"No negatives needed": weakly-supervised regression for interpretable tumor detection in whole-slide histopathology images

Accurate tumor detection in digital pathology whole-slide images (WSIs) is crucial for cancer diagnosis and treatment planning. Multiple Instance Learning (MIL) has emerged as a widely used approach for weakly-supervised tumor detection with large-scale data without the need for manual annotations. However, traditional MIL methods often depend on classification tasks that require tumor-free cases as negative examples, which are challenging to obtain in real-world clinical workflows, especially for surgical resection specimens. We address this limitation by reformulating tumor detection as a regression task, estimating tumor percentages from WSIs, a clinically available target across multiple cancer types. In this paper, we provide an analysis of the proposed weakly-supervised regression framework by applying it to multiple organs, specimen types and clinical scenarios. We characterize the robustness of our framework to tumor percentage as a noisy regression target, and introduce a novel concept of amplification technique to improve tumor detection sensitivity when learning from small tumor regions. Finally, we provide interpretable insights into the model's predictions by analyzing visual attention and logit maps. Our code is available at https://github.com/DIAGNijmegen/tumor-percentage-mil-regression.

Improving Quality Control of Whole Slide Images by Explicit Artifact Augmentation

The problem of artifacts in whole slide image acquisition, prevalent in both clinical workflows and research-oriented settings, necessitates human intervention and re-scanning. Overcoming this challenge requires developing quality control algorithms, that are hindered by the limited availability of relevant annotated data in histopathology. The manual annotation of ground-truth for artifact detection methods is expensive and time-consuming. This work addresses the issue by proposing a method dedicated to augmenting whole slide images with artifacts. The tool seamlessly generates and blends artifacts from an external library to a given histopathology dataset. The augmented datasets are then utilized to train artifact classification methods. The evaluation shows their usefulness in classification of the artifacts, where they show an improvement from 0.10 to 0.01 AUROC depending on the artifact type. The framework, model, weights, and ground-truth annotations are freely released to facilitate open science and reproducible research.

Benchmarking Hierarchical Image Pyramid Transformer for the classification of colon biopsies and polyps in histopathology images

Training neural networks with high-quality pixel-level annotation in histopathology whole-slide images (WSI) is an expensive process due to gigapixel resolution of WSIs. However, recent advances in self-supervised learning have shown that highly descriptive image representations can be learned without the need for annotations. We investigate the application of the recent Hierarchical Image Pyramid Transformer (HIPT) model for the specific task of classification of colorectal biopsies and polyps. After evaluating the effectiveness of TCGA-learned features in the original HIPT model, we incorporate colon biopsy image information into HIPT's pretraining using two distinct strategies: (1) fine-tuning HIPT from the existing TCGA weights and (2) pretraining HIPT from random weight initialization. We compare the performance of these pretraining regimes on two colorectal biopsy classification tasks: binary and multiclass classification.