Transcriptomics

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

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  1. CellMSA: Context Modeling for Single-Cell Representation Learning

    Sep 30, 2026Suyuan Zhao, Minghao Liu, Yizhen Luo +1TranscriptomicsRepresentation Learning

    Institute for AI Industry Research (AIR), Tsinghua University · Department of Computer Science and Technology, Tsinghua University · Tsinghua Institute of Multidisciplinary Biomedical Research (TIMBR), Tsinghua University +2

  2. Language as the Interface: Foundation-Model Contrastive Learning Links Transcriptomes and Electrophysiology

    Sep 29, 2026Junbo Shen, Jinying Gao, Bo LeiElectroencephalography Foundation ModelsMultimodal Foundation Model

    Department of Computer Science and Engineering, The Chinese University of Hong Kong · State Key Laboratory of Brain Cognition and Brain-inspired Intelligence Technology, Institute of Automation, Chinese Academy of Sciences, Beijing, China · Beijing Academy of Artificial Intelligence, Beijing, China +1

  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. Discover, Falsify, Revise: Auditing Input-Use Claims from Source Code to Predictive Contribution in Agent-Discovered Cell Models

    Sep 23, 2026Mengran Li, Bo Li, Chengyang Zhang +3Virtual CellModel Auditing

    Sun Yat-sen University · University of Macau · Sichuan University +3

  6. Density-Ratio Rescoring for Imbalanced Classification Using Raking Duals and Classifier Scores

    Sep 20, 2026Dongha Kim, Seunghwan ParkImbalanced ClassificationRarity

    School of Mathematics, Statistics and Data Science, Sungshin Women’s University, 2, Bomun-ro 34da-gil, Seongbuk-gu, Seoul, 02844, Republic of Korea · Department of Information Statistics, Kangwon National University, 1, Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea

  7. MIRCID: Inferred Hub-miRNAs Drive Cross-Task Improvements in Drug Mechanistic Modeling

    Sep 18, 2026Xin Cao, Yigang Chen, Jiatong Xu +11TranscriptomicsImprovement

    School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China · School of Data Science, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China · Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China +2

  8. A Transformer-Based Delta Expression Encoder for Psilocybin Transcriptional Response: Architecture, Representations, and Biological Validation

    Sep 8, 2026Sai JayakumarTranscriptomicsResponses

    Stanford School of Medicine, Biomedical Data Science Program, Stanford, CA

  9. PopPert: Population-level Joint-Distribution Modeling for Single-Cell Perturbation Prediction

    Sep 1, 2026Handong Wang, Jiaxin Qi, Haochen Feng +1Single-Cell Perturbation PredictionTranscriptomics

    Computer Network Information Center, Chinese Academy of Sciences · University of Chinese Academy of Sciences

  10. Novel Knowledge-Guided Generative Methods for Synthetic Transcriptomic Data

    Aug 13, 2026Francesca Pia Panaccione, Sofia Mongardi, Marco Masseroli +1TranscriptomicsSynthetic Data

    DEIB - Dipartimento Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy

  11. Control-Anchored Residual Flow Matching Conditioned on Gene Geometry for Virtual Cell Perturbation Modeling

    Aug 7, 2026Quanquan Li, Yihe Chi, Liuyang Song +10Single-Cell Perturbation PredictionTranscriptomics

    1East China Normal University · 2Peking University · University of Science and Technology of China +2

  12. CASCADE: An Agentic Regulatory Network Framework for Patient-Data-Validated Downstream Perturbation Prediction

    Aug 5, 2026Jose A. BirdTranscriptomicsRegulatory Networks

    Independent Researcher

  13. MS-MLB: An Open Machine Learning Benchmark for Blood-Based MS Classification

    Aug 4, 2026Adam Simson, Ankush Dutta, Quang BuiMultiple SclerosisTranscriptomics

    Synthica Research Group

  14. LLM-Guided Retrieval for Prediction of Molecular Perturbation Responses

    Aug 3, 2026Betty Xiong, Jan-Christian Huetter, Gabriele Scalia +2Single-Cell Perturbation PredictionTranscriptomics

    Department of Biomedical Data Science Stanford University Stanford, CA 94305, USA · Biology Research & AI Development, Genentech DNA Way, South San Francisco, CA 94080, USA

