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Xing Y, van Erp TG, Pearlson GD, Kochunov P, Calhoun VD, Du Y. More reliable biomarkers and more accurate prediction for mental disorders using a label-noise filtering-based dimensional prediction method. iScience 2024; 27:109319. [PMID: 38482500 PMCID: PMC10933544 DOI: 10.1016/j.isci.2024.109319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/17/2023] [Accepted: 02/19/2024] [Indexed: 04/26/2024] Open
Abstract
The integration of neuroimaging with artificial intelligence is crucial for advancing the diagnosis of mental disorders. However, challenges arise from incomplete matching between diagnostic labels and neuroimaging. Here, we propose a label-noise filtering-based dimensional prediction (LAMP) method to identify reliable biomarkers and achieve accurate prediction for mental disorders. Our method proposes to utilize a label-noise filtering model to automatically filter out unclear cases from a neuroimaging perspective, and then the typical subjects whose diagnostic labels align with neuroimaging measures are used to construct a dimensional prediction model to score independent subjects. Using fMRI data of schizophrenia patients and healthy controls (n = 1,245), our method yields consistent scores to independent subjects, leading to more distinguishable relabeled groups with an enhanced classification accuracy of 31.89%. Additionally, it enables the exploration of stable abnormalities in schizophrenia. In summary, our LAMP method facilitates the identification of reliable biomarkers and accurate diagnosis of mental disorders using neuroimages.
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Affiliation(s)
- Ying Xing
- School of Computer and Information Technology, Shanxi University, Taiyuan 030006, China
| | - Theo G.M. van Erp
- Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, Irvine, CA 92617, USA
- Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, CA 92617, USA
| | - Godfrey D. Pearlson
- Departments of Psychiatry and of Neurobiology, Yale University, New Haven, CT 06519, USA
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT 06106, USA
| | - Peter Kochunov
- Maryland Psychiatric Research Center and Department of Psychiatry, University of Maryland, School of Medicine, Baltimore, MD 21201, USA
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA 30030, USA
| | - Yuhui Du
- School of Computer and Information Technology, Shanxi University, Taiyuan 030006, China
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Porter A, Fei S, Damme KSF, Nusslock R, Gratton C, Mittal VA. A meta-analysis and systematic review of single vs. multimodal neuroimaging techniques in the classification of psychosis. Mol Psychiatry 2023; 28:3278-3292. [PMID: 37563277 PMCID: PMC10618094 DOI: 10.1038/s41380-023-02195-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Psychotic disorders are characterized by structural and functional abnormalities in brain networks. Neuroimaging techniques map and characterize such abnormalities using unique features (e.g., structural integrity, coactivation). However, it is unclear if a specific method, or a combination of modalities, is particularly effective in identifying differences in brain networks of someone with a psychotic disorder. METHODS A systematic meta-analysis evaluated machine learning classification of schizophrenia spectrum disorders in comparison to healthy control participants using various neuroimaging modalities (i.e., T1-weighted imaging (T1), diffusion tensor imaging (DTI), resting state functional connectivity (rs-FC), or some combination (multimodal)). Criteria for manuscript inclusion included whole-brain analyses and cross-validation to provide a complete picture regarding the predictive ability of large-scale brain systems in psychosis. For this meta-analysis, we searched Ovid MEDLINE, PubMed, PsychInfo, Google Scholar, and Web of Science published between inception and March 13th 2023. Prediction results were averaged for studies using the same dataset, but parallel analyses were run that included studies with pooled sample across many datasets. We assessed bias through funnel plot asymmetry. A bivariate regression model determined whether differences in imaging modality, demographics, and preprocessing methods moderated classification. Separate models were run for studies with internal prediction (via cross-validation) and external prediction. RESULTS 93 studies were identified for quantitative review (30 T1, 9 DTI, 40 rs-FC, and 14 multimodal). As a whole, all modalities reliably differentiated those with schizophrenia spectrum disorders from controls (OR = 2.64 (95%CI = 2.33 to 2.95)). However, classification was relatively similar across modalities: no differences were seen across modalities in the classification of independent internal data, and a small advantage was seen for rs-FC studies relative to T1 studies in classification in external datasets. We found large amounts of heterogeneity across results resulting in significant signs of bias in funnel plots and Egger's tests. Results remained similar, however, when studies were restricted to those with less heterogeneity, with continued small advantages for rs-FC relative to structural measures. Notably, in all cases, no significant differences were seen between multimodal and unimodal approaches, with rs-FC and unimodal studies reporting largely overlapping classification performance. Differences in demographics and analysis or denoising were not associated with changes in classification scores. CONCLUSIONS The results of this study suggest that neuroimaging approaches have promise in the classification of psychosis. Interestingly, at present most modalities perform similarly in the classification of psychosis, with slight advantages for rs-FC relative to structural modalities in some specific cases. Notably, results differed substantially across studies, with suggestions of biased effect sizes, particularly highlighting the need for more studies using external prediction and large sample sizes. Adopting more rigorous and systematized standards will add significant value toward understanding and treating this critical population.
