharya, Debayan

AU - Betz, Christian

AU - Eggert, Dennis

AU - Schlaefer, Alexander

PY - 2022/4/4

Y1 - 2022/4/4

N2 - Colorectal Cancer(CRC) poses a great risk to public health. It is the third most common cause of cancer in the US. Development of colorectal polyps is one of the earliest signs of cancer. Early detection and resection of polyps can greatly increase survival rate to 90%. Manual inspection can cause misdetections because polyps vary in color, shape, size and appearance. To this end, Computer-Aided Diagnosis systems(CADx) has been proposed that detect polyps by processing the colonoscopic videos. The system acts a secondary check to help clinicians reduce misdetections so that polyps may be resected before they transform to cancer. Polyps vary in color, shape, size, texture and appearance. As a result, the miss rate of polyps is between 6% and 27% despite the prominence of CADx solutions. Furthermore, sessile and flat polyps which have diameter less than 10 mm are more likely to be undetected. Convolutional Neural Networks(CNN) have shown promising results in polyp segmentation. However, all of these works have a supervised approach and are limited by the size of the dataset. It was observed that smaller datasets reduce the segmentation accuracy of ResUNet++. Self-supervision is a stronger alternative to fully supervised learning especially in medical image analysis since it redresses the limitations posed by small annotated datasets. From the self-supervised approach proposed by Jamaludin et al., it is evident that pretraining a network with a proxy task helps in extracting meaningful representations from the underlying data which can then be used to improve the performance of the final downstream supervised task. In summary, we train a U-Net to inpaint randomly dropped out pixels in the image as a proxy task. The dataset we use for pretraining is Kvasir-SEG dataset. This is followed by a supervised training on the limited Kvasir-Sessile dataset. Our experimental results demonstrate that with limited annotated dataset and a larger unlabeled dataset, self-supervised approach is a better alternative than fully supervised approach. Specifically, our self-supervised U-Net performs better than five segmentation models which were trained in supervised manner on the Kvasir-Sessile dataset.

AB - Colorectal Cancer(CRC) poses a great risk to public health. It is the third most common cause of cancer in the US. Development of colorectal polyps is one of the earliest signs of cancer. Early detection and resection of polyps can greatly increase survival rate to 90%. Manual inspection can cause misdetections because polyps vary in color, shape, size and appearance. To this end, Computer-Aided Diagnosis systems(CADx) has been proposed that detect polyps by processing the colonoscopic videos. The system acts a secondary check to help clinicians reduce misdetections so that polyps may be resected before they transform to cancer. Polyps vary in color, shape, size, texture and appearance. As a result, the miss rate of polyps is between 6% and 27% despite the prominence of CADx solutions. Furthermore, sessile and flat polyps which have diameter less than 10 mm are more likely to be undetected. Convolutional Neural Networks(CNN) have shown promising results in polyp segmentation. However, all of these works have a supervised approach and are limited by the size of the dataset. It was observed that smaller datasets reduce the segmentation accuracy of ResUNet++. Self-supervision is a stronger alternative to fully supervised learning especially in medical image analysis since it redresses the limitations posed by small annotated datasets. From the self-supervised approach proposed by Jamaludin et al., it is evident that pretraining a network with a proxy task helps in extracting meaningful representations from the underlying data which can then be used to improve the performance of the final downstream supervised task. In summary, we train a U-Net to inpaint randomly dropped out pixels in the image as a proxy task. The dataset we use for pretraining is Kvasir-SEG dataset. This is followed by a supervised training on the limited Kvasir-Sessile dataset. Our experimental results demonstrate that with limited annotated dataset and a larger unlabeled dataset, self-supervised approach is a better alternative than fully supervised approach. Specifically, our self-supervised U-Net performs better than five segmentation models which were trained in supervised manner on the Kvasir-Sessile dataset.

U2 - 10.1117/12.2611364

DO - 10.1117/12.2611364

M3 - SCORING: Contribution to collected editions/anthologies

SN - 9781510649415

T3 - Proceedings of SPIE

BT - Medical Imaging 2022: Computer-Aided Diagnosis

A2 - Drukker, Karen

A2 - Iftekharuddin, Khan M.

PB - SPIE

CY - Bellingham, Wash.

ER -