Gene Expression Prediction from Histopathology Images

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7 papers in the last four weeks, with none the four weeks before. 0.1% of all new papers.

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  1. Cross-Modal Contrastive Learning for the Retrieval of Immunotherapy-Associated Molecular Signatures from Histopathology

    Oct 4, 2026Sigrid Vila-Bagaria, Mar Teixidó, Miquel Piñol +3Computational PathologyCross-Modal Retrieval

    Signal Theory and Communications Department (TSC) Universitat Politècnica de Catalunya - BarcelonaTech (UPC) · Cancer Biomarkers Research Group (GReBiC) - IRB Lleida

  2. 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

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

    Sep 29, 2026Zijun Gao, Chunbin Gu, Jinxi Xiang +2Spatial TranscriptomicsSpatial Gene Expression Prediction

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

  4. MoSPR: Histology-to-Gene Expression Prediction with Morpho-Spatial Macrostates and Low-Rank Molecular Programs

    Sep 28, 2026Dongmyung Shin, Geongyu Lee, Yesung Cho +1Computational PathologyExplainable Medical Image Analysis

    OmixAI Co. Ltd. · Oncocross Co. Ltd. · Kyunghee University

  5. 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

  6. 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

  7. 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

  8. 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

  9. Zero-Cost Virtual RNA: Approximating Immunotherapy Signatures via Cross-Modal WSI Retrieval

    Aug 1, 2026Sigrid Vila-Bagaria, Mar Teixidó, Miquel Piñol +3Computational PathologyCross-Modal Retrieval

    Image Processing Group, Universitat Politècnica de Catalunya, Spain · Research group of Cancer Biomarkers & Oncological Pathology, IRB Lleida, Spain

  10. 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

  11. What Carries the Signal in Pathology Foundation-Model Atlases? A Patient-Level Controlled Benchmark in Breast Cancer

    Jul 31, 2026Chimdi Walter NdubuisiBreast CancerComputational Pathology

    Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA

  12. 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

  13. 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

  14. 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

  15. 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

  16. Data-Efficient Multimodal Alignment for Histopathology-based Molecular Prediction

    Jun 29, 2026Dominik Winter, Dominik Vonficht, Loïc Le Bescond +6Computational PathologyCross-Modal Alignment

    AstraZeneca Computational Pathology and Biomarkers, Munich, Germany · AstraZeneca, Early Oncology and Translation Medicine, Cambridge, UK

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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.

  22. RNA-FM: Flow-Matching Generative Model for Genome-wide RNA-Seq Prediction

    May 12, 2026Yaxuan Song, Jianan Fan, Tianyi Wang +4Computational PathologyGenomics

    School of Computer Science, The University of Sydney, Australia · Biological Systems and Engineering Division, Lawrence Berkeley National Lab, USA · Berkeley Biomedical Data Science Center, Lawrence Berkeley National Lab, USA +1

  23. CHRep: Cross-modal Histology Representation and Post-hoc Calibration for Spatial Gene Expression Prediction

    Apr 23, 2026Changfan Wang, Xinran Wang, Donghai Liu +4Spatial TranscriptomicsPost-Hoc Calibration

    Beijing University of Posts and Telecommunications, Beijing 100876, China, and also with the Beijing Key Laboratory of Network System and Network Culture, Beijing 100876, China · Peking University Third Hospital, Beijing 100191, China