  15. Beyond Gene Reconstruction: Learning Cell Representations through Complementary Transcriptomic Views

    Aug 2, 2026Jiaqi Xiong, Yuntao hu, Yu Zheng +3Single-Cell RnaTranscriptomics

    University of Oxford, Oxford, United Kingdom · Tongji University, Shanghai, China · Hunan University, Changsha, China +2

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

    Aug 1, 2026Sigrid Vila-Bagaria, Mar Teixidó, Miquel Piñol +3TranscriptomicsBiomarker

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

  17. Can We Trust In-Distribution Success? Locked Evaluation Reveals Transfer Failure and Sampling-Depth Entanglement in CRISPRi Perturbation Prediction

    Jul 31, 2026Mehrdad Shoeibi, Niloofar YousefiTranscriptomicsText Dominance

    University of Central Florida

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

    Jul 31, 2026Chimdi Walter NdubuisiPathology Foundation ModelsTranscriptomics

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

  19. Continuous surrogates versus threshold Boolean networks for modeling Arabidopsis ISR gene regulation

    Jul 25, 2026Gonzalo A. RuzRegulatory NetworksSurrogate Models

    Facultad de Ingenier´ıa y Ciencias, Universidad Adolfo Ib´a˜nez · Millennium Nucleus for Social Data Science (SODAS) · Millennium Nucleus in Data Science for Plant Resilience (PhytoLearning) +1

  20. M3^3-Gen: Interpretable Multimodal Generation of Gene Expression Profiles Using Clinical and Imaging Data

    Jul 23, 2026Francesca Pia Panaccione, Carlo Sgaravatti, Marco VenereMultimodal Clinical DataTranscriptomics

    DEIB - Dipartimento Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, 20133, Italy

  21. GeneSpeak-FP: Target and Compound Retrieval from Observed Cell-Level Perturbation Signatures

    Jul 20, 2026Kseniia Vaniushkina, Jeongmin Lim, Jinyong ParkSingle-Cell Perturbation PredictionTranscriptomics

    AIFFEL Research, Modulabs, Republic of Korea

  22. 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

  23. CoDiffGRN: Rethinking Gene Regulatory Network Inference via the BEELINE-KGC Benchmark and Co-evolutionary Discrete Diffusion

    Jul 14, 2026Jiaze Song, Runhao Zhao, Minghao Xu +2Regulatory NetworksTranscriptomics

    Peking University · National University of Defense Technology

  24. Gene Expression-Informed Jointly Controlled Generative Modeling for Precision Molecular Design

    Jul 13, 2026Hang Yuan, Chen Li, Wenjun Ma +2Molecular DesignMolecular Generation

    School of Artificial Intelligence South China Normal University Foshan, Guangdong, China · D3 Center The University of Osaka Suita, Osaka, Japan · School of Computer Science South China Normal University Guangzhou, Guangdong, China

  25. 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

  26. Predicting Therapeutic Outcome via Aligning Patient-Specific Knowledge Graph and Gene-Level Perturbation Representations

    Jul 6, 2026Dongmin Bang, Sugyun An, Inyoung Sung +3TranscriptomicsBiomedical Knowledge Graph

    Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea · AIGENDRUG Co., Ltd., Seoul, Republic of Korea · BK21 FOUR Intelligence Computing, Seoul National University, Seoul, Republic of Korea +2

  27. 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

  28. ParaPairAudioBench: Paralinguistic Pairwise Audio Benchmark for LALM-as-a-Judge

    Jun 23, 2026Jisu Jeon, Seungyeon Jwa, Joosung Lee +6Paralinguistic CuesLarge Audio Language Models

    Hongik University, South Korea · Seoul National University, South Korea · NAVER Cloud, South Korea +1

  29. Stable-Shift: Biologically Structured Prediction of Transcriptional Responses to Unseen Gene Perturbations

    Jun 22, 2026Sajib Acharjee Dip, Liqing ZhangTranscriptomicsRegulatory Networks

    Department of Computer Science, Virginia Tech Blacksburg, VA, USA · Fralin Biomedical Research Institute, Virginia Tech Roanoke, VA, USA · FBRI Cancer Research Center Washington, DC, USA

  30. How Post-Training Shapes Biological Reasoning Models

    Jun 15, 2026Lukas Fesser, Hanlin Zhang, Michelle M. Li +5Large Reasoning ModelsPost-Training

