Phenotypes

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9 papers in the last four weeks, up 80% on the four weeks before. 0.1% of all new papers.

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  1. Flattening the Connectome Spectrum: A Spectral Filter for FC Induces a Pretraining Target for fMRI Encoders

    Sep 29, 2026Giovanni Marraffini, Victoria Shevchenko, Carlo Alberto Barbano +1Functional ConnectivityHuman Connectome Project

    UNITO · MIND

  2. 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

  3. RareDx: Controlled Knowledge Integration and Graph-Grounded Policy Optimization for Rare-Disease Diagnosis

    Sep 28, 2026Bo Zhang, Yuchen Wang, Dongbai Li +6Rare DiseaseBiomedical Knowledge Graph

    Xi’an Jiaotong University · UIUC · Tsinghua University +4

  4. Recent Advances in Agentic Agri-Robotic Phenotyping: A Perspective Review from Fragmented Multimodal Sensing to Unified PhenoAgent Intelligence

    Sep 28, 2026Muhammad Owais, Ehtesham Iqbal, Samee Ullah Khan +3Tomato DiseasesAgricultural Monitoring

    Khalifa University Center for Autonomous Robotic Systems (KU-CARS), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. · Advanced Research and Innovation Center (ARIC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. · Department of Computer Science and Engineering, Chung-Ang University, Seoul, South Korea. +1

  5. On Growth and Form, and Function: Reusable Regulatory Handles Control Phenotypic Variation

    Sep 24, 2026Benedikt Hartl, Milton L. Montero, Marcello Barylli +2Neural Cellular AutomataSelf-Organization

    Allen Discovery Center at Tufts University, Medford, MA, USA · IT University of Copenhagen, Denmark · Sakana AI, Japan +1

  6. ERCPMP-Gx: Endoscopic Image and Video Dataset for Morphological, Histopathological, and Genomic Characterization of Colorectal Polyposis

    Sep 17, 2026Zahra Ghaffari, Massih Bahar, Mojgan Forootan +2Polyp SegmentationColorectal Cancer

    Shahid Beheshti University of Medical Sciences, Tehran, Iran. · Familial & Hereditary Cancers Institute, Tehran, Iran. · Shiraz University of Medical Sciences, Shiraz, Iran. +1

  7. Self-Replicating Neural Cellular Automata: Quantifying Emergent Phenotypic and Genotypic Diversity in an OpenEnded Substrate

    Sep 17, 2026Sanyam Jain, Felix Simon Reimers, Stefano NicheleNeural Cellular AutomataSelf-Organization

    Department of Computer Science and Communication, Østfold University of Applied Sciences, B R A veien 4, 1757 Halden, Norway · Department of Computer Science, Oslo Metropolitan University, Pilestredet 35, 0166 Oslo, Norway

  8. Large Language Model Agents for Evidence Based Genetic Disease Severity Classification

    Sep 17, 2026Tohid Ghasemnejad, Ahmadreza Argha, Mark Grosser +7PhenotypesSeverity

    UNSW BioMedical Machine Learning Lab (BML), School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia · School of Biomedical Engineering, UNSW Sydney, NSW 2052, Australia · 23Strands, Pyrmont, Australia +8

  9. Zero-Shot 3D Plant Organ Segmentation with SAM3 and Semantic NeRFs

    Sep 7, 2026Andreas Gilson, Laura Hennig, Peter PietrzykInteractive 3D SegmentationPoint Clouds

    Fraunhofer Institute for Integrated Circuits (IIS), Fürth, Germany · Otto-Friedrich-Universität Bamberg, Germany · Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany

  10. PhenoBench: Mapping What a Deeply Phenotyped Human Cohort Can Tell Us

    Sep 5, 2026Gal Sapir, Alon Diament, Adva Wolf +7PhenotypesCohort

    Pheno.AI, Tel Aviv, Israel · Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel · Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel +1

  11. AI-enabled Low-Cost 3D Maize Ear Morphometry Platform at Breeding Scale

    Aug 31, 2026Therin Young, Elijah Rodriguez, Lisa Coffey +4Morphometric AnalysisPrecision Agriculture

