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Shahzad MN, Ali H. Deep learning based diagnosis of PTSD using 3D-CNN and resting-state fMRI data. Psychiatry Res Neuroimaging 2024; 343:111845. [PMID: 38908302 DOI: 10.1016/j.pscychresns.2024.111845] [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: 01/24/2024] [Revised: 05/26/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024]
Abstract
BACKGROUND The incidence rate of Posttraumatic stress disorder (PTSD) is currently increasing due to wars, terrorism, and pandemic disease situations. Therefore, accurate detection of PTSD is crucial for the treatment of the patients, for this purpose, the present study aims to classify individuals with PTSD versus healthy control. METHODS The resting-state functional MRI (rs-fMRI) scans of 19 PTSD and 24 healthy control male subjects have been used to identify the activation pattern in most affected brain regions using group-level independent component analysis (ICA) and t-test. To classify PTSD-affected subjects from healthy control six machine learning techniques including random forest, Naive Bayes, support vector machine, decision tree, K-nearest neighbor, linear discriminant analysis, and deep learning three-dimensional 3D-CNN have been performed on the data and compared. RESULTS The rs-fMRI scans of the most commonly investigated 11 regions of trauma-exposed and healthy brains are analyzed to observe their level of activation. Amygdala and insula regions are determined as the most activated regions from the regions-of-interest in the brain of PTSD subjects. In addition, machine learning techniques have been applied to the components extracted from ICA but the models provided low classification accuracy. The ICA components are also fed into the 3D-CNN model, which is trained with a 5-fold cross-validation method. The 3D-CNN model demonstrated high accuracies, such as 98.12%, 98.25 %, and 98.00 % on average with training, validation, and testing datasets, respectively. CONCLUSION The findings indicate that 3D-CNN is a surpassing method than the other six considered techniques and it helps to recognize PTSD patients accurately.
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Affiliation(s)
| | - Haider Ali
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
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Huang Y, Li Y, Yuan Y, Zhang X, Yan W, Li T, Niu Y, Xu M, Yan T, Li X, Li D, Xiang J, Wang B, Yan T. Beta-informativeness-diffusion multilayer graph embedding for brain network analysis. Front Neurosci 2024; 18:1303741. [PMID: 38525375 PMCID: PMC10957763 DOI: 10.3389/fnins.2024.1303741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/07/2024] [Indexed: 03/26/2024] Open
Abstract
Brain network analysis provides essential insights into the diagnosis of brain disease. Integrating multiple neuroimaging modalities has been demonstrated to be more effective than using a single modality for brain network analysis. However, a majority of existing brain network analysis methods based on multiple modalities often overlook both complementary information and unique characteristics from various modalities. To tackle this issue, we propose the Beta-Informativeness-Diffusion Multilayer Graph Embedding (BID-MGE) method. The proposed method seamlessly integrates structural connectivity (SC) and functional connectivity (FC) to learn more comprehensive information for diagnosing neuropsychiatric disorders. Specifically, a novel beta distribution mapping function (beta mapping) is utilized to increase vital information and weaken insignificant connections. The refined information helps the diffusion process concentrate on crucial brain regions to capture more discriminative features. To maximize the preservation of the unique characteristics of each modality, we design an optimal scale multilayer brain network, the inter-layer connections of which depend on node informativeness. Then, a multilayer informativeness diffusion is proposed to capture complementary information and unique characteristics from various modalities and generate node representations by incorporating the features of each node with those of their connected nodes. Finally, the node representations are reconfigured using principal component analysis (PCA), and cosine distances are calculated with reference to multiple templates for statistical analysis and classification. We implement the proposed method for brain network analysis of neuropsychiatric disorders. The results indicate that our method effectively identifies crucial brain regions associated with diseases, providing valuable insights into the pathology of the disease, and surpasses other advanced methods in classification performance.
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Affiliation(s)
- Yin Huang
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, China
| | - Ying Li
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, China
| | - Yuting Yuan
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, China
| | - Xingyu Zhang
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, China
| | - Wenjie Yan
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, China
| | - Ting Li
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yan Niu
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, China
| | - Mengzhou Xu
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing, China
| | - Ting Yan
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, China
| | - Xiaowen Li
- Computer Information Engineering Institute, Shanxi Technology and Business College, Taiyuan, China
| | - Dandan Li
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, China
| | - Jie Xiang
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, China
| | - Bin Wang
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, China
| | - Tianyi Yan
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing, China
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3
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Krämer C, Stumme J, da Costa Campos L, Dellani P, Rubbert C, Caspers J, Caspers S, Jockwitz C. Prediction of cognitive performance differences in older age from multimodal neuroimaging data. GeroScience 2024; 46:283-308. [PMID: 37308769 PMCID: PMC10828156 DOI: 10.1007/s11357-023-00831-4] [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: 03/02/2023] [Accepted: 05/17/2023] [Indexed: 06/14/2023] Open
Abstract
Differences in brain structure and functional and structural network architecture have been found to partly explain cognitive performance differences in older ages. Thus, they may serve as potential markers for these differences. Initial unimodal studies, however, have reported mixed prediction results of selective cognitive variables based on these brain features using machine learning (ML). Thus, the aim of the current study was to investigate the general validity of cognitive performance prediction from imaging data in healthy older adults. In particular, the focus was with examining whether (1) multimodal information, i.e., region-wise grey matter volume (GMV), resting-state functional connectivity (RSFC), and structural connectivity (SC) estimates, may improve predictability of cognitive targets, (2) predictability differences arise for global cognition and distinct cognitive profiles, and (3) results generalize across different ML approaches in 594 healthy older adults (age range: 55-85 years) from the 1000BRAINS study. Prediction potential was examined for each modality and all multimodal combinations, with and without confound (i.e., age, education, and sex) regression across different analytic options, i.e., variations in algorithms, feature sets, and multimodal approaches (i.e., concatenation vs. stacking). Results showed that prediction performance differed considerably between deconfounding strategies. In the absence of demographic confounder control, successful prediction of cognitive performance could be observed across analytic choices. Combination of different modalities tended to marginally improve predictability of cognitive performance compared to single modalities. Importantly, all previously described effects vanished in the strict confounder control condition. Despite a small trend for a multimodal benefit, developing a biomarker for cognitive aging remains challenging.
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Affiliation(s)
- Camilla Krämer
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Institute for Anatomy I, Medical Faculty & University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Johanna Stumme
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Institute for Anatomy I, Medical Faculty & University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lucas da Costa Campos
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Institute for Anatomy I, Medical Faculty & University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Paulo Dellani
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Institute for Anatomy I, Medical Faculty & University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christian Rubbert
- Department of Diagnostic and Interventional Radiology, Medical Faculty & University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Julian Caspers
- Department of Diagnostic and Interventional Radiology, Medical Faculty & University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Svenja Caspers
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Institute for Anatomy I, Medical Faculty & University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christiane Jockwitz
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany.
- Institute for Anatomy I, Medical Faculty & University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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4
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Alves CL, Toutain TGLDO, Porto JAM, Aguiar PMDC, de Sena EP, Rodrigues FA, Pineda AM, Thielemann C. Analysis of functional connectivity using machine learning and deep learning in different data modalities from individuals with schizophrenia. J Neural Eng 2023; 20:056025. [PMID: 37673060 DOI: 10.1088/1741-2552/acf734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
Objective. Schizophrenia(SCZ) is a severe mental disorder associated with persistent or recurrent psychosis, hallucinations, delusions, and thought disorders that affect approximately 26 million people worldwide, according to the World Health Organization. Several studies encompass machine learning (ML) and deep learning algorithms to automate the diagnosis of this mental disorder. Others study SCZ brain networks to get new insights into the dynamics of information processing in individuals suffering from the condition. In this paper, we offer a rigorous approach with ML and deep learning techniques for evaluating connectivity matrices and measures of complex networks to establish an automated diagnosis and comprehend the topology and dynamics of brain networks in SCZ individuals.Approach.For this purpose, we employed an functional magnetic resonance imaging (fMRI) and electroencephalogram (EEG) dataset. In addition, we combined EEG measures, i.e. Hjorth mobility and complexity, with complex network measurements to be analyzed in our model for the first time in the literature.Main results.When comparing the SCZ group to the control group, we found a high positive correlation between the left superior parietal lobe and the left motor cortex and a positive correlation between the left dorsal posterior cingulate cortex and the left primary motor. Regarding complex network measures, the diameter, which corresponds to the longest shortest path length in a network, may be regarded as a biomarker because it is the most crucial measure in different data modalities. Furthermore, the SCZ brain networks exhibit less segregation and a lower distribution of information. As a result, EEG measures outperformed complex networks in capturing the brain alterations associated with SCZ.Significance. Our model achieved an area under receiver operating characteristic curve (AUC) of 100% and an accuracy of 98.5% for the fMRI, an AUC of 95%, and an accuracy of 95.4% for the EEG data set. These are excellent classification results. Furthermore, we investigated the impact of specific brain connections and network measures on these results, which helped us better describe changes in the diseased brain.
