Spatial Gene Expression Prediction

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Overview

The field predicts gene activity at tissue spots or individual cells from H&E images, with the goal of extending costly spatial assays to more samples. Approaches combine pathology foundation-model features with local and global context from transformers or graphs, and add cell-type, gene-program, or ontology priors; some also use retrieval or generative models and sparse measured expression. Methods are commonly evaluated on HEST-1k and spatial platforms such as Visium and Xenium, using expression correlations and measures of spatial-pattern recovery, including held-out-slide or held-out-organ tests. A key challenge is generalizing across patients, tissues, and platforms while preserving spatial heterogeneity and biologically meaningful gene relationships, rather than optimizing pointwise accuracy alone.

Latest papers

CardsList

39 papers6 papers in the last four weeks, up 20% on the four weeks before. 0.0% of all new papers.

  1. Biology-Guided Context-Aware Residual Propagation for Spatial Gene Expression Prediction from Histology

    Oct 26, 2026Vu Van An, Long D. Nguyen, Ho Viet Duc Luong +1Spatial Gene Expression PredictionGene Expression Prediction from Histopathology Images

    Hanoi University of Science and Technology Hanoi, 10000, Vietnam · Victoria University of Wellington Wellington, 6012, New Zealand

  2. HistoLoop: Iterative Contextual Inference with a Looped Transformer for Histology-Based Spatial Gene Expression Prediction

    Oct 20, 2026Ziang Liu, Jie Liu, Shuai Li +2Spatial Gene Expression PredictionGene Expression Prediction from Histopathology Images

    Laboratory of Digitizing Software for Frontier Equipment, National University of Defense Technology · National Key Laboratory of Parallel and Distributed Computing, National University of Defense Technology · College of Computer Science and Technology, National University of Defense Technology, Changsha 410073, China

  3. VGL-stGen: Learning a shared multimodal model for lung histology and spatial transcriptomics

    Oct 20, 2026Haenara Shin, Dongjoo Lee, Sungwoo Bae +3Gene Expression Prediction from Histopathology ImagesMedical VLMs

    Portrai, Inc., Seoul, Republic of Korea

  4. REST: Reliability-Guided Spatial Transcriptomics Supervision for Gene Expression Prediction from Histopathological HE-Stained Images

    Oct 19, 2026Lanfeng Zhong, Xiangyu Sun, Guixuan Xu +4Gene Expression Prediction from Histopathology ImagesSpatial Gene Expression Prediction

    School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China · Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China · Department of Pathology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China

  5. MIST: Multi-Scale Spatial Context for Gene Expression Prediction from Histology

    Oct 13, 2026Koushik Howlader, Tirtho Roy, Md Tauhidul Islam +1Spatial Context ModelingSpatial Gene Expression Prediction

    Iowa State University, Iowa, USA · Stanford University, CA, USA

  6. GATE-ST: Gene-Aware Text-image Encoder for Spatial Transcriptomics

    Sep 30, 2026Lucas Ni, Jian Luo, Wentao Huang +1Spatial TranscriptomicsMultimodal Embedding

    Ridge High School Basking Ridge, United States · Stony Brook University Stony Brook, United States

  7. Towards Scalable Context-Aware Single-Cell Spatial Transcriptomics Prediction from Histology Images

    Sep 29, 2026Zijun Gao, Chunbin Gu, Jinxi Xiang +2Spatial TranscriptomicsSpatial Attention

    The Chinese University of Hong Kong · Stanford University School of Medicine

  8. Preserving DEG Rankings for Gene Discovery in Histology-Based Spatial Gene Expression Prediction

    Sep 27, 2026Kaito Shiku, Kazuya Nishimura, Yasuhiro Kojima +1Spatial TranscriptomicsLearning to Rank

    Kyushu University, Japan · The University of Osaka, Japan · National Cancer Center, Japan

  9. Is H&E Image-to-Spatial Transcriptomics Simpler Than It Looks?

    Sep 26, 2026Duc T. Nguyen, Thanh Ha Do, Phuong M. Cao +1Gene Expression Prediction from Histopathology ImagesSpatial Gene Expression Prediction

