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Peng L, Su J, Hu D, Yu Y, Wei H, Li M. Measuring functional connectivity in frequency-domain helps to better characterize brain function. Hum Brain Mapp 2024; 45:e26726. [PMID: 38949487 PMCID: PMC11215841 DOI: 10.1002/hbm.26726] [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: 08/19/2023] [Revised: 03/25/2024] [Accepted: 05/09/2024] [Indexed: 07/02/2024] Open
Abstract
Resting-state functional connectivity (FC) is widely used in multivariate pattern analysis of functional magnetic resonance imaging (fMRI), including identifying the locations of putative brain functional borders, predicting individual phenotypes, and diagnosing clinical mental diseases. However, limited attention has been paid to the analysis of functional interactions from a frequency perspective. In this study, by contrasting coherence-based and correlation-based FC with two machine learning tasks, we observed that measuring FC in the frequency domain helped to identify finer functional subregions and achieve better pattern discrimination capability relative to the temporal correlation. This study has proven the feasibility of coherence in the analysis of fMRI, and the results indicate that modeling functional interactions in the frequency domain may provide richer information than that in the time domain, which may provide a new perspective on the analysis of functional neuroimaging.
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Affiliation(s)
- Limin Peng
- College of Intelligence Science and TechnologyNational University of Defense TechnologyChangshaChina
| | - Jianpo Su
- College of Intelligence Science and TechnologyNational University of Defense TechnologyChangshaChina
| | - Dewen Hu
- College of Intelligence Science and TechnologyNational University of Defense TechnologyChangshaChina
| | - Yang Yu
- College of Intelligence Science and TechnologyNational University of Defense TechnologyChangshaChina
| | - Huilin Wei
- Systems Engineering InstituteAcademy of Military SciencesBeijingChina
| | - Ming Li
- College of Intelligence Science and TechnologyNational University of Defense TechnologyChangshaChina
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2
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Su J, Shen H, Peng L, Hu D. Few-Shot Domain-Adaptive Anomaly Detection for Cross-Site Brain Images. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2024; 46:1819-1835. [PMID: 34748478 DOI: 10.1109/tpami.2021.3125686] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Early screening is essential for effective intervention and treatment of individuals with mental disorders. Functional magnetic resonance imaging (fMRI) is a noninvasive tool for depicting neural activity and has demonstrated strong potential as a technique for identifying mental disorders. Due to the difficulty in data collection and diagnosis, imaging data from patients are rare at a single site, whereas abundant healthy control data are available from public datasets. However, joint use of these data from multiple sites for classification model training is hindered by cross-domain distribution discrepancy and diverse label spaces. Herein, we propose few-shot domain-adaptive anomaly detection (FAAD) to achieve cross-site anomaly detection of brain images based on only a few labeled samples. We introduce domain adaptation to mitigate cross-domain distribution discrepancy and jointly align the general and conditional feature distributions of imaging data across multiple sites. We utilize fMRI data of healthy subjects in the Human Connectome Project (HCP) as the source domain and fMRI images from six independent sites, including patients with mental disorders and demographically matched healthy controls, as target domains. Experiments showed the superiority of the proposed method compared with binary classification, traditional anomaly detection methods, and several recognized domain adaptation methods.
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Shinn AK, Hurtado-Puerto AM, Roh YS, Ho V, Hwang M, Cohen BM, Öngür D, Camprodon JA. Cerebellar transcranial magnetic stimulation in psychotic disorders: intermittent, continuous, and sham theta-burst stimulation on time perception and symptom severity. Front Psychiatry 2023; 14:1218321. [PMID: 38025437 PMCID: PMC10679721 DOI: 10.3389/fpsyt.2023.1218321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background The cerebellum contributes to the precise timing of non-motor and motor functions, and cerebellum abnormalities have been implicated in psychosis pathophysiology. In this study, we explored the effects of cerebellar theta burst stimulation (TBS), an efficient transcranial magnetic stimulation protocol, on temporal discrimination and self-reported mood and psychotic symptoms. Methods We conducted a case-crossover study in which patients with psychosis (schizophrenias, schizoaffective disorders, or bipolar disorders with psychotic features) were assigned to three sessions of TBS to the cerebellar vermis: one session each of intermittent (iTBS), continuous (cTBS), and sham TBS. Of 28 enrolled patients, 26 underwent at least one TBS session, and 20 completed all three. Before and immediately following TBS, participants rated their mood and psychotic symptoms and performed a time interval discrimination task (IDT). We hypothesized that cerebellar iTBS and cTBS would modulate these measures in opposing directions, with iTBS being adaptive and cTBS maladaptive. Results Reaction time (RT) in the IDT decreased significantly after iTBS vs. Sham (LS-mean difference = -73.3, p = 0.0001, Cohen's d = 1.62), after iTBS vs. cTBS (LS-mean difference = -137.6, p < 0.0001, d = 2.03), and after Sham vs. cTBS (LS-mean difference = -64.4, p < 0.0001, d = 1.33). We found no effect on IDT accuracy. We did not observe any effects on symptom severity after correcting for multiple comparisons. Conclusion We observed a frequency-dependent dissociation between the effects of iTBS vs. cTBS to the cerebellar midline on the reaction time of interval discrimination in patients with psychosis. iTBS showed improved (adaptive) while cTBS led to worsening (maladaptive) speed of response. These results demonstrate behavioral target engagement in a cognitive dimension of relevance to patients with psychosis and generate testable hypotheses about the potential therapeutic role of cerebellar iTBS in this clinical population. Clinical Trial Registration clinicaltrials.gov, identifier NCT02642029.
