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5 papers in the last four weeks, down 17% on the four weeks before. 0.1% of all new papers.

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  1. Auditable Algebraic Counting Field for Cryptic-Pocket Detection from Apo Structures

    Oct 1, 2026Shan Yu, Xuening WuMolecular Property PredictionRoc-Auc

    Pfizer, Shanghai, China

  2. scTrilemma: Balancing Identity, Invariance, and Fidelity in Single-Cell Representation Learning

    Sep 30, 2026Yunhak Oh, Yoonho Lee, Junseok Lee +9CellsMolecular Representation Learning

    KAIST · Work done during an internship at HITS · HITS

  3. 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

  4. From Retrieval to Reasoning: Agentic Mechanism Prediction from Cell Painting Profiles

    Sep 29, 2026Jiayuan Chen, Botao Yu, Tianyu Liu +3PhenotypesCells

    Department of Computer Science and Engineering, The Ohio State University · Department of Biomedical Informatics, The Ohio State University · Department of Biostatistics, Yale University +1

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

    Sep 28, 2026Mustapha Bounoua, Giulio Franzese, Pietro MichiardiSingle-Cell Perturbation PredictionCells

    Department of Data Science EURECOM, France

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

    Sep 28, 2026Haojie Yang, Ran SuSingle-Cell Perturbation PredictionCells

    College of Intelligence and Computing Tianjin University, Tianjin, China

  7. See, Measure, and Reason: Learning Visually Grounded Reasoning in Pathology

    Sep 28, 2026Chengyang Zhang, Wenchuan Zhang, Bo Li +8Pathology Foundation ModelsCells

    College of Computer Science, Sichuan University · Department of Pathology and Institute of Clinical Pathology, West China Hospital, Sichuan University · Department of Computer Science, School of Computing, National University of Singapore +1

  8. End-to-End Cell Detection via Instance-aware Graph Modeling

    Sep 14, 2026Ruochen Liu, Yalin Zheng, Jingxin Liu +5CellsGraph Representation Learning

    Faculty of Science and Engineering, University of Liverpool, Liverpool, L69 3GJ, U.K. · Department of Eye and Vision Sciences, University of Liverpool, Liverpool, L7 8TX, U.K. · School of AI and Advanced Computing, Xi’an Jiaotong-Liverpool University, Suzhou, 215400, China +3

  9. Beyond Accuracy: Uncertainty-Guided Boundary Refinement for Reliable Biomedical Image Segmentation

    Sep 14, 2026Anima KujurSemi-Supervised Medical Image SegmentationDelineation

    Interdisciplinary Centre for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany

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

    Sep 9, 2026Murthy DevarakondaSingle-Cell Perturbation PredictionCells

    Causal Data AI (causaldata.ai)

  11. Multi-label versus multi-class classification of blood cells and their aggregates in microfluidic channels

    Sep 7, 2026Igor Zingman, Shada Abuhattum, Sara Kaliman +8Acute Myeloid LeukemiaCells

    Max Planck Institute for the Science of Light, Erlangen, Germany · Max-Planck-Zentrum für Physik und Medizin · Friedrich-Alexander Universiät Erlangen-Nürnberg, Erlangen, Germany

  12. Semantic-Guided Multimodal Preprocessing for Vision Transformer-Based Clear Cell Renal Cell Carcinoma Grading

    Sep 1, 2026Fatemeh Javadian, Zhu Chen, Zahra Aminparast +1Cancer DetectionDigital Pathology

    Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany · Machine Learning for Medical Data, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany · Institute of Medical Sciences, Kermanshah University, Medical School,Sep Kermanshah, Iran

  13. Topology Inference for Immune System Networks by Using Cell Amount Data

    Aug 7, 2026Yushan Li, Rikard Forlin, Dimos V. Dimarogonas +1CellsTopology

    Department of Decision and Control Systems, KTH Royal Institute of Technology, Sweden · Department of Women’s and Children’s Health, Karolinska Institutet, Sweden

  14. JUMP-lite: Compact, reproducible benchmarking of cell representations

    Aug 7, 2026Alán F. Muñoz, Johan Fredin Haslum, Runxi Shen +2CellsPhenotypes

    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

  15. 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

  16. CohortHijack: Robustness of Single Cell Annotation to Companion Cell Removal

    Aug 6, 2026Arash Vashagh, Yasmin VashaghCellsCohort

    Faculty of Computer Science, University of New Brunswick, Fredericton, New Brunswick E3B 5A3, Canada · Farzanegan Amin 2 High School, Isfahan, Iran

