SpaFactor is a lightweight framework that predicts spatial gene expression from hematoxylin and eosin images by fusing central spot visuals with multiscale neighborhood context. It uses a residual MLP to map tissue microenvironment to low‑dimensional latent gene programs, which are decoded into coordinated multi‑gene predictions. Across five public cohorts, SpaFactor outperforms existing methods, especially for spatially variable genes, and better recovers biologically organized spatial patterns.
By Shiting Ruan, Xitong Ling, Qiming He, Ziyou Yan, Huaitian Yuan, Tian Guan, Ying Xiao, Xu Guan, Yonghong He
arXiv:2608.20548v1 Announce Type: cross
Abstract: Disaster damage is spatial: buildings rarely fail in isolation. Yet using spatial context for damage classification remains surprisingly underexplore...
By Fuad Hasan, Chul Min Yeum
arXiv:2607. 02990v1 Announce Type: new Abstract: We propose MABLE (Masked Autoencoding with Bi-Lipschitz Decoding for Embeddings and Graph Metric Learning), a self-supervised framework for learning node and graph embeddings from large, heterogeneous graphs, demonstrated here on geospatial mineral-exploration data.
By Yaniv Shulman, Shaghayegh Akbarpour, Jack B. Muir
arXiv:2506. 11152v4 Announce Type: replace-cross Abstract: Single-cell transcriptomics and proteomics have become a great source for data-driven insights into biology, enabling the use of advanced deep learning methods to understand cellular heterogeneity and gene expression at the single-cell level.
By Hiren Madhu, Jo\~ao Felipe Rocha, Tinglin Huang, Siddharth Viswanath, Smita Krishnaswamy, Rex Ying
arXiv:2610.28579v1 Announce Type: cross
Abstract: Cellular states are shaped by both intrinsic gene expression programs and the spatial microenvironment in which cells reside. Spatial transcriptomics...
By Azim Dehghani Amirabad, Ali Khodabandeh Yalabadi, Artem Moskalev, Yun-Ching Chen, Mehdi Pirooznia, Scott Oloff, Rui Liao
arXiv:2608.24823v1 Announce Type: new
Abstract: Spatially resolved biology requires representations that preserve biological neighborhood structure rather than only exact cross-modal correspondences....
By Seungik Cho, Betul Orcan-Ekmekci