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Affiliation(s)
- Alexis Porter
- Department of Psychology, Northwestern University, Evanston, IL, USA.
| | - Sihan Fei
- Department of Psychology, Northwestern University, Evanston, IL, USA
| | - Katherine S F Damme
- Department of Psychology, Northwestern University, Evanston, IL, USA
- Institute for Innovations in Developmental Sciences, Northwestern University, Evanston and Chicago, IL, USA
| | - Robin Nusslock
- Department of Psychology, Northwestern University, Evanston, IL, USA
| | - Caterina Gratton
- Department of Psychology, Florida State University, Tallahassee, FL, USA
| | - Vijay A Mittal
- Department of Psychology, Northwestern University, Evanston, IL, USA
- Institute for Innovations in Developmental Sciences, Northwestern University, Evanston and Chicago, IL, USA
- Department of Psychiatry, Northwestern University, Chicago, IL, USA
- Medical Social Sciences, Northwestern University, Chicago, IL, USA
- Institute for Policy Research, Northwestern University, Chicago, IL, USA
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Rokham H, Falakshahi H, Calhoun VD. A Deep Learning Approach for Psychosis Spectrum Label Noise Detection from Multimodal Neuroimaging Data. Annu Int Conf IEEE Eng Med Biol Soc 2023; 2023:1-4. [PMID: 38082903 DOI: 10.1109/embc40787.2023.10339949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Understanding the structural and functional mechanisms of the brain is challenging for mood and mental disorders. Many neuroimaging techniques are widely used to reveal hidden patterns from different brain imaging modalities. However, these findings are bounded by the limitation of each modality. In addition, the lack of validity of current psychosis nosology created more complications in understanding biomarkers. In this study, we introduced a deep convolutional framework to classify and identify label noises using structural and functional magnetic resonance imaging data. We applied our method to functional and structural MRI data from a schizophrenia dataset and evaluated the model's performance in a cross-validated form. In addition, we introduced a noise criterion to distinguish a potentially noisy subject for each modality. Our results show the learned model using resting-state functional MRI data is more informative and has higher performance in comparison with structural MRI data. Lastly, based on the noise level, we investigated potential borderline subjects as possible subtypes and made a statistical analysis to distinguish differences between resting-state static functional connectivity features.Clinical Relevance- Results show schizophrenia patients are separable from the healthy control group based on their neuroimaging data and resting-state functional MRI data is more informative than structural MRI data and hence contains less label noise.