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Affiliation(s)
- Ann K. Shinn
- Psychotic Disorders Division, McLean Hospital, Belmont, MA, United States
- Department of Psychiatry, Harvard Medical School, Boston, MA, United States
| | - Aura M. Hurtado-Puerto
- Laboratory for Neuropsychiatry and Neuromodulation, Massachusetts General Hospital, Boston, MA, United States
| | - Youkyung S. Roh
- Psychotic Disorders Division, McLean Hospital, Belmont, MA, United States
| | - Victoria Ho
- Laboratory for Neuropsychiatry and Neuromodulation, Massachusetts General Hospital, Boston, MA, United States
| | - Melissa Hwang
- Psychotic Disorders Division, McLean Hospital, Belmont, MA, United States
| | - Bruce M. Cohen
- Department of Psychiatry, Harvard Medical School, Boston, MA, United States
- Program for Neuropsychiatric Research, McLean Hospital, Belmont, MA, United States
| | - Dost Öngür
- Psychotic Disorders Division, McLean Hospital, Belmont, MA, United States
- Department of Psychiatry, Harvard Medical School, Boston, MA, United States
| | - Joan A. Camprodon
- Department of Psychiatry, Harvard Medical School, Boston, MA, United States
- Laboratory for Neuropsychiatry and Neuromodulation, Massachusetts General Hospital, Boston, MA, United States
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Zhang J, Yang Y, Liu T, Shi Z, Pei G, Wang L, Wu J, Funahashi S, Suo D, Wang C, Yan T. Functional connectivity in people at clinical and familial high risk for schizophrenia. Psychiatry Res 2023; 328:115464. [PMID: 37690192 DOI: 10.1016/j.psychres.2023.115464] [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: 01/28/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Patients diagnosed with schizophrenia (SZ) exhibit compromised functional connectivity within extensive brain networks. However, the precise development of this impairment during disease progression in the clinical high-risk (CHR) population and their relatives remains unclear. Our study leveraged data from 128 resting electroencephalography (EEG) channels acquired from 30 SZ patients, 21 CHR individuals, 17 unaffected healthy relatives (RSs; those at heightened SZ risk due to family history), and 31 healthy controls (HCs). These data were harnessed to establish functional connectivity patterns. By calculating the geometric distance between EEG sequences, we unveiled local and global nonlinear relationships within the entire brain. The process of dimensionality reduction led to low-dimensional representations, providing insights into high-dimensional EEG data. Our findings indicated that CHR participants exhibited aberrant functional connectivity across hemispheres, whereas RS individuals showcased anomalies primarily concentrated within hemispheres. In the realm of low-dimensional analysis, RS participants' third-dimensional occipital lobe values lay between those of the CHR individuals and HCs, significantly correlating with scale scores. This low-dimensional approach facilitated the visualization of brain states, potentially offering enhanced comprehension of brain structure, function, and early-stage functional impairment, such as occipital visual deficits, in RS individuals before cognitive decline onset.
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Affiliation(s)
- Jian Zhang
- School of Medical Technology, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China
| | - Yaxin Yang
- School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China
| | - Tiantian Liu
- School of Medical Technology, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China
| | - Zhongyan Shi
- School of Medical Technology, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China
| | - Guangying Pei
- School of Medical Technology, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China
| | - Li Wang
- School of Medical Technology, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China
| | - Jinglong Wu
- School of Medical Technology, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China
| | - Shintaro Funahashi
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China
| | - Dingjie Suo
- School of Medical Technology, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China
| | - Changming Wang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Tianyi Yan
- School of Medical Technology, Beijing Institute of Technology, 5 South Zhongguancun St, Haidian District, Beijing 100081, China.
