Single-Cell Perturbation Modeling

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

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  1. DRIFT: Disentangled Responsive-Invariant Flow Transport for Single-Cell Perturbation Prediction

    Sep 28, 2026Mustapha Bounoua, Giulio Franzese, Pietro MichiardiDisentangled Representation LearningConditional Flow Matching

    Department of Data Science EURECOM, France

  2. P2P: Cross-View Population Denoising for Unpaired Single-Cell Perturbation Response Prediction

    Sep 28, 2026Haojie Yang, Ran SuSingle-Cell Perturbation ModelingSingle-Cell Transcriptomics

    College of Intelligence and Computing Tianjin University, Tianjin, China

  3. 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 +3AI Agents for Scientific DiscoveryAI Agent Auditing

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

  4. CellRFT: Reinforcement Fine-Tuning for Single-Cell Perturbation Modeling

    Sep 17, 2026Jie Yan, Li Liu, Hanze Guo +7Multi-Objective Reinforcement LearningSingle-Cell Perturbation Modeling

    Chinese Academy of Sciences · Peking University · Renmin University of China +2

  5. scDEFT: A deep learning framework for drug-effect prediction and counterfactual reasoning

    Sep 9, 2026Murthy DevarakondaSingle-Cell Perturbation ModelingClinical Outcome Prediction

    Causal Data AI (causaldata.ai)

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

    Sep 8, 2026Sai JayakumarTransformerSingle-Cell Perturbation Modeling

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

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

    Sep 1, 2026Handong Wang, Jiaxin Qi, Haochen Feng +1Single-Cell Perturbation ModelingSingle-Cell RNA Sequencing

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

  8. PertMind: Eliciting Emergent Biological Reasoning in LLM via Reinforcement Learning on Cellular Perturbation Data

    Aug 17, 2026Zhenchao Tang, Xiaogang Xu, Jiafei Wu +16RL for Language Model ReasoningSingle-Cell Perturbation Modeling

    Zhejiang University

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

    Aug 7, 2026Quanquan Li, Yihe Chi, Liuyang Song +10Flow MatchingSingle-Cell Perturbation Modeling

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

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

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

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

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

    Jul 31, 2026Mehrdad Shoeibi, Niloofar YousefiOOD GeneralizationSingle-Cell Perturbation Modeling

    University of Central Florida

  12. PerturbMap: Cross-Context Transfer of Single-Cell Perturbation Responses

    Jul 30, 2026Panpan Cui, Yiqi Liu, Wenhao SunSingle-Cell Perturbation ModelingCross-Domain Transfer Learning

    School of Advanced Interdisciplinary Sciences, University of Chinese Academy of Sciences · Institute of Computing Technology, CAS; University of Chinese Academy of Sciences · 3Hong Kong University of Science and Technology

  13. PerturbPFN: Probing the Limits of Synthetic Priors in Drug Perturbation Modelling

    Jul 26, 2026Yuche Gao, José Miguel Hernández-Lobato, Siyuan GuoSynthetic Data PretrainingStructural Causal Models

    University of Cambridge, Cambridge, United Kingdom · Prior Labs, Freiburg, Germany

  14. PertReason: A Knowledge-Grounded Benchmark and Framework for Cell-State-Conditioned Mechanistic Reasoning of Perturbation Effects

    Jul 21, 2026Dongkwan Kim, Yiming Gao, Yining Yang +1LLM GroundingSingle-Cell Perturbation Modeling

    Department of Electrical and Computer Engineering, Texas A&M University

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

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

    AIFFEL Research, Modulabs, Republic of Korea

  16. Score Distributions, Not Cells: Evaluating Single-Cell Perturbations Under Class Overlap

    Jul 6, 2026Youssef Marrakchi, Davide D'Ascenzo, Sebastiano Cultrera di MontesanoSingle-Cell Perturbation ModelingClassification

    Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA. · Department of Computer Science, University of Milan, Milan, Italy. · Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy. +1

  17. Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses

    Jun 29, 2026Dingping Zhao, Jie Lin, Feng Xu +1Single-Cell Perturbation ModelingSingle-Cell RNA Sequencing

    Division of Pharmacognosy, School of Pharmaceutical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China · Department of Computer Science at School of Informatics, Xiamen University, Xiamen, China · Peking University Health Science Center, Peking University, Beijing, China

  18. SVC-Probe: A Framework for Evaluating Perturbation Generalization in Spatial Foundation-Model Embeddings

    Jun 26, 2026Jake Y. Chen, Huu Phong Nguyen, Fuad Al Abir +1Single-Cell Perturbation ModelingRepresentation Probing

    Department of Biomedical Informatics and Data Science, University of Alabama at Birmingham, Birmingham, AL, USA. · System Pharmacology and AI Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.

