Detection of Prostate Cancer in Whole-Slide Images Through End-to-End Training With Image-Level Labels

• 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. Themethod enables the use of entire biopsy images at high-resolution directly by reducing the GPUmemory requirements by 2.4 TB. We show thatmodern 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.

Subject headings

TEKNIK OCH TEKNOLOGIER  -- Medicinteknik -- Medicinsk bildbehandling (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Medical Engineering -- Medical Image Processing (hsv//eng)

Keyword

Deep learning; deep convolutional neural networks; computational pathology; prostate cancer

Publication and Content Type

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