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Teng J, Liu W, Mi C, Zhang H, Shi J, Li N. Extracting the most discriminating functional connections in mild traumatic brain injury based on machine learning. Neurosci Lett 2023; 810:137311. [PMID: 37236344 DOI: 10.1016/j.neulet.2023.137311] [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: 04/10/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Mild traumatic brain injury (mTBI) is characterized as brain microstructural damage, which may cause a wide range of brain functional disturbances and emotional problems. Brain network analysis based on machine learning is an important means of neuroimaging research. Obtaining the most discriminating functional connection is of great significance to analyze the pathological mechanism of mTBI. METHODS To better obtain the most discriminating features of functional connection networks, this study proposes a hierarchical feature selection pipeline (HFSP) composed of Variance Filtering (VF), Lasso, and Principal Component Analysis (PCA). Ablation experiments indicate that each module plays a positive role in classification, validating the robustness and reliability of the HFSP. Furthermore, the HFSP is compared with recursive feature elimination (RFE), elastic net (EN), and locally linear embedding (LLE), verifying its superiority. In addition, this study also utilizes random forest (RF), SVM, Bayesian, linear discriminant analysis (LDA), and logistic regression (LR) as classifiers to evaluate the generalizability of HFSP. RESULTS The results show that the indexes obtained from RF are the highest, with accuracy = 89.74%, precision = 91.26%, recall = 89.74%, and F1 score = 89.42%. The HFSP selects 25 pairs of the most discriminating functional connections, mainly distributed in the frontal lobe, occipital lobe, and cerebellum. Nine brain regions show the largest node degree. LIMITATIONS The number of samples is small. This study only includes acute mTBI. CONCLUSIONS The HFSP is a useful tool for extracting discriminating functional connections and may contribute to the diagnostic processes.
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Affiliation(s)
- Jing Teng
- The School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, Beijing, China.
| | - Wuyi Liu
- The School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, Beijing, China.
| | - Chunlin Mi
- The School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, Beijing, China.
| | - Honglei Zhang
- The School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, Beijing, China.
| | - Jian Shi
- Department of Critical Care Medicine and Hematology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan Province, China; Department of Spine Surgery, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan Province, China.
| | - Na Li
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan Province, China.
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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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Bedel HA, Sivgin I, Dalmaz O, Dar SUH, Çukur T. BolT: Fused window transformers for fMRI time series analysis. Med Image Anal 2023; 88:102841. [PMID: 37224718 DOI: 10.1016/j.media.2023.102841] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/07/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023]
Abstract
Deep-learning models have enabled performance leaps in analysis of high-dimensional functional MRI (fMRI) data. Yet, many previous methods are suboptimally sensitive for contextual representations across diverse time scales. Here, we present BolT, a blood-oxygen-level-dependent transformer model, for analyzing multi-variate fMRI time series. BolT leverages a cascade of transformer encoders equipped with a novel fused window attention mechanism. Encoding is performed on temporally-overlapped windows within the time series to capture local representations. To integrate information temporally, cross-window attention is computed between base tokens in each window and fringe tokens from neighboring windows. To gradually transition from local to global representations, the extent of window overlap and thereby number of fringe tokens are progressively increased across the cascade. Finally, a novel cross-window regularization is employed to align high-level classification features across the time series. Comprehensive experiments on large-scale public datasets demonstrate the superior performance of BolT against state-of-the-art methods. Furthermore, explanatory analyses to identify landmark time points and regions that contribute most significantly to model decisions corroborate prominent neuroscientific findings in the literature.
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Affiliation(s)
- Hasan A Bedel
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey
| | - Irmak Sivgin
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey
| | - Onat Dalmaz
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey
| | - Salman U H Dar
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey
| | - Tolga Çukur
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey; Neuroscience Program, Bilkent University, Ankara 06800, Turkey.
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Keyvanfard F, Nasab AR, Nasiraei-Moghaddam A. Brain subnetworks most sensitive to alterations of functional connectivity in Schizophrenia: a data-driven approach. Front Neuroinform 2023; 17:1175886. [PMID: 37274751 PMCID: PMC10232974 DOI: 10.3389/fninf.2023.1175886] [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: 02/28/2023] [Accepted: 04/24/2023] [Indexed: 06/06/2023] Open
Abstract
Functional connectivity (FC) of the brain changes in various brain disorders. Its complexity, however, makes it difficult to obtain a systematic understanding of these alterations, especially when they are found individually and through hypothesis-based methods. It would be easier if the variety of brain connectivity alterations is extracted through data-driven approaches and expressed as variation modules (subnetworks). In the present study, we modified a blind approach to determine inter-group brain variations at the network level and applied it specifically to schizophrenia (SZ) disorder. The analysis is based on the application of independent component analysis (ICA) over the subject's dimension of the FC matrices, obtained from resting-state functional magnetic resonance imaging (rs-fMRI). The dataset included 27 SZ people and 27 completely matched healthy controls (HC). This hypothesis-free approach led to the finding of three brain subnetworks significantly discriminating SZ from HC. The area associated with these subnetworks mostly covers regions in visual, ventral attention, and somatomotor areas, which are in line with previous studies. Moreover, from the graph perspective, significant differences were observed between SZ and HC for these subnetworks, while there was no significant difference when the same parameters (path length, network strength, global/local efficiency, and clustering coefficient) across the same limited data were calculated for the whole brain network. The increased sensitivity of those subnetworks to SZ-induced alterations of connectivity suggested whether an individual scoring method based on their connectivity values can be applied to classify subjects. A simple scoring classifier was then suggested based on two of these subnetworks and resulted in acceptable sensitivity and specificity with an area under the ROC curve of 77.5%. The third subnetwork was found to be a less specific building block (module) for describing SZ alterations. It projected a wider range of inter-individual variations and, therefore, had a lower chance to be considered as a SZ biomarker. These findings confirmed that investigating brain variations from a modular viewpoint can help to find subnetworks that are more sensitive to SZ-induced alterations. Altogether, our study results illustrated the developed method's ability to systematically find brain alterations caused by SZ disorder from a network perspective.
