Genome-Wide Association Study

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8 papers in the last four weeks, up 167% on the four weeks before. 0.1% of all new papers.

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Surface-volume self-supervised representation learning of brain MRI for genetic discovery
Oct 1, 2026Tian Xia, Nuo Chen, Zihao Zhu +4Functional Magnetic Resonance Imaging Genome-Wide Association Study
D. Bradley McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, US. · Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, US. · Department of Electrical and Computer Engineering, Texas A&M University, College Station, US. +1
VANDAM: Viewing a nucleotide sequence with DNA molecular priors
Sep 30, 2026Jeremy Levy, Ariel Larey, Yury Nahshan +18Genome-Wide Association Study Sequence Modeling
Applied AI Architecture, NVIDIA, Israel. · Worldwide Field Ops, NVIDIA, Israel. · Developer Programs, NVIDIA, Israel. +3
GenoMorph: Pathway-Grounded Genomic Disease Reasoning via Adaptive Latent Computation
Sep 28, 2026Tanmoy Kanti Halder, Akash Ghosh, Arijit Roy +1Genome-Wide Association Study Biomedical Knowledge Graph
Department of Computer Science and Engineering, Indian Institute of Technology Patna, Bihta, 801106, Bihar, India · Prasannadeb Women’s College, India
Weighted Spline-Expanded Networks with Distributional Balancing for Continuous Treatment Effects
Sep 27, 2026Shucheng Liu, Chan Park, Guanhua ChenHeterogeneous Treatment Effects Covariate Balancing
University of North Carolina at Chapel Hill · University of Illinois Urbana-Champaign · University of Wisconsin–Madison
Null importance: Disentangling relevance for interpretable machine learning
Sep 16, 2026Garvesh Raskutti, Kris Sankaran, Jiaxin YeFeature Importance Importance
Department of Statistics, University of Wisconsin–Madison
HyCoSeq: Contextual Hyperbolic Representation Learning for Genomic Sequences
Sep 15, 2026Chenhao Zeng, Zhibin Pu, Shufei GeHyperbolic Learning Genome-Wide Association Study
Institute of Mathematical Sciences, ShanghaiTech University, Shanghai, China
SeqMaestro: From nucleotide sequences to biological hypotheses through interpretable machine learning
Sep 14, 2026Evgeny S. Saveliev, Krzysztof Kacprzyk, Charlotte Capitanchik +7Genome-Wide Association Study Bioinformatics
Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK · The Francis Crick Institute, London, UK · UK Dementia Research Institute at King’s College London, London, UK +1
Human mutation field reveals an equilibrium-like structure with irreversible circulation
Sep 7, 2026Isabella Caranzano, Daniel Maria Busiello, Stefano Priorelli +2Lattice Mutation Free-Energy Landscape
AI and Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, Torino, Italy · Department of Physics, University of Padova, Padova, Italy · Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
Science sandboxes measure the scientific capability of AI agents
Aug 31, 2026Arya S. Rao, Rodrigo I. Castro, Sager J. Gosai +8Scientific Discovery Sandbox
The Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA. · Department of Biomedical Informatics, Harvard Medical School; Boston, MA 02115, USA. · The Jackson Laboratory; Bar Harbor, ME 04609, USA. +10
Homo-RAG: Homology-Guided Retrieval-Augmented Generation for Cross-Species Gene Function Prediction
Aug 26, 2026Azrin SultanaGenome-Wide Association Study Hievi-Rag
Department of Computer Science, American International University-Bangladesh, 408/1, Kuratoli, Khilkhet, 1229, Dhaka, Bangladesh.
