arXiv Machine Learning By Hiren Madhu, Jo\~ao Felipe Rocha, Tinglin Huang, Siddharth Viswanath, Smita Krishnaswamy, Rex Ying

HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data

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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.

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arXiv Machine Learning
Sep 25

SpaFactor: Lightweight Spatial Context-Aware Gene Program Modeling for Histology-to-Transcriptomics Inference

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 Machine Learning
Jul 24

HierarchicalDAEW: Domain-Aware Edge-Weighted Graph Convolution with Evidential Uncertainty for Multi-Section Spatial Gene Expression Prediction from H&E Histology

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