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Affiliation(s)
- Farzaneh Keyvanfard
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Alireza Rahimi Nasab
- Biomedical Engineering Department, Amirkabir University of Technology, Tehran, Iran
| | - Abbas Nasiraei-Moghaddam
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- Biomedical Engineering Department, Amirkabir University of Technology, Tehran, Iran
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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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Wang Y, Wang J, Su W, Hu H, Xia M, Zhang T, Xu L, Zhang X, Taylor H, Osipowicz K, Young IM, Lin YH, Nicholas P, Tanglay O, Sughrue ME, Tang Y, Doyen S. Symptom-circuit mappings of the schizophrenia connectome. Psychiatry Res 2023; 323:115122. [PMID: 36889161 DOI: 10.1016/j.psychres.2023.115122] [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: 08/26/2022] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 02/27/2023]
Abstract
OBJECTIVE This paper aims to model the anatomical circuits underlying schizophrenia symptoms, and to explore patterns of abnormal connectivity among brain networks affected by psychopathology. METHODS T1 magnetic resonance imaging (MRI), diffusion weighted imaging (DWI), and resting-state functional MRI (rsfMRI) were obtained from a total of 126 patients with schizophrenia who were recruited for the study. The images were processed using the Omniscient software (https://www.o8t. com). We further apply the use of the Hollow-tree Super (HoTS) method to gain insights into what brain regions had abnormal connectivity that might be linked to the symptoms of schizophrenia. RESULTS The Positive and Negative Symptom Scale is characterised into 6 factors. Each symptom is mapped with specific anatomical abnormalities and circuits. Comparison between factors reveals co-occurrence in parcels in Factor 1 and Factor 2. Multiple large-scale networks are involved in SCZ symptomatology, with functional connectivity within Default Mode Network (DMN) and Central Executive Network (CEN) regions most frequently associated with measures of psychopathology. CONCLUSION We present a summary of the relevant anatomy for regions of the cortical areas as part of a larger effort to understand its contribution in schizophrenia. This unique machine learning-type approach maps symptoms to specific brain regions and circuits by bridging the diagnostic subtypes and analysing the features of the connectome.
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Affiliation(s)
- Yingchan Wang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Jijun Wang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China.
| | - Wenjun Su
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Hao Hu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Mengqing Xia
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Tianhong Zhang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Lihua Xu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Xia Zhang
- Xijia Medical Technology Company Limited, Shenzhen 518000, China; International Joint Research Center on Precision Brain Medicine, XD Group Hospital, Xi'an 710082, China
| | - Hugh Taylor
- Omniscient Neurotechnology, Sydney, Australia
| | | | | | - Yueh-Hsin Lin
- Department of Neurosurgery, Prince of Wales Private Hospital, Sydney, Australia
| | | | | | - Michael E Sughrue
- International Joint Research Center on Precision Brain Medicine, XD Group Hospital, Xi'an 710082, China; Omniscient Neurotechnology, Sydney, Australia
| | - Yingying Tang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China.
