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Zhu X, Kim Y, Ravid O, He X, Suarez-Jimenez B, Zilcha-Mano S, Lazarov A, Lee S, Abdallah CG, Angstadt M, Averill CL, Baird CL, Baugh LA, Blackford JU, Bomyea J, Bruce SE, Bryant RA, Cao Z, Choi K, Cisler J, Cotton AS, Daniels JK, Davenport ND, Davidson RJ, DeBellis MD, Dennis EL, Densmore M, deRoon-Cassini T, Disner SG, Hage WE, Etkin A, Fani N, Fercho KA, Fitzgerald J, Forster GL, Frijling JL, Geuze E, Gonenc A, Gordon EM, Gruber S, Grupe DW, Guenette JP, Haswell CC, Herringa RJ, Herzog J, Hofmann DB, Hosseini B, Hudson AR, Huggins AA, Ipser JC, Jahanshad N, Jia-Richards M, Jovanovic T, Kaufman ML, Kennis M, King A, Kinzel P, Koch SBJ, Koerte IK, Koopowitz SM, Korgaonkar MS, Krystal JH, Lanius R, Larson CL, Lebois LAM, Li G, Liberzon I, Lu GM, Luo Y, Magnotta VA, Manthey A, Maron-Katz A, May G, McLaughlin K, Mueller SC, Nawijn L, Nelson SM, Neufeld RWJ, Nitschke JB, O'Leary EM, Olatunji BO, Olff M, Peverill M, Phan KL, Qi R, Quidé Y, Rektor I, Ressler K, Riha P, Ross M, Rosso IM, Salminen LE, Sambrook K, Schmahl C, Shenton ME, Sheridan M, Shih C, Sicorello M, Sierk A, Simmons AN, Simons RM, Simons JS, Sponheim SR, Stein MB, Stein DJ, Stevens JS, Straube T, Sun D, Théberge J, Thompson PM, Thomopoulos SI, van der Wee NJA, van der Werff SJA, van Erp TGM, van Rooij SJH, van Zuiden M, Varkevisser T, Veltman DJ, Vermeiren RRJM, Walter H, Wang L, Wang X, Weis C, Winternitz S, Xie H, Zhu Y, Wall M, Neria Y, Morey RA. Neuroimaging-based classification of PTSD using data-driven computational approaches: A multisite big data study from the ENIGMA-PGC PTSD consortium. Neuroimage 2023; 283:120412. [PMID: 37858907 PMCID: PMC10842116 DOI: 10.1016/j.neuroimage.2023.120412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/10/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Recent advances in data-driven computational approaches have been helpful in devising tools to objectively diagnose psychiatric disorders. However, current machine learning studies limited to small homogeneous samples, different methodologies, and different imaging collection protocols, limit the ability to directly compare and generalize their results. Here we aimed to classify individuals with PTSD versus controls and assess the generalizability using a large heterogeneous brain datasets from the ENIGMA-PGC PTSD Working group. METHODS We analyzed brain MRI data from 3,477 structural-MRI; 2,495 resting state-fMRI; and 1,952 diffusion-MRI. First, we identified the brain features that best distinguish individuals with PTSD from controls using traditional machine learning methods. Second, we assessed the utility of the denoising variational autoencoder (DVAE) and evaluated its classification performance. Third, we assessed the generalizability and reproducibility of both models using leave-one-site-out cross-validation procedure for each modality. RESULTS We found lower performance in classifying PTSD vs. controls with data from over 20 sites (60 % test AUC for s-MRI, 59 % for rs-fMRI and 56 % for d-MRI), as compared to other studies run on single-site data. The performance increased when classifying PTSD from HC without trauma history in each modality (75 % AUC). The classification performance remained intact when applying the DVAE framework, which reduced the number of features. Finally, we found that the DVAE framework achieved better generalization to unseen datasets compared with the traditional machine learning frameworks, albeit performance was slightly above chance. CONCLUSION These results have the potential to provide a baseline classification performance for PTSD when using large scale neuroimaging datasets. Our findings show that the control group used can heavily affect classification performance. The DVAE framework provided better generalizability for the multi-site data. This may be more significant in clinical practice since the neuroimaging-based diagnostic DVAE classification models are much less site-specific, rendering them more generalizable.
