Traditional statistical approaches have advanced our understanding of the genetics of complex diseases, yet are limited to linear additive models. Here we applied machine learning (ML) to genome-wide data from 41,686 individuals in the largest European consortium on Alzheimer's disease (AD) to investigate the effectiveness of various ML algorithms in replicating known findings, discovering novel loci, and predicting individuals at risk. We utilised Gradient Boosting Machines (GBMs), biological pathway-informed Neural Networks (NNs), and Model-based Multifactor Dimensionality Reduction (MB-MDR) models. ML approaches successfully captured all genome-wide significant genetic variants identified in the training set and 22% of associations from larger meta-analyses. They highlight 6 novel loci which replicate in an external dataset, including variants which map to ARHGAP25, LY6H, COG7, SOD1 and ZNF597. They further identify novel association in AP4E1, refining the genetic landscape of the known SPPL2A locus. Our results demonstrate that machine learning methods can achieve predictive performance comparable to classical approaches in genetic epidemiology and have the potential to uncover novel loci that remain undetected by traditional GWAS. These insights provide a complementary avenue for advancing the understanding of AD genetics.

1st Department of Neurology Aiginition Hospital National and Kapodistrian University of Athens Medical School Athens Greece

1st Department of Neurology Medical school Aristotle University of Thessaloniki Thessaloniki Makedonia Greece

ACE Alzheimer Center Barcelona Universitat Internacional de Catalunya Barcelona Spain

Aging Research Center Department of Neurobiology Care Sciences and Society Karolinska Institutet and Stockholm University Stockholm Sweden

Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam The Netherlands

Alzheimer Research Center and Memory Clinic Andalusian Institute for Neuroscience Málaga Spain

Alzheimer's Centre Reina Sofia CIEN Foundation ISCIII 28031 Madrid Spain

Alzheimer's Disease and Other Cognitive Disorders Unit Neurology Service Hospital Clínic of Barcelona Fundació Recerca Clinic Barcelona Institut d'Investigacions Biomèdiques August Pi i Sunyer and University of Barcelona Barcelona Spain

Alzheimer's disease and other cognitive disorders unit Service of Neurology Hospital Clínic of Barcelona Institut d'Investigacions Biomèdiques August Pi i Sunyer University of Barcelona Barcelona Spain

Biggs Institute for Alzheimer's and Neurodegenerative Diseases University of Texas Health Science Center San Antonio Texas USA

BIO3 Systems Genetics GIGA R Molecular and Computational Biology University of Liege Liege Belgium

BIO3 Systems Medicine Department of Human Genetics KU Leuven Leuven Belgium

Center for Cognitive Disorders Department of Psychiatry and Psychotherapy Technical University of Munich School of Medicine and Health Klinikum rechts der Isar Munich Germany

Centre for Artificial Intelligence in Precision Medicine University of Oxford Oxford United Kingdom

Centre for Memory Disturbances Lab of Clinical Neurochemistry Section of Neurology University of Perugia Perugia Italy

Centre for Neuropsychiatric Genetics and Genomics Division of Psychological Medicine and Clinical Neuroscience School of Medicine Cardiff University Cardiff UK

Centro de Biología Molecular Severo Ochoa Madrid Spain

Charité Universitätsmedizin Berlin corporate member of Freie Universität Berlin Humboldt Universität zu Berlin and Berlin Institute of Health Institute of Psychiatry and Psychotherapy Hindenburgdamm 30 12203 Berlin Germany

CHU de Bordeaux Pole santé publique Bordeaux France

CHUV Old Age Psychiatry Department of Psychiatry Lausanne Switzerland

CIBERNED Network Center for Biomedical Research in Neurodegenerative Diseases National Institute of Health Carlos 3 Madrid Spain

Clinic of Neurology UH Alexandrovska Medical University Sofia Sofia Bulgaria

Cluster of Excellence Cellular Stress Responses in Aging associated Diseases University of Cologne Cologne Germany

Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Disease University of Cologne Cologne Germany

Complex Genetics of Alzheimer's Disease Group VIB Center for Molecular Neurology VIB Antwerp Belgium

Department of Biomedical Sciences Section of Neuroscience and Clinical Pharmacology University of Cagliari Cagliari Italy

Department of Biomedical Sciences University of Antwerp Antwerp Belgium

Department of Child and Adolescent Psychiatry and Psychotherapy University Hospital of Psychiatry Zurich University of Zurich Zurich Switzerland

Department of Clinical and Experimental Sciences University of Brescia Brescia Italy

Department of Clinical Biochemistry Copenhagen University Hospital Rigshospitalet Copenhagen Denmark

Department of Clinical Genetics VU University Medical Centre Amsterdam The Netherlands