Uncertainty-Aware Deep Learning for Genomics Applications: Insights from an Empirical Study
Aug 11, 2026Sepideh Saran, Mahsa Ghanbari, Uwe OhlerGenome-Wide Association Study Uncertainty-Aware Classification
The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Germany · Department of Electrical Engineering and Computer Science, Technical University of Berlin, Germany · Department of Biology, Humboldt University of Berlin, Germany +1
Decoding Phenotypes: A Framework for Fusing Genomic Language Models and Neuroimaging
Aug 9, 2026Tianli Tao, Ziyang Wang, Emma Robinson +2Multimodal Neuroimaging Genome-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
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 Transcriptomics Single-Cell Rna
University of Michigan Ann Arbor, Michigan, USA · Weill Cornell Medicine New York, New York, USA
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 Prediction Transcriptomics
1East China Normal University · 2Peking University · University of Science and Technology of China +2
Self-supervised DXA representations encode multi-system disease risk, biological aging and heritability
Aug 3, 2026Gil Sasson, Zachary Levine, Smadar Shilo +9Vascular Age Biomarker
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. · Gray Faculty of Medical and Health Sciences, Tel Aviv University, Tel-Aviv, Israel. · The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children’s Medical Center of Israel, Petah Tikva, Israel. +5
Gene Ontology-Guided Hierarchical Spatial Gene Expression Prediction from Histopathology Images
Aug 1, 2026Zhiwen Xu, Xiaoming Yan, Chengkun Wu +3Spatial Transcriptomics Genome-Wide Association Study
National University of Defense Technology Changsha, China
VESTIGE: A Knowledge-Guided Masking Strategy for Corruption-Aware Fine-Tuning of Genomic Transformers, Validated on Ancient DNA Reconstruction
Jul 30, 2026Angshuman Chakravertty, Rahul MaheshwariGenome-Wide Association Study Corrupted Inputs
School of Technology Management & Engineering, SVKM’s Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-be-University, Jadcherla, Hyderabad 509301, Telangana, India, Hyderabad, India · School of Pharmacy and Technology Management, SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-be-University, Hyderabad, Jadcheral-509301, Telangana, India · School of Pharmacy and Technology Management, SVKM's Narsee Monjee Institute of Management Studies (NMIMS) Deemed-to-University, Hyderabad, Jadcheral-509301, Telangana, India
PlantBGC: Transformer for Plant BGC Discovery via Label-Free Domain Adaptation and Weak Supervision
Jul 29, 2026Yuhan Zhao, Nidhi Grover, Zhishan Guo +1Genome-Wide Association Study Tomato Diseases
North Carolina State University Department of Computer Science Raleigh, North Carolina, USA · North Carolina State University Department of Molecular and Structural Biochemistry Raleigh, North Carolina, USA
Foundation-model-guided radiogenomic discovery linking cancer genomes to cancer scans
Jul 22, 2026Frederik Hauke, Jeremias Krause, Patrick Wienholt +6Radiomics Genome-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
Deep and Probabilistic Models for Gene Regulatory Network Inference
Jul 17, 2026Claudia Skok GibbsRegulatory Networks Genome-Wide Association Study
Center for Data Science New York University
NVAITC AI Scientist: A Governed End-to-End Research System -- A Hypertension GWAS Case Study
Jul 13, 2026Eddie Huang, Ken Liao, Iven Fu +14Scientific Workflows Artificial Intelligence Scientists
NVIDIA AI Technology Center, NVIDIA Corporation · NVIDIA AI Technology Center (NVAITC), NVIDIA Corporation · Department of Medical Research, China Medical University Hospital, Taichung, Taiwan +12
The Regularization Parameter: Sparse Precision Matrix Estimation
Jul 7, 2026Aryan Eftekhari, Daniel Sergio Vega, Ernst-Jan Camiel Wit +1Maximum Likelihood Regularization
Institute of Computing, Faculty of Informatics, Universit`a della Svizzera italiana (USI), Lugano, Switzerland
SHIFT: Survival Prediction from Incomplete and Heterogeneous Genomic Data
Jul 4, 2026Muhammet Sami Yavuz, Ayhan Can Erdur, Sabri Mustafa Kahya +2Survival Predictions Genome-Wide Association Study
AI for Image-Guided Diagnosis and Therapy, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany · Munich Center for Machine Learning (MCML) · Department of Radiation Oncology, TUM University Hospital +4
EVOTS: Evolutionary Transformer Search for Time Series Forecasting
Jun 30, 2026AbdElRahman ElSaid, Damir PulatovTime Series Forecasting Autoregressive Transformers
University of North Carolina Wilmington Wilmington, North Carolina, USA