  12. Evaluation of Clinically Steerable Retinal Image Generation from Foundation Model Latent Spaces

    Aug 13, 2026Zuzanna A. Wakefield-Skórniewska, Bartłomiej W. PapieżMedical Image GenerationLatent Space

    Big Data Institute, Nuffield Department of Population Health, University of Oxford, United Kingdom

  13. Multi-Level Evidence Aggregation for Robust Facial Phenotype Retrieval in Rare Genetic Disorder Prioritization

    Aug 11, 2026Alexander Hustinx, Carolin Kaffiné, Behnam Javanmardi +2PhenotypesRare Disease

    Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany

  14. One-Time Training for All Grains: Open-Set Grain Recognition and Quantitative Analysis

    Aug 10, 2026Qihe Su, Mengyu Sun, Yuxi Ke +4Precision AgricultureFine-Grained Perception

    National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China · College of Engineering, Huazhong Agricultural University, Wuhan, 430070, China · Engineering Research Center of Intelligent Technology for Agriculture, Ministry of Education +1

  15. Decoding Phenotypes: A Framework for Fusing Genomic Language Models and Neuroimaging

    Aug 9, 2026Tianli Tao, Ziyang Wang, Emma Robinson +2Multimodal NeuroimagingGenome-Wide Association Study

    School of Biomedical Engineering and Imaging Science, Faculty of Life Science and Medicine, King’s College London, UK · School of Computer Science and Digital Technologies, Aston University, UK · School of Engineering, College of Engineering and Physical Sciences, University of Birmingham, UK

  16. 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

  17. GraphRareBench: An Auditable Graph-Evidence Benchmark for Phenotype-Driven Rare-Disease Diagnosis

    Jul 27, 2026Guiling Guo, Jia Yang, Jiahao Xu +3Rare DiseaseBiomedical Knowledge Graph

    National Institute for Data Science in Health and Medicine, Xiamen University · Institute of Artificial Intelligence, Xiamen University · School of Medicine, Xiamen University +1

  18. Foundation-model-guided radiogenomic discovery linking cancer genomes to cancer scans

    Jul 22, 2026Frederik Hauke, Jeremias Krause, Patrick Wienholt +6RadiomicsGenome-Wide Association Study

    Department of Diagnostic and Interventional Radiology, University Hospital RWTH Aachen, Aachen, Germany · Center for Human Genetics and Genomic Medicine, University Hospital RWTH Aachen, Aachen, Germany · Department of Nephrology, Rheumatology and Immunology (Medical Clinic II), University Hospital RWTH Aachen, Aachen, Germany +3

  19. Text-conditioned Segmentation for Tomato Phenotyping via Procedural Synthetic Data

    Jul 20, 2026Samy Mounir, Mikolaj Cieslak, Najmeddine Dhieb +8Synthetic-To-Real Domain GapTomato Diseases

    Computer, Electrical and Mathematical Sciences and Engineering Division, KAUST, KSA · Department of Computer Science, University of Calgary, Canada · Department of Computer Science, Kiel University, Germany +2

  20. Using binary silver labels in electronic health records-based computable phenotyping algorithms

    Jul 20, 2026Shuhe Wang, Matthew T. Slaughter, Jennifer C. Nelson +1Electronic Health RecordsPhenotypes

    Department of Biostatistics, University of Washington · Kaiser Permanente Center for Health Research · Biostatistics Division, Kaiser Permanente Washington Health Research Institute +1

  21. Still image and spatial-temporal tomato data enabling detection, segmentation, tracking, and video-instance segmentation using strong and weak labels

    Jul 16, 2026Michael Halstead, Esra Guclu, Mohamed Farag +7Tomato DiseasesFruit

    University of Bonn, Bonn, Germany · CSIRO, Pullenvale, Australia

  22. A Unified Framework for Comprehensive Cardiac CT Segmentation and Phenotyping: Human-in-the-Loop Data Annotation, Vision Foundation Model Development, Multicenter Evaluation and Clinical Validation

