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:2607. 14410v1 Announce Type: new Abstract: Spatially resolved omics studies increasingly combine transcriptomic and epigenomic assays, yet downstream analysis is often still performed using single-modality pipelines.
By Jagan Mohan Reddy Dwarampudi, Veena Kochat, Suresh Satpati, Kunal Rai, Tania Banerjee
arXiv:2607. 20896v1 Announce Type: new Abstract: Spatial transcriptomics assays remain costly and technically demanding, restricting transcriptome-wide profiling to specialist settings and preventing routine clinical deployment.
By Kritanu Chattopadhyay, Soumya Chatterjee, Ondrej Krejcar, Debotosh Bhattacharjee
arXiv:2606. 08712v1 Announce Type: cross Abstract: Purpose: Spatial transcriptomics (ST) enables gene expression measurements within the tissue context.
By Hongyi Yu, Yaoyu Fang, Jiahe Qian, Xinkun Wang, Lee A. Cooper, Bo Zhou
arXiv:2609.36429v1 Announce Type: new
Abstract: Predicting gene expression from H&E-stained histology images offers a scalable alternative to costly spatial transcriptomics, yet most existing methods...
By Zijun Gao, Chunbin Gu, Jinxi Xiang, Xiangde Luo, Pheng-Ann Heng
arXiv:2608. 14710v1 Announce Type: cross Abstract: Predicting spatial gene expression from hematoxylin and eosin (H\&E)-stained images offers a cost-effective alternative to spatial transcriptomics (ST).
By Ruochen Liu, Wei Lou