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Affiliation(s)
- Xi Zhu
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA
| | - Yoojean Kim
- New York State Psychiatric Institute, New York, NY, USA
| | - Orren Ravid
- New York State Psychiatric Institute, New York, NY, USA
| | - Xiaofu He
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
| | | | | | | | - Seonjoo Lee
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA
| | - Chadi G Abdallah
- Baylor College of Medicine, Houston, TX, USA; Yale University School of Medicine, New Haven, CT, USA
| | | | - Christopher L Averill
- Baylor College of Medicine, Houston, TX, USA; Yale University School of Medicine, New Haven, CT, USA
| | | | - Lee A Baugh
- Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | | | | | - Steven E Bruce
- Center for Trauma Recovery, Department of Psychological Sciences, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Richard A Bryant
- School of Psychology, University of New South Wales, Sydney, NSW, Australia
| | - Zhihong Cao
- Department of Radiology, The Affiliated Yixing Hospital of Jiangsu University, Yixing, Jiangsu, China
| | - Kyle Choi
- University of California San Diego, La Jolla, CA, USA
| | - Josh Cisler
- Department of Psychiatry, University of Texas at Austin, Austin, TX, USA
| | | | | | | | | | | | - Emily L Dennis
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Maria Densmore
- Departments of Psychology and Psychiatry, Neuroscience Program, Western University, London, ON, Canada; Department of Psychology, University of British Columbia, Okanagan, Kelowna, British Columbia, Canada
| | | | - Seth G Disner
- Minneapolis VA Health Care System, Minneapolis, MN, USA
| | - Wissam El Hage
- UMR 1253, CIC 1415, University of Tours, CHRU de Tours, INSERM, France
| | | | - Negar Fani
- Emory University Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Kelene A Fercho
- Civil Aerospace Medical Institute, US Federal Aviation Administration, Oklahoma City, OK, USA
| | | | - Gina L Forster
- Brain Health Research Centre, Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Jessie L Frijling
- Department of Psychiatry, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Elbert Geuze
- Brain Research and Innovation Centre, Ministry of Defence, Utrecht, The Netherlands
| | - Atilla Gonenc
- Cognitive and Clinical Neuroimaging Core, McLean Hospital, Belmont, MA, USA
| | - Evan M Gordon
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Staci Gruber
- Cognitive and Clinical Neuroimaging Core, McLean Hospital, Belmont, MA, USA
| | | | - Jeffrey P Guenette
- Division of Neuroradiology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Ryan J Herringa
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | | | | | | | - Neda Jahanshad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, CA, USA
| | | | | | - Milissa L Kaufman
- Division of Women's Mental Health, McLean Hospital, Belmont, MA, USA
| | - Mitzy Kennis
- Brain Research and Innovation Centre, Ministry of Defence, Utrecht, The Netherlands
| | | | - Philipp Kinzel
- Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig Maximilian University of Munich, Munich, Germany; Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Boston, MA, USA
| | - Saskia B J Koch
- Donders Institute for Brain, Cognition and Behavior, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Inga K Koerte
- Department of Child and Adolescent Psychiatry, Psychosomatic and Psychotherapy, Ludwig Maximilian University of Munich, Munich, Germany; Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Ruth Lanius
- Department of Neuroscience, Western University, London, ON, Canada
| | | | - Lauren A M Lebois
- McLean Hospital, Belmont, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Gen Li
- Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Israel Liberzon
- Psychiatry and Behavioral Science, Texas A&M University Health Science Center, College Station, TX, USA
| | - Guang Ming Lu
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Yifeng Luo
- Department of Radiology, The Affiliated Yixing Hospital of Jiangsu University, Yixing, Jiangsu, China
| | | | - Antje Manthey
- Charité Universitätsmedizin Berlin Campus Charite Mitte: Charite Universitatsmedizin Berlin, Berlin, Germany
| | | | - Geoffery May
- VISN 17 Center of Excellence for Research on Returning War Veterans, Waco, TX, USA
| | | | | | - Laura Nawijn
- Department of Psychiatry, Amsterdam University Medical Centers, VU University Medical Center, VU University, Amsterdam, The Netherlands
| | - Steven M Nelson
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Richard W J Neufeld
- Departments of Psychology and Psychiatry, Neuroscience Program, Western University, London, ON, Canada; Department of Psychology, University of British Columbia, Okanagan, Kelowna, British Columbia, Canada
| | | | | | - Bunmi O Olatunji
- Department of Psychology, Vanderbilt University, Nashville, TN, USA
| | - Miranda Olff
- Department of Psychiatry, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | | - K Luan Phan
- Department of Psychiatry and Behavioral Health, Ohio State University, Columbus, OH, USA
| | - Rongfeng Qi
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Yann Quidé
- School of Psychology, University of New South Wales, Sydney, NSW, Australia; Neuroscience Research Australia, Randwick, NSW, Australia
| | | | - Kerry Ressler
- McLean Hospital, Belmont, MA, USA; Harvard Medical School, Boston, MA, USA
| | | | - Marisa Ross
- Northwestern Neighborhood and Networks Initiative, Northwestern University Institute for Policy Research, Evanston, IL, USA
| | - Isabelle M Rosso
- McLean Hospital, Belmont, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Lauren E Salminen
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, CA, USA
| | | | | | - Martha E Shenton
- Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Anika Sierk
- Charité Universitätsmedizin Berlin Campus Charite Mitte: Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Alan N Simmons
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, CA, USA
| | | | | | - Scott R Sponheim
- Minneapolis VA Health Care System, Minneapolis, MN, USA; University of Minnesota, Minneapolis, MN, USA
| | | | - Dan J Stein