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Affiliation(s)
- Caroline L Alves
- University of São Paulo (USP), Institute of Mathematical and Computer Sciences (ICMC), São Paulo, Brazil
- BioMEMS Lab, Aschaffenburg University of Applied Sciences, Aschaffenburg, Germany
| | | | | | - Patrícia Maria de Carvalho Aguiar
- Hospital Israelita Albert Einstein, São Paulo, Brazil
- Federal University of São Paulo, Department of Neurology and Neurosurgery, São Paulo, Brazil
| | | | - Francisco A Rodrigues
- University of São Paulo (USP), Institute of Mathematical and Computer Sciences (ICMC), São Paulo, Brazil
| | - Aruane M Pineda
- University of São Paulo (USP), Institute of Mathematical and Computer Sciences (ICMC), São Paulo, Brazil
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5
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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] [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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6
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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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Chen Z, Liu X, Yang Q, Wang YJ, Miao K, Gong Z, Yu Y, Leonov A, Liu C, Feng Z, Chuan-Peng H. Evaluation of Risk of Bias in Neuroimaging-Based Artificial Intelligence Models for Psychiatric Diagnosis: A Systematic Review. JAMA Netw Open 2023; 6:e231671. [PMID: 36877519 PMCID: PMC9989906 DOI: 10.1001/jamanetworkopen.2023.1671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
IMPORTANCE Neuroimaging-based artificial intelligence (AI) diagnostic models have proliferated in psychiatry. However, their clinical applicability and reporting quality (ie, feasibility) for clinical practice have not been systematically evaluated. OBJECTIVE To systematically assess the risk of bias (ROB) and reporting quality of neuroimaging-based AI models for psychiatric diagnosis. EVIDENCE REVIEW PubMed was searched for peer-reviewed, full-length articles published between January 1, 1990, and March 16, 2022. Studies aimed at developing or validating neuroimaging-based AI models for clinical diagnosis of psychiatric disorders were included. Reference lists were further searched for suitable original studies. Data extraction followed the CHARMS (Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modeling Studies) and PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines. A closed-loop cross-sequential design was used for quality control. The PROBAST (Prediction Model Risk of Bias Assessment Tool) and modified CLEAR (Checklist for Evaluation of Image-Based Artificial Intelligence Reports) benchmarks were used to systematically evaluate ROB and reporting quality. FINDINGS A total of 517 studies presenting 555 AI models were included and evaluated. Of these models, 461 (83.1%; 95% CI, 80.0%-86.2%) were rated as having a high overall ROB based on the PROBAST. The ROB was particular high in the analysis domain, including inadequate sample size (398 of 555 models [71.7%; 95% CI, 68.0%-75.6%]), poor model performance examination (with 100% of models lacking calibration examination), and lack of handling data complexity (550 of 555 models [99.1%; 95% CI, 98.3%-99.9%]). None of the AI models was perceived to be applicable to clinical practices. Overall reporting completeness (ie, number of reported items/number of total items) for the AI models was 61.2% (95% CI, 60.6%-61.8%), and the completeness was poorest for the technical assessment domain with 39.9% (95% CI, 38.8%-41.1%). CONCLUSIONS AND RELEVANCE This systematic review found that the clinical applicability and feasibility of neuroimaging-based AI models for psychiatric diagnosis were challenged by a high ROB and poor reporting quality. Particularly in the analysis domain, ROB in AI diagnostic models should be addressed before clinical application.
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Affiliation(s)
- Zhiyi Chen
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Xuerong Liu
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Qingwu Yang
- Department of Neurology, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Yan-Jiang Wang
- Department of Neurology, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Kuan Miao
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Zheng Gong
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Yang Yu
- School of Psychology, Third Military Medical University, Chongqing, China
| | - Artemiy Leonov
- Department of Psychology, Clark University, Worcester, Massachusetts
| | - Chunlei Liu
- School of Psychology, Qufu Normal University, Qufu, China
| | - Zhengzhi Feng
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Hu Chuan-Peng
- School of Psychology, Nanjing Normal University, Nanjing, China
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Ferrara M, Franchini G, Funaro M, Cutroni M, Valier B, Toffanin T, Palagini L, Zerbinati L, Folesani F, Murri MB, Caruso R, Grassi L. Machine Learning and Non-Affective Psychosis: Identification, Differential Diagnosis, and Treatment. Curr Psychiatry Rep 2022; 24:925-936. [PMID: 36399236 PMCID: PMC9780131 DOI: 10.1007/s11920-022-01399-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/12/2022] [Indexed: 11/19/2022]
Abstract
PURPOSE OF REVIEW This review will cover the most relevant findings on the use of machine learning (ML) techniques in the field of non-affective psychosis, by summarizing the studies published in the last three years focusing on illness detection and treatment. RECENT FINDINGS Multiple ML tools that include mostly supervised approaches such as support vector machine, gradient boosting, and random forest showed promising results by applying these algorithms to various sources of data: socio-demographic information, EEG, language, digital content, blood biomarkers, neuroimaging, and electronic health records. However, the overall performance, in the binary classification case, varied from 0.49, which is to be considered very low (i.e., noise), to over 0.90. These results are fully justified by different factors, some of which may be attributable to the preprocessing of the data, the wide variety of the data, and the a-priori setting of hyperparameters. One of the main limitations of the field is the lack of stratification of results based on biological sex, given that psychosis presents differently in men and women; hence, the necessity to tailor identification tools and data analytic strategies. Timely identification and appropriate treatment are key factors in reducing the consequences of psychotic disorders. In recent years, the emergence of new analytical tools based on artificial intelligence such as supervised ML approaches showed promises as a potential breakthrough in this field. However, ML applications in everyday practice are still in its infancy.
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Affiliation(s)
- Maria Ferrara
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy.
- Department of Psychiatry, Yale School of Medicine, 34 Park Street, New Haven, CT, USA.
| | - Giorgia Franchini
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Via Campi 213/B, Modena, Italy
- Department of Mathematics and Computer Science, University of Ferrara, Via Macchiavelli 33, Ferrara, Italy
| | - Melissa Funaro
- Harvey Cushing/John Hay Whitney Medical Library, Yale University, 333 Cedar St., New Haven, CT, USA
| | - Marcello Cutroni
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy
| | - Beatrice Valier
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy
| | - Tommaso Toffanin
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy
| | - Laura Palagini
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy
| | - Luigi Zerbinati
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy
| | - Federica Folesani
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy
| | - Martino Belvederi Murri
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy
| | - Rosangela Caruso
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy
| | - Luigi Grassi
- Department of Neuroscience and Rehabilitation, Institute of Psychiatry, University of Ferrara, via Fossato di Mortara 64/A, Ferrara, Italy
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9
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Wang J, Lu S, Wang SH, Zhang YD. A review on extreme learning machine. MULTIMEDIA TOOLS AND APPLICATIONS 2022; 81:41611-41660. [DOI: 10.1007/s11042-021-11007-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/26/2021] [Accepted: 05/05/2021] [Indexed: 08/30/2023]
Abstract
AbstractExtreme learning machine (ELM) is a training algorithm for single hidden layer feedforward neural network (SLFN), which converges much faster than traditional methods and yields promising performance. In this paper, we hope to present a comprehensive review on ELM. Firstly, we will focus on the theoretical analysis including universal approximation theory and generalization. Then, the various improvements are listed, which help ELM works better in terms of stability, efficiency, and accuracy. Because of its outstanding performance, ELM has been successfully applied in many real-time learning tasks for classification, clustering, and regression. Besides, we report the applications of ELM in medical imaging: MRI, CT, and mammogram. The controversies of ELM were also discussed in this paper. We aim to report these advances and find some future perspectives.
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10
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Rahaman MA, Chen J, Fu Z, Lewis N, Iraji A, van Erp TGM, Calhoun VD. Deep multimodal predictome for studying mental disorders. Hum Brain Mapp 2022; 44:509-522. [PMID: 36574598 PMCID: PMC9842924 DOI: 10.1002/hbm.26077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 01/25/2023] Open
Abstract
Characterizing neuropsychiatric disorders is challenging due to heterogeneity in the population. We propose combining structural and functional neuroimaging and genomic data in a multimodal classification framework to leverage their complementary information. Our objectives are two-fold (i) to improve the classification of disorders and (ii) to introspect the concepts learned to explore underlying neural and biological mechanisms linked to mental disorders. Previous multimodal studies have focused on naïve neural networks, mostly perceptron, to learn modality-wise features and often assume equal contribution from each modality. Our focus is on the development of neural networks for feature learning and implementing an adaptive control unit for the fusion phase. Our mid fusion with attention model includes a multilayer feed-forward network, an autoencoder, a bi-directional long short-term memory unit with attention as the features extractor, and a linear attention module for controlling modality-specific influence. The proposed model acquired 92% (p < .0001) accuracy in schizophrenia prediction, outperforming several other state-of-the-art models applied to unimodal or multimodal data. Post hoc feature analyses uncovered critical neural features and genes/biological pathways associated with schizophrenia. The proposed model effectively combines multimodal neuroimaging and genomics data for predicting mental disorders. Interpreting salient features identified by the model may advance our understanding of their underlying etiological mechanisms.
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Affiliation(s)
- Md Abdur Rahaman
- Department of Computational Science and EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA,Tri‐Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)Georgia State University, Georgia Institute of Technology, Emory UniversityAtlantaGeorgiaUSA
| | - Jiayu Chen
- Tri‐Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)Georgia State University, Georgia Institute of Technology, Emory UniversityAtlantaGeorgiaUSA
| | - Zening Fu
- Tri‐Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)Georgia State University, Georgia Institute of Technology, Emory UniversityAtlantaGeorgiaUSA
| | - Noah Lewis
- Department of Computational Science and EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA,Tri‐Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)Georgia State University, Georgia Institute of Technology, Emory UniversityAtlantaGeorgiaUSA
| | - Armin Iraji
- Tri‐Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)Georgia State University, Georgia Institute of Technology, Emory UniversityAtlantaGeorgiaUSA
| | - Theo G. M. van Erp
- Clinical Translational Neuroscience Laboratory, Department of Psychiatry and Human BehaviorUniversity of California IrvineIrvineCaliforniaUSA,Center for the Neurobiology of Learning and MemoryUniversity of California IrvineIrvineCaliforniaUSA
| | - Vince D. Calhoun
- Department of Computational Science and EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA,Tri‐Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)Georgia State University, Georgia Institute of Technology, Emory UniversityAtlantaGeorgiaUSA
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11
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Sadeghi D, Shoeibi A, Ghassemi N, Moridian P, Khadem A, Alizadehsani R, Teshnehlab M, Gorriz JM, Khozeimeh F, Zhang YD, Nahavandi S, Acharya UR. An overview of artificial intelligence techniques for diagnosis of Schizophrenia based on magnetic resonance imaging modalities: Methods, challenges, and future works. Comput Biol Med 2022; 146:105554. [DOI: 10.1016/j.compbiomed.2022.105554] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 12/21/2022]
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12
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Algumaei AH, Algunaid RF, Rushdi MA, Yassine IA. Feature and decision-level fusion for schizophrenia detection based on resting-state fMRI data. PLoS One 2022; 17:e0265300. [PMID: 35609033 PMCID: PMC9129055 DOI: 10.1371/journal.pone.0265300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 02/28/2022] [Indexed: 12/01/2022] Open
Abstract
Mental disorders, especially schizophrenia, still pose a great challenge for diagnosis in early stages. Recently, computer-aided diagnosis techniques based on resting-state functional magnetic resonance imaging (Rs-fMRI) have been developed to tackle this challenge. In this work, we investigate different decision-level and feature-level fusion schemes for discriminating between schizophrenic and normal subjects. Four types of fMRI features are investigated, namely the regional homogeneity, voxel-mirrored homotopic connectivity, fractional amplitude of low-frequency fluctuations and amplitude of low-frequency fluctuations. Data denoising and preprocessing were first applied, followed by the feature extraction module. Four different feature selection algorithms were applied, and the best discriminative features were selected using the algorithm of feature selection via concave minimization (FSV). Support vector machine classifiers were trained and tested on the COBRE dataset formed of 70 schizophrenic subjects and 70 healthy subjects. The decision-level fusion method outperformed the single-feature-type approaches and achieved a 97.85% accuracy, a 98.33% sensitivity, a 96.83% specificity. Moreover, feature-fusion scheme resulted in a 98.57% accuracy, a 99.71% sensitivity, a 97.66% specificity, and an area under the ROC curve of 0.9984. In general, decision-level and feature-level fusion schemes boosted the performance of schizophrenia detectors based on fMRI features.
