Spatial Transcriptomics

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5 papers in the last four weeks, against 2 the four weeks before. 0.1% of all new papers.

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

    Sep 30, 2026Lucas Ni, Jian Luo, Wentao Huang +1Spatial TranscriptomicsImage-Text Alignment

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

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

    Sep 29, 2026Zijun Gao, Chunbin Gu, Jinxi Xiang +2Spatial TranscriptomicsDigital Pathology

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

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

    Sep 28, 2026Dongmyung Shin, Geongyu Lee, Yesung Cho +1Spatial TranscriptomicsDigital Pathology

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

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

    Sep 27, 2026Kaito Shiku, Kazuya Nishimura, Yasuhiro Kojima +1Spatial TranscriptomicsTranscriptomics

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

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

    Sep 23, 2026Shiting Ruan, Xitong Ling, Qiming He +6Spatial TranscriptomicsDigital Pathology

    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

  6. 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

  7. Dynamic Generalized Gromov-Wasserstein Optimal Transport

    Sep 17, 2026Junda Ying, Zhiwei Zeng, Peijie Zhou +1Optimal Transport ApproachSpatial Transcriptomics

    Beijing International Center for Mathematical Research, Peking University · Center for Quantitative Biology, Peking University · Center for Machine Learning Research, Peking University +4

  8. Hyperbolic Contrastive Learning with Entailment for Spatial Transcriptomics

    Sep 14, 2026Daniela Vega, Paula Cárdenas, Hannah Ceballos +2Spatial TranscriptomicsSpatio-Temporal Transformers

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

  9. 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 +6Spatial TranscriptomicsSingle-Cell Rna

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

  10. CellWorld: From Gene-Level Reconstruction to Latent Cell Prediction in Spatial Transcriptomics Foundation Models

    Aug 7, 2026Haiping Liu, Qian Zhao, Lijing Lin +2Spatial TranscriptomicsCells

    University of Manchester

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

    Aug 1, 2026Zhiwen Xu, Xiaoming Yan, Chengkun Wu +3Spatial TranscriptomicsGenome-Wide Association Study

    National University of Defense Technology Changsha, China

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

    Jul 27, 2026Ziang Liu, Xinhai Chen, Yigui Feng +3Spatial TranscriptomicsDigital Pathology

    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 +1Spatial TranscriptomicsDigital Pathology

    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. LATTICE: Graph Self-Supervised Learning for Multimodal Spatial Omics Integration

    Jul 15, 2026Jagan Mohan Reddy Dwarampudi, Veena Kochat, Suresh Satpati +2Spatial TranscriptomicsMulti-Omic Integration

    University of Houston · MD Anderson Cancer Center

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

    Jul 10, 2026Keunho Byeon, Sunhong Park, Jeewoo Lim +1Spatial TranscriptomicsTranscriptomics

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

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

    Jul 6, 2026Yuhang Yang, Yonggan Bu, Shengyuan Zhou +2Spatial TranscriptomicsDigital Pathology

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

  17. Resolving superposition in AI for interpretability and cross-modal alignment in patient-neuronal images

    Jun 30, 2026Jisung Park, Seohyeon Kang, Daeun Yoo +8Multimodal NeuroimagingSpatial Transcriptomics

    1KAIST · 2Konyang University · 4UCL Queen Square Institute of Neurology & The Francis Crick Institute +1

  18. 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 +5Spatial TranscriptomicsDigital Pathology

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

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

    Jun 19, 2026Joohyeok Kim, Taejin Jeong, Jinyeong Kim +1Spatial Transcriptomics3D Masked Autoencoders

    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

  20. Structured Nonparametric Variational Inference for Dependent Latent Modeling

    Jun 13, 2026Yuda Shao, Zhiling Gu, Shan YuVariational InferenceLatent Variable

    Department of Statistics, University of Virginia · Department of Biostatistics, Yale University

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

    Jun 12, 2026Weiyi Wu, Xinwen Xu, Xingjian Diao +4Spatial TranscriptomicsSpatio-Temporal Transformers

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

  22. SNR-ST-Mix: Sample-specific Neighborhood Regression Mixup for Augmented Spatial Transcriptomics Imputation with Deep Neural Network

    Jun 7, 2026Hongyi Yu, Yaoyu Fang, Jiahe Qian +3Spatial TranscriptomicsData Augmentation

    Northwestern University, Department of Radiology, Chicago, IL, USA · Yale University, Department of Biostatistics, New Haven, CT, USA · Northwestern University, Department of Cell and Developmental Biology, Chicago, IL, USA +1

  23. Single-Cell Cross-Modal Transfer by Adversarial Fine-Tuning of Foundation Models

    Jun 4, 2026Joseph Boyd, Matthew Lyon, Martino Mansoldo +2Spatial TranscriptomicsSingle-Cell Rna

    GSK.ai, GlaxoSmithKline, London, United Kingdom.