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Rokham H, Falakshahi H, Fu Z, Pearlson G, Calhoun VD. Evaluation of boundaries between mood and psychosis disorder using dynamic functional network connectivity (dFNC) via deep learning classification. Hum Brain Mapp 2023; 44:3180-3195. [PMID: 36919656 PMCID: PMC10171526 DOI: 10.1002/hbm.26273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
The validity and reliability of diagnoses in psychiatry is a challenging topic in mental health. The current mental health categorization is based primarily on symptoms and clinical course and is not biologically validated. Among multiple ongoing efforts, neurological observations alongside clinical evaluations are considered to be potential solutions to address diagnostic problems. The Bipolar-Schizophrenia Network on Intermediate Phenotypes (B-SNIP) has published multiple papers attempting to reclassify psychotic illnesses based on biological rather than symptomatic measures. However, the effort to investigate the relationship between this new categorization approach and other neuroimaging techniques, including resting-state fMRI data, is still limited. This study focused on investigating the relationship between different psychotic disorders categorization methods and resting-state fMRI-based measures called dynamic functional network connectivity (dFNC) using state-of-the-art artificial intelligence (AI) approaches. We applied our method to 613 subjects, including individuals with psychosis and healthy controls, which were classified using both the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) and the B-SNIP biomarker-based (Biotype) approach. Statistical group differences and cross-validated classifiers were performed within each framework to assess how different categories. Results highlight interesting differences in occupancy in both DSM-IV and Biotype categorizations compared to healthy individuals, which are distributed across specific transient connectivity states. Biotypes tended to show less distinctiveness in occupancy level and included fewer cellwise differences. Classification accuracy obtained by DSM-IV and Biotype categories were both well above chance. Results provided new insights and highlighted the benefits of both DSM-IV and biology-based categories while also emphasizing the importance of future work in this direction, including employing further data types.
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Affiliation(s)
- Hooman Rokham
- Department of Electrical and Computer EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
- Tri‐institutional Center of Translational Research in Neuroimaging and Data Science (TReNDS), Georgia Institute of Technology, and Emory UniversityGeorgia State UniversityAtlantaGeorgiaUSA
| | - Haleh Falakshahi
- Department of Electrical and Computer EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
- Tri‐institutional Center of Translational Research in Neuroimaging and Data Science (TReNDS), Georgia Institute of Technology, and Emory UniversityGeorgia State UniversityAtlantaGeorgiaUSA
| | - Zening Fu
- Tri‐institutional Center of Translational Research in Neuroimaging and Data Science (TReNDS), Georgia Institute of Technology, and Emory UniversityGeorgia State UniversityAtlantaGeorgiaUSA
| | - Godfrey Pearlson
- Department of PsychiatryYale UniversityNew HavenConnecticutUSA
- Department of NeuroscienceYale UniversityNew HavenConnecticutUSA
- Olin Neuropsychiatry Research CenterHartford HospitalHartfordConnecticutUSA
| | - Vince D. Calhoun
- Department of Electrical and Computer EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
- Tri‐institutional Center of Translational Research in Neuroimaging and Data Science (TReNDS), Georgia Institute of Technology, and Emory UniversityGeorgia State UniversityAtlantaGeorgiaUSA
- Department of PsychiatryYale UniversityNew HavenConnecticutUSA
- Department of Computer ScienceGeorgia State UniversityAtlantaGeorgiaUSA
- Department of PsychologyGeorgia State UniversityAtlantaGeorgiaUSA
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Falakshahi H, Rokham H, Fu Z, Iraji A, Mathalon DH, Ford JM, Mueller BA, Preda A, van Erp TGM, Turner JA, Plis S, Calhoun VD. Path Analysis: A Method to Estimate Altered Pathways in Time-varying Graphs of Neuroimaging Data. Netw Neurosci 2022; 6:634-664. [PMID: 36204419 PMCID: PMC9531579 DOI: 10.1162/netn_a_00247] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 03/23/2022] [Indexed: 11/16/2022] Open
Abstract
Graph-theoretical methods have been widely used to study human brain networks in psychiatric disorders. However, the focus has primarily been on global graphic metrics with little attention to the information contained in paths connecting brain regions. Details of disruption of these paths may be highly informative for understanding disease mechanisms. To detect the absence or addition of multistep paths in the patient group, we provide an algorithm estimating edges that contribute to these paths with reference to the control group. We next examine where pairs of nodes were connected through paths in both groups by using a covariance decomposition method. We apply our method to study resting-state fMRI data in schizophrenia versus controls. Results show several disconnectors in schizophrenia within and between functional domains, particularly within the default mode and cognitive control networks. Additionally, we identify new edges generating additional paths. Moreover, although paths exist in both groups, these paths take unique trajectories and have a significant contribution to the decomposition. The proposed path analysis provides a way to characterize individuals by evaluating changes in paths, rather than just focusing on the pairwise relationships. Our results show promise for identifying path-based metrics in neuroimaging data.