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11
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Zhang S, Goodale SE, Gold BP, Morgan VL, Englot DJ, Chang C. Vigilance associates with the low-dimensional structure of fMRI data. Neuroimage 2023; 267:119818. [PMID: 36535323 PMCID: PMC10074161 DOI: 10.1016/j.neuroimage.2022.119818] [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: 08/21/2022] [Revised: 11/24/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The human brain exhibits rich dynamics that reflect ongoing functional states. Patterns in fMRI data, detected in a data-driven manner, have uncovered recurring configurations that relate to individual and group differences in behavioral, cognitive, and clinical traits. However, resolving the neural and physiological processes that underlie such measurements is challenging, particularly without external measurements of brain state. A growing body of work points to underlying changes in vigilance as one driver of time-windowed fMRI connectivity states, calculated on the order of tens of seconds. Here we examine the degree to which the low-dimensional spatial structure of instantaneous fMRI activity is associated with vigilance levels, by testing whether vigilance-state detection can be carried out in an unsupervised manner based on individual BOLD time frames. To investigate this question, we first reduce the spatial dimensionality of fMRI data, and apply Gaussian Mixture Modeling to cluster the resulting low-dimensional data without any a priori vigilance information. Our analysis includes long-duration task and resting-state scans that are conducive to shifts in vigilance. We observe a close alignment between low-dimensional fMRI states (data-driven clusters) and measurements of vigilance derived from concurrent electroencephalography (EEG) and behavior. Whole-brain coactivation analysis revealed cortical anti-correlation patterns that resided primarily during higher behavioral- and EEG-defined levels of vigilance, while cortical activity was more often spatially uniform in states corresponding to lower vigilance. Overall, these findings indicate that vigilance states may be detected in the low-dimensional structure of fMRI data, even within individual time frames.
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Affiliation(s)
- Shengchao Zhang
- Department of Electrical and Computer Engineering, Vanderbilt University, 400 24th Avenue S., Nashville, TN 37212, USA.
| | - Sarah E Goodale
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Benjamin P Gold
- Department of Electrical and Computer Engineering, Vanderbilt University, 400 24th Avenue S., Nashville, TN 37212, USA; Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Victoria L Morgan
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dario J Englot
- Department of Electrical and Computer Engineering, Vanderbilt University, 400 24th Avenue S., Nashville, TN 37212, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Catie Chang
- Department of Electrical and Computer Engineering, Vanderbilt University, 400 24th Avenue S., Nashville, TN 37212, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Department of Computer Science, Vanderbilt University, Nashville, TN, USA; Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA.
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12
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Xu N, Zhou Y, Patel A, Zhang N, Liu Y. Parkinson's Disease Diagnosis beyond Clinical Features: A Bio-marker using Topological Machine Learning of Resting-state Functional Magnetic Resonance Imaging. Neuroscience 2023; 509:43-50. [PMID: 36436700 DOI: 10.1016/j.neuroscience.2022.11.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
Parkinson's disease (PD) is one of the leading causes of neurological disability, and its prevalence is expected to increase rapidly in the following few decades. PD diagnosis heavily depends on clinical features using the patient's symptoms. Therefore, an accurate, robust, and non-invasive bio-marker is of critical clinical importance for PD. This study proposes to develop a new bio-marker for PD diagnosis using resting-state functional Magnetic Resonance Imaging (rs-fMRI). Unlike most existing rs-fMRI data analytics using correlational analysis, a Topological Machine Learning approach is proposed to construct the bio-marker. The default functional network is identified first using rs-fMRI. Next, rs-fMRI's high dimensional spatial-temporal data structure is mapped on a Riemann Manifold using topological dimensional reduction. Following the topological dimensional reduction, machine learning is used for classification and sensitivity analysis. The proposed methodology is applied to three open fMRI databases for demonstration and validation. The PD diagnosis accuracy can reach 96.4% when the proposed methodology is used. Thus, rs-fMRI and topological machine learning provide a quantifiable and verifiable bio-marker for future PD early detection and treatment evaluation.
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Affiliation(s)
- Nan Xu
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Yuxiang Zhou
- Department of Radiology, Mayo Clinic, Scottsdale, AZ, USA.
| | - Ameet Patel
- Department of Radiology, Mayo Clinic, Scottsdale, AZ, USA
| | - Na Zhang
- Independent Researcher, Chandler, AZ, USA
| | - Yongming Liu
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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13
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Weaver C, Xiao L, Lindquist MA. Single-index models with functional connectivity network predictors. Biostatistics 2022; 24:52-67. [PMID: 33948617 DOI: 10.1093/biostatistics/kxab015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
Functional connectivity is defined as the undirected association between two or more functional magnetic resonance imaging (fMRI) time series. Increasingly, subject-level functional connectivity data have been used to predict and classify clinical outcomes and subject attributes. We propose a single-index model wherein response variables and sparse functional connectivity network valued predictors are linked by an unspecified smooth function in order to accommodate potentially nonlinear relationships. We exploit the network structure of functional connectivity by imposing meaningful sparsity constraints, which lead not only to the identification of association of interactions between regions with the response but also the assessment of whether or not the functional connectivity associated with a brain region is related to the response variable. We demonstrate the effectiveness of the proposed model in simulation studies and in an application to a resting-state fMRI data set from the Human Connectome Project to model fluid intelligence and sex and to identify predictive links between brain regions.
