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Avants BB, Tustison NJ, Stone JR. Similarity-driven multi-view embeddings from high-dimensional biomedical data. NATURE COMPUTATIONAL SCIENCE 2021; 1:143-152. [PMID: 33796865 PMCID: PMC8009088 DOI: 10.1038/s43588-021-00029-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 01/19/2021] [Indexed: 12/31/2022]
Abstract
Diverse, high-dimensional modalities collected in large cohorts present new opportunities for the formulation and testing of integrative scientific hypotheses. Similarity-driven multi-view linear reconstruction (SiMLR) is an algorithm that exploits inter-modality relationships to transform large scientific datasets into smaller, more well-powered and interpretable low-dimensional spaces. SiMLR contributes an objective function for identifying joint signal, regularization based on sparse matrices representing prior within-modality relationships and an implementation that permits application to joint reduction of large data matrices. We demonstrate that SiMLR outperforms closely related methods on supervised learning problems in simulation data, a multi-omics cancer survival prediction dataset and multiple modality neuroimaging datasets. Taken together, this collection of results shows that SiMLR may be applied to joint signal estimation from disparate modalities and may yield practically useful results in a variety of application domains.
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Affiliation(s)
- Brian B Avants
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA
| | - Nicholas J Tustison
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA
| | - James R Stone
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA
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Adhikari BM, Jahanshad N, Shukla D, Turner J, Grotegerd D, Dannlowski U, Kugel H, Engelen J, Dietsche B, Krug A, Kircher T, Fieremans E, Veraart J, Novikov DS, Boedhoe PSW, van der Werf YD, van den Heuvel OA, Ipser J, Uhlmann A, Stein DJ, Dickie E, Voineskos AN, Malhotra AK, Pizzagalli F, Calhoun VD, Waller L, Veer IM, Walter H, Buchanan RW, Glahn DC, Hong LE, Thompson PM, Kochunov P. A resting state fMRI analysis pipeline for pooling inference across diverse cohorts: an ENIGMA rs-fMRI protocol. Brain Imaging Behav 2020; 13:1453-1467. [PMID: 30191514 DOI: 10.1007/s11682-018-9941-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Large-scale consortium efforts such as Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) and other collaborative efforts show that combining statistical data from multiple independent studies can boost statistical power and achieve more accurate estimates of effect sizes, contributing to more reliable and reproducible research. A meta- analysis would pool effects from studies conducted in a similar manner, yet to date, no such harmonized protocol exists for resting state fMRI (rsfMRI) data. Here, we propose an initial pipeline for multi-site rsfMRI analysis to allow research groups around the world to analyze scans in a harmonized way, and to perform coordinated statistical tests. The challenge lies in the fact that resting state fMRI measurements collected by researchers over the last decade vary widely, with variable quality and differing spatial or temporal signal-to-noise ratio (tSNR). An effective harmonization must provide optimal measures for all quality data. Here we used rsfMRI data from twenty-two independent studies with approximately fifty corresponding T1-weighted and rsfMRI datasets each, to (A) review and aggregate the state of existing rsfMRI data, (B) demonstrate utility of principal component analysis (PCA)-based denoising and (C) develop a deformable ENIGMA EPI template based on the representative anatomy that incorporates spatial distortion patterns from various protocols and populations.
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Affiliation(s)
- Bhim M Adhikari
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Neda Jahanshad
- Imaging Genetics Center, Keck School of Medicine of USC, Marina del Rey, Los Angeles, CA, USA
| | - Dinesh Shukla
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jessica Turner
- Department of Psychology, Georgia State University, Atlanta, GA, USA
| | | | - Udo Dannlowski
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Harald Kugel
- Department of Clinical Radiology, University of Münster, Münster, Germany
| | - Jennifer Engelen
- Department of Psychiatry and Psychotherapy, Philipps-University Marburg, Marburg, Germany
| | - Bruno Dietsche
- Department of Psychiatry and Psychotherapy, Philipps-University Marburg, Marburg, Germany
| | - Axel Krug
- Department of Psychiatry and Psychotherapy, Philipps-University Marburg, Marburg, Germany
| | - Tilo Kircher
- Department of Psychiatry and Psychotherapy, Philipps-University Marburg, Marburg, Germany
| | - Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
| | - Jelle Veraart
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
| | - Dmitry S Novikov
- Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA
| | - Premika S W Boedhoe
- Department of Psychiatry, Department of Anatomy & Neurosciences, VU University Medical Center, Amsterdam, Netherlands
| | - Ysbrand D van der Werf
- Department of Psychiatry, Department of Anatomy & Neurosciences, VU University Medical Center, Amsterdam, Netherlands
| | - Odile A van den Heuvel
- Department of Psychiatry, Department of Anatomy & Neurosciences, VU University Medical Center, Amsterdam, Netherlands
| | - Jonathan Ipser
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Anne Uhlmann
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Erin Dickie
- Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Aristotle N Voineskos
- Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Anil K Malhotra
- Department of Psychiatry, The Zucker Hillside Hospital, Glen Oaks, New York, NY, USA
| | - Fabrizio Pizzagalli
- Imaging Genetics Center, Keck School of Medicine of USC, Marina del Rey, Los Angeles, CA, USA
| | - Vince D Calhoun
- The Mind Research Network & The University of New Mexico, Albuquerque, NM, USA
| | - Lea Waller
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Campus Matte, Berlin, Germany
| | - Ilja M Veer
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Campus Matte, Berlin, Germany
| | - Hernik Walter
- Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Campus Matte, Berlin, Germany
| | - Robert W Buchanan
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - David C Glahn
- Department of Psychiatry, Yale University, School of Medicine, New Haven, CT, USA
| | - L Elliot Hong
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Paul M Thompson
- Imaging Genetics Center, Keck School of Medicine of USC, Marina del Rey, Los Angeles, CA, USA
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
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