    Jul 13, 2026Pooya Mohammadi Kazaj, Leo Fridolin Weber, Wen Xie +17EchocardiographyMulti Organ Computed Tomography Segmentation

    Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland · Department of Digital Medicine, University of Bern, Bern, Switzerland · Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland +4

  23. The Effects of Synthetic Data and Label Distribution on Canola Branch Counting

    Jul 10, 2026Amirsalar Darvishpour, Mikolaj Cieslak, Adam RunionsTomato DiseasesSynthetic Data

    Department of Computer Science, University of Calgary

  24. AI-guided stimuli discovery and generation to optimize facial emotion perception studies in autism

    Jul 9, 2026Kushin Mukherjee, Na Yeon Kim, Maren Wehrheim +2Autism Spectrum DisorderFacial Expression Recognition

    Centre for Integrative and Applied Neuroscience, York University, Canada · Department of Psychology, Stanford University, USA · Department of Psychology, University of California, Riverside, USA +2

  25. A Transdiagnostic Space of Disorder Like Phenotypes in Reinforcement Learning Agents

    Jul 8, 2026Hari PrasadOffline Reinforcement LearningMental Health

  26. Hierarchical Classification via Cascading Feature Elimination: Application to Human Phenotype Ontology-Aligned Facial Phenotyping (FaceMesh2HPO)

    Jul 6, 2026Fabio Hellmann, Alexander Hustinx, Benjamin D. Solomon +4PhenotypesSkin Lesion Classification

    1*Chair for Human-centered Artificial Intelligence, University of Augsburg, Universitätsstr. 6a, Augsburg, 86159, Bavaria, Germany. · Institute for Genomic Statistics and Bioinformatics, University of Bonn, Venusberg-Campus 1, Bonn, 53127, North Rhine-Westphalia, Germany. · 3National Human Genome Research Institute, National Institutes of2026 Health, 10 Center Dr, Bethesda, 20892, MD, United States of America.

  27. Population-Scale Segmentation of Penile Tissue in DIXON MRI using Deep Learning for Quantitative Phenotyping in Male Reproductive Health

    Jul 2, 2026Jan Ernsting, Gunnar Paul Kordes, Nils Johannaber +5Prostate Magnetic Resonance ImagingMulti Organ Computed Tomography Segmentation

    University of Münster Germany

  28. Structured Gaussian Processes for Uncertainty-Aware Classification of High-Dimensional, Small-Sampled Omics Data

    Jul 2, 2026Yue Zhang, Nandini Amit Gadhia, Georgios Karagiannis +1Multi-Omic IntegrationBacterial Colony Counting

    Department of Mathematical Sciences Durham University Durham, United Kingdom · STFC Hartree Centre University of Liverpool Liverpool, United Kingdom · STFC Hartree Centre Daresbury, United Kingdom

  29. Evolutionary Wave Function Collapse

    Jul 2, 2026Dipika Rajesh, Ahmed Khalifa, Julian TogeliusMotion GenerationMaze Task

    UC Santa Cruz Santa Cruz, USA · University of Malta Msida, Malta · New York University New York, USA

  30. The Turning Point of 3D Plant Phenotyping: 3D Foundation Models Enable Minute-to-Second Cross-Crop Reconstruction and Beyond

    Jul 2, 2026Hanyue Jia, Wei Zhou, Wenbo Zhou +3Tomato Diseases3D Foundation Models

    Northwest A&F University, Yangling, 712100, China · Huazhong University of Science and Technology, Wuhan, 430074, China · Wuhan Institute of Technology, Wuhan, 430205, China

  31. CW-B: Class Weighted Boosting Framework for Imbalance Resilient Multi Class Cardiac Phenotyping

    Jun 29, 2026Sijia Li, Xiaoyu Tan, Chen Zhan +3Imbalanced ClassificationXgboost Model

    School of Electronic and Electrical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China · Tencent YouTu Lab, Shanghai 200232, China · Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China +1

