论文标题
通过图像级标签通过端到端训练在全扫描图像中检测前列腺癌
Detection of prostate cancer in whole-slide images through end-to-end training with image-level labels
论文作者
论文摘要
前列腺癌是西方国家男性中最普遍的癌症,每年有110万个新诊断。前列腺癌诊断的黄金标准是病理学家对前列腺组织的评估。 为了协助病理学家,已经开发了深度学习的癌症检测系统。许多最先进的模型都是基于补丁的卷积神经网络,因为加速器卡上的内存限制会阻碍整个扫描载玻片的使用。基于补丁的系统通常需要详细的像素级注释来有效培训。但是,与包含幻灯片级标签的病理学家的临床报道相比,这种注释很少很容易获得。因此,开发不需要手动像素注释的算法,但只能使用临床报告学习将是该领域的重大进步。 在本文中,我们建议使用卷积层的流式实施,以训练4712个前列腺活检的现代CNN(Resnet-34),其端到端的2100万参数。该方法通过将GPU内存需求减少2.4 TB,可以直接将整个活检图像直接使用。我们表明,使用我们的流媒体方法训练的现代CNN可以从高分辨率图像中提取有意义的功能,而无需额外的启发式方法,其性能与基于最先进的补丁和基于多种现实的学习方法相似。通过规避对手动注释的需求,这种方法可以作为组织病理学诊断其他任务的蓝图。 重现流媒体模型的源代码可在https://github.com/diaghijmegen/pathology-streaming-pipeline上获得。
Prostate cancer is the most prevalent cancer among men in Western countries, with 1.1 million new diagnoses every year. The gold standard for the diagnosis of prostate cancer is a pathologists' evaluation of prostate tissue. To potentially assist pathologists deep-learning-based cancer detection systems have been developed. Many of the state-of-the-art models are patch-based convolutional neural networks, as the use of entire scanned slides is hampered by memory limitations on accelerator cards. Patch-based systems typically require detailed, pixel-level annotations for effective training. However, such annotations are seldom readily available, in contrast to the clinical reports of pathologists, which contain slide-level labels. As such, developing algorithms which do not require manual pixel-wise annotations, but can learn using only the clinical report would be a significant advancement for the field. In this paper, we propose to use a streaming implementation of convolutional layers, to train a modern CNN (ResNet-34) with 21 million parameters end-to-end on 4712 prostate biopsies. The method enables the use of entire biopsy images at high-resolution directly by reducing the GPU memory requirements by 2.4 TB. We show that modern CNNs, trained using our streaming approach, can extract meaningful features from high-resolution images without additional heuristics, reaching similar performance as state-of-the-art patch-based and multiple-instance learning methods. By circumventing the need for manual annotations, this approach can function as a blueprint for other tasks in histopathological diagnosis. The source code to reproduce the streaming models is available at https://github.com/DIAGNijmegen/pathology-streaming-pipeline .