论文标题
REET:计算病理学的鲁棒性评估和增强工具箱
REET: Robustness Evaluation and Enhancement Toolbox for Computational Pathology
论文作者
论文摘要
动机:通过数字幻灯片扫描仪进行病理实验室的数字化以及对客观组织学评估的深度学习方法的进步,导致计算病理学(CPATH)领域的快速进步,并在医学和药品研究中广泛应用以及临床工作流程。但是,估计CPATH模型对输入图像中的变化的鲁棒性是一个开放的问题,对这些方法的下游实际适用性,部署和可接受性有重大影响。此外,开发特定领域的策略以增强这种模型的鲁棒性也很重要。 实施和可用性:在这项工作中,我们建议针对计算病理学应用的第一个特定领域的鲁棒性评估和增强工具箱(REET)。它提供了一系列算法策略,可实现有关预测模型的鲁棒性评估,以染色,压缩,聚焦,模糊,空间分辨率的变化,亮度变化,几何变化,几何变化以及像素级级别的对手级别的逆转。此外,REET还可以在计算病理学中对深度学习管道进行有效而强大的培训。 REET在Python中实现,可在以下URL:https://github.com/alexjfoote/reetoolbox上找到。 联系人:[email protected]
Motivation: Digitization of pathology laboratories through digital slide scanners and advances in deep learning approaches for objective histological assessment have resulted in rapid progress in the field of computational pathology (CPath) with wide-ranging applications in medical and pharmaceutical research as well as clinical workflows. However, the estimation of robustness of CPath models to variations in input images is an open problem with a significant impact on the down-stream practical applicability, deployment and acceptability of these approaches. Furthermore, development of domain-specific strategies for enhancement of robustness of such models is of prime importance as well. Implementation and Availability: In this work, we propose the first domain-specific Robustness Evaluation and Enhancement Toolbox (REET) for computational pathology applications. It provides a suite of algorithmic strategies for enabling robustness assessment of predictive models with respect to specialized image transformations such as staining, compression, focusing, blurring, changes in spatial resolution, brightness variations, geometric changes as well as pixel-level adversarial perturbations. Furthermore, REET also enables efficient and robust training of deep learning pipelines in computational pathology. REET is implemented in Python and is available at the following URL: https://github.com/alexjfoote/reetoolbox. Contact: [email protected]