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Affiliation(s)
- Ali H. Algumaei
- Department of Biomedical Engineering and Systems, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Rami F. Algunaid
- Department of Biomedical Engineering and Systems, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Muhammad A. Rushdi
- Department of Biomedical Engineering and Systems, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Inas A. Yassine
- Department of Biomedical Engineering and Systems, Faculty of Engineering, Cairo University, Giza, Egypt
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13
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Machine Learning in Neuro-Oncology, Epilepsy, Alzheimer's Disease, and Schizophrenia. ACTA NEUROCHIRURGICA. SUPPLEMENT 2021; 134:349-361. [PMID: 34862559 DOI: 10.1007/978-3-030-85292-4_39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Applications of machine learning (ML) in translational medicine include therapeutic drug creation, diagnostic development, surgical planning, outcome prediction, and intraoperative assistance. Opportunities in the neurosciences are rich given advancement in our understanding of the brain, expanding indications for intervention, and diagnostic challenges often characterized by multiple clinical and environmental factors. We present a review of ML in neuro-oncology, epilepsy, Alzheimer's disease, and schizophrenia to highlight recent progression in these field, optimizing machine learning capabilities in their current forms. Supervised learning models appear to be the most commonly incorporated algorithm models for machine learning across the reviewed neuroscience disciplines with primary aim of diagnosis. Accuracy ranges are high from 63% to 99% across all algorithms investigated. Machine learning contributions to neurosurgery, neurology, psychiatry, and the clinical and basic science neurosciences may enhance current medical best practices while also broadening our understanding of dynamic neural networks and the brain.
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14
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Jiang X, Zhou C, Ao N, Gu W, Li J, Chen Y. Scarcity Mindset Neuro Network Decoding With Reward: A Tree-Based Model and Functional Near-Infrared Spectroscopy Study. Front Hum Neurosci 2021; 15:736415. [PMID: 34899213 PMCID: PMC8652088 DOI: 10.3389/fnhum.2021.736415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Resource scarcity imposes challenging demands on the human cognitive system. Insufficient resources cause the scarcity mindset to affect cognitive performance, while reward enhances cognitive function. Here, we examined how reward and scarcity simultaneously contribute to cognitive performance. Experimental manipulation to induce a polar scarcity mindset and reward conditions within participants under functional near-infrared spectroscopy (fNIRS) recording was implemented to explore the mechanism underlying the scarcity mindset and reward in terms of behavior and neurocognition. Participants showed decreased functional connectivity from the dorsolateral prefrontal cortex (DLPFC) to the ventrolateral prefrontal cortex (VLPFC) with a scarcity mindset, a region often implicated in cognitive control. Moreover, under reward conditions, the brain activation of the maximum total Hb bold signal was mainly located in the left hemisphere [channels 1, 3, and 4, left ventrolateral prefrontal cortex (L-VLPFC) and channel 6, left dorsolateral prefrontal cortex (L-DLPFC)], and there was also significant brain activation of the right dorsolateral prefrontal cortex (R-DLPFC) in the right hemisphere (channel 17). Furthermore, these data indicate the underlying neural changes of the scarcity mentality and demonstrate that brain activities may underlie reward processing. Additionally, the base-tree machine learning model was trained to detect the mechanism of reward function in the prefrontal cortex (PFC). According to SHapley Additive exPlanations (SHAP), channel 8 contributed the most important effect, as well as demonstrating a high-level interrelationship with other channels.
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Affiliation(s)
- Xiaowei Jiang
- Institute of Psychology and Behavior, Henan University, Kaifeng, China
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Chenghao Zhou
- Institute of Psychology and Behavior, Henan University, Kaifeng, China
| | - Na Ao
- Institute of Psychology and Behavior, Henan University, Kaifeng, China
| | - Wenke Gu
- Institute of Psychology and Behavior, Henan University, Kaifeng, China
| | - Jingyi Li
- Institute of Psychology and Behavior, Henan University, Kaifeng, China
| | - Yanan Chen
- Institute of Psychology and Behavior, Henan University, Kaifeng, China
- Institute of Cognition, Brain and Health, Henan University, Kaifeng, China
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15
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Rahaman MA, Chen J, Fu Z, Lewis N, Iraji A, Calhoun VD. Multi-modal deep learning of functional and structural neuroimaging and genomic data to predict mental illness. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:3267-3272. [PMID: 34891938 DOI: 10.1109/embc46164.2021.9630693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Neuropsychiatric disorders such as schizophrenia are very heterogeneous in nature and typically diagnosed using self-reported symptoms. This makes it difficult to pose a confident prediction on the cases and does not provide insight into the underlying neural and biological mechanisms of these disorders. Combining neuroimaging and genomic data with a multi-modal 'predictome' paves the way for biologically informed markers and may improve prediction reliability. With that, we develop a multi-modal deep learning framework by fusing data from different modalities to capture the interaction between the latent features and evaluate their complementary information in characterizing schizophrenia. Our deep model uses structural MRI, functional MRI, and genome-wide polymorphism data to perform the classification task. It includes a multi-layer feed-forward network, an encoder, and a long short-term memory (LSTM) unit with attention to learn the latent features and adopt a joint training scheme capturing synergies between the modalities. The hybrid network also uses different regularizers for addressing the inherent overfitting and modality-specific bias in the multi-modal setup. Next, we run the network through a saliency model to analyze the learned features. Integrating modalities enhances the performance of the classifier, and our framework acquired 88% (P < 0.0001) accuracy on a dataset of 437 subjects. The trimodal accuracy is comparable to the state-of-the-art performance on a data collection of this size and outperforms the unimodal and bimodal baselines we compared. Model introspection was used to expose the salient neural features and genes/biological pathways associated with schizophrenia. To our best knowledge, this is the first approach that fuses genomic information with structural and functional MRI biomarkers for predicting schizophrenia. We believe this type of modality blending can better explain the disorder's dynamics by adding cross-modal prospects.Clinical Relevance- This study combinedly learns imaging and genomic features for the classification of schizophrenia. The data fusion scheme extracts modality interactions, and the saliency experiments report multiple functional and structural networks closely connected to the disorder.
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16
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Jain P, Sao AK, Minhas AS. Analyzing the Effect of Resolution of Network Nodes on the Resting State Functional Connectivity Maps of Schizophrenic Human Brains. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:6695-6698. [PMID: 34892644 DOI: 10.1109/embc46164.2021.9630822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Functional connectivity (FC) mapping from resting-state functional magnetic resonance imaging (rsfMRI) data is a widely used technique to characterize the brain abnormalities in mental health disorders. Using atlases for brain parcellation is an important intermediate step in calculation of FC maps. Atlases with varying resolution (number of nodes in an atlas) have been deployed by researchers to study the abnormal brain functions in Schizophrenia. In this work, we compared the variations in FC maps of Schizophrenic brains obtained from three different atlases: AAL atlas (2002), Dosenbach atlas (2010), and the Brainnetome atlas (2016). To evaluate the atlas-dependent variations in FC maps, we relied on the capability of the features of FC maps in accurately classifying a given data into healthy or Schizophrenia group. Our results indicate that the high-resolution Dosenbach and Brainnetome atlases perform better than AAL atlas in terms of the accuracy, sensitivity and specificity of the SVM classifier.
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17
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Gallos IK, Galaris E, Siettos CI. Construction of embedded fMRI resting-state functional connectivity networks using manifold learning. Cogn Neurodyn 2021; 15:585-608. [PMID: 34367362 PMCID: PMC8286923 DOI: 10.1007/s11571-020-09645-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/26/2020] [Accepted: 10/06/2020] [Indexed: 11/26/2022] Open
Abstract
We construct embedded functional connectivity networks (FCN) from benchmark resting-state functional magnetic resonance imaging (rsfMRI) data acquired from patients with schizophrenia and healthy controls based on linear and nonlinear manifold learning algorithms, namely, Multidimensional Scaling, Isometric Feature Mapping, Diffusion Maps, Locally Linear Embedding and kernel PCA. Furthermore, based on key global graph-theoretic properties of the embedded FCN, we compare their classification potential using machine learning. We also assess the performance of two metrics that are widely used for the construction of FCN from fMRI, namely the Euclidean distance and the cross correlation metric. We show that diffusion maps with the cross correlation metric outperform the other combinations.
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Affiliation(s)
- Ioannis K. Gallos
- School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Athens, Greece
| | - Evangelos Galaris
- Dipartimento di Matematica e Applicazioni “Renato Caccioppoli”, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Constantinos I. Siettos
- Dipartimento di Matematica e Applicazioni “Renato Caccioppoli”, Università degli Studi di Napoli Federico II, Napoli, Italy
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18
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Zang J, Huang Y, Kong L, Lei B, Ke P, Li H, Zhou J, Xiong D, Li G, Chen J, Li X, Xiang Z, Ning Y, Wu F, Wu K. Effects of Brain Atlases and Machine Learning Methods on the Discrimination of Schizophrenia Patients: A Multimodal MRI Study. Front Neurosci 2021; 15:697168. [PMID: 34385901 PMCID: PMC8353157 DOI: 10.3389/fnins.2021.697168] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 11/24/2022] Open
Abstract
Recently, machine learning techniques have been widely applied in discriminative studies of schizophrenia (SZ) patients with multimodal magnetic resonance imaging (MRI); however, the effects of brain atlases and machine learning methods remain largely unknown. In this study, we collected MRI data for 61 first-episode SZ patients (FESZ), 79 chronic SZ patients (CSZ) and 205 normal controls (NC) and calculated 4 MRI measurements, including regional gray matter volume (GMV), regional homogeneity (ReHo), amplitude of low-frequency fluctuation and degree centrality. We systematically analyzed the performance of two classifications (SZ vs NC; FESZ vs CSZ) based on the combinations of three brain atlases, five classifiers, two cross validation methods and 3 dimensionality reduction algorithms. Our results showed that the groupwise whole-brain atlas with 268 ROIs outperformed the other two brain atlases. In addition, the leave-one-out cross validation was the best cross validation method to select the best hyperparameter set, but the classification performances by different classifiers and dimensionality reduction algorithms were quite similar. Importantly, the contributions of input features to both classifications were higher with the GMV and ReHo features of brain regions in the prefrontal and temporal gyri. Furthermore, an ensemble learning method was performed to establish an integrated model, in which classification performance was improved. Taken together, these findings indicated the effects of these factors in constructing effective classifiers for psychiatric diseases and showed that the integrated model has the potential to improve the clinical diagnosis and treatment evaluation of SZ.