    Harvard University · Google DeepMind · Google Research

  31. scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing

    Jun 11, 2026Ping Xu, Pengjiang Li, Tian Du +6Single-Cell RnaTranscriptomics

    Computer Network Information Center, Chinese Academy of Sciences, Beijing, China · University of Chinese Academy of Sciences, Beijing, China · School of Computing and Information Technology, Great Bay University, Dongguan, China +2

  32. OCOO-T : A Simple and Scalable Virtual Cell Model for Transcriptional Perturbation Response Prediction

    Jun 11, 2026Danning Jiang, Zheming An, Yalong Zhao +1Single-Cell Perturbation PredictionSingle-Cell Rna

    INFevo

  33. The Metric Picks the Winner: Evaluation Choice Flips Model Rankings for Drug-Response Prediction in Unseen Chemistry

    Jun 10, 2026Dhruv Agarwal, Riya BishtPharmacokineticsTranscriptomics

  34. Finding Multiple Interpretations in Datasets

    Jun 10, 2026Matthew Chak, Paul AndersonTranscriptomicsData Mining

    Department of Computer Science California Polytechnic State University San Luis Obispo, CA, US

  35. Skill-Augmented AI Agents for Medical Research Analysis: An Exploratory Multi-Model Human Evaluation in an NSCLC Transcriptomic Biomarker Task

    Jun 10, 2026Qianyu Yao, Fei Sun, Bocheng Huang +10Multidisciplinary Tumor BoardsTranscriptomics

    AIPOCH PTE. LTD., Singapore

  36. Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors

    Jun 7, 2026Jake Fawkes, Liam Hodgson, Jason HartfordBiomedical Knowledge GraphTranscriptomics

    Department of Computer Science, University College London, UK · Valence Labs, London, UK · Recursion, London, UK +1

  37. GIFT: LLM-Guided State-Reward Interface for Financial Reinforcement Learning

    Jun 7, 2026Yanyan Wu, Boyi Zhang, Yanlin Liu +10Large Language Model Reinforcement LearningOffline Reinforcement Learning

    East China University of Science and Technology · University of Science and Technology of China · Southwestern University of Finance and Economics +5

  38. The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models

    Jun 5, 2026Chahat Baranwal, Aaditya Baranwal, Lakshya Nitin TandonGenome-Wide Association StudyTranscriptomics

    IIT Jodhpur · University of Central Florida · Northeastern University

  39. 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.

  40. 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.

  41. 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

  42. A Fast Screening Approach for High-dimensional Outcomes and High-dimensional Predictors

    Jun 2, 2026Hongju Park, Zhenyao Ye, Shuo ChenScreeningHigh-Dimensional

    School of Pharmacy, University of North Carolina, Chapel Hill · Maryland Psychiatric Research Center, School of Medicine, University of Maryland

  43. Pathway-Structured Privileged Distillation for Deployable Computational Pathology

    Jun 1, 2026Yongxin Guo, Hao Lu, Onur Koyun +2Computational PathologyTranscriptomics

    1*School of Medicine, Wake Forest University, Winston-Salem, NC, USA.

  44. Plausibility Is Not Prediction: Contrastive Evidence for LLM-Based Cellular Perturbation Reasoning

    May 31, 2026Xinyu Yuan, Xixian Liu, Jianan Zhao +3Single-Cell Perturbation PredictionTranscriptomics

    1Mila - Québec AI Institute · University of Montréal · University of Ottawa +3

  45. On the Recoverability of Causal Relations from Bulk Gene Expression Data

    May 30, 2026Gongxu Luo, Boyang Sun, Kun ZhangTranscriptomicsCausal

    Mohamed bin Zayed University of Artificial Intelligence · Carnegie Mellon University

  46. Effective Biological Representation Learning by Masking Gene Expression

    May 29, 2026Kian Kenyon-Dean, Alina Selega, Ihab Bendidi +5TranscriptomicsGenome-Wide Association Study

    Recursion · Valence Labs · École Normale Supérieure PSL

  47. Chem-PerturBridge: a harmonized compendium of small molecule perturbation transcriptomic effects

    May 29, 2026Artur Szałata, Olga Novitskaia, Maiia Shulman +3TranscriptomicsHarmonization

    Institute of Computational Biology, Helmholtz Center Munich · TUM School of Life Sciences Weihenstephan, Technical University of Munich · Institut Curie, INSERM U1331, Computational Oncology +1

