ProtoPathway: Biologically Structured Prototype-Pathway Fusion for Multimodal Cancer Survival Prediction

We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of the fusion. On the histopathology side, $K$ learnable morphological prototypes, trained end-to-end with the survival objective, serve as the slide representation itself: patches flow into prototype tokens via soft assignment, compressing variable-length patch sets into fixed task-adaptive tokens. On the genomic side, a bipartite graph neural network encodes gene expression within the Reactome pathway hierarchy, producing pathway embeddings that reflect both constituent genes and their broader biological context through bidirectional message passing over a shared gene--pathway graph. Cross-modal attention then operates over a compact prototype $\times$ pathway matrix in which prototypes query pathways, modeling the biological direction in which molecular programs give rise to tissue morphology. Because both axes carry stable task-learned identity, the attention matrix is itself an interpretability output, yielding native inference-time attribution across the full biological hierarchy, from genes through pathways and prototypes to spatial tissue maps. We evaluate on five TCGA cancer cohorts, demonstrating competitive or superior survival prediction with substantially improved biological interpretability and reduced computational cost, with interpretability claims validated through fold-stratified rank-based population-level analysis. Our source code, model weights, and Reactome pathways, together with a unified codebase reimplementing all multimodal survival baselines under identical preprocessing and evaluation, are available at: https://github.com/AmayaGS/ProtoPathway.

BioX-CPath: Biologically-driven Explainable Diagnostics for Multistain IHC Computational Pathology

The development of biologically interpretable and explainable models remains a key challenge in computational pathology, particularly for multistain immunohistochemistry (IHC) analysis. We present BioX-CPath, an explainable graph neural network architecture for whole slide image (WSI) classification that leverages both spatial and semantic features across multiple stains. At its core, BioX-CPath introduces a novel Stain-Aware Attention Pooling (SAAP) module that generates biologically meaningful, stain-aware patient embeddings. Our approach achieves state-of-the-art performance on both Rheumatoid Arthritis and Sjogren's Disease multistain datasets. Beyond performance metrics, BioX-CPath provides interpretable insights through stain attention scores, entropy measures, and stain interaction scores, that permit measuring model alignment with known pathological mechanisms. This biological grounding, combined with strong classification performance, makes BioX-CPath particularly suitable for clinical applications where interpretability is key. Source code and documentation can be found at: https://github.com/AmayaGS/BioX-CPath.

Multi-Stain Self-Attention Graph Multiple Instance Learning Pipeline for Histopathology Whole Slide Images

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.

Automated segmentation of rheumatoid arthritis immunohistochemistry stained synovial tissue

Rheumatoid Arthritis (RA) is a chronic, autoimmune disease which primarily affects the joint's synovial tissue. It is a highly heterogeneous disease, with wide cellular and molecular variability observed in synovial tissues. Over the last two decades, the methods available for their study have advanced considerably. In particular, Immunohistochemistry stains are well suited to highlighting the functional organisation of samples. Yet, analysis of IHC-stained synovial tissue samples is still overwhelmingly done manually and semi-quantitatively by expert pathologists. This is because in addition to the fragmented nature of IHC stained synovial tissue, there exist wide variations in intensity and colour, strong clinical centre batch effect, as well as the presence of many undesirable artefacts present in gigapixel Whole Slide Images (WSIs), such as water droplets, pen annotation, folded tissue, blurriness, etc. There is therefore a strong need for a robust, repeatable automated tissue segmentation algorithm which can cope with this variability and provide support to imaging pipelines. We train a UNET on a hand-curated, heterogeneous real-world multi-centre clinical dataset R4RA, which contains multiple types of IHC staining. The model obtains a DICE score of 0.865 and successfully segments different types of IHC staining, as well as dealing with variance in colours, intensity and common WSIs artefacts from the different clinical centres. It can be used as the first step in an automated image analysis pipeline for synovial tissue samples stained with IHC, increasing speed, reproducibility and robustness.