Department of Clinical Medicine University of Copenhagen Copenhagen Denmark

Department of Clinical Sciences and Community Health University of Milan 20122 Milan Italy

Department of Cognitive Disorders and Old Age Psychiatry University Hospital Bonn Medical Faculty Bonn Germany

Department of Cognitive Disorders and Old Age Psychiatry University Hospital Bonn Venusberg Campus 1 53127 Bonn Germany

Department of Complex Trait Genetics Center for Neurogenomics and Cognitive Research Amsterdam Neuroscience Vrije University Amsterdam The Netherlands

Department of Epidemiology Erasmus MC Rotterdam The Netherlands

Department of Epidemiology ErasmusMC Rotterdam The Netherlands

Department of Geriatric Psychiatry Central Institute for Mental Health Mannheim Faculty Mannheim University of Heidelberg Heidelberg Germany

Department of Geriatric Psychiatry University Hospital of Psychiatry Zürich Zürich Switzerland

Department of Hematology and Stem Cell Transplant Vito Fazzi Hospital Lecce Italy

Department of Medicine and Surgery Unit of Neurology University Hospital of Parma Parma Italy

Department of Neurology Bordeaux University Hospital Bordeaux France

Department of Neurology ErasmusMC Rotterdam Netherlands

Department of Neurology Hospital Universitario Donostia San Sebastian Spain

Department of Neurology Medical University Sofia Sofia Bulgaria

Department of Neuroscience Psychology Drug Research and Child Health University of Florence Florence Italy

Department of Neuroscience Rita Levi Montalcini University of Torino Torino Italy

Department of Neuroscience Università Cattolica del Sacro Cuore Rome Italy

Department of Psychiatry and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases San Antonio TX USA

Department of Psychiatry and Psychotherapy Comprehensive Center for Clinical Neurosciences and Mental Health Medical University of Vienna Vienna Austria

Department of Psychiatry and Psychotherapy Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany

Department of Psychiatry and Psychotherapy LVR Klinikum Essen University of Duisburg Essen Germany Medical Faculty Essen Germany

Department of Psychiatry and Psychotherapy University Medical Center Goettingen Goettingen Germany

Department of Psychiatry Psychosomatics and Psychotherapy Center of Mental Health University Hospital of Würzburg Würzburg Germany

Department of Radiology and Nuclear Medicine Erasmus MC Rotterdam The Netherlands

Depatamento de Especialidades Quirúrgicas Bioquímica e Inmunología Facultad de Medicina Universidad de Málaga Málaga Spain

Dept of Biomedical Surgical and Dental Sciences University of Milan Milan IT Italy

Dept of Public Health and Caring Sciences Geriatrics Uppsala University Uppsala Sweden

Dept of Public Health and Carins Sciences Geriatrics Uppsala University Uppsala Sweden

Division of Clinical Geriatrics Department of Neurobiology Care Sciences and Society Karolinska Institutet Stockholm Sweden

Division of Neurogenetics and Molecular Psychiatry Department of Psychiatry and Psychotherapy Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany

Estudios en Neurociencias y Sistemas Complejos CONICET HEC UNAJ Buenos Aires Argentina

Faculty of Medicine University of Lisbon Lisbon Portugal

Fundació Docència i Recerca MútuaTerrassa Terrassa Barcelona Spain

Geriatric Unit Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico 20122 Milan Italy

German Center for Neurodegenerative Diseases Berlin Germany

German Center for Neurodegenerative Diseases Bonn Germany

German Center for Neurodegenerative Diseases Goettingen Germany

German Center for Neurodegenerative Diseases Magdeburg Germany

German Center for Neurodegenerative Diseases Munich Germany

Inserm Bordeaux Population Health Research Center UMR 1219 Univ Bordeaux ISPED CIC 1401 EC Univ Bordeaux Bordeaux France

Institut de Recerca Biomedica de Lleida Lleida Spain

Institute for Stroke and Dementia Research University Hospital LMU Munich Munich Germany

Institute for Urban Public Health University Hospital of University Duisburg Essen Essen Germany

Institute of Biomedicine University of Eastern Finland Kuopio Finland

Institute of Clinical Medicine Neurology University of Eastern Finland Kuopio Finland

Institute of Clinical Medicine University of Oslo Oslo Norway

Institute of Cognitive Neurology and Dementia Research Otto von Guericke University Magdeburg Germany

Institute of Gerontology and Geriatrics Department of Medicine and Surgery University of Perugia Perugia Italy

Institute of Human Genetics University of Bonn School of Medicine and University Hospital Bonn Bonn Germany

Institute of Neurology Catholic University of the Sacred Heart Rome Italy

Institute of Social Medicine Occupational Health and Public Health University of Leipzig 04103 Leipzig Germany