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Affiliation(s)
- Jinyu Zang
- Department of Biomedical Engineering, School of Material Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
| | - Yuanyuan Huang
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou Huiai Hospital, Guangzhou, China
| | - Lingyin Kong
- Department of Biomedical Engineering, School of Material Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
| | - Bingye Lei
- Department of Biomedical Engineering, School of Material Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
| | - Pengfei Ke
- Department of Biomedical Engineering, School of Material Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
| | - Hehua Li
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou Huiai Hospital, Guangzhou, China
| | - Jing Zhou
- Department of Biomedical Engineering, School of Material Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
| | - Dongsheng Xiong
- Department of Biomedical Engineering, School of Material Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
| | - Guixiang Li
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou, China
- National Engineering Research Center for Healthcare Devices, Guangzhou, China
| | - Jun Chen
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou, China
- National Engineering Research Center for Healthcare Devices, Guangzhou, China
| | - Xiaobo Li
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, United States
| | - Zhiming Xiang
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou, China
- Department of Radiology, Panyu Central Hospital of Guangzhou, Guangzhou, China
| | - Yuping Ning
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou Huiai Hospital, Guangzhou, China
| | - Fengchun Wu
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou Huiai Hospital, Guangzhou, China
| | - Kai Wu
- Department of Biomedical Engineering, School of Material Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, China
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou Huiai Hospital, Guangzhou, China
- Guangdong Engineering Technology Research Center for Diagnosis and Rehabilitation of Dementia, Guangzhou, China
- National Engineering Research Center for Healthcare Devices, Guangzhou, China
- Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, China
- Department of Nuclear Medicine and Radiology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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19
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Masoudi B, Daneshvar S, Razavi SN. Multi-modal neuroimaging feature fusion via 3D Convolutional Neural Network architecture for schizophrenia diagnosis. INTELL DATA ANAL 2021. [DOI: 10.3233/ida-205113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Early and precise diagnosis of schizophrenia disorder (SZ) has an essential role in the quality of a patient’s life and future treatments. Structural and functional neuroimaging provides robust biomarkers for understanding the anatomical and functional changes associated with SZ. Each of the neuroimaging techniques shows only a different perspective on the functional or structural of the brain, while multi-modal fusion can reveal latent connections in the brain. In this paper, we propose an approach for the fusion of structural and functional brain data with a deep learning-based model to take advantage of data fusion and increase the accuracy of schizophrenia disorder diagnosis. The proposed method consists of an architecture of 3D convolutional neural networks (CNNs) that applied to magnetic resonance imaging (MRI), functional magnetic resonance imaging (fMRI), and diffusion tensor imaging (DTI) extracted features. We use 3D MRI patches, fMRI spatial independent component analysis (ICA) map, and DTI fractional anisotropy (FA) as model inputs. Our method is validated on the COBRE dataset, and an average accuracy of 99.35% is obtained. The proposed method demonstrates promising classification performance and can be applied to real data.
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Affiliation(s)
- Babak Masoudi
- Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
| | - Sabalan Daneshvar
- Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
- Department of Electronic and Computer Engineering, College of Engineering, Design and Physical Sciences, Brunel University, London, UK
| | - Seyed Naser Razavi
- Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
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20
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Mansourian M, Khademi S, Marateb HR. A Comprehensive Review of Computer-Aided Diagnosis of Major Mental and Neurological Disorders and Suicide: A Biostatistical Perspective on Data Mining. Diagnostics (Basel) 2021; 11:393. [PMID: 33669114 PMCID: PMC7996506 DOI: 10.3390/diagnostics11030393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/13/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
The World Health Organization (WHO) suggests that mental disorders, neurological disorders, and suicide are growing causes of morbidity. Depressive disorders, schizophrenia, bipolar disorder, Alzheimer's disease, and other dementias account for 1.84%, 0.60%, 0.33%, and 1.00% of total Disability Adjusted Life Years (DALYs). Furthermore, suicide, the 15th leading cause of death worldwide, could be linked to mental disorders. More than 68 computer-aided diagnosis (CAD) methods published in peer-reviewed journals from 2016 to 2021 were analyzed, among which 75% were published in the year 2018 or later. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol was adopted to select the relevant studies. In addition to the gold standard, the sample size, neuroimaging techniques or biomarkers, validation frameworks, the classifiers, and the performance indices were analyzed. We further discussed how various performance indices are essential based on the biostatistical and data mining perspective. Moreover, critical information related to the Transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD) guidelines was analyzed. We discussed how balancing the dataset and not using external validation could hinder the generalization of the CAD methods. We provided the list of the critical issues to consider in such studies.
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Affiliation(s)
- Mahsa Mansourian
- Department of Medical Physics, School of Medicine, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran;
| | - Sadaf Khademi
- Biomedical Engineering Department, Faculty of Engineering, University of Isfahan, Isfahan 8174-67344, Iran;
| | - Hamid Reza Marateb
- Biomedical Engineering Department, Faculty of Engineering, University of Isfahan, Isfahan 8174-67344, Iran;
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21
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Quaak M, van de Mortel L, Thomas RM, van Wingen G. Deep learning applications for the classification of psychiatric disorders using neuroimaging data: Systematic review and meta-analysis. Neuroimage Clin 2021; 30:102584. [PMID: 33677240 PMCID: PMC8209481 DOI: 10.1016/j.nicl.2021.102584] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 12/20/2022]
Abstract
Deep learning (DL) methods have been increasingly applied to neuroimaging data to identify patients with psychiatric and neurological disorders. This review provides an overview of the different DL applications within psychiatry and compares DL model accuracy to standard machine learning (SML). Fifty-three articles were included for qualitative analysis, primarily investigating autism spectrum disorder (ASD; n = 22), schizophrenia (SZ; n = 22) and attention-deficit/hyperactivity disorder (ADHD; n = 9). Thirty-two of the thirty-five studies that directly compared DL to SML reported a higher accuracy for DL. Only sixteen studies could be included in a meta-regression to quantitatively compare DL and SML performance. This showed a higher odds ratio for DL models, though the comparison attained significance only for ASD. Our results suggest that deep learning of neuroimaging data is a promising tool for the classification of individual psychiatric patients. However, it is not yet used to its full potential: most studies use pre-engineered features, whereas one of the main advantages of DL is its ability to learn representations of minimally processed data. Our current evaluation is limited by minimal reporting of performance measures to enable quantitative comparisons, and the restriction to ADHD, SZ and ASD as current research focusses on large publicly available datasets. To truly uncover the added value of DL, we need carefully designed comparisons of SML and DL models which are yet rarely performed.
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Affiliation(s)
- Mirjam Quaak
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Meibergdreef 5, 1105 AZ Amsterdam, The Netherlands
| | - Laurens van de Mortel
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Meibergdreef 5, 1105 AZ Amsterdam, The Netherlands
| | - Rajat Mani Thomas
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Meibergdreef 5, 1105 AZ Amsterdam, The Netherlands
| | - Guido van Wingen
- Amsterdam UMC, University of Amsterdam, Department of Psychiatry, Meibergdreef 5, 1105 AZ Amsterdam, The Netherlands.
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22
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Todeva-Radneva A, Paunova R, Kandilarova S, St Stoyanov D. The Value of Neuroimaging Techniques in the Translation and Transdiagnostic Validation of Psychiatric Diagnoses - Selective Review. Curr Top Med Chem 2021; 20:540-553. [PMID: 32003690 DOI: 10.2174/1568026620666200131095328] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 01/05/2023]
Abstract
Psychiatric diagnosis has long been perceived as more of an art than a science since its foundations lie within the observation, and the self-report of the patients themselves and objective diagnostic biomarkers are lacking. Furthermore, the diagnostic tools in use not only stray away from the conventional medical framework but also remain invalidated with evidence-based concepts. However, neuroscience, as a source of valid objective knowledge has initiated the process of a paradigm shift underlined by the main concept of psychiatric disorders being "brain disorders". It is also a bridge closing the explanatory gap among the different fields of medicine via the translation of the knowledge within a multidisciplinary framework. The contemporary neuroimaging methods, such as fMRI provide researchers with an entirely new set of tools to reform the current status quo by creating an opportunity to define and validate objective biomarkers that can be translated into clinical practice. Combining multiple neuroimaging techniques with the knowledge of the role of genetic factors, neurochemical imbalance and neuroinflammatory processes in the etiopathophysiology of psychiatric disorders is a step towards a comprehensive biological explanation of psychiatric disorders and a final differentiation of psychiatry as a well-founded medical science. In addition, the neuroscientific knowledge gained thus far suggests a necessity for directional change to exploring multidisciplinary concepts, such as multiple causality and dimensionality of psychiatric symptoms and disorders. A concomitant viewpoint transition of the notion of validity in psychiatry with a focus on an integrative validatory approach may facilitate the building of a collaborative bridge above the wall existing between the scientific fields analyzing the mind and those studying the brain.