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Affiliation(s)
- Caleb Weaver
- Department of Statistics, North Carolina State University, 2311 Stinson Drive, Raleigh, NC 27606, USA
| | - Luo Xiao
- Department of Statistics, North Carolina State University, 2311 Stinson Drive, Raleigh, NC 27606, USA
| | - Martin A Lindquist
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205, USA
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14
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Lin K, Jie B, Dong P, Ding X, Bian W, Liu M. Convolutional Recurrent Neural Network for Dynamic Functional MRI Analysis and Brain Disease Identification. Front Neurosci 2022; 16:933660. [PMID: 35873806 PMCID: PMC9298744 DOI: 10.3389/fnins.2022.933660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 06/13/2022] [Indexed: 12/12/2022] Open
Abstract
Dynamic functional connectivity (dFC) networks derived from resting-state functional magnetic resonance imaging (rs-fMRI) help us understand fundamental dynamic characteristics of human brains, thereby providing an efficient solution for automated identification of brain diseases, such as Alzheimer's disease (AD) and its prodromal stage. Existing studies have applied deep learning methods to dFC network analysis and achieved good performance compared with traditional machine learning methods. However, they seldom take advantage of sequential information conveyed in dFC networks that could be informative to improve the diagnosis performance. In this paper, we propose a convolutional recurrent neural network (CRNN) for automated brain disease classification with rs-fMRI data. Specifically, we first construct dFC networks from rs-fMRI data using a sliding window strategy. Then, we employ three convolutional layers and long short-term memory (LSTM) layer to extract high-level features of dFC networks and also preserve the sequential information of extracted features, followed by three fully connected layers for brain disease classification. Experimental results on 174 subjects with 563 rs-fMRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) demonstrate the effectiveness of our proposed method in binary and multi-category classification tasks.
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Affiliation(s)
- Kai Lin
- School of Computer and Information, Anhui Normal University, Wuhu, China
| | - Biao Jie
- School of Computer and Information, Anhui Normal University, Wuhu, China
| | - Peng Dong
- School of Computer and Information, Anhui Normal University, Wuhu, China
| | - Xintao Ding
- School of Computer and Information, Anhui Normal University, Wuhu, China
| | - Weixin Bian
- School of Computer and Information, Anhui Normal University, Wuhu, China
| | - Mingxia Liu
- Department of Radiology and Biomedical Research Imaging Center (BRIC), University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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15
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Wang T, Bezerianos A, Cichocki A, Li J. Multikernel Capsule Network for Schizophrenia Identification. IEEE TRANSACTIONS ON CYBERNETICS 2022; 52:4741-4750. [PMID: 33259321 DOI: 10.1109/tcyb.2020.3035282] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Schizophrenia seriously affects the quality of life. To date, both simple (e.g., linear discriminant analysis) and complex (e.g., deep neural network) machine-learning methods have been utilized to identify schizophrenia based on functional connectivity features. The existing simple methods need two separate steps (i.e., feature extraction and classification) to achieve the identification, which disables simultaneous tuning for the best feature extraction and classifier training. The complex methods integrate two steps and can be simultaneously tuned to achieve optimal performance, but these methods require a much larger amount of data for model training. To overcome the aforementioned drawbacks, we proposed a multikernel capsule network (MKCapsnet), which was developed by considering the brain anatomical structure. Kernels were set to match partition sizes of the brain anatomical structure in order to capture interregional connectivities at the varying scales. With the inspiration of the widely used dropout strategy in deep learning, we developed capsule dropout in the capsule layer to prevent overfitting of the model. The comparison results showed that the proposed method outperformed the state-of-the-art methods. Besides, we compared performances using different parameters and illustrated the routing process to reveal characteristics of the proposed method. MKCapsnet is promising for schizophrenia identification. Our study first utilized the capsule neural network for analyzing functional connectivity of magnetic resonance imaging (MRI) and proposed a novel multikernel capsule structure with the consideration of brain anatomical parcellation, which could be a new way to reveal brain mechanisms. In addition, we provided useful information in the parameter setting, which is informative for further studies using a capsule network for other neurophysiological signal classification.
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16
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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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17
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Panda R, Kalmady SV, Greiner R. Multi-Source Domain Adaptation Techniques for Mitigating Batch Effects: A Comparative Study. Front Neuroinform 2022; 16:805117. [PMID: 35528213 PMCID: PMC9067602 DOI: 10.3389/fninf.2022.805117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
The past decade has seen an increasing number of applications of deep learning (DL) techniques to biomedical fields, especially in neuroimaging-based analysis. Such DL-based methods are generally data-intensive and require a large number of training instances, which might be infeasible to acquire from a single acquisition site, especially for data, such as fMRI scans, due to the time and costs that they demand. We can attempt to address this issue by combining fMRI data from various sites, thereby creating a bigger heterogeneous dataset. Unfortunately, the inherent differences in the combined data, known as batch effects, often hamper learning a model. To mitigate this issue, techniques such as multi-source domain adaptation [Multi-source Domain Adversarial Networks (MSDA)] aim at learning an effective classification function that uses (learned) domain-invariant latent features. This article analyzes and compares the performance of various popular MSDA methods [MDAN, Domain AggRegation Networks (DARN), Multi-Domain Matching Networks (MDMN), and Moment Matching for MSDA (M3SDA)] at predicting different labels (illness, age, and sex) of images from two public rs-fMRI datasets: ABIDE 1and ADHD-200. It also evaluates the impact of various conditions such as class imbalance, the number of sites along with a comparison of the degree of adaptation of each of the methods, thereby presenting the effectiveness of MSDA models in neuroimaging-based applications.