  24. Cross-scale spatially-aware generative modeling of transcriptomic programs underlying neurodegenerative brain organization

    Jun 4, 2026Krishnakumar VaithianathanSpatial TranscriptomicsTranscriptomics

    for the Alzheimer's Disease Neuroimaging Initiative · Department of Computer Engineering, Karaikal Polytechnic College,2026 Karaikal, Puducherry, India.

  25. Do Foundation Models See Biology? Evaluating Attention Coherence with Spatial Transcriptomics in Glioblastoma

    Jun 3, 2026Dilakshan Srikanthan, Amoon Jamzad, Paul Wilson +5Spatial TranscriptomicsPathology Foundation Models

    Translational Medicine, School of Medicine, Queen’s University, Kingston, ON, Canada · School of Computing, Queen’s University, Kingston, ON, Canada · Department of Surgery, Queen’s University, Kingston, ON, Canada

  26. 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 +4Spatial TranscriptomicsCells

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

  27. Spatial Transcriptomics-Guided Alignment Enhances Molecular Profiling in Pathology Foundation Model

    May 29, 2026Fengtao Zhou, Yingxue Xu, Zhengyu Zhang +20Spatial TranscriptomicsPathology Foundation Models

    Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China · Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China · Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China +16

  28. Geometry-First Generative Spatial Single-Cell Reconstruction

    May 27, 2026Ehtesamul Azim, Muhtasim Noor Alif, Tae Hyun Hwang +2Spatial TranscriptomicsDistance

    University of Central Florida Orlando, Florida, USA · Vanderbilt University Medical Center Nashville, Tennessee, USA · Arizona State University Tempe, Arizona, USA

  29. Benchmarking Pathology Foundation Models for Spatial Domain Understanding

    May 25, 2026Bokai Zhao, Yiyang Zhang, Yuanchi Zhu +6Computational PathologySpatial Transcriptomics

    School of Artificial Intelligence, University of Chinese Academy of Sciences. · Brainnetome Center, Institute of Automation, Chinese Academy of Sciences. · Beijing Key Laboratory of Brainnetome and Brain-Computer Interface, Institute of Automation, Chinese Academy of Sciences. +2

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

    May 18, 2026Qi Si, Penglei Wang, Yushuai Wu +5Spatial TranscriptomicsSpatio-Temporal Correlations

    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.

  31. STS: Efficient Sparse Attention with Speculative Token Sparsity

    May 15, 2026Ceyu Xu, Jiangnan Yu, Yongji Wu +1Dynamic Sparse AttentionSpatial Transcriptomics

    The Hong Kong University of Science and Technology · UC Berkeley

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

    May 13, 2026Junchao Zhu, Ruining Deng, Junlin Guo +11Spatial TranscriptomicsSingle-Cell Rna

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

  33. Bridging the Modality Bottleneck in Pathology MIL through Virtual Molecular Staining

    May 12, 2026Yucheng Xing, Pei Liu, Jingying Ma +6Computational PathologyPathology Foundation Models

    National University of Singapore, Singapore · Hunan University, China · Peking Union Medical College Hospital (PUMCH), China +1

  34. Transformed Latent Variable Multi-Output Gaussian Processes

    May 6, 2026Xiaoyu Jiang, Xinxing Shi, Sokratia Georgaka +2Gaussian ProcessHigh-Dimensional

    Department of Computer Science, University of Manchester, Manchester, UK · Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK

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

    May 6, 2026Keunho Byeon, Jin Tae KwakSpatial TranscriptomicsSpatio-Temporal Transformers

    School of Electrical Engineering, Korea University, Seoul

  36. Leveraging Spatial Transcriptomics as Alternative to Manual Annotations for Deep Learning-Based Nuclei Analysis

    Apr 26, 2026Kazuya Nishimura, Ryoma Bise, Haruka Hirose +1Spatial TranscriptomicsDigital Pathology

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

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

    Apr 23, 2026Changfan Wang, Xinran Wang, Donghai Liu +4Spatial TranscriptomicsDigital Pathology

    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

  38. Audio Spoof Detection with GaborNet

    Apr 21, 2026Waldek MaciejkoConvolutionalSpatial Transcriptomics

  39. Spatial Transcriptomics as Images for Large-Scale Pretraining

    Mar 13, 2026Yishun Zhu, Jiaxin Qi, Jian Wang +2Spatial TranscriptomicsSpatio-Temporal Transformers

    Computer Network Information Center, Chinese Academy of Sciences, Beijing, China · Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Zhejiang, China