    VinUniversity, Hanoi, Vietnam · VinUni-Illinois Smart Health Center (VISHC), VinUniversity, Hanoi, Vietnam · Posts and Telecommunications Institute of Technology, Hanoi, Vietnam +1

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

    Sep 23, 2026Shiting Ruan, Xitong Ling, Qiming He +6Computational PathologySpatial Transcriptomics

    Shenzhen International Graduate School, Tsinghua University, Shenzhen, China · Fuzhou University, Fuzhou, Fujian, China · Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China +1

  11. Benchmarking Active Spot Selection for Cost-Efficient Spatial Transcriptomics

    Sep 23, 2026Zheyu Zhu, Junchao Zhu, Fengbei Liu +7Spatial TranscriptomicsActive Learning

    University of Pennsylvania, Philadelphia, PA 19104, USA · Vanderbilt University, Nashville, TN, USA · Cornell Tech, New York, NY 10044, USA +4

  12. Hyperbolic Contrastive Learning with Entailment for Spatial Transcriptomics

    Sep 14, 2026Daniela Vega, Paula Cárdenas, Hannah Ceballos +2Contrastive LearningSpatial Transcriptomics

    Center for Research and Formation in Artificial Intelligence Universidad de los Andes, Colombia

  13. Correlation-Guided Flow Matching with Annealed Masking for Spatial Transcriptomics Generation

    Aug 28, 2026Yupei Zhang, Hao Chen, Li Pan +2Spatial Gene Expression PredictionGene Expression Prediction from Histopathology Images

    Department of Clinical Neurosciences University of Cambridge UK · Usher Institute The University of Edinburgh EH16 RUX · Department of Diagnostic Radiology National University of Singapore Singapore

  14. Towards Trustworthy Biological Alignment in TabPFN-Probed Pathology Foundation Models

    Aug 25, 2026Ushashi Bhattacharjee, Alloy Das, Saria Hannan +3Pathology Foundation ModelsGene Expression Prediction from Histopathology Images

  15. Concept-based explanation of gene expression prediction from H&E images

    Aug 17, 2026Amos Muench, Jonathan Thielmann, Reduan Achtibat +9Gene Expression Prediction from Histopathology ImagesComputational Pathology

    Institute of Pathology – Charité Universitätsmedizin, Berlin, Germany · Fraunhofer Heinrich-Hertz-Institute, Berlin, Germany · Center for Computational Biology (CBIO), Mines Paris, PSL University, Paris, France +5

  16. Program-space Diffusion for Morphology-to-Transcriptomics Prediction

    Aug 14, 2026Ruyter Swann, Dorent Reuben, Racoceanu DanielGene Expression Prediction from Histopathology ImagesSpatial Gene Expression Prediction

    Sorbonne Université, CNRS, Inserm, AP-HP, Inria, Paris Brain Institute – ICM, Paris, France

  17. Path2ST: Hierarchical Cell-Tissue Grounded Cross-Modal Translation for Spatial Transcriptomics

    Aug 11, 2026Ruochen Liu, Wei LouSpatial Gene Expression PredictionGene Expression Prediction from Histopathology Images

    Faculty of Science and Engineering University of Liverpool Liverpool, United Kingdom · College of Mathematical Medicine Zhejiang Normal University Jinhua, China

  18. VOICE: A Vision-Omics Foundation Model Integrating Direct and Retrieval-Based Prediction of In-situ Single-Cell Gene Expression

    Aug 8, 2026Xin Luo, Yicheng Tao, Haoxuan Zeng +6Computational PathologySpatial Transcriptomics

    University of Michigan Ann Arbor, Michigan, USA · Weill Cornell Medicine New York, New York, USA

  19. Gene Ontology-Guided Hierarchical Spatial Gene Expression Prediction from Histopathology Images

    Aug 1, 2026Zhiwen Xu, Xiaoming Yan, Chengkun Wu +3Computational PathologySpatial Transcriptomics

    National University of Defense Technology Changsha, China

  20. HistoGPA: A Context-Conditioned Gene-Prior Attention Framework for Histology-Based Spatial Gene Expression Prediction

    Jul 27, 2026Ziang Liu, Xinhai Chen, Yigui Feng +3Computational PathologySpatial Transcriptomics

