Efficient Self-Supervised Barlow Twins from Limited Tissue Slide Cohorts for Colonic Pathology Diagnostics

• URL: http://arxiv.org/abs/2411.05959v1
• Date: Fri, 08 Nov 2024 20:43:53 GMT
• Title: Efficient Self-Supervised Barlow Twins from Limited Tissue Slide Cohorts for Colonic Pathology Diagnostics
• Authors: Cassandre Notton, Vasudev Sharma, Vincent Quoc-Huy Trinh, Lina Chen, Minqi Xu, Sonal Varma, Mahdi S. Hosseini,
• Abstract summary: Colorectal cancer (CRC) is one of the few cancers that has an established dysplasia-carcinoma sequence that benefits from screening. DL models face significant challenges in computational pathology (CPath) because of the gigapixel image size of whole-slide images and the scarcity of detailed annotated datasets. This paper proposes an optimized Barlow Twins framework for colorectal polyps screening.
• Score: 14.177695952155213
• License:
• Abstract: Colorectal cancer (CRC) is one of the few cancers that have an established dysplasia-carcinoma sequence that benefits from screening. Everyone over 50 years of age in Canada is eligible for CRC screening. About 20\% of those people will undergo a biopsy for a pre-neoplastic polyp and, in many cases, multiple polyps. As such, these polyp biopsies make up the bulk of a pathologist's workload. Developing an efficient computational model to help screen these polyp biopsies can improve the pathologist's workflow and help guide their attention to critical areas on the slide. DL models face significant challenges in computational pathology (CPath) because of the gigapixel image size of whole-slide images and the scarcity of detailed annotated datasets. It is, therefore, crucial to leverage self-supervised learning (SSL) methods to alleviate the burden and cost of data annotation. However, current research lacks methods to apply SSL frameworks to analyze pathology data effectively. This paper aims to propose an optimized Barlow Twins framework for colorectal polyps screening. We adapt its hyperparameters, augmentation strategy and encoder to the specificity of the pathology data to enhance performance. Additionally, we investigate the best Field of View (FoV) for colorectal polyps screening and propose a new benchmark dataset for CRC screening, made of four types of colorectal polyps and normal tissue, by performing downstream tasking on MHIST and NCT-CRC-7K datasets. Furthermore, we show that the SSL representations are more meaningful and qualitative than the supervised ones and that Barlow Twins benefits from the Swin Transformer when applied to pathology data. Codes are avaialble from https://github.com/AtlasAnalyticsLab/PathBT.

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