Instituto de Investigacion Sanitaria 'Hospital la Paz' Madrid Spain

Instituto de Investigación Sanitaria del Principado de Asturias Asturias Spain

Interdisciplinary Department of Medicine Geriatric Medicine and Memory Unit University of Bari A Moro Bari Italy

International Clinical Research Center St Anne's University Hospital Brno Brno Czech Republic

IRCCS Fondazione Don Carlo Gnocchi Florence Italy

Krembil Brain Institute University Health Network Toronto Ontario Canada

Laboratorio de Genética Hospital Universitario Central de Asturias Oviedo Spain

Laboratory of Genetics Immunology and Human Pathology Faculty of Science of Tunis University of Tunis El Manar 2092 Tunis Tunisia

Laboratory of Neuropsychiatry IRCCS Santa Lucia Foundation Rome Italy

Maastricht University Department of Psychiatry and Neuropsychologie Alzheimer Center Limburg Maastricht the Netherlands

Medical Science Department iBiMED Aveiro Portugal

Memory Clinic Department of Neurology Charles University 2nd Faculty of Medicine and Motol University Hospital Praha Czech Republic

Memory Disorders Unit Department of Neurology Hospital Universitari Mutua de Terrassa Terrassa Barcelona Spain

Molecular Markers Laboratory IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy

Munich Cluster for Systems Neurology Munich Germany

Networking Research Center on Neurodegenerative Diseases Instituto de Salud Carlos 3 Madrid Spain

Neurodegenerative Diseases Unit Fondazione IRCCS Ca' Granda Ospedale Policlinico Milan IT Italy

Neurological Tissue Bank Biobank Hospital Clinic FRCB IDIBAPS Barcelona Spain

Neurology Service Marqués de Valdecilla University Hospital Santander Spain

Neurology Unit IRCCS Fondazione Policlinico Universitario A Gemelli Rome Italy

Neurology Unit San Gerardo hospital Monza and University of Milano Bicocca Milan Italy

Neuroscience Center Zurich University of Zurich and ETH Zurich Zurich Switzerland

Neurosciences Area Instituto Biogipuzkoa San Sebastian Spain

NORMENT Centre Division of Mental Health and Addiction Oslo University Hospital Oslo Norway

Nuffield Department of Population Health University of Oxford Oxford United Kingdom

Old Age Psychiatry Department of Psychiatry Lausanne University Hospital Lausanne Switzerland

Research Center and Memory clinic ACE Alzheimer Center Barcelona Universitat Internacional de Catalunya Barcelona Spain

Research Center and Memory Clinic ACE Alzheimer Center Barcelona Universitat Internacional de Catalunya Catalunya Spain

Research Center and Memory clinic Fundació ACE Institut Català de Neurociències Aplicades Universitat Internacional de Catalunya Barcelona Spain

Sant Pau Memory Unit Institut de Recerca Sant Pau Department of Neurology Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona Barcelona Spain

School of Medicine Cardiff University Cardiff UK

Tanz Centre for Research in Neurodegenerative Diseases Departments of Medicine and Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada

Taub Institute for Research in Alzheimer's Disease and the Aging Brain The Gertrude H Sergievsky Center Depatment of Neurology Columbia University New York NY USA

Translational Health Sciences Bristol Medical School University of Bristol Bristol UK

Unidad Clínica de Enfermedades Infecciosas y Microbiología Hospital Universitario de Valme Sevilla Spain

Unidad de Trastornos del Movimiento Servicio de Neurología y Neurofisiología Instituto de Biomedicina de Sevilla Hospital Universitario Virgen del Rocío CSIC Universidad de Sevilla Seville Spain

Unit for Hereditary Dementias Theme Aging Karolinska University Hospital Solna 171 64 Stockholm Sweden

Unit of Neurology 5 Neuropathology Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy

Unitat de Genètica Molecular Institut de Biomedicina de València CSIC Valencia Spain

Unitat Trastorns Cognitius Hospital Universitari Santa Maria de Lleida Lleida Spain

Univ Lille Inserm 1171 CHU Clinical and Research Memory Research Centre of Distalz Lille France Lille France

Univ Lille Inserm CHU Lille Institut Pasteur de Lille LabEx DISTALZ U1167 RID AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement Lille France

Univ Rouen Normandie Normandie Univ Inserm U1245 and CHU Rouen Department of Genetics and CNRMAJ F 76000 Rouen France

Universidad Autónoma de Madrid Madrid Spain

Université de Paris EA 4468 APHP Hôpital Broca Paris France

Université Paris Saclay CEA Centre National de Recherche en Génomique Humaine 91057 Evry France

University Bordeaux Inserm Bordeaux Population Health Research Center Bordeaux France

Zurich Center for Integrative Human Physiology University of Zurich Zurich Switzerland

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Machine learning in Alzheimer's disease genetics