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Affiliation(s)
- Anna Todeva-Radneva
- Department of Psychiatry and Medical Psychology and Scientific Research Institute, The Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Rositsa Paunova
- Department of Psychiatry and Medical Psychology and Scientific Research Institute, The Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Sevdalina Kandilarova
- Department of Psychiatry and Medical Psychology and Scientific Research Institute, The Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Drozdstoy St Stoyanov
- Department of Psychiatry and Medical Psychology and Scientific Research Institute, The Medical University of Plovdiv, Plovdiv, Bulgaria
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23
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Park SM, Jeong B, Oh DY, Choi CH, Jung HY, Lee JY, Lee D, Choi JS. Identification of Major Psychiatric Disorders From Resting-State Electroencephalography Using a Machine Learning Approach. Front Psychiatry 2021; 12:707581. [PMID: 34483999 PMCID: PMC8416434 DOI: 10.3389/fpsyt.2021.707581] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/20/2021] [Indexed: 12/03/2022] Open
Abstract
We aimed to develop a machine learning (ML) classifier to detect and compare major psychiatric disorders using electroencephalography (EEG). We retrospectively collected data from medical records, intelligence quotient (IQ) scores from psychological assessments, and quantitative EEG (QEEG) at resting-state assessments from 945 subjects [850 patients with major psychiatric disorders (six large-categorical and nine specific disorders) and 95 healthy controls (HCs)]. A combination of QEEG parameters including power spectrum density (PSD) and functional connectivity (FC) at frequency bands was used to establish models for the binary classification between patients with each disorder and HCs. The support vector machine, random forest, and elastic net ML methods were applied, and prediction performances were compared. The elastic net model with IQ adjustment showed the highest accuracy. The best feature combinations and classification accuracies for discrimination between patients and HCs with adjusted IQ were as follows: schizophrenia = alpha PSD, 93.83%; trauma and stress-related disorders = beta FC, 91.21%; anxiety disorders = whole band PSD, 91.03%; mood disorders = theta FC, 89.26%; addictive disorders = theta PSD, 85.66%; and obsessive-compulsive disorder = gamma FC, 74.52%. Our findings suggest that ML in EEG may predict major psychiatric disorders and provide an objective index of psychiatric disorders.
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Affiliation(s)
- Su Mi Park
- Department of Psychiatry, SMG-SNU Boramae Medical Center, Seoul, South Korea
| | - Boram Jeong
- Department of Statistics, Ewha Womans University, Seoul, South Korea
| | - Da Young Oh
- Department of Psychiatry, SMG-SNU Boramae Medical Center, Seoul, South Korea
| | - Chi-Hyun Choi
- Department of Psychiatry, SMG-SNU Boramae Medical Center, Seoul, South Korea
| | - Hee Yeon Jung
- Department of Psychiatry, SMG-SNU Boramae Medical Center, Seoul, South Korea.,Department of Psychiatry and Behavioral Science, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Human Behavioral Medicine, Seoul National University Medical Research Center, Seoul, South Korea
| | - Jun-Young Lee
- Department of Psychiatry, SMG-SNU Boramae Medical Center, Seoul, South Korea.,Department of Psychiatry and Behavioral Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Donghwan Lee
- Department of Statistics, Ewha Womans University, Seoul, South Korea
| | - Jung-Seok Choi
- Department of Psychiatry, SMG-SNU Boramae Medical Center, Seoul, South Korea.,Department of Psychiatry and Behavioral Science, Seoul National University College of Medicine, Seoul, South Korea
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24
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Faria AV, Zhao Y, Ye C, Hsu J, Yang K, Cifuentes E, Wang L, Mori S, Miller M, Caffo B, Sawa A. Multimodal MRI assessment for first episode psychosis: A major change in the thalamus and an efficient stratification of a subgroup. Hum Brain Mapp 2020; 42:1034-1053. [PMID: 33377594 PMCID: PMC7856640 DOI: 10.1002/hbm.25276] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/29/2020] [Accepted: 10/18/2020] [Indexed: 02/06/2023] Open
Abstract
Multi‐institutional brain imaging studies have emerged to resolve conflicting results among individual studies. However, adjusting multiple variables at the technical and cohort levels is challenging. Therefore, it is important to explore approaches that provide meaningful results from relatively small samples at institutional levels. We studied 87 first episode psychosis (FEP) patients and 62 healthy subjects by combining supervised integrated factor analysis (SIFA) with a novel pipeline for automated structure‐based analysis, an efficient and comprehensive method for dimensional data reduction that our group recently established. We integrated multiple MRI features (volume, DTI indices, resting state fMRI—rsfMRI) in the whole brain of each participant in an unbiased manner. The automated structure‐based analysis showed widespread DTI abnormalities in FEP and rs‐fMRI differences between FEP and healthy subjects mostly centered in thalamus. The combination of multiple modalities with SIFA was more efficient than the use of single modalities to stratify a subgroup of FEP (individuals with schizophrenia or schizoaffective disorder) that had more robust deficits from the overall FEP group. The information from multiple MRI modalities and analytical methods highlighted the thalamus as significantly abnormal in FEP. This study serves as a proof‐of‐concept for the potential of this methodology to reveal disease underpins and to stratify populations into more homogeneous sub‐groups.
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Affiliation(s)
- Andreia V Faria
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yi Zhao
- Department of Biostatistics, Indiana University, School of Medicine, Indianapolis, Indiana, USA
| | - Chenfei Ye
- Department of Electronics and Information, Harbin Institute of Technology Shenzhen Graduate School, Guangdong, China
| | - Johnny Hsu
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kun Yang
- Department Psychiatry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth Cifuentes
- Department Psychiatry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lei Wang
- Department of Psychiatry and Behavioral Sciences and Radiology, Northwestern University, Evanston, Illinois, USA
| | - Susumu Mori
- Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Miller
- Department of Biomedical Engineering, The Whiting School of Engineering, Baltimore, Maryland, USA
| | - Brian Caffo
- Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Akira Sawa
- Department Psychiatry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Biomedical Engineering, The Whiting School of Engineering, Baltimore, Maryland, USA.,Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Mental Health, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
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25
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Cortical abnormalities and identification for first-episode schizophrenia via high-resolution magnetic resonance imaging. Biomark Neuropsychiatry 2020. [DOI: 10.1016/j.bionps.2020.100022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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26
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3D-Deep Learning Based Automatic Diagnosis of Alzheimer's Disease with Joint MMSE Prediction Using Resting-State fMRI. Neuroinformatics 2020; 18:71-86. [PMID: 31093956 DOI: 10.1007/s12021-019-09419-w] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We performed this research to 1) evaluate a novel deep learning method for the diagnosis of Alzheimer's disease (AD) and 2) jointly predict the Mini Mental State Examination (MMSE) scores of South Korean patients with AD. Using resting-state functional Magnetic Resonance Imaging (rs-fMRI) scans of 331 participants, we obtained functional 3-dimensional (3-D) independent component spatial maps for use as features in classification and regression tasks. A 3-D convolutional neural network (CNN) architecture was developed for the classification task. MMSE scores were predicted using: linear least square regression (LLSR), support vector regression, bagging-based ensemble regression, and tree regression with group independent component analysis (gICA) features. To improve MMSE regression performance, we applied feature optimization methods including least absolute shrinkage and selection operator and support vector machine-based recursive feature elimination (SVM-RFE). The mean balanced test accuracy was 85.27% for the classification of AD versus healthy controls. The medial visual, default mode, dorsal attention, executive, and auditory related networks were mainly associated with AD. The maximum clinical MMSE score prediction accuracy with the LLSR method applied on gICA combined with SVM-RFE features had the lowest root mean square error (3.27 ± 0.58) and the highest R2 value (0.63 ± 0.02). Classification of AD and healthy controls can be successfully achieved using only rs-fMRI and MMSE scores can be accurately predicted using functional independent component features. In the absence of trained clinicians, AD disease status and clinical MMSE scores can be jointly predicted using 3-D deep learning and regression learning approaches with rs-fMRI data.
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27
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Rashid B, Calhoun V. Towards a brain-based predictome of mental illness. Hum Brain Mapp 2020; 41:3468-3535. [PMID: 32374075 PMCID: PMC7375108 DOI: 10.1002/hbm.25013] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 01/10/2023] Open
Abstract
Neuroimaging-based approaches have been extensively applied to study mental illness in recent years and have deepened our understanding of both cognitively healthy and disordered brain structure and function. Recent advancements in machine learning techniques have shown promising outcomes for individualized prediction and characterization of patients with psychiatric disorders. Studies have utilized features from a variety of neuroimaging modalities, including structural, functional, and diffusion magnetic resonance imaging data, as well as jointly estimated features from multiple modalities, to assess patients with heterogeneous mental disorders, such as schizophrenia and autism. We use the term "predictome" to describe the use of multivariate brain network features from one or more neuroimaging modalities to predict mental illness. In the predictome, multiple brain network-based features (either from the same modality or multiple modalities) are incorporated into a predictive model to jointly estimate features that are unique to a disorder and predict subjects accordingly. To date, more than 650 studies have been published on subject-level prediction focusing on psychiatric disorders. We have surveyed about 250 studies including schizophrenia, major depression, bipolar disorder, autism spectrum disorder, attention-deficit hyperactivity disorder, obsessive-compulsive disorder, social anxiety disorder, posttraumatic stress disorder, and substance dependence. In this review, we present a comprehensive review of recent neuroimaging-based predictomic approaches, current trends, and common shortcomings and share our vision for future directions.
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Affiliation(s)
- Barnaly Rashid
- Department of PsychiatryHarvard Medical SchoolBostonMassachusettsUSA
| | - Vince Calhoun
- Tri‐Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)Georgia State University, Georgia Institute of Technology, and Emory UniversityAtlantaGeorgiaUSA
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28
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Peng Y, Zhang X, Li Y, Su Q, Wang S, Liu F, Yu C, Liang M. MVPANI: A Toolkit With Friendly Graphical User Interface for Multivariate Pattern Analysis of Neuroimaging Data. Front Neurosci 2020; 14:545. [PMID: 32742251 PMCID: PMC7364177 DOI: 10.3389/fnins.2020.00545] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/04/2020] [Indexed: 12/03/2022] Open
Abstract
With the rapid development of machine learning techniques, multivariate pattern analysis (MVPA) is becoming increasingly popular in the field of neuroimaging data analysis. Several software packages have been developed to facilitate its application in neuroimaging studies. As most of these software packages are based on command lines, researchers are required to learn how to program, which has greatly limited the use of MVPA for researchers without programming skills. Moreover, lacking a graphical user interface (GUI) also hinders the standardization of the application of MVPA in neuroimaging studies and, consequently, the replication of previous studies or comparisons of results between different studies. Therefore, we developed a GUI-based toolkit for MVPA of neuroimaging data: MVPANI (MVPA for Neuroimaging). Compared with other existing software packages, MVPANI has several advantages. First, MVPANI has a GUI and is, thus, more friendly for non-programmers. Second, MVPANI offers a variety of machine learning algorithms with the flexibility of parameter modification so that researchers can test different algorithms and tune parameters to identify the most suitable algorithms and parameters for their own data. Third, MVPANI also offers the function of data fusion at two levels (feature level or decision level) to utilize complementary information contained in different measures obtained from multimodal neuroimaging techniques. In this paper, we introduce this toolkit and provide four examples to demonstrate its usage, including (1) classification between patients and controls, (2) identification of brain areas containing discriminating information, (3) prediction of clinical scores, and (4) multimodal data fusion.