When to Truncate a Feature Ranking: A Residual-Overlap Stopping Rule for Subset Selection
Jun 30, 2026Jesus S. Aguilar-RuizFeature Selection False Discovery Rate
School of Engineering Pablo de Olavide University ES-41013 Seville, Spain
KG-TRACE: A Neuro-Symbolic Framework for Mechanistic Grounding in Antimicrobial Resistance Prediction
Jun 24, 2026Naman Garg, Sarika Jain, Sourav Yadav +4Genome-Wide Association Study Clinical Prediction
National Institute of Technology Kurukshetra, Kurukshetra, India · Indian Institute of Information Technology Manipur, Manipur, India · Purdue University, West Lafayette, IN, USA +1
Evolutional Math: Cross-Validated Island-Model Genetic Programming for Interpretable Symbolic Regression on Small, Wide Datasets
Jun 20, 2026Artem AndrianovSymbolic Regression Genetic Algorithms
Cyntegrity Germany GmbH, Hofheim am Taunus, Germany · Independent Researcher, Muensterer Str. 49, 65719 Hofheim am Taunus, Germany
A Bayesian Boolean Matrix Factorization with Application to Copy Number Analysis in Cancer
Jun 16, 2026Adolphus Wagala, Mehmet Samur, Giovanni ParmigianiRestricted Bernoulli Matrix Factorization Genome-Wide Association Study
Department of Data Science, Dana-Farber Cancer Institute · Department of Biostatistics, Harvard T.H. Chan School of Public Health
Is It You or Your Environment? A Bayesian Inference Framework for Genomically-Anchored Personalized Physiological Interpretation
Jun 11, 2026Aruna Dey, Suraj BiswasPhysiological Data Genome-Wide Association Study
Dots-In
From Genes to Tokens: a GWAS-inspired Approach for Interpretable Stylometric Analysis
Jun 8, 2026Dmitry Pronin, Evgeny KazartsevStylometric Authorship
HSE University
The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models
Jun 5, 2026Chahat Baranwal, Aaditya Baranwal, Lakshya Nitin TandonGenome-Wide Association Study Transcriptomics
IIT Jodhpur · University of Central Florida · Northeastern University
$p$ -adic Bi-Filtrations for Topological Machine Learning on Genomic Sequences
Jun 4, 2026Tirtharaj Dash, Gunja SachdevaGenome-Wide Association Study Topological Learning
Department of CS & IS, BITS Pilani, K K Birla Goa Campus, Zuarinagar, Goa 403726, India. · Department of Mathematics, BITS Pilani, K K Birla Goa Campus, Zuarinagar, Goa 403726, India.
LDARNet: DNA Adaptive Representation Network with Learnable Tokenization for Genomic Modeling
Jun 3, 2026Daria Ledneva, Denis KuznetsovGenome-Wide Association Study Deep Learning Architectures
Moscow Independent Research Institute of Artificial Intelligence, Moscow, Russia.
GENEB: Why Genomic Models Are Hard to Compare
Jun 3, 2026Daria Ledneva, Mikhail Nuridinov, Denis KuznetsovGenome-Wide Association Study Model Evaluation
Moscow Independent Research Institute of Artificial Intelligence, Moscow, Russia · Moscow State Institute of Steel and Alloys, Moscow, Russia
A Robust Optimization Approach to Sparse Principal Component Analysis
Jun 2, 2026David Vävinggren, Francis Bach, André M. H. Teixeira +2Principal Component Analysis Sparsity
Uppsala University, Sweden · PSL Research University / INRIA, France · Science for Life Laboratory, Sweden
Annotation-Informed Block-Sparse Bayesian Modeling for cis-Expression Prediction
May 30, 2026Lei Huang, Hui Shen, Kuan-Jui Su +9Genome-Wide Association Study Generalized Linear Model
School of Computing Sciences and Computer Engineering, University of Southern Mississippi, Hattiesburg, MS, USA · Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA · Texas Tech University Health Sciences Center, School of Medicine, Texas Tech University
Agentic Authoring of Interactive Multiview Visualizations in Genomics
May 29, 2026Astrid van den Brandt, Kiroong Choe, Sehi L'Yi +2Visual Analytics Genome-Wide Association Study
Harvard Medical School · Boston College
Cluster Analysis with Resampling for Validation and Exploration (CARVE)
May 29, 2026Kai R. Wycik, Tiffany M. Tang, Tarek M. Zikry +1Clustering Cluster
Department of Statistics, Columbia University, New York, NY, USA · Center for Theoretical Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA · Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, USA +2
Effective Biological Representation Learning by Masking Gene Expression
May 29, 2026Kian Kenyon-Dean, Alina Selega, Ihab Bendidi +5Transcriptomics Genome-Wide Association Study
Recursion · Valence Labs · École Normale Supérieure PSL
Position: Genomic Model Research Must Move Beyond Anecdotal Evaluation of Interpretability Methods
May 29, 2026Shasha Zhou, Mingyu Huang, Ke LiGenome-Wide Association Study Interpretability
Department of Computer Science, University of Exeter, Exeter, UK.
