Multi-site benchmark classification of major depressive disorder using machine learning on cortical and subcortical measures
Scientific Reports, vol. 14, pp. 1084
Abstract
Machine learning (ML) techniques have gained popularity in the neuroimaging field due to their potential for classifying neuropsychiatric disorders. However, the diagnostic predictive power of the existing algorithms has been limited by small sample sizes, lack of representativeness, data leakage, and/or overfitting. Here, we overcome these limitations with the largest multi-site sample size to date (N = 5365) to provide a generalizable ML classification benchmark of major depressive disorder (MDD) using shallow linear and non-linear models. Leveraging brain measures from standardized ENIGMA analysis pipelines in FreeSurfer, we were able to classify MDD versus healthy controls (HC) with a balanced accuracy of around 62%. But after harmonizing the data, e.g., using ComBat, the balanced accuracy dropped to approximately 52%. Accuracy results close to random chance levels were also observed in stratified groups according to age of onset, antidepressant use, number of episodes and sex. Future studies incorporating higher dimensional brain imaging/phenotype features, and/or using more advanced machine and deep learning methods may yield more encouraging prospects.
Authors 64
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Universitätsmedizin Göttingen · University of Göttingen
Affiliation as printed
Laboratory of Systems Neuroscience and Imaging in Psychiatry (SNIP-Lab), Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August University, Von-Siebold-Str. 5, 37075, Göttingen, Germany
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Leiden University · Amsterdam Neuroscience · Amsterdam Public Health · Amsterdam University Medical Centers · Vrije Universiteit Amsterdam
Affiliation as printed
Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
Institute of Education and Child Studies, Section Forensic Family and Youth Care, Leiden University, Leiden, The Netherlands
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University Medical Center Groningen · University of Groningen
Affiliation as printed
Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Affiliation as printed
Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
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Affiliation as printed
Department of Psychiatry and Behavioral Science, University of Minnesota Medical School, Minneapolis, MN, USA
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Affiliation as printed
Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Affiliation as printed
Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany
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Universitätsmedizin Greifswald · Universität Greifswald
Affiliation as printed
Institute for Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
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University of Southern California
Affiliation as printed
Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
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Affiliation as printed
Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
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Affiliation as printed
Department of Psychiatry and Behavioral Science, University of Minnesota Medical School, Minneapolis, MN, USA
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Affiliation as printed
Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, VIC, Australia
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City, University of London · King's College London
Affiliation as printed
Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
Department of Psychology, School of Arts and Social Sciences, City, University of London, London, UK
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Amsterdam Neuroscience · Amsterdam Public Health · Amsterdam University Medical Centers · Vrije Universiteit Amsterdam
Affiliation as printed
Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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National Institutes of Health · National Institute of Mental Health
Affiliation as printed
Experimental Therapeutics and Pathophysiology Branch, National Institute for Mental Health, National Institutes of Health, Bethesda, MD, USA
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University of East London · King's College London
Affiliation as printed
Centre for Affective Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
School of Psychology, University of East London, London, UK
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Affiliation as printed
SoCAT Lab, Department of Psychiatry, School of Medicine, Ege University, Izmir, Turkey
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Affiliation as printed
Department of Psychology, Stanford University, Stanford, CA, USA
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Universitätsmedizin Greifswald · Universität Greifswald
Affiliation as printed
Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
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Affiliation as printed
Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
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Affiliation as printed
Center for Medical Imaging and Visualization, Linköping University, Linköping, Sweden
Center for Social and Affective Neuroscience, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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Affiliation as printed
Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, VIC, Australia
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University of California, Los Angeles · University of California, San Francisco
Affiliation as printed
Department of Psychiatry and Behavioral Sciences, Division of Child and Adolescent Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
Department of Psychology, University of California, Los Angeles, Los Angeles, CA, USA
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The University of Texas Health Science Center at Houston
Affiliation as printed
Center Of Excellence On Mood Disorders, Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences at McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
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Affiliation as printed
Department of Psychiatry, McGill University, Montreal, QC, Canada
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University of Southern California
Affiliation as printed
Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
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Affiliation as printed
Department of Psychology, University of Minnesota, Minneapolis, MN, USA
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Affiliation as printed
Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
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Affiliation as printed
Cardiff University Brain Research Imaging Center, Cardiff University, Cardiff, UK
MRC Center for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
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Affiliation as printed
Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany
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Maastricht University · Cardiff University
Affiliation as printed
Cardiff University Brain Research Imaging Center, Cardiff University, Cardiff, UK
Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
MRC Center for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