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Affiliation(s)
- Yanmin Peng
- School of Medical Imaging, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China
| | - Xi Zhang
- School of Medical Imaging, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China
| | - Yifan Li
- School of Medical Imaging, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China
| | - Qian Su
- School of Medical Imaging, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China
| | - Sijia Wang
- School of Medical Imaging, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China
| | - Feng Liu
- Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China.,Department of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Chunshui Yu
- School of Medical Imaging, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China.,Department of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Meng Liang
- School of Medical Imaging, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China
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29
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A Systematic Characterization of Structural Brain Changes in Schizophrenia. Neurosci Bull 2020; 36:1107-1122. [PMID: 32495122 DOI: 10.1007/s12264-020-00520-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/13/2020] [Indexed: 01/10/2023] Open
Abstract
A systematic characterization of the similarities and differences among different methods for detecting structural brain abnormalities in schizophrenia, such as voxel-based morphometry (VBM), tensor-based morphometry (TBM), and projection-based thickness (PBT), is important for understanding the brain pathology in schizophrenia and for developing effective biomarkers for a diagnosis of schizophrenia. However, such studies are still lacking. Here, we performed VBM, TBM, and PBT analyses on T1-weighted brain MR images acquired from 116 patients with schizophrenia and 116 healthy controls. We found that, although all methods detected wide-spread structural changes, different methods captured different information - only 10.35% of the grey matter changes in cortex were detected by all three methods, and VBM only detected 11.36% of the white matter changes detected by TBM. Further, pattern classification between patients and controls revealed that combining different measures improved the classification accuracy (81.9%), indicating that fusion of different structural measures serves as a better neuroimaging marker for the objective diagnosis of schizophrenia.
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30
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Steardo L, Carbone EA, de Filippis R, Pisanu C, Segura-Garcia C, Squassina A, De Fazio P, Steardo L. Application of Support Vector Machine on fMRI Data as Biomarkers in Schizophrenia Diagnosis: A Systematic Review. Front Psychiatry 2020; 11:588. [PMID: 32670113 PMCID: PMC7326270 DOI: 10.3389/fpsyt.2020.00588] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/08/2020] [Indexed: 01/06/2023] Open
Abstract
Non-invasive measurements of brain function and structure as neuroimaging in patients with mental illnesses are useful and powerful tools for studying discriminatory biomarkers. To date, functional MRI (fMRI), structural MRI (sMRI) represent the most used techniques to provide multiple perspectives on brain function, structure, and their connectivity. Recently, there has been rising attention in using machine-learning (ML) techniques, pattern recognition methods, applied to neuroimaging data to characterize disease-related alterations in brain structure and function and to identify phenotypes, for example, for translation into clinical and early diagnosis. Our aim was to provide a systematic review according to the PRISMA statement of Support Vector Machine (SVM) techniques in making diagnostic discrimination between SCZ patients from healthy controls using neuroimaging data from functional MRI as input. We included studies using SVM as ML techniques with patients diagnosed with Schizophrenia. From an initial sample of 660 papers, at the end of the screening process, 22 articles were selected, and included in our review. This technique can be a valid, inexpensive, and non-invasive support to recognize and detect patients at an early stage, compared to any currently available assessment or clinical diagnostic methods in order to save crucial time. The higher accuracy of SVM models and the new integrated methods of ML techniques could play a decisive role to detect patients with SCZ or other major psychiatric disorders in the early stages of the disease or to potentially determine their neuroimaging risk factors in the near future.
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Affiliation(s)
- Luca Steardo
- Department of Health Sciences, School of Medicine and Surgery, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Elvira Anna Carbone
- Department of Health Sciences, School of Medicine and Surgery, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Renato de Filippis
- Department of Health Sciences, School of Medicine and Surgery, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Claudia Pisanu
- Section of Neuroscience and Clinical Pharmacology, Department of Biomedical Sciences, Faculty of Medicine and Surgery, University of Cagliari, Cagliari, Italy
| | - Cristina Segura-Garcia
- Department of Medical and Surgical Science, University of Magna Graecia, Catanzaro, Italy
| | - Alessio Squassina
- Section of Neuroscience and Clinical Pharmacology, Department of Biomedical Sciences, Faculty of Medicine and Surgery, University of Cagliari, Cagliari, Italy.,Department of Psychiatry, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Pasquale De Fazio
- Department of Health Sciences, School of Medicine and Surgery, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Luca Steardo
- Department of Physiology and Pharmacology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome, Italy.,Department of Psychiatry, Giustino Fortunato University, Benevento, Italy
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31
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Lei D, Pinaya WHL, Young J, van Amelsvoort T, Marcelis M, Donohoe G, Mothersill DO, Corvin A, Vieira S, Huang X, Lui S, Scarpazza C, Arango C, Bullmore E, Gong Q, McGuire P, Mechelli A. Integrating machining learning and multimodal neuroimaging to detect schizophrenia at the level of the individual. Hum Brain Mapp 2019; 41:1119-1135. [PMID: 31737978 PMCID: PMC7268084 DOI: 10.1002/hbm.24863] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 02/05/2023] Open
Abstract
Schizophrenia is a severe psychiatric disorder associated with both structural and functional brain abnormalities. In the past few years, there has been growing interest in the application of machine learning techniques to neuroimaging data for the diagnostic and prognostic assessment of this disorder. However, the vast majority of studies published so far have used either structural or functional neuroimaging data, without accounting for the multimodal nature of the disorder. Structural MRI and resting‐state functional MRI data were acquired from a total of 295 patients with schizophrenia and 452 healthy controls at five research centers. We extracted features from the data including gray matter volume, white matter volume, amplitude of low‐frequency fluctuation, regional homogeneity and two connectome‐wide based metrics: structural covariance matrices and functional connectivity matrices. A support vector machine classifier was trained on each dataset separately to distinguish the subjects at individual level using each of the single feature as well as their combination, and 10‐fold cross‐validation was used to assess the performance of the model. Functional data allow higher accuracy of classification than structural data (mean 82.75% vs. 75.84%). Within each modality, the combination of images and matrices improves performance, resulting in mean accuracies of 81.63% for structural data and 87.59% for functional data. The use of all combined structural and functional measures allows the highest accuracy of classification (90.83%). We conclude that combining multimodal measures within a single model is a promising direction for developing biologically informed diagnostic tools in schizophrenia.
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Affiliation(s)
- Du Lei
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China.,Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, De Crespigny Park, London, UK
| | - Walter H L Pinaya
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, De Crespigny Park, London, UK
| | - Jonathan Young
- Department of Neuroimaging, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Therese van Amelsvoort
- Department of Psychiatry and Neuropsychology, School of Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Machteld Marcelis
- Department of Psychiatry and Neuropsychology, School of Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherlands.,Mental Health Care Institute Eindhoven (GGzE), Eindhoven, The Netherlands
| | - Gary Donohoe
- School of Psychology & Center for neuroimaging and Cognitive Genomics, NUI Galway University, Galway, Ireland
| | - David O Mothersill
- School of Psychology & Center for neuroimaging and Cognitive Genomics, NUI Galway University, Galway, Ireland
| | - Aiden Corvin
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Sandra Vieira
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, De Crespigny Park, London, UK
| | - Xiaoqi Huang
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Su Lui
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Cristina Scarpazza
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, De Crespigny Park, London, UK.,Department of General Psychology, University of Padua, Padua, Italy
| | - Celso Arango
- Child and Adolescent Department of Psychiatry, Hospital General Universitario Gregorio Marañon, School of Medicine, Universidad Complutense Madrid, IiSGM, CIBERSAM, Madrid, Spain
| | - Ed Bullmore
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Qiyong Gong
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China.,Psychoradiology Research Unit of Chinese Academy of Medical Sciences, West China Hospital of Sichuan University, Chengdu, Sichuan, China.,Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Philip McGuire
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, De Crespigny Park, London, UK
| | - Andrea Mechelli
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, De Crespigny Park, London, UK
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32
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Qureshi MNI, Oh J, Lee B. 3D-CNN based discrimination of schizophrenia using resting-state fMRI. Artif Intell Med 2019; 98:10-17. [DOI: 10.1016/j.artmed.2019.06.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/23/2019] [Accepted: 06/21/2019] [Indexed: 11/30/2022]
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33
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Finotelli P, Forlim CG, Klock L, Pini A, Bächle J, Stoll L, Giemsa P, Fuchs M, Schoofs N, Montag C, Dulio P, Gallinat J, Kühn S. New Graph-Theoretical-Multimodal Approach Using Temporal and Structural Correlations Reveals Disruption in the Thalamo-Cortical Network in Patients with Schizophrenia. Brain Connect 2019; 9:760-769. [PMID: 31232080 DOI: 10.1089/brain.2018.0654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Schizophrenia has been understood as a network disease with altered functional and structural connectivity in multiple brain networks compatible to the extremely broad spectrum of psychopathological, cognitive, and behavioral symptoms in this disorder. When building brain networks, functional and structural networks are typically modeled independently: Functional network models are based on temporal correlations among brain regions, whereas structural network models are based on anatomical characteristics. Combining both features may give rise to more realistic and reliable models of brain networks. In this study, we applied a new flexible graph-theoretical-multimodal model called FD (F, the functional connectivity matrix, and D, the structural matrix) to construct brain networks combining functional, structural, and topological information of magnetic resonance imaging (MRI) measurements (structural and resting-state imaging) to patients with schizophrenia (n = 35) and matched healthy individuals (n = 41). As a reference condition, the traditional pure functional connectivity (pFC) analysis was carried out. By using the FD model, we found disrupted connectivity in the thalamo-cortical network in schizophrenic patients, whereas the pFC model failed to extract group differences after multiple comparison correction. We interpret this observation as evidence that the FD model is superior to conventional connectivity analysis, by stressing relevant features of the whole-brain connectivity, including functional, structural, and topological signatures. The FD model can be used in future research to model subtle alterations of functional and structural connectivity, resulting in pronounced clinical syndromes and major psychiatric disorders. Lastly, FD is not limited to the analysis of resting-state functional MRI, and it can be applied to electro-encephalography, magneto-encephalography, etc.