AnnotateMissense: a genome-wide annotation and benchmarking framework for missense pathogenicity prediction
May 23, 2026Muhammad Muneeb, David B. AscherGenome-Wide Association Study Clinical Prediction
School of Chemistry and Molecular Biology, The University of Queensland, Queen Street, 4067, Queensland, Australia · 2Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Commercial Road, 3004, Victoria, Australia
TaxDistill: Improving Metagenomic Taxonomic Annotation via Distilled Genomic Foundation Models
May 22, 2026Rongye Ye, Lun Li, Zheng Luo +3Bacterial Colony Counting Genome-Wide Association Study
National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China · Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China · University of Chinese Academy of Sciences, Beijing 100049, China +1
$\textit{BlockFormer}$ : Transformer-based inference from genomic contact maps
May 20, 2026Eloïse Touron, Pedro L. C. Rodrigues, Julyan Arbel +2Genome-Wide Association Study Flow Map
Univ. Grenoble Alpes, Inria CNRS, Grenoble INP, LJK, France · TIMC, Univ. Grenoble Alpes CNRS, Grenoble INP, France
HDMoE: A Hierarchical Decoupling-Fusion Mixture-of-Experts Framework for Multimodal Cancer Survival Prediction
May 20, 2026Huayi Wang, Haochao Ying, Yuyang Xu +5Multimodal Clinical Data Genome-Wide Association Study
Zhejiang University Hangzhou, China · Xinjiang University Urumqi, China · Hangzhou City University Hangzhou, China +1
AgentCo-op: Retrieval-Based Synthesis of Interoperable Multi-Agent Workflows
May 19, 2026Shuaike Shen, Wenduo Cheng, Shike Wang +2Multi-Agent Workflows Scientific Agents
1Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University · 2Machine Learning Department, School of Computer Science, Carnegie Mellon University
AttnGen: Attention-Guided Saliency Learning for Interpretable Genomic Sequence Classification
May 13, 2026Rayhaneh Shabani Nia, Ali KarkehabadiGenome-Wide Association Study Attention-Guided Training
University of California, Davis California, USA
Texture Regenerating and Grafting Using Genome-Driven Neural Cellular Automata
May 13, 2026Mirela-Magdalena Catrina, Ioana Cristina Plajer, Alexandra BăicoianuNeural Cellular Automata Texture
Transilvania University of Brașov, Faculty of Mathematics and Informatics 29 Eroilor, 500036, Brașov, Romania
Bridging Sequence and Graph Structure for Epigenetic Age Prediction
May 11, 2026Yao Li, Xikun Zhang, Xiaotao Shen +4Vascular Age Genome-Wide Association Study
School of Computing and Information Systems The University of Melbourne · School of Computing Technologies RMIT University · Lee Kong Chian School of Medicine Nanyang Technological University Singapore +1
MicroFuse: Protein-to-Genome Expert Fusion for Microbial Operon Reasoning
May 9, 2026Seungik ChoBacterial Colony Counting Genome-Wide Association Study
Department of Physics and Astronomy, Rice University, Texas, USA.
