Contrastive Multiple Instance Learning: An Unsupervised Framework for Learning Slide-Level Representations of Whole Slide Histopathology Images without Labels

Abstract

Recent methods in computational pathology have trended towards semi- and weakly-supervised methods requiring only slide-level labels. Yet, even slide-level labels may be absent or irrelevant to the application of interest, such as in clinical trials. Hence, we present a fully unsupervised method to learn meaningful, compact representations of WSIs. Our method initially trains a tile-wise encoder using SimCLR, from which subsets of tile-wise embeddings are extracted and fused via an attention-based multiple-instance learning framework to yield slide-level representations. The resulting set of intra-slide-level and inter-slide-level embeddings are attracted and repelled via contrastive loss, respectively. This resulted in slide-level representations with self-supervision. We applied our method to two tasks— (1) non-small cell lung cancer subtyping (NSCLC) as a classification prototype and (2) breast cancer proliferation scoring (TUPAC16) as a regression prototype—and achieved an AUC of 0.8641 ± 0.0115 and correlation (R2) of 0.5740 ± 0.0970, respectively. Ablation experiments demonstrate that the resulting unsupervised slide-level feature space can be fine-tuned with small datasets for both tasks. Overall, our method approaches computational pathology in a novel manner, where meaningful features can be learned from whole-slide images without the need for annotations of slide-level labels. The proposed method stands to benefit computational pathology, as it theoretically enables researchers to benefit from completely unlabeled whole-slide images.