Interpretable Multimodal Cancer Prototyping with Whole Slide Images and Incompletely Paired Genomics

• URL: http://arxiv.org/abs/2511.21937v1
• Date: Wed, 26 Nov 2025 21:53:17 GMT
• Title: Interpretable Multimodal Cancer Prototyping with Whole Slide Images and Incompletely Paired Genomics
• Authors: Yupei Zhang, Yating Huang, Wanming Hu, Lequan Yu, Hujun Yin, Chao Li,
• Abstract summary: We propose a flexible multimodal prototyping framework to integrate whole slide images and incomplete genomics for precision oncology.<n>Our approach has four key components: 1) Biological Prototyping using text prompting and prototype-wise weighting; 2) Multiview Alignment through sample- and distribution-wise alignments; 3) Bipartite Fusion to capture both shared and modality-specific information for multimodal fusion; and 4) Semantic Genomics Imputation to handle missing data.
• Score: 26.503881136106965
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Multimodal approaches that integrate histology and genomics hold strong potential for precision oncology. However, phenotypic and genotypic heterogeneity limits the quality of intra-modal representations and hinders effective inter-modal integration. Furthermore, most existing methods overlook real-world clinical scenarios where genomics may be partially missing or entirely unavailable. We propose a flexible multimodal prototyping framework to integrate whole slide images and incomplete genomics for precision oncology. Our approach has four key components: 1) Biological Prototyping using text prompting and prototype-wise weighting; 2) Multiview Alignment through sample- and distribution-wise alignments; 3) Bipartite Fusion to capture both shared and modality-specific information for multimodal fusion; and 4) Semantic Genomics Imputation to handle missing data. Extensive experiments demonstrate the consistent superiority of the proposed method compared to other state-of-the-art approaches on multiple downstream tasks. The code is available at https://github.com/helenypzhang/Interpretable-Multimodal-Prototyping.

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