用自监督方法提升小样本病理切片分析效率,助力结肠病变筛查。
Efficient Self-Supervised Barlow Twins from Limited Tissue Slide Cohorts for Colonic Pathology Diagnostics
- 优化巴洛双子框架适配病理图像特性,改进超参数与增强策略。
- 在4类结肠息肉数据上实现优于监督学习的表示质量,提升诊断效率。
- 为结肠癌筛查构建新基准数据集,适合病理人工智能研究者使用。
结直肠癌(CRC)具有明确的异型增生-癌变序列,适合筛查。加拿大所有50岁以上人群均可接受筛查,约20%需进行活检,常涉及多个息肉,构成病理科医生主要工作量。开发高效计算模型辅助筛查可优化工作流程并引导关注关键区域。深度学习在计算病理学中受限于全切片图像的吉字节级大小及标注数据稀缺。因此,需借助自监督学习(SSL)降低标注成本。然而现有方法难以有效应用于病理数据。本文提出针对结肠息肉筛查的优化版巴洛双子框架,通过调整超参数、增强策略和编码器以适配病理数据特点。同时研究最佳视野范围,并基于MHIST与NCT-CRC-7K数据集构建包含四类结肠息肉与正常组织的新基准数据集。实验表明,该方法所得的自监督表征比监督学习更优,且在病理数据上应用Swin Transformer效果显著。代码已开源。
原文摘要 · Abstract (English)
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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