- University of Cape Town, Cape Town, South Africa
| | - Jennifer S Stevens
- Emory University Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | | | | | - Jean Théberge
- Departments of Psychology and Psychiatry, Neuroscience Program, Western University, London, ON, Canada; Department of Psychology, University of British Columbia, Okanagan, Kelowna, British Columbia, Canada
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, CA, USA
| | - Sophia I Thomopoulos
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, CA, USA
| | | | | | | | - Sanne J H van Rooij
- Emory University Department of Psychiatry and Behavioral Sciences, Atlanta, GA, USA
| | - Mirjam van Zuiden
- Department of Psychiatry, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tim Varkevisser
- Brain Research and Innovation Centre, Ministry of Defence, Utrecht, The Netherlands
| | - Dick J Veltman
- Department of Psychiatry, Amsterdam University Medical Centers, VU University Medical Center, VU University, Amsterdam, The Netherlands
| | | | - Henrik Walter
- Charité Universitätsmedizin Berlin Campus Charite Mitte: Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Li Wang
- Institute of Psychology, Chinese Academy of Sciences, Beijing, China; Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- University of Toledo, Toledo, OH, USA
| | - Carissa Weis
- Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sherry Winternitz
- Division of Women's Mental Health, McLean Hospital, Belmont, MA, USA
| | - Hong Xie
- University of Toledo, Toledo, OH, USA
| | - Ye Zhu
- Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Melanie Wall
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA
| | - Yuval Neria
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
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5
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Chen Z, Hu B, Liu X, Becker B, Eickhoff SB, Miao K, Gu X, Tang Y, Dai X, Li C, Leonov A, Xiao Z, Feng Z, Chen J, Chuan-Peng H. Sampling inequalities affect generalization of neuroimaging-based diagnostic classifiers in psychiatry. BMC Med 2023; 21:241. [PMID: 37400814 DOI: 10.1186/s12916-023-02941-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/13/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND The development of machine learning models for aiding in the diagnosis of mental disorder is recognized as a significant breakthrough in the field of psychiatry. However, clinical practice of such models remains a challenge, with poor generalizability being a major limitation. METHODS Here, we conducted a pre-registered meta-research assessment on neuroimaging-based models in the psychiatric literature, quantitatively examining global and regional sampling issues over recent decades, from a view that has been relatively underexplored. A total of 476 studies (n = 118,137) were included in the current assessment. Based on these findings, we built a comprehensive 5-star rating system to quantitatively evaluate the quality of existing machine learning models for psychiatric diagnoses. RESULTS A global sampling inequality in these models was revealed quantitatively (sampling Gini coefficient (G) = 0.81, p < .01), varying across different countries (regions) (e.g., China, G = 0.47; the USA, G = 0.58; Germany, G = 0.78; the UK, G = 0.87). Furthermore, the severity of this sampling inequality was significantly predicted by national economic levels (β = - 2.75, p < .001, R2adj = 0.40; r = - .84, 95% CI: - .41 to - .97), and was plausibly predictable for model performance, with higher sampling inequality for reporting higher classification accuracy. Further analyses showed that lack of independent testing (84.24% of models, 95% CI: 81.0-87.5%), improper cross-validation (51.68% of models, 95% CI: 47.2-56.2%), and poor technical transparency (87.8% of models, 95% CI: 84.9-90.8%)/availability (80.88% of models, 95% CI: 77.3-84.4%) are prevailing in current diagnostic classifiers despite improvements over time. Relating to these observations, model performances were found decreased in studies with independent cross-country sampling validations (all p < .001, BF10 > 15). In light of this, we proposed a purpose-built quantitative assessment checklist, which demonstrated that the overall ratings of these models increased by publication year but were negatively associated with model performance. CONCLUSIONS Together, improving sampling economic equality and hence the quality of machine learning models may be a crucial facet to plausibly translating neuroimaging-based diagnostic classifiers into clinical practice.
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Affiliation(s)
- Zhiyi Chen
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China.
- Faculty of Psychology, Southwest University, Chongqing, China.
| | - Bowen Hu
- Faculty of Psychology, Southwest University, Chongqing, China
| | - Xuerong Liu
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China
| | - Benjamin Becker
- The Center of Psychosomatic Medicine, Sichuan Provincial Center for Mental Health, Sichuan Provincial People's Hospital, Chengdu, China
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Simon B Eickhoff
- Institute of Systems Neuroscience, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kuan Miao
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China
| | - Xingmei Gu
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China
| | - Yancheng Tang
- School of Business and Management, Shanghai International Studies University, Shanghai, China
| | - Xin Dai
- Faculty of Psychology, Southwest University, Chongqing, China
| | - Chao Li
- Department of Radiology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangdong, China
| | - Artemiy Leonov
- School of Psychology, Clark University, Worcester, MA, USA
| | - Zhibing Xiao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Zhengzhi Feng
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China
| | - Ji Chen
- Department of Psychology and Behavioral Sciences, Zhejiang University, Hangzhou, China.
- Department of Psychiatry, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
| | - Hu Chuan-Peng
- School of Psychology, Nanjing Normal University, Nanjing, China
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