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Affiliation(s)
- Rohan Panda
- Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Sunil Vasu Kalmady
- Canadian VIGOUR Centre, University of Alberta, Edmonton, AB, Canada
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada
| | - Russell Greiner
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada
- Alberta Machine Intelligence Institute, Edmonton, AB, Canada
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
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18
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Benkarim O, Paquola C, Park BY, Kebets V, Hong SJ, Vos de Wael R, Zhang S, Yeo BTT, Eickenberg M, Ge T, Poline JB, Bernhardt BC, Bzdok D. Population heterogeneity in clinical cohorts affects the predictive accuracy of brain imaging. PLoS Biol 2022; 20:e3001627. [PMID: 35486643 PMCID: PMC9094526 DOI: 10.1371/journal.pbio.3001627] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/11/2022] [Accepted: 04/11/2022] [Indexed: 12/18/2022] Open
Abstract
Brain imaging research enjoys increasing adoption of supervised machine learning for single-participant disease classification. Yet, the success of these algorithms likely depends on population diversity, including demographic differences and other factors that may be outside of primary scientific interest. Here, we capitalize on propensity scores as a composite confound index to quantify diversity due to major sources of population variation. We delineate the impact of population heterogeneity on the predictive accuracy and pattern stability in 2 separate clinical cohorts: the Autism Brain Imaging Data Exchange (ABIDE, n = 297) and the Healthy Brain Network (HBN, n = 551). Across various analysis scenarios, our results uncover the extent to which cross-validated prediction performances are interlocked with diversity. The instability of extracted brain patterns attributable to diversity is located preferentially in regions part of the default mode network. Collectively, our findings highlight the limitations of prevailing deconfounding practices in mitigating the full consequences of population diversity.
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Affiliation(s)
- Oualid Benkarim
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Casey Paquola
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Jülich, Germany
| | - Bo-yong Park
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
- Department of Data Science, Inha University, Incheon, South Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon, South Korea
| | - Valeria Kebets
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Seok-Jun Hong
- Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon, South Korea
- Center for the Developing Brain, Child Mind Institute, New York, New York, United States of America
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Reinder Vos de Wael
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Shaoshi Zhang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Centre for Sleep and Cognition (CSC) & Centre for Translational Magnetic Resonance Research (TMR), National University of Singapore, Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine (WisDM), National University of Singapore, Singapore, Singapore
| | - B. T. Thomas Yeo
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Centre for Sleep and Cognition (CSC) & Centre for Translational Magnetic Resonance Research (TMR), National University of Singapore, Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine (WisDM), National University of Singapore, Singapore, Singapore
| | | | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jean-Baptiste Poline
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Boris C. Bernhardt
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Danilo Bzdok
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, Canada
- School of Computer Science, McGill University, Montreal, Canada
- Mila—Quebec Artificial Intelligence Institute, Montreal, Canada
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19
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Plechawska-Wójcik M, Karczmarek P, Krukow P, Kaczorowska M, Tokovarov M, Jonak K. Recognition of Electroencephalography-Related Features of Neuronal Network Organization in Patients With Schizophrenia Using the Generalized Choquet Integrals. Front Neuroinform 2022; 15:744355. [PMID: 34970131 PMCID: PMC8712566 DOI: 10.3389/fninf.2021.744355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, we focused on the verification of suitable aggregation operators enabling accurate differentiation of selected neurophysiological features extracted from resting-state electroencephalographic recordings of patients who were diagnosed with schizophrenia (SZ) or healthy controls (HC). We built the Choquet integral-based operators using traditional classification results as an input to the procedure of establishing the fuzzy measure densities. The dataset applied in the study was a collection of variables characterizing the organization of the neural networks computed using the minimum spanning tree (MST) algorithms obtained from signal-spaced functional connectivity indicators and calculated separately for predefined frequency bands using classical linear Granger causality (GC) measure. In the series of numerical experiments, we reported the results of classification obtained using numerous generalizations of the Choquet integral and other aggregation functions, which were tested to find the most appropriate ones. The obtained results demonstrate that the classification accuracy can be increased by 1.81% using the extended versions of the Choquet integral called in the literature, namely, generalized Choquet integral or pre-aggregation operators.