Learning Multi-Relational Graph Representations for DNA Methylation-Based Biological Age Estimation
May 8, 2026Qing Qing, Xikun Zhang, Zhongyuan Zhang +7Vascular Age Genome-Wide Association Study
Jilin University · RMIT University · The Chinese University of Hong Kong +1
Wisteria: A Unified Multi-Scale Feature Learning Framework for DNA Language Model
May 7, 2026Weihua Wang, Haoji Li, Feilong Bao +2Genome-Wide Association Study Sequence Modeling
College of Computer Science, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China · National and Local Joint Engineering Research Center of Intelligent Information Processing Technology for Mongolian, Hohhot, Inner Mongolia, 010021, China · Inner Mongolia Key Laboratory of Multilingual Artificial Intelligence Technology, Hohhot, Inner Mongolia, 010021, China +1
Simple Self-Conditioning Adaptation for Masked Diffusion Models
Apr 28, 2026Michael Cardei, Huu Binh Ta, Ferdinando FiorettoMasked Diffusion Language Models Diffusion Models
University of Virginia
Mining Negative Sequential Patterns to Improve Viral Genomic Feature Representation and Classification
Apr 28, 2026Wenxi Zhu, Wensheng Gan, Zhenlian QiSirus Genome-Wide Association Study
College of Information Science and Technology, Jinan University, Guangzhou 510632, China · College of Cyber Security, Jinan University, Guangzhou 510632, China · Guangdong Eco-Engineering Polytechnic, Guangzhou 510520, China
StackFeat RL: Reinforcement Learning over Iterative Dual Criterion Feature Selection for Stable Biomarker Discovery
Apr 24, 2026A. Yermekov, D. A. Herrera-MartíFeature Selection Genome-Wide Association Study
PAfoS.AI, Almaty, Kazakhstan · CEA List, Université Grenoble Alpes, France
Evaluating Post-hoc Explanations of the Transformer-based Genome Language Model DNABERT-2
Apr 23, 2026Isabel Kurth, Paulo Yanez Sarmiento, Bernhard Y. RenardGenome-Wide Association Study Explainable AI Methods
Hasso Plattner Institute University of Potsdam
Multimodal Feature Prototype Learning for Interpretable and Discriminative Cancer Survival Prediction
Oct 7, 2025Shuo Jiang, Zhuwen Chen, Liaoman Xu +6Survival Predictions Learnable Prototypes
Hangzhou Dianzi University, Hangzhou 310018, China · School of Information and Communication Technology, Griffith University, QLD 4215, Australia · Shenzhen Research Institute of Big Data, Shenzhen 518172, China +3
Stacked SVD or SVD stacked? A Random Matrix Theory perspective on data integration
Jul 29, 2025Tavor Z. Baharav, Phillip B. Nicol, Rafael A. Irizarry +1Singular Value Decomposition Low-Rank Structure
Eric and Wendy Schmidt Center, Broad Institute, Cambridge, MA, 02142, USA · Department of Data Science, Dana Farber Cancer Institute, Boston, MA, 02115, USA · Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics
Jun 2, 2025Ella Rannon, David BursteinGenome-Wide Association Study Transcriptomics
The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel

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Surface-volume self-supervised representation learning of brain MRI for genetic discovery

Tian Xia, Nuo Chen, Zihao Zhu, Huiwen Han+3

D. Bradley McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, US. · Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, US. · Department of Electrical and Computer Engineering, Texas A&M University, College Station, US.+1

Functional Magnetic Resonance Imaging Genome-Wide Association Study Self-Supervised Representations Representation Learning Bioinformatics

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Existing genome-wide association studies (GWAS) of brain imaging provide predefined or deep-learning-derived imaging phenotypes, yet these phenotypes come from either volumetric scans or cortical surface meshes, so each captures only part of the heritable variation in brain anatomy. Here we introduce MEVA (Mesh-Enhanced Volumetric Autoencoder), a self-supervised framework that encodes voxel-level image intensity together with cortical mesh geometry, including curvature and cortical thickness at each surface vertex, into one shared set of imaging features. Combining the mesh and volumetric inputs in MEVA yields modest performance gains in age and sex prediction over models that use either input alone. When these features serve as phenotypes for GWAS in the UK Biobank, they reveal more genome-wide significant loci than features learned from volumes alone or from meshes alone. These results suggest that adding cortical surface geometry to volumetric self-supervised learning captures additional heritable variation and so increases the number of loci detected.

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