  17. Learning Molecular Representations from Cellular Phenotypes with Structure Preservation

    Aug 3, 2026Xuan Lin, Jingyu Sheng, Tengfei Ma +2Molecular Representation LearningChemical Structures

    School of Computer Science, Xiangtan University, Xiangtan, Hunan, China · College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan, China · School of Computer Science, Beijing University of Posts and Telecommunications, Beijing, China +1

  18. 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

  19. 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

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

    Jul 30, 2026Panpan Cui, Yiqi Liu, Wenhao SunSingle-Cell Perturbation PredictionCells

    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

  21. Neural Circuit Function Inference with LLMs

    Jul 27, 2026Yijie Yin, Albert CardonaNeural CircuitsConnectome

    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK · MRC Laboratory of Molecular Biology, Cambridge, UK

  22. Auditing Retrieval-Augmented LLM Hypotheses for Longitudinal Cell Painting Morphology

    Jul 17, 2026Gilchan Park, Guang Zhao, Byung-Jun Yoon +1CellsModel Auditing

    Brookhaven National Laboratory Upton, New York, USA

  23. Transient State Reorganization and Cell Differentiation in the Developmental Dynamics of Growing Neural Cellular Automata

    Jul 17, 2026Hiroki Sato, Atsushi Masumori, Takashi IkegamiNeural Cellular AutomataCells

    1The University of Tokyo, Japan · 2Alternative Machine Inc., Japan · 3Atomi University, Japan

  24. Virtual Chromoendscopy with Tunable Visibility Enhancement

    Jul 14, 2026Yuhi Kanno, Yusuke Monno, Sho Suzuki +2ColonoscopyColorectal Cancer

    Department of Systems and Control Engineering, School of Engineering, Institute of Science Tokyo, Meguro-ku, Tokyo 152-8550, Japan · Department of Gastroenterology, International University of Health and Welfare Ichikawa Hospital, Ichikawa-shi, Chiba 272-0827, Japan · AI Medical Service Inc., Toshima-ku, Tokyo 170-0013, Japan

  25. Higher-Order Cell Tracking Transformer

    Jul 13, 2026Jordão Bragantini, Ilan Theodoro, Loïc A. RoyerCellsSpatio-Temporal Transformers

    Biohub San Francisco, CA

  26. Data-Driven Soft Labeling Scales DNA Read Classification to Whole-Body Cell-Type Deconvolution

    Jul 6, 2026Dmytro Rizdvanetskyi, Nathan Roos, Pavlo LutsikCellsMulti-Label Classification

    Department of Oncology KU Leuven Leuven, Belgium

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

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

    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

  28. MalariAI: A Label-Resilient Decoupled Framework for Universal Cell Segmentation and Explainable Stage Classification in Dense Malaria Blood Smears

    Jul 1, 2026Kaysarul Anas Apurba, Md Hasibul Hasan, Mohammed Ali +1Acute Myeloid LeukemiaMultiple Instance Learning

    Department of Electrical and Computer Engineering, North South University, Dhaka 1229, Bangladesh · Department of Computer Science and Engineering, International University of Business Agriculture and Technology (IUBAT), Dhaka 1230, Bangladesh

  29. CellDETR: A Detection-Guided Framework for Scalable Cell Representation Learning from Histopathology Images

    Jun 28, 2026Shikang Zhang, Guojun Li, Yicong Mao +1Digital PathologyWhole-Slide Images

    Zhejiang University of Technology · Tianjin University · Hangzhou Institute of Medicine, Chinese Academy of Sciences

  30. 3D Masked Autoencoders are Robust Learners of Volumetric and Multimodal Cellular Representations for Microscopy

    Jun 22, 2026Amirhossein Kardoost, Lion Gleiter, Tingying Peng +13D Masked AutoencodersMicroscopy

    Institute of AI for Health & Helmholtz AI, Computational Health Center, Helmholtz Munich – German Research Center for Environmental Health, Neuherberg, Germany · Munich Center for Machine Learning (MCML), Munich, Germany · Department of Medicine III, Ludwig-Maximilian-University Hospital, Munich, Germany +2