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Affiliation(s)
- Paolo Finotelli
- Department of Mathematics, Politecnico di Milano, Milan, Italy
| | - Caroline Garcia Forlim
- Clinic and Policlinic for Psychiatry and Psychotherapy, University Medical Center Hamburg - Eppendorf, Hamburg, Germany
| | - Leonie Klock
- Clinic and Policlinic for Psychiatry and Psychotherapy, University Medical Center Hamburg - Eppendorf, Hamburg, Germany
| | - Alessia Pini
- Department of Statistical Sciences, Università Cattolica del Sacro Cuore, Milan, Italy
| | - Johanna Bächle
- Department of Psychiatry and Psychotherapy, Charité University Medicine and St. Hedwig-Krankenhaus, Berlin, Germany
| | - Laura Stoll
- Department of Psychiatry and Psychotherapy, Charité University Medicine and St. Hedwig-Krankenhaus, Berlin, Germany
| | - Patrick Giemsa
- Department of Psychiatry and Psychotherapy, Charité University Medicine and St. Hedwig-Krankenhaus, Berlin, Germany
| | - Marie Fuchs
- Department of Psychiatry and Psychotherapy, Charité University Medicine and St. Hedwig-Krankenhaus, Berlin, Germany
| | - Nikola Schoofs
- Department of Psychiatry and Psychotherapy, Charité University Medicine and St. Hedwig-Krankenhaus, Berlin, Germany
| | - Christiane Montag
- Department of Psychiatry and Psychotherapy, Charité University Medicine and St. Hedwig-Krankenhaus, Berlin, Germany
| | - Paolo Dulio
- Department of Mathematics, Politecnico di Milano, Milan, Italy
| | - Jürgen Gallinat
- Clinic and Policlinic for Psychiatry and Psychotherapy, University Medical Center Hamburg - Eppendorf, Hamburg, Germany
| | - Simone Kühn
- Clinic and Policlinic for Psychiatry and Psychotherapy, University Medical Center Hamburg - Eppendorf, Hamburg, Germany
- Lise-Meitner Group for Environmental Neuroscience, Max Planck Institute for Human Development, Berlin, Germany
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Nguyen DT, Ryu S, Qureshi MNI, Choi M, Lee KH, Lee B. Hybrid multivariate pattern analysis combined with extreme learning machine for Alzheimer's dementia diagnosis using multi-measure rs-fMRI spatial patterns. PLoS One 2019; 14:e0212582. [PMID: 30794629 PMCID: PMC6386400 DOI: 10.1371/journal.pone.0212582] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 02/05/2019] [Indexed: 12/20/2022] Open
Abstract
Background Early diagnosis of Alzheimer’s disease (AD) and Mild Cognitive Impairment (MCI) is essential for timely treatment. Machine learning and multivariate pattern analysis (MVPA) for the diagnosis of brain disorders are explicitly attracting attention in the neuroimaging community. In this paper, we propose a voxel-wise discriminative framework applied to multi-measure resting-state fMRI (rs-fMRI) that integrates hybrid MVPA and extreme learning machine (ELM) for the automated discrimination of AD and MCI from the cognitive normal (CN) state. Materials and methods We used two rs-fMRI cohorts: the public Alzheimer’s disease Neuroimaging Initiative database (ADNI2) and an in-house Alzheimer’s disease cohort from South Korea, both including individuals with AD, MCI, and normal controls. After extracting three-dimensional (3-D) patterns measuring regional coherence and functional connectivity during the resting state, we performed univariate statistical t-tests to generate a 3-D mask that retained only voxels showing significant changes. Given the initial univariate features, to enhance discriminative patterns, we implemented MVPA feature reduction using support vector machine-recursive feature elimination (SVM-RFE), and least absolute shrinkage and selection operator (LASSO), in combination with the univariate t-test. Classifications were performed by an ELM, and its efficiency was compared to linear and nonlinear (radial basis function) SVMs. Results The maximal accuracies achieved by the method in the ADNI2 cohort were 98.86% (p<0.001) and 98.57% (p<0.001) for AD and MCI vs. CN, respectively. In the in-house cohort, the same accuracies were 98.70% (p<0.001) and 94.16% (p<0.001). Conclusion From a clinical perspective, combining extreme learning machine and hybrid MVPA applied on concatenations of multiple rs-fMRI biomarkers can potentially assist the clinicians in AD and MCI diagnosis.
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Affiliation(s)
- Duc Thanh Nguyen
- Department of Biomedical Science and Engineering (BMSE), Institute of Integrated Technology (IIT), Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Seungjun Ryu
- Department of Biomedical Science and Engineering (BMSE), Institute of Integrated Technology (IIT), Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Muhammad Naveed Iqbal Qureshi
- Translational Neuroimaging Laboratory, The McGill University Research Center for Studies in Aging (MCSA), McGill University, Montreal, Canada
- Alzheimer’s Disease Research Unit, Douglas Mental Health University Institute, McGill University, Montreal, Canada
- Department of Psychiatry, McGill University, Montreal, Canada
- Montreal Neurological Institute and Hospital, Montreal, Canada
| | - Min Choi
- Department of Biomedical Science and Engineering (BMSE), Institute of Integrated Technology (IIT), Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Kun Ho Lee
- National Research Center for Dementia, Chosun University, Gwangju, Republic of Korea
- Department of Biomedical Science, Chosun University, Gwangju, Republic of Korea
| | - Boreom Lee
- Department of Biomedical Science and Engineering (BMSE), Institute of Integrated Technology (IIT), Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
- * E-mail:
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Qureshi MNI, Ryu S, Song J, Lee KH, Lee B. Evaluation of Functional Decline in Alzheimer's Dementia Using 3D Deep Learning and Group ICA for rs-fMRI Measurements. Front Aging Neurosci 2019; 11:8. [PMID: 30804774 PMCID: PMC6378312 DOI: 10.3389/fnagi.2019.00008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/10/2019] [Indexed: 12/21/2022] Open
Abstract
Purpose: To perform automatic assessment of dementia severity using a deep learning framework applied to resting-state functional magnetic resonance imaging (rs-fMRI) data. Method: We divided 133 Alzheimer’s disease (AD) patients with clinical dementia rating (CDR) scores from 0.5 to 3 into two groups based on dementia severity; the groups with very mild/mild (CDR: 0.5–1) and moderate to severe (CDR: 2–3) dementia consisted of 77 and 56 subjects, respectively. We used rs-fMRI to extract functional connectivity features, calculated using independent component analysis (ICA), and performed automated severity classification with three-dimensional convolutional neural networks (3D-CNNs) based on deep learning. Results: The mean balanced classification accuracy was 0.923 ± 0.042 (p < 0.001) with a specificity of 0.946 ± 0.019 and sensitivity of 0.896 ± 0.077. The rs-fMRI data indicated that the medial frontal, sensorimotor, executive control, dorsal attention, and visual related networks mainly correlated with dementia severity. Conclusions: Our CDR-based novel classification using rs-fMRI is an acceptable objective severity indicator. In the absence of trained neuropsychologists, dementia severity can be objectively and accurately classified using a 3D-deep learning framework with rs-fMRI independent components.
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Affiliation(s)
- Muhammad Naveed Iqbal Qureshi
- Department of Biomedical Science and Engineering (BMSE), Institute of Integrated Technology (IIT), Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea.,Translational Neuroimaging Laboratory, The McGill University Research Centre for Studies in Aging, McGill University, Montreal, QC, Canada.,Alzheimer's Disease Research Unit, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada.,Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Seungjun Ryu
- Department of Biomedical Science and Engineering (BMSE), Institute of Integrated Technology (IIT), Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea
| | - Joonyoung Song
- Department of Biomedical Science and Engineering (BMSE), Institute of Integrated Technology (IIT), Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea
| | - Kun Ho Lee
- National Research Center for Dementia, Chosun University, Gwangju, South Korea.,Department of Biomedical Science, Chosun University, Gwangju, South Korea
| | - Boreom Lee
- Department of Biomedical Science and Engineering (BMSE), Institute of Integrated Technology (IIT), Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea
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de Filippis R, Carbone EA, Gaetano R, Bruni A, Pugliese V, Segura-Garcia C, De Fazio P. Machine learning techniques in a structural and functional MRI diagnostic approach in schizophrenia: a systematic review. Neuropsychiatr Dis Treat 2019; 15:1605-1627. [PMID: 31354276 PMCID: PMC6590624 DOI: 10.2147/ndt.s202418] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/09/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Diagnosis of schizophrenia (SCZ) is made exclusively clinically, since specific biomarkers that can predict the disease accurately remain unknown. Machine learning (ML) represents a promising approach that could support clinicians in the diagnosis of mental disorders. OBJECTIVES A systematic review, according to the PRISMA statement, was conducted to evaluate its accuracy to distinguish SCZ patients from healthy controls. METHODS We systematically searched PubMed, Embase, MEDLINE, PsychINFO and the Cochrane Library through December 2018 using generic terms for ML techniques and SCZ without language or time restriction. Thirty-five studies were included in this review: eight of them used structural neuroimaging, twenty-six used functional neuroimaging and one both, with a minimum accuracy >60% (most of them 75-90%). Sensitivity, Specificity and accuracy were extracted from each publication or obtained directly from authors. RESULTS Support vector machine, the most frequent technique, if associated with other ML techniques achieved accuracy close to 100%. The prefrontal and temporal cortices appeared to be the most useful brain regions for the diagnosis of SCZ. ML analysis can efficiently detect significantly altered brain connectivity in patients with SCZ (eg, default mode network, visual network, sensorimotor network, frontoparietal network and salience network). CONCLUSION The greater accuracy demonstrated by these predictive models and the new models resulting from the integration of multiple ML techniques will be increasingly decisive for early diagnosis and evaluation of the treatment response and to establish the prognosis of patients with SCZ. To achieve a real benefit for patients, the future challenge is to reach an accurate diagnosis not only through clinical evaluation but also with the aid of ML algorithms.