  32. CPAgents: Agentic Composite Phenotype Generation for Cardiac Disease Association

    Jun 26, 2026Zuoou Li, Wenlong Zhao, Kelly Yu +5PhenotypesCardiovascular Risk Prediction

    Department of Mechanical Engineering, University College London, London, UK · CSIG Group, Tencent, Beijing, China · Department of Computing, Imperial College London, London, UK +5

  33. GRAFT: Biological Graph and Hypergraph Benchmarks for Linked Gene Expression and Phenotypic Trait Prediction in Arabidopsis thaliana

    Jun 25, 2026Manuel Serna-Aguilera, Vanshika Jindal, Fiona L. Goggin +5PhenotypesRegulatory Networks

    Department of Electrical Engineering and Computer Science, University of Arkansas, AR · CVIU Lab, University of Arkansas, AR · Department of Entomology and Plant Pathology, University of Arkansas, AR +3

  34. Dementia-Agents: A Multi-Modal Multi-Agent System for Dementia Staging and Phenotyping

    Jun 19, 2026Yaling Shen, Maja Christensen, Yiwen Jiang +4AlzheimerMultimodal Clinical Data

    Monash University · Eastern Health · Lived Experience Advisor

  35. Robust Image-Driven Phenotyping of Ovarian Tumor Cells using Optimized Dynamic Features in Hyperbolic Channels

    Jun 15, 2026Hong-Fei Li, Xi-Lin Gao, Yi-Juan Xiang +6Mitotic FiguresPhenotypes

    Cancer Hospital of Dalian University of Technology, Dalian University of Technology, Shenyang 110000, China · Faculty of Medicine, Dalian University of Technology, Dalian 116024, China · Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410000, China +2

  36. From Genes to Tokens: a GWAS-inspired Approach for Interpretable Stylometric Analysis

    Jun 8, 2026Dmitry Pronin, Evgeny KazartsevStylometricAuthorship

    HSE University

  37. Comparison of Deep Learning Frameworks For Rice Disease Mapping From UAV Multispectral Imaging

    Jun 4, 2026Yadav Raj Ghimire, Jagrati Talreja, Tewodros Syum Gebre +3Leaf Disease ClassificationTomato Diseases

    North Carolina A&T State University Greensboro, North Carolina, USA.

  38. DXA-Derived Skeletal Phenotypes and Hip Fracture Risk: A Backdoor-Adjusted Causal Analysis

    May 29, 2026Zixin Shi, Chen Zhao, Meiling Zhou +8PhenotypesSkeleton

    Department of Applied Computing, Michigan Technological University, Houghton, MI, 49931, USA · Department of Computer Science, Kennesaw State University, Marietta, GA, 30060, USA · Department of Statistics, Grand Valley State University, Allendale, MI, USA +6

  39. Frontier LLM-based agents can overcome the ontology curation bottleneck for natural phenotypes

    May 27, 2026James P. Balhoff, Hilmar LappPhenotypesData-Curation

    Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina, USA · Neuromatch, USA

  40. PhAME: Phenotype-Aware Molecular Editing via Latent Diffusion

    May 27, 2026Łukasz Janisiów, Sebastian Musiał, Bartosz Zieliński +2Molecular OptimizationDrug Design

    Faculty of Mathematics and Computer Science, Jagiellonian University · Doctoral School of Exact and Natural Sciences, Jagiellonian University · Jagiellonian Center for Artificial Intelligence, Jagiellonian University +2

  41. Polymorphism Is Rotation: Operational Mechanistic Interpretability from a Two-Layer Transformer to Pythia-70m

    May 23, 2026Jordan F. McCannTransformer ArchitecturesImproving Sparse Autoencoders

    Independent Researcher

  42. GEESE: Genotype-aware End-to-End Spatio-temporal Embedding for Behavioral Phenotyping

    May 23, 2026Yiran Ding, Yuen Gao, Chunqi Qian +1PhenotypesAutism Spectrum Disorder

    Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, USA · Department of Radiology, Michigan State University, East Lansing, Michigan, USA