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Affiliation as printed
Departments of Psychiatry and Pediatrics, University of Calgary, Calgary, AB, Canada
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Cardiff University · RWTH Aachen University
Affiliation as printed
Cardiff University Brain Research Imaging Center, Cardiff University, Cardiff, UK
Department of Psychiatry, Psychotherapy and Psychosomatics, Medical School, RWTH Aachen University, Aachen, Germany
MRC Center for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
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Affiliation as printed
Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Affiliation as printed
Department of Psychiatry and Behavioral Science, University of Minnesota Medical School, Minneapolis, MN, USA
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University of Pittsburgh · Center for the Neural Basis of Cognition
Affiliation as printed
Center for Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA
Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
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Amsterdam Neuroscience · Amsterdam Public Health · Amsterdam University Medical Centers · Vrije Universiteit Amsterdam
Affiliation as printed
Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Amsterdam Neuroscience · Amsterdam Public Health · Amsterdam University Medical Centers · Vrije Universiteit Amsterdam
Affiliation as printed
Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Affiliation as printed
Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Centro de Investigación Biomédica en Red de Salud Mental · Fidmag Sisters Hospitallers
Affiliation as printed
FIDMAG Germanes Hospitalàries Research Foundation, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Barcelona, Catalonia, Spain
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Hospital de Sant Pau · Institut de Recerca Sant Pau
Affiliation as printed
Sant Pau Mental Health Research Group, Institut de Recerca de L'Hospital de La Santa Creu I Sant Pau, Barcelona, Catalonia, Spain
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The University of Melbourne · Orygen
Affiliation as printed
Centre for Youth Mental Health, The University of Melbourne, Parkville, VIC, Australia
Orygen, Parkville, VIC, Australia
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Amsterdam University Medical Centers
Affiliation as printed
Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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Harvard University · Massachusetts General Hospital
Affiliation as printed
Meditation Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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Max Planck Institute of Psychiatry
Affiliation as printed
Max Planck Institute of Psychiatry, Munich, Germany
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Amsterdam University Medical Centers
Affiliation as printed
Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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National University of Singapore · Nanyang Technological University · Institute of Mental Health
Affiliation as printed
Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
West Region, Institute of Mental Health, Singapore, Singapore
Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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The University of Texas Health Science Center at Houston
Affiliation as printed
Center Of Excellence On Mood Disorders, Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences at McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
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Affiliation as printed
SA MRC Research Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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University of Southern California
Affiliation as printed
Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
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Affiliation as printed
SoCAT Lab, Department of Psychiatry, School of Medicine, Ege University, Izmir, Turkey
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Leiden University Medical Center
Affiliation as printed
Leiden Institute for Brain and Cognition, Leiden University Medical Center, Leiden, The Netherlands
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Steven J.A. van der Werff Aachen Department of Psychiatry, Leiden University Medical Center Leiden Institute for Brain and Cognition
Leiden University Medical Center
Affiliation as printed
Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
Leiden Institute for Brain and Cognition, Leiden University Medical Center, Leiden, The Netherlands
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Universitätsmedizin Greifswald · Universität Greifswald
Affiliation as printed
Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
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The University of Melbourne · Melbourne Health
Affiliation as printed
Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Melbourne, VIC, Australia
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Universitätsmedizin Greifswald · German Center for Neurodegenerative Diseases · Universität Greifswald
Affiliation as printed
Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
German Center for Neurodegenerative Diseases (DZNE), Site Rostock/ Greifswald, Greifswald, Germany
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Affiliation as printed
Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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The University of Texas Health Science Center at Houston
Affiliation as printed
Center Of Excellence On Mood Disorders, Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences at McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
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University of California, San Francisco
Affiliation as printed
Department of Psychiatry and Behavioral Sciences, Division of Child and Adolescent Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
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National Institutes of Health · National Institute of Mental Health
Affiliation as printed
Section on the Neurobiology and Treatment of Mood Disorders, National Institute of Mental Health, Bethesda, MD, USA
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Amsterdam Neuroscience · Amsterdam Public Health · Amsterdam University Medical Centers · Vrije Universiteit Amsterdam
Affiliation as printed
Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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The University of Melbourne · Orygen
Affiliation as printed
Centre for Youth Mental Health, The University of Melbourne, Parkville, VIC, Australia
Orygen, Parkville, VIC, Australia
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University of Southern California
Affiliation as printed
Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
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Roberto Goya‐Maldonado corresponding
Universitätsmedizin Göttingen · University of Göttingen
Affiliation as printed
Laboratory of Systems Neuroscience and Imaging in Psychiatry (SNIP-Lab), Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August University, Von-Siebold-Str. 5, 37075, Göttingen, Germany. roberto.goya@med.uni-goettingen.de
Laboratory of Systems Neuroscience and Imaging in Psychiatry (SNIP-Lab), Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August University, Von-Siebold-Str. 5, 37075, Göttingen, Germany
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