A Good Feature Extractor Is All You Need for Weakly Supervised Learning in Histopathology

Deep learning is revolutionising pathology, offering novel opportunities in disease prognosis and personalised treatment. Historically, stain normalisation has been a crucial preprocessing step in computational pathology pipelines, and persists into the deep learning era. Yet, with the emergence of feature extractors trained using self-supervised learning (SSL) on diverse pathology datasets, we call this practice into question. In an empirical evaluation of publicly available feature extractors, we find that omitting stain normalisation and image augmentations does not compromise downstream performance, while incurring substantial savings in memory and compute. Further, we show that the top-performing feature extractors are remarkably robust to variations in stain and augmentations like rotation in their latent space. Contrary to previous patch-level benchmarking studies, our approach emphasises clinical relevance by focusing on slide-level prediction tasks in a weakly supervised setting with external validation cohorts. This work represents the most comprehensive robustness evaluation of public pathology SSL feature extractors to date, involving more than 6,000 training runs across nine tasks, five datasets, three downstream architectures, and various preprocessing setups. Our findings stand to streamline digital pathology workflows by minimising preprocessing needs and informing the selection of feature extractors.

Using Multiple Dermoscopic Photographs of One Lesion Improves Melanoma Classification via Deep Learning: A Prognostic Diagnostic Accuracy Study

Background: Convolutional neural network (CNN)-based melanoma classifiers face several challenges that limit their usefulness in clinical practice. Objective: To investigate the impact of multiple real-world dermoscopic views of a single lesion of interest on a CNN-based melanoma classifier. Methods: This study evaluated 656 suspected melanoma lesions. Classifier performance was measured using area under the receiver operating characteristic curve (AUROC), expected calibration error (ECE) and maximum confidence change (MCC) for (I) a single-view scenario, (II) a multiview scenario using multiple artificially modified images per lesion and (III) a multiview scenario with multiple real-world images per lesion. Results: The multiview approach with real-world images significantly increased the AUROC from 0.905 (95% CI, 0.879-0.929) in the single-view approach to 0.930 (95% CI, 0.909-0.951). ECE and MCC also improved significantly from 0.131 (95% CI, 0.105-0.159) to 0.072 (95% CI: 0.052-0.093) and from 0.149 (95% CI, 0.125-0.171) to 0.115 (95% CI: 0.099-0.131), respectively. Comparing multiview real-world to artificially modified images showed comparable diagnostic accuracy and uncertainty estimation, but significantly worse robustness for the latter. Conclusion: Using multiple real-world images is an inexpensive method to positively impact the performance of a CNN-based melanoma classifier.

Test Time Transform Prediction for Open Set Histopathological Image Recognition

Tissue typology annotation in Whole Slide histological images is a complex and tedious, yet necessary task for the development of computational pathology models. We propose to address this problem by applying Open Set Recognition techniques to the task of jointly classifying tissue that belongs to a set of annotated classes, e.g. clinically relevant tissue categories, while rejecting in test time Open Set samples, i.e. images that belong to categories not present in the training set. To this end, we introduce a new approach for Open Set histopathological image recognition based on training a model to accurately identify image categories and simultaneously predict which data augmentation transform has been applied. In test time, we measure model confidence in predicting this transform, which we expect to be lower for images in the Open Set. We carry out comprehensive experiments in the context of colorectal cancer assessment from histological images, which provide evidence on the strengths of our approach to automatically identify samples from unknown categories. Code is released at https://github.com/agaldran/t3po .