  31. Chem2Gen-Bench: Benchmarking Chemical-to-Genetic Translation in Perturbation Response Space

    Jun 19, 2026Yuxiang Lin, Ying ChenCells

    National Institute for Data Science in Health and Medicine, Xiamen University · School of Informatics, Xiamen University

  32. Revisiting Structural Dependency in Autoregressive Multi-Task Table Recognition via Order-Independent Cell-Level Representations

    Jun 16, 2026Takaya KawakatsuTabular LearningMulti--Task Learning

    Preferred Networks, Inc., 1-6-1 Otemachi, Chiyoda, Tokyo, Japan.

  33. Towards a Pseudo-Labeling Workflow for Celltype-Classification from Explanted Brain Slice Recordings

    Jun 15, 2026Cora Jostock, Jonas Ort, Henner Koch +2Neural RecordingsCells

    University of Duisburg-Essen, Intelligent Embedded Systems Lab, Duisburg, Germany · RWTH University Hospital, Department of Neurosurgery, Aachen, Germany · RWTH University Hospital, Department of Epileptology, Aachen, Germany

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

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

    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.

  35. CellNet -- Localizing Cells using Sparse and Noisy Point Annotations

    Jun 10, 2026Benjamin Eckhardt, Dmytro Fishman, Stuart Fawke +3CellsMicroscopy

    University of Göttingen · University of Tartu · Wellcome Sanger Institute

  36. Small Experiments, Cheaper Decisions: A Case Study in Staged Promotion for Micro-Pretraining

    Jun 9, 2026Felipe Chavarro PolaniaToken Budget AllocationPretraining

    Hewlett Packard Enterprise

  37. Incremental Sheaf Cohomology on Cellular Complexes: O(1)-in-n Lazy Edit Processing under Bounded Local Geometry

    Jun 2, 2026Jason L. VolkSheafPersistent Homology

    Invariant Research

  38. Quantifying the biophysical properties of stomatocytes in health and disease

    Jun 2, 2026Zhaojie Chai, Jianlu Zheng, He Li +2Acute Myeloid LeukemiaCells

    Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States · Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts · College of Engineering, University of Georgia, Athens, Georgia, United States

  39. Toward Pre-Deployment Assurance for Enterprise AI Agents: Ontology-Grounded Simulation and Trust Certification

    Jun 2, 2026Thanh Luong Tuan, Abhijit SanyalAgentic DeploymentsPre-Deployment Safety Assessments

    Golden Gate University, San Francisco, CA, USA · Data, Digital & IT, Novartis Healthcare Pvt. Ltd., Hyderabad, India

  40. 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

  41. CodeCytos: AI-assisted spatial molecular imaging analysis via code-augmented agent action space

    May 30, 2026Hung Q. Vo, Huy Q. Vo, Son T. Ly +6MicroscopyCells

    University of Houston, Department of Electrical and Computer Engineering, Houston, Texas, 77004, USA · Houston Methodist Hospital, Department of Systems Medicine and Biomedical Engineering, Houston, Texas, 77030, USA

  42. AI-Guided Design and Optimization of Graphite-Based Anodes via Iterative Experimental Feedback

    May 29, 2026Qian Du, Mark M. Sullivan, James E. Saal +1Lithium-Ion BatteriesGenerative Inverse Design

    hte GmbH, Kurpfalzring 104, 69123 Heidelberg, Germany · Citrine Informatics, 2629 Broadway St., Redwood City, CA 94063, USA

  43. One Click per Cell Type Suffices: Training-free Group Interaction for Cell Instance Segmentation

    May 28, 2026Sanghyun Jo, Seo Jin Lee, Seohyung Hong +4CellsMultiple Instance Learning

    1OGQ, Korea · 2Seoul National University, Korea · 3LG CNS, Korea

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

    May 27, 2026Mufan Qiu, Genhui Zheng, Yinuo Xu +4CellsDevelopmental Trajectories

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

  45. Cell Phantom Video Generation in Elliptical Fourier Descriptor Domain

    May 21, 2026Francesco Benedetto, Roberto Basla, Luca Magri +1Long Video GenerationCells

    Department of Electronics Information and Bioengineering, Politecnico di Milano, Italy

