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: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
The paper introduces BCARP, a Biology‑Guided Context‑Aware Residual Propagation framework that predicts spatial gene expression from H&E‑stained histology images. Rather than directly decoding expression from visual features, BCARP treats histology embeddings as morphological priors and iteratively refines spot representations in a transcriptomics‑oriented latent space, integrating nuclei‑guided local context and prototype‑guided global propagation. Evaluations on three spatial transcriptomics datasets and ten HEST‑1k cohorts show that BCARP outperforms existing baselines in mean correlation‑based metrics, demonstrating the effectiveness of biology‑guided local‑global residual propagation for histology‑to‑transcriptomics prediction.
By Vu Van An, Long D. Nguyen, Ho Viet Duc Luong, Binh P. Nguyen
arXiv:2609.18578v1 Announce Type: new
Abstract: Pathologists diagnose diseases by first locating suspicious tissue and then examining it at higher magnification, whereas self-supervised vision transf...
By Anabel Stammer, Valay Bundele, Mehran Hosseinzadeh, Hendrik P. A. Lensch
GATE-ST is a gene-aware text-image encoder that enhances spatial transcriptomics predictions by integrating gene descriptions into image-based models. The method encodes gene summaries with a text encoder and fuses these embeddings with image features via cross‑attention, aligning them with morphological cues. Benchmarks show GATE‑ST outperforms random gene embeddings and other image‑text fusion architectures, indicating its potential to improve accuracy while reducing time and cost in spatial gene expression analysis.
By Lucas Ni, Jian Luo, Wentao Huang, Chao Chen
arXiv:2606. 07222v1 Announce Type: cross Abstract: Cell detection in histopathology images strongly depends on surrounding tissue context, where visually similar cells may belong to different classes under different microenvironments.
By Bahman Jafari Tabaghsar, Son Tran, K. Devaraja, Atul Sajjanhar