  43. Towards Label-Free Single-Cell Phenotyping Using Multi-Task Learning

    May 14, 2026Saqib Nazir, Ardhendu BeheraAcute Myeloid LeukemiaPhenotypes

    Department of Computer Science, Edge Hill University, UK

  44. The Geno-Synthetic Algorithm: Type-Factored Coevolutionary Optimization for Heterogeneous Genotypes and Assembled Phenotypes

    May 13, 2026Alex BogdanGenetic AlgorithmsEvolutionary Optimization

    Evolutionairy AI Toronto, Canada

  45. AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents

    May 11, 2026Edward De Brouwer, Carl Edwards, Alexander Wu +9PhenotypesVirtual Cell

    Genentech

  46. CT-IDP: Segmentation-Derived Quantitative Phenotypes for Interpretable Abdominal CT Disease Classification

    May 9, 2026Lavsen Dahal, Joseph Y. LoPhenotypesDisease

    1. Center for Virtual Imaging Trials, Carl E. Ravin Advanced Imaging Laboratories · 3. Electrical and Computer Engineering, Pratt School of Engineering, Duke University · 4. Medical Physics Graduate Program, Duke University +1

  47. A Linear-Transformer Hybrid for SNP-Based Genotype-to-Phenotype Prediction in Grapevine

    May 7, 2026Yibin Wang, Murukarthick Jayakodi, Silvas Kirubakaran +2Phenotypes

    Department of Biological and Agricultural Engineering, Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, 75252, USA · Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, 75252, USA · USDA-ARS, Grape Genetics Research Unit, 630 West North Street, Geneva, New York 14456, USA

  48. EFGPP: Exploratory framework for genotype-phenotype prediction

    May 2, 2026Muhammad Muneeb, David B. AscherPhenotypesClinical Prediction

    School of Chemistry and Molecular Biology, The University of Queensland, Brisbane, 4067, Australia · Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, 3004, Australia

  49. Active Inference: A method for Phenotyping Agency in AI systems?

    Apr 25, 2026Philip Wilson, Axel Constant, Mahault Albarracin +4Artificial Intelligence GovernanceArtificial Intelligence Systems

    Independent Researcher · Department of Engineering and Informatics, University of Sussex, Falmer, Brighton, BN1 9RH, UK · Laboratoire d’Analyse Cognitive de l’Information, Université du Québec à Montréal, Québec, Canada +4

  50. Phonological Subspace Collapse Is Aetiology-Specific and Cross-Lingually Stable: Evidence from 3,374 Speakers

    Apr 23, 2026Bernard Muller, Antonio Armando Ortiz Barrañón, LaVonne RobertsDysarthric SpeechGrapheme-To-Phoneme

    The Scott-Morgan Foundation, Torquay, United Kingdom · Tecnológico de Monterrey, Monterrey, Mexico

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

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

    The Ohio State University

  52. A phenotype-driven and evidence-governed framework for knowledge graph enrichment and hypotheses discovery in population data

    Apr 18, 2026Adela Bâra, Simona-Vasilica OpreaKnowledge GraphsLocal Causal Structures

    Department of Economic Informatics and Cybernetics, Bucharest University of Economic Studies, Bucharest, Romania

  53. LLM-MINE: Large Language Model based Alzheimer's Disease and Related Dementias Phenotypes Mining from Clinical Notes

    Mar 14, 2026Mingchen Shao, Yuzhang Xie, Carl Yang +1AlzheimerClinical Notes

    Northwestern University, Evanston, IL · Emory University, Atlanta, GA

  54. ECGFlowCMR: Pretraining with ECG-Generated Cine CMR Helps Cardiac Disease Classification and Phenotype Prediction

    Jan 28, 2026Xiaocheng Fang, Zhengyao Ding, Guangkun Nie +9Cardiac Magnetic Resonance ImagingCardiac

    State Key Laboratory of General Artificial Intelligence, Peking University · School of Intelligence Science and Technology, Peking University, Beijing, China · Polytechnic Institute of Zhejiang University, Zhejiang University, Hangzhou, China +4