  46. Training distribution determines the ceiling of drug-blind cancer sensitivity prediction

    May 20, 2026Taekyung HeoPharmacokineticsCells

  47. WBCAtt+: Fine-Grained Pixel-Level Morphological Annotations for White Blood Cell Images

    May 19, 2026Satoshi Tsutsui, Winnie Pang, Shuting He +1Acute Myeloid LeukemiaPixel-Level Annotation

    Rapid-Rich Object Search (ROSE) Lab, School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore · Shanghai University of Finance and Economics, Shanghai, China

  48. 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

  49. From Table to Cell: Attention for Better Reasoning with TABALIGN

    May 14, 2026Tung Sum Thomas Kwok, Zeyong Zhang, Xinyu Wang +6Tabular DataLLM Reasoning Strategies

    University of California, Los Angeles · SimpleWay · New Jersey Institute of Technology +4

  50. Neurally-plausible radial basis kernels using distributed Fourier embeddings

    May 8, 2026Jakeb ChouinardRadial Basis FunctionSemantic Geometry

    Department of Systems Design Engineering, University of Waterloo · Centre for Theoretical Neuroscience, University of Waterloo

  51. Inference of Qualitative Models from Steady-State Data via Weighted MaxSMT

    May 8, 2026Ondřej Huvar, Nikola Beneš, Martin Jonáš +2CellsStructural Constraints

    Masaryk University, Brno, Czechia

  52. Donor-Aware scRNA-seq Benchmarks for IBD Classification

    May 5, 2026Jonathan MuhireSingle-Cell RnaCells

    Department of Computer Science, Oklahoma Christian University

  53. Approaching human parity in the quality of automated organoid image segmentation

    May 4, 2026Chase Cartwright, Gongbo Guo, Sai Teja Pusuluri +3TissueComputer Vision

    Department of Physics and Astronomy and Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, USA · The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA. · Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA. +1

  54. A Cellular Doctrine of Morality: Intrinsic Active Precision and the Mind-Reality Overload Dilemma

    May 2, 2026Ahsan AdeelMoral ReasoningNeuroscience

    Conscious Multisensory Integration (CMI) Lab, University of Stirling, UK

  55. AblateCell: A Reproduce-then-Ablate Agent for Virtual Cell Repositories

    Apr 21, 2026Xue Xia, Chengkai Yao, Mingyu Tsoi +10Virtual CellCells

    Shanghai Artificial Intelligence Laboratory · The Hong Kong University of Science and Technology (Guangzhou) · University of California San Diego +4

  56. Cell-Based Representation of Relational Binding in Language Models

    Apr 21, 2026Qin Dai, Benjamin Heinzerling, Kentaro InuiLanguage ModelingRelational

    1Tohoku University · 2RIKEN AIP · 3MBZUAI

  57. Efficient Search of Implantable Adaptive Cells for Medical Image Segmentation

    Apr 16, 2026Emil Benedykciuk, Marcin Denkowski, Grzegorz M. WójcikSemi-Supervised Medical Image SegmentationU-Net

    Institute of Computer Science and Mathematics, Maria Curie Sklodowska University, Akademicka 9, Lublin, 20-033,, Poland

  58. Intermediate Layers Encode Optimal Biological Representations in Single-Cell Foundation Models

    Apr 16, 2026Vincenzo Yuto Civale, Roberto Semeraro, Andrew David Bagdanov +1CellsLayer-Wise

    University of Siena · University of di Firenze · University of Firenze

  59. Residual RL-MPC for Robust Microrobotic Cell Pushing Under Time-Varying Flow

    Mar 5, 2026Yanda Yang, Sambeeta DasFluid ControlsModel Predictive Control

    Department of Mechanical Engineering, University of Delaware, Newark, DE 19716, USA

  60. CytoCLIP: Learning Cytoarchitectural Characteristics in Developing Human Brain Using Contrastive Language Image Pre-Training

    Jan 18, 2026Pralaypati Ta, Sriram Venkatesaperumal, Keerthi Ram +1Mitotic FiguresMultimodal Neuroimaging

    Sudha Gopalakrishnan Brain Centre, Indian Institute of Technology, Madras, Chennai, India. · Department of Electrical Engineering, Indian Institute of Technology, Madras, Chennai, India.