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Affiliation(s)
- Haleh Falakshahi
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Hooman Rokham
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Zening Fu
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, USA
| | - Armin Iraji
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, USA
| | - Daniel H. Mathalon
- Department of Psychiatry, University of California, San Francisco, CA, USA
- San Francisco VA Medical Center, San Francisco, CA, USA
| | - Judith M. Ford
- Department of Psychiatry, University of California, San Francisco, CA, USA
- San Francisco VA Medical Center, San Francisco, CA, USA
| | - Bryon A. Mueller
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Adrian Preda
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
| | - Theo G. M. van Erp
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, USA
- Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, USA
| | - Jessica A. Turner
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, USA
- Department of Psychology, Georgia State University, Atlanta, GA, USA
| | - Sergey Plis
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, USA
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
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Calhoun VD, Pearlson GD, Sui J. Data-driven approaches to neuroimaging biomarkers for neurological and psychiatric disorders: emerging approaches and examples. Curr Opin Neurol 2021; 34:469-479. [PMID: 34054110 PMCID: PMC8263510 DOI: 10.1097/wco.0000000000000967] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE OF REVIEW The 'holy grail' of clinical applications of neuroimaging to neurological and psychiatric disorders via personalized biomarkers has remained mostly elusive, despite considerable effort. However, there are many reasons to continue to be hopeful, as the field has made remarkable advances over the past few years, fueled by a variety of converging technical and data developments. RECENT FINDINGS We discuss a number of advances that are accelerating the push for neuroimaging biomarkers including the advent of the 'neuroscience big data' era, biomarker data competitions, the development of more sophisticated algorithms including 'guided' data-driven approaches that facilitate automation of network-based analyses, dynamic connectivity, and deep learning. Another key advance includes multimodal data fusion approaches which can provide convergent and complementary evidence pointing to possible mechanisms as well as increase predictive accuracy. SUMMARY The search for clinically relevant neuroimaging biomarkers for neurological and psychiatric disorders is rapidly accelerating. Here, we highlight some of these aspects, provide recent examples from studies in our group, and link to other ongoing work in the field. It is critical that access and use of these advanced approaches becomes mainstream, this will help propel the community forward and facilitate the production of robust and replicable neuroimaging biomarkers.
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Affiliation(s)
- Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia
| | - Godfrey D Pearlson
- Department of Psychiatry and Neuroscience, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jing Sui
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia
- Institute of Automation, Chinese Academy of Sciences, and the University of Chinese Academy of Sciences, Beijing, China
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Paulus MP. Pragmatic and Explanatory Progress Using Statistical Models of Disturbed Mind, Brain, and Behavior to Improve Mental Health. Biol Psychiatry Cogn Neurosci Neuroimaging 2020; 5:723-725. [PMID: 32771178 DOI: 10.1016/j.bpsc.2020.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 11/30/2022]
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Barch DM. Understanding the Nature and Treatment of Psychopathology: Can the Data Guide the Way? Biol Psychiatry Cogn Neurosci Neuroimaging 2020; 5:719-722. [PMID: 32771177 DOI: 10.1016/j.bpsc.2020.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Deanna M Barch
- Departments of Psychological and Brain Sciences, Psychiatry, and Radiology, Washington University in St. Louis, St. Louis, Missouri.
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