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Affiliation(s)
- Renato de Filippis
- Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Elvira Anna Carbone
- Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Raffaele Gaetano
- Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Antonella Bruni
- Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Valentina Pugliese
- Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Cristina Segura-Garcia
- Department of Medical and Surgical Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
| | - Pasquale De Fazio
- Department of Health Sciences, University Magna Graecia of Catanzaro, Catanzaro 88100, Italy
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37
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Kong Y, Gao J, Xu Y, Pan Y, Wang J, Liu J. Classification of autism spectrum disorder by combining brain connectivity and deep neural network classifier. Neurocomputing 2019. [DOI: 10.1016/j.neucom.2018.04.080] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Tulay EE, Metin B, Tarhan N, Arıkan MK. Multimodal Neuroimaging: Basic Concepts and Classification of Neuropsychiatric Diseases. Clin EEG Neurosci 2019; 50:20-33. [PMID: 29925268 DOI: 10.1177/1550059418782093] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Neuroimaging techniques are widely used in neuroscience to visualize neural activity, to improve our understanding of brain mechanisms, and to identify biomarkers-especially for psychiatric diseases; however, each neuroimaging technique has several limitations. These limitations led to the development of multimodal neuroimaging (MN), which combines data obtained from multiple neuroimaging techniques, such as electroencephalography, functional magnetic resonance imaging, and yields more detailed information about brain dynamics. There are several types of MN, including visual inspection, data integration, and data fusion. This literature review aimed to provide a brief summary and basic information about MN techniques (data fusion approaches in particular) and classification approaches. Data fusion approaches are generally categorized as asymmetric and symmetric. The present review focused exclusively on studies based on symmetric data fusion methods (data-driven methods), such as independent component analysis and principal component analysis. Machine learning techniques have recently been introduced for use in identifying diseases and biomarkers of disease. The machine learning technique most widely used by neuroscientists is classification-especially support vector machine classification. Several studies differentiated patients with psychiatric diseases and healthy controls with using combined datasets. The common conclusion among these studies is that the prediction of diseases increases when combining data via MN techniques; however, there remain a few challenges associated with MN, such as sample size. Perhaps in the future N-way fusion can be used to combine multiple neuroimaging techniques or nonimaging predictors (eg, cognitive ability) to overcome the limitations of MN.
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Affiliation(s)
| | | | - Nevzat Tarhan
- 1 Uskudar University, Istanbul, Turkey.,2 NPIstanbul Hospital, Istanbul, Turkey
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Sakai K, Yamada K. Machine learning studies on major brain diseases: 5-year trends of 2014–2018. Jpn J Radiol 2018; 37:34-72. [DOI: 10.1007/s11604-018-0794-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022]
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40
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Multiclass Classification of Word Imagination Speech With Hybrid Connectivity Features. IEEE Trans Biomed Eng 2018; 65:2168-2177. [DOI: 10.1109/tbme.2017.2786251] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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41
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Li Y, Liu J, Huang J, Li Z, Liang P. Learning Brain Connectivity Sub-networks by Group- Constrained Sparse Inverse Covariance Estimation for Alzheimer's Disease Classification. Front Neuroinform 2018; 12:58. [PMID: 30258358 PMCID: PMC6143825 DOI: 10.3389/fninf.2018.00058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/17/2018] [Indexed: 11/15/2022] Open
Abstract
Background/Aims: Brain functional connectivity networks constructed from resting-state functional magnetic resonance imaging (rs-fMRI) have been widely used for classifying Alzheimer's disease (AD) from normal controls (NC). However, conventional correlation analysis methods only capture the pairwise information, which may not be capable of revealing an adequate and accurate functional connectivity relationship among brain regions in the whole brain. Additionally, the non-sparse connectivity networks commonly contain a large number of spurious or insignificant connections, which are inconsistent with the sparse connectivity of actual brain networks in nature and may deteriorate the classification performance of Alzheimer's disease. Methods: To address these problems, in this paper, a new classification framework is proposed by combining the Group-constrained topology structure detection with sparse inverse covariance estimation (SICE) method to build the functional brain sub-network for each brain region. Particularly, to tune the sensitive analysis of the regularized parameters in the SICE method, a nested leave-one-out cross-validation (LOOCV) method is adopted. Sparse functional connectivity networks are thus effectively constructed by using the optimal regularized parameters. Finally, a decision classification tree (DCT) classifier is trained for classifying AD from NC based on these optimal functional brain sub-networks. The convergence performance of our proposed method is furthermore evaluated by the trend of coefficient variation. Results: Experiment results indicate that a LOOCV classification accuracy of 81.82% with a sensitivity of 80.00%, and a specificity of 83.33% can be obtained by using the proposed method for the classification AD from NC, and outperforms the most state-of-the-art methods in terms of the classification accuracy. Additionally, the experiment results of the convergence performance further suggest that our proposed scheme has a high rate of convergence. Particularly, the abnormal brain regions and functional connections identified by our proposed framework are highly associated with the underpinning pathological mechanism of the AD, which are consistent with previous studies. Conclusion: These results have demonstrated the effectiveness of the proposed Group- constrained SICE method, and are capable of clinical value to the diagnosis of Alzheimer's disease.
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Affiliation(s)
- Yang Li
- School of Automation Sciences and Electrical Engineering, Beihang University, Beijing, China.,Beijing Advanced Innovation Center for Big Data and Brain Computing, Beihang University, Beijing, China.,Beijing Advanced Innovation Center for Big Date-Based Precision Medicine, Beihang University, Beijing, China.,Fujian Provincial Key Laboratory of Information Processing and Intelligent Control, Minjiang University, Fujian, China
| | - Jingyu Liu
- School of Automation Sciences and Electrical Engineering, Beihang University, Beijing, China
| | - Jie Huang
- School of Automation Sciences and Electrical Engineering, Beihang University, Beijing, China
| | - Zuoyong Li
- Fujian Provincial Key Laboratory of Information Processing and Intelligent Control, Minjiang University, Fujian, China
| | - Peipeng Liang
- Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing, China.,School of Psychology, Capital Normal University, Beijing, China
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Du Y, Fu Z, Calhoun VD. Classification and Prediction of Brain Disorders Using Functional Connectivity: Promising but Challenging. Front Neurosci 2018; 12:525. [PMID: 30127711 PMCID: PMC6088208 DOI: 10.3389/fnins.2018.00525] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022] Open
Abstract
Brain functional imaging data, especially functional magnetic resonance imaging (fMRI) data, have been employed to reflect functional integration of the brain. Alteration in brain functional connectivity (FC) is expected to provide potential biomarkers for classifying or predicting brain disorders. In this paper, we present a comprehensive review in order to provide guidance about the available brain FC measures and typical classification strategies. We survey the state-of-the-art FC analysis methods including widely used static functional connectivity (SFC) and more recently proposed dynamic functional connectivity (DFC). Temporal correlations among regions of interest (ROIs), data-driven spatial network and functional network connectivity (FNC) are often computed to reflect SFC from different angles. SFC can be extended to DFC using a sliding-window framework, and intrinsic connectivity states along the time-varying connectivity patterns are typically extracted using clustering or decomposition approaches. We also briefly summarize window-less DFC approaches. Subsequently, we highlight various strategies for feature selection including the filter, wrapper and embedded methods. In terms of model building, we include traditional classifiers as well as more recently applied deep learning methods. Moreover, we review representative applications with remarkable classification accuracy for psychosis and mood disorders, neurodevelopmental disorder, and neurological disorders using fMRI data. Schizophrenia, bipolar disorder, autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), Alzheimer's disease and mild cognitive impairment (MCI) are discussed. Finally, challenges in the field are pointed out with respect to the inaccurate diagnosis labeling, the abundant number of possible features and the difficulty in validation. Some suggestions for future work are also provided.
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Affiliation(s)
- Yuhui Du
- The Mind Research Network, Albuquerque, NM, United States
- School of Computer & Information Technology, Shanxi University, Taiyuan, China
| | - Zening Fu
- The Mind Research Network, Albuquerque, NM, United States
| | - Vince D. Calhoun
- The Mind Research Network, Albuquerque, NM, United States
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, United States
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Takahashi T, Suzuki M. Brain morphologic changes in early stages of psychosis: Implications for clinical application and early intervention. Psychiatry Clin Neurosci 2018; 72:556-571. [PMID: 29717522 DOI: 10.1111/pcn.12670] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2018] [Indexed: 12/20/2022]
Abstract
To date, a large number of magnetic resonance imaging (MRI) studies have been conducted in schizophrenia, which generally demonstrate gray matter reduction, predominantly in the frontal and temporo-limbic regions, as well as gross brain abnormalities (e.g., a deviated sulcogyral pattern). Although the causes as well as timing and course of these findings remain elusive, these morphologic changes (especially gross brain abnormalities and medial temporal lobe atrophy) are likely present at illness onset, possibly reflecting early neurodevelopmental abnormalities. In addition, longitudinal MRI studies suggest that patients with schizophrenia and related psychoses also have progressive gray matter reduction during the transition period from prodrome to overt psychosis, as well as initial periods after psychosis onset, while such changes may become almost stable in the chronic stage. These active brain changes during the early phases seem to be relevant to the development of clinical symptoms in a region-specific manner (e.g., superior temporal gyrus atrophy and positive psychotic symptoms), but may be at least partly ameliorated by antipsychotic medication. Recently, increasing evidence from MRI findings in individuals at risk for developing psychosis has suggested that those who subsequently develop psychosis have baseline brain changes, which could be at least partly predictive of later transition into psychosis. In this article, we selectively review previous MRI findings during the course of psychosis and also refer to the possible clinical applicability of these neuroimaging research findings, especially in the diagnosis of schizophrenia and early intervention for psychosis.
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Affiliation(s)
- Tsutomu Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Michio Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
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Oh J, Cho D, Park J, Na SH, Kim J, Heo J, Shin CS, Kim JJ, Park JY, Lee B. Prediction and early detection of delirium in the intensive care unit by using heart rate variability and machine learning. Physiol Meas 2018; 39:035004. [PMID: 29376502 DOI: 10.1088/1361-6579/aaab07] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Delirium is an important syndrome found in patients in the intensive care unit (ICU), however, it is usually under-recognized during treatment. This study was performed to investigate whether delirious patients can be successfully distinguished from non-delirious patients by using heart rate variability (HRV) and machine learning. APPROACH Electrocardiography data of 140 patients was acquired during daily ICU care, and HRV data were analyzed. Delirium, including its type, severity, and etiologies, was evaluated daily by trained psychiatrists. HRV data and various machine learning algorithms including linear support vector machine (SVM), SVM with radial basis function (RBF) kernels, linear extreme learning machine (ELM), ELM with RBF kernels, linear discriminant analysis, and quadratic discriminant analysis were utilized to distinguish delirium patients from non-delirium patients. MAIN RESULTS HRV data of 4797 ECGs were included, and 39 patients had delirium at least once during their ICU stay. The maximum classification accuracy was acquired using SVM with RBF kernels. Our prediction method based on HRV with machine learning was comparable to previous delirium prediction models using massive amounts of clinical information. SIGNIFICANCE Our results show that autonomic alterations could be a significant feature of patients with delirium in the ICU, suggesting the potential for the automatic prediction and early detection of delirium based on HRV with machine learning.
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Affiliation(s)
- Jooyoung Oh
- Department of Biomedical Science and Engineering (BMSE), Institute of Integrated Technology (IIT), Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea. These authors contributed equally to this work
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