  48. CellBRIDGE: Learning Cellular Trajectories via Interaction-Aware Alignment

    May 28, 2026Silas Ruhrberg Estévez, Nicolas Huynh, Tennison Liu +4Single-Cell RnaTranscriptomics

    DAMTP, University of Cambridge · Francis Crick Institute · University of Colorado Anschutz Medical Campus

  49. ScaleMAP: Preserving Local Density and Neighborhood Structure in Low-Dimensional Embeddings

    May 28, 2026Rajas Poorna, Marcus T. CiceroneDimensionality ReductionMultiscale

    Georgia Institute of Technology · School of Chemical and Biomolecular Engineering Georgia Institute of Technology · School of Chemistry and Biochemistry Georgia Institute of Technology

  50. FPLIER: Federated Pathway-Level Information Extractor

    May 28, 2026Daniele Malpetti, Christian Berchtold, Francesco Gualdi +3TranscriptomicsMembership Inference Attacks

    1Dalle Molle Institute for Artificial Intelligence (IDSIA), USI-SUPSI, Lugano, Switzerland · 2Swiss Institute of Bioinformatics (SIB), Lugano, Switzerland

  51. Controlling False Discovery in Arbitrarily Structured Hypothesis Spaces via Reproducing Kernels

    May 17, 2026Binyamin Perets, Shie MannorFalse Discovery RateReproducing Kernel Hilbert Spaces

    Technion – Israel Institute of Technology · NVIDIA

  52. Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design

    May 14, 2026Ziyu Xu, Zijian Zhang, Liang Wang +4Drug DesignTranscriptomics

    NLPR, MAIS, Institute of Automation, Chinese Academy of Sciences, Beijing, China · School of Advanced Interdisciplinary Sciences, University of Chinese Academy of Sciences, Beijing, China · School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China +1

  53. CPEMH: An Agentic Framework for Prompt-Driven Behavior Evaluation and Assurance in Foundation-Model Systems for Mental Health Screening

    May 11, 2026Giuliano Lorenzoni, Ivens Portugal, Paulo Alencar +1Mental HealthAgentic Framework

    University of Waterloo · University of Waterloo Waterloo, ON, Canada

  54. Learning predictive models for combinations of heterogeneous proteomic data sources

    May 9, 2026Michal Valko, Richard Pelikan, Miloš HauskrechtMulti-Omic IntegrationTranscriptomics

    Computer Science Department University of Pittsburgh, Pittsburgh, Pennsylvania

  55. Prototype Guided Post-pretraining for Single-Cell Representation Learning

    May 8, 2026Sachini Weerasekara, Natasha Darras, Sagar Kamarthi +2TranscriptomicsSingle-Cell Foundation Models

    Sachini Weerasekara∗ · Natasha Darras · Sagar Kamarthi +2

  56. Feature Dimensionality Outweighs Model Complexity in Breast Cancer Subtype Classification Using TCGA-BRCA Gene Expression Data

    May 7, 2026Meena Al HasaniTranscriptomicsIntrinsic Dimensionality

    Independent Researcher

  57. OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning

    May 7, 2026Maciej Sypetkowski, Joanna Krawczyk, Łukasz Smoliński +4Multi-Omic IntegrationTranscriptomics

    Ingenix.AI, Warsaw, Poland

  58. CellxPert: Inference-Time MCMC Steering of a Multi-Omics Single-Cell Foundation Model for In-Silico Perturbation

    Apr 30, 2026Andac Demir, Erik W. Anderson, Jeremy L. Jenkins +1Single-Cell Perturbation PredictionTranscriptomics

    Novartis Biomedical Research

  59. HATS: An Open data set Integrating Human Perception Applied to the Evaluation of Automatic Speech Recognition Metrics

    Apr 30, 2026Thibault Bañeras Roux, Jane Wottawa, Mickael Rouvier +2Automatic Speech Recognition EvaluationCharacter Error Rate

    Nantes University, France · Le Mans University, France · Avignon University, France

  60. Intervention-Aware Multiscale Representation Learning from Imaging Phenomics and Perturbation Transcriptomics

    Apr 19, 2026Jiayuan Chen, Ruoqi Liu, Zishan Gu +1TranscriptomicsPhenotypes

    The Ohio State University