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BioKERN: Biological Kernel Regularization for Histology-to-Transcriptomics Neighborhood Retrieval

arXiv · AI, language, vision and robotics · article · Aug 25, 2026 · UTC

Spatially resolved biology requires representations that preserve biological neighborhood structure rather than only exact cross-modal correspondences. Existing histology--transcriptomics objectives can emphasize instance-level matching even when non-paired spots share molecular or spatial context. We introduce BioKERN, a multimodal spatial representation-learning framework that incorporates biological structure as an explicit, learnable inductive bias. BioKERN constructs a training-time biological kernel by combining transcriptomic similarity and spatial proximity, then uses it to provide gra

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