  19. PerturbCellRL: Verifier-Guided Reinforcement Learning for Single-Cell Perturbation Prediction

    Jun 26, 2026Dongxia Wu, Mingyu Li, Yuhui Zhang +4Single-Cell Perturbation ModelingReinforcement Learning with Verifiable Rewards

    Peking University Beijing, China · Stanford University Stanford, CA

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

    Jun 22, 2026Sajib Acharjee Dip, Liqing ZhangSingle-Cell Perturbation ModelingGenomics

    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

  21. 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 ModelingSingle-Cell Transcriptomics

    INFevo

  22. CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context

    Jun 10, 2026Wei Zhang, Xun Jiang, Yuesi Xi +1Single-Cell Perturbation ModelingGenomics

    1L3S Research Center, Leibniz Universität Hannover, Germany · School of Clinical Medicine & Laboratory Medicine, Jiangsu University, China · Institute for Information Processing (tnt), Leibniz Universität Hannover, Germany.

  23. FreeBridge: Variational Schrödinger Bridges for Cellular Transition Dynamics

    Jun 9, 2026Xurui Wang, Qin Ren, Jun Ma +2Schrödinger BridgesSingle-Cell Perturbation Modeling

    Stony Brook University, Stony Brook, NY, USA · University of Toronto, Toronto, ON, Canada · University Health Network, Toronto, ON, Canada

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

    Jun 7, 2026Jake Fawkes, Liam Hodgson, Jason HartfordRL for Language Model ReasoningSingle-Cell Perturbation Modeling

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

  25. Querying Counterfactuals on Tissue Graphs with Supervised Disentanglement

    Jun 7, 2026Abdul Moeed, Stefan Schrod, Martin Rohbeck +4Spatial TranscriptomicsDisentangled Representation Learning

    Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany · Helmholtz Information & Data Science School for Health, Germany · Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany +4

  26. scCBGM: Interpretable Single-Cell Counterfactual Editing

    Jun 5, 2026Alma Andersson, Aya Abdelsalam Ismail, Edward De Brouwer +6Concept Bottleneck ModelsCausal Counterfactual Generation

    Genentech · Guide Labs · Department of Computer Science, New York University +1

  27. Chreode: A Cell World Model for One-Step Temporal Dynamics and Perturbation Prediction

    May 27, 2026Mufan Qiu, Genhui Zheng, Yinuo Xu +4World Model LearningLatent Dynamics Modeling

    University of North Carolina at Chapel Hill · The University of Texas at Austin · University of Pennsylvania

  28. Learning Latent Dynamical Causal Processes for Single-Cell Perturbation Prediction

    May 25, 2026Wenkang Jiang, Yuhang Liu, Erdun Gao +3Causal Representation LearningLatent Dynamics Modeling

  29. What Makes a Representation Good for Single-Cell Perturbation Prediction?

    May 19, 2026Wenkang Jiang, Yuhang Liu, Yichao Cai +5Variational AutoencodersDisentangled Representation Learning

    Australian Institute for Machine Learning, Adelaide University, Australia · Responsible AI Research Centre, Australia · College of Computer Science and Artificial Intelligence, Fudan University, China +3

  30. CellScientist: From Execution Feedback to Auditable Model-Revision Trajectories for Cellular Perturbation Prediction

    May 8, 2026Mengran Li, Bo Li, Jiaying Wang +7Single-Cell Perturbation ModelingScientific Workflow Automation

    Center for Artificial Intelligence and Robotics (CAIR), Hong Kong Institute of Science and Innovation (HKISI)