MUSTANG: Multi-Stain Self-Attention Graph Multiple Instance Learning Pipeline for Histopathology Whole Slide Images
This addresses the challenge of weakly supervised classification in histopathology for clinical diagnosis, though it appears incremental as an extension of attention-based MIL methods.
The authors tackled the problem of classifying gigapixel whole slide images (WSIs) with only patient-level labels by proposing MUSTANG, a multi-stain self-attention graph multiple instance learning pipeline, which achieved a state-of-the-art F1-score of 0.89 and AUC of 0.92, outperforming the CLAM model.
Whole Slide Images (WSIs) present a challenging computer vision task due to their gigapixel size and presence of numerous artefacts. Yet they are a valuable resource for patient diagnosis and stratification, often representing the gold standard for diagnostic tasks. Real-world clinical datasets tend to come as sets of heterogeneous WSIs with labels present at the patient-level, with poor to no annotations. Weakly supervised attention-based multiple instance learning approaches have been developed in recent years to address these challenges, but can fail to resolve both long and short-range dependencies. Here we propose an end-to-end multi-stain self-attention graph (MUSTANG) multiple instance learning pipeline, which is designed to solve a weakly-supervised gigapixel multi-image classification task, where the label is assigned at the patient-level, but no slide-level labels or region annotations are available. The pipeline uses a self-attention based approach by restricting the operations to a highly sparse k-Nearest Neighbour Graph of embedded WSI patches based on the Euclidean distance. We show this approach achieves a state-of-the-art F1-score/AUC of 0.89/0.92, outperforming the widely used CLAM model. Our approach is highly modular and can easily be modified to suit different clinical datasets, as it only requires a patient-level label without annotations and accepts WSI sets of different sizes, as the graphs can be of varying sizes and structures. The source code can be found at https://github.com/AmayaGS/MUSTANG.