    Laboratory of Digitizing Software for Frontier Equipment, National University of Defense Technology · National Key Laboratory of Parallel and Distributed Computing, National University of Defense Technology · College of Computer Science and Technology, National University of Defense Technology, Changsha 410073, China

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

    Jul 23, 2026Kritanu Chattopadhyay, Soumya Chatterjee, Ondrej Krejcar +1Computational PathologySpatial Transcriptomics

    Department of Mechanical Engineering, National Institute of Technology Durgapur,, Durgapur, 713209, West Bengal, India · Department of Electrical Engineering, National Institute of Technology Durgapur,, Durgapur, 713209, West Bengal, India · Research Center, Skoda Auto University, Na Karmeli 1457, Mlada Boleslav, 293 01,, Czech Republic +1

  22. COAST: Context-Aware Differential Learning for Gene Expression Prediction in Spatial Transcriptomics

    Jul 10, 2026Keunho Byeon, Sunhong Park, Jeewoo Lim +1Spatial TranscriptomicsSpatial Gene Expression Prediction

    School of Electrical Engineering, Korea University, Seoul 02841, Republic of Korea

  23. DriftST: One-Step Generative Inference of Spatial Transcriptomics from H&E Histology

    Jul 6, 2026Yuhang Yang, Yonggan Bu, Shengyuan Zhou +2Computational PathologySpatial Transcriptomics

    University of Science and Technology of China, Hefei, China · Peking University Cancer Hospital, Beijing, China

  24. JASPR: Joint Spatial Representation learning of histology and spatial genomics for improved virtual genomic screening and clinical prognostication

    Jun 24, 2026Marija Pizurica, Eric Zimmermann, Neil Tenenholtz +5Cancer GenomicsComputational Pathology

    Microsoft Research, Cambridge, MA, United States · Stanford University, CA, United States

  25. Contrastive and Adaptive Multi-modal Masked Autoencoder for Spatial Transcriptomics

    Jun 19, 2026Joohyeok Kim, Taejin Jeong, Jinyeong Kim +1Computational PathologySpatial Transcriptomics

    Department of Artificial Intelligence, Yonsei University, Seoul, Republic of Korea · Department of Computer Science, Yonsei University, Seoul, Republic of Korea · Yonsei University College of Medicine, Seoul, Republic of Korea

  26. HiST: A Hierarchical Sparse Transformer for Cross-Modal Spatial Transcriptomics Modeling

    Jun 12, 2026Weiyi Wu, Xinwen Xu, Xingjian Diao +4Computational PathologySpatial Transcriptomics

    Dartmouth College · Mass General Hospital · New Jersey Institute of Technology +1

  27. GC-MoE: Genomics-Guided Cell-Type-Specific Mixture of Experts for Histology-Based Single-Cell Spatial Transcriptomics

    Jun 1, 2026Kaito Shiku, Ahtisham Fazeel Abbasi, Ryoma Bise +4Computational PathologySpatial Transcriptomics

    Kyushu University, Japan · German Research Center for Artificial Intelligence (DFKI GmbH), Germany · RPTU University Kaiserslautern-Landau, Germany +3

  28. FLAG: Foundation model representation with Latent diffusion Alignment via Graph for spatial gene expression prediction

    May 18, 2026Qi Si, Penglei Wang, Yushuai Wu +5Spatial TranscriptomicsSpatial Gene Expression Prediction

    Shanghai Academy of Artificial Intelligence for Science, Shanghai, China. · School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. · Artificial Intelligence Innovation and Incubation Institute, Fudan University, Shanghai, China.

  29. DUET: Dual-Paradigm Adaptive Expert Triage with Single-cell Inductive Prior for Spatial Transcriptomics Prediction

    May 13, 2026Junchao Zhu, Ruining Deng, Junlin Guo +11Spatial TranscriptomicsSpatial Gene Expression Prediction

    Vanderbilt University, Tennessee, USA · Weill Cornell Medicine, New York, USA · Vanderbilt University Medical Center, Tennessee, USA

  30. HEXST: Hexagonal Shifted-Window Transformer for Spatial Transcriptomics Gene Expression Prediction

    May 6, 2026Keunho Byeon, Jin Tae KwakComputational PathologySpatial Transcriptomics

    School of Electrical Engineering, Korea University, Seoul