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Affiliation(s)
| | - Paweł Karczmarek
- Department of Computer Science, Lublin University of Technology, Lublin, Poland
| | - Paweł Krukow
- Department of Clinical Neuropsychiatry, Medical University of Lublin, Lublin, Poland
| | - Monika Kaczorowska
- Department of Computer Science, Lublin University of Technology, Lublin, Poland
| | - Mikhail Tokovarov
- Department of Computer Science, Lublin University of Technology, Lublin, Poland
| | - Kamil Jonak
- Department of Computer Science, Lublin University of Technology, Lublin, Poland.,Department of Clinical Neuropsychiatry, Medical University of Lublin, Lublin, Poland
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20
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Okamoto N, Akama H. Extended Invariant Information Clustering Is Effective for Leave-One-Site-Out Cross-Validation in Resting State Functional Connectivity Modeling. Front Neuroinform 2021; 15:709179. [PMID: 34924987 PMCID: PMC8671136 DOI: 10.3389/fninf.2021.709179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Herein, we propose a new deep neural network model based on invariant information clustering (IIC), proposed by Ji et al., to improve the modeling performance of the leave-one-site-out cross-validation (LOSO-CV) for a multi-source dataset. Our Extended IIC (EIIC) is a type of contrastive learning; however, unlike the original IIC, it is characterized by transfer learning with labeled data pairs, but without the need for a data augmentation technique. Each site in LOSO-CV is left out in turn from the remaining sites used for training and receives a value for modeling evaluation. We applied the EIIC to the resting state functional connectivity magnetic resonance imaging dataset of the Autism Brain Imaging Data Exchange. The challenging nature of brain analysis for autism spectrum disorder (ASD) can be attributed to the variability of subjects, particularly the rapid change in the neural system of children as the target ASD age group. However, EIIC demonstrated higher LOSO-CV classification accuracy for the majority of scanning locations than previously used methods. Particularly, with the adjustment of a mini-batch size, EIIC outperformed other classifiers with an accuracy >0.8 for the sites with highest mean age of the subjects. Considering its effectiveness, our proposed method might be promising for harmonization in other domains, owing to its simplicity and intrinsic flexibility.
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Affiliation(s)
- Naoki Okamoto
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Hiroyuki Akama
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Institute for Liberal Arts, Tokyo Institute of Technology, Tokyo, Japan
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21
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Machine learning approaches for parsing comorbidity/heterogeneity in antisociality and substance use disorders: A primer. PERSONALITY NEUROSCIENCE 2021; 4:e6. [PMID: 34909565 PMCID: PMC8640675 DOI: 10.1017/pen.2021.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/30/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022]
Abstract
By some accounts, as many as 93% of individuals diagnosed with antisocial personality disorder (ASPD) or psychopathy also meet criteria for some form of substance use disorder (SUD). This high level of comorbidity, combined with an overlapping biopsychosocial profile, and potentially interacting features, has made it difficult to delineate the shared/unique characteristics of each disorder. Moreover, while rarely acknowledged, both SUD and antisociality exist as highly heterogeneous disorders in need of more targeted parcellation. While emerging data-driven nosology for psychiatric disorders (e.g., Research Domain Criteria (RDoC), Hierarchical Taxonomy of Psychopathology (HiTOP)) offers the opportunity for a more systematic delineation of the externalizing spectrum, the interrogation of large, complex neuroimaging-based datasets may require data-driven approaches that are not yet widely employed in psychiatric neuroscience. With this in mind, the proposed article sets out to provide an introduction into machine learning methods for neuroimaging that can help parse comorbid, heterogeneous externalizing samples. The modest machine learning work conducted to date within the externalizing domain demonstrates the potential utility of the approach but remains highly nascent. Within the paper, we make suggestions for how future work can make use of machine learning methods, in combination with emerging psychiatric nosology systems, to further diagnostic and etiological understandings of the externalizing spectrum. Finally, we briefly consider some challenges that will need to be overcome to encourage further progress in the field.
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22
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Kim JH, Zhang Y, Han K, Wen Z, Choi M, Liu Z. Representation learning of resting state fMRI with variational autoencoder. Neuroimage 2021; 241:118423. [PMID: 34303794 PMCID: PMC8485214 DOI: 10.1016/j.neuroimage.2021.118423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/18/2021] [Accepted: 07/21/2021] [Indexed: 11/24/2022] Open
Abstract
Resting state functional magnetic resonance imaging (rsfMRI) data exhibits complex but structured patterns. However, the underlying origins are unclear and entangled in rsfMRI data. Here we establish a variational auto-encoder, as a generative model trainable with unsupervised learning, to disentangle the unknown sources of rsfMRI activity. After being trained with large data from the Human Connectome Project, the model has learned to represent and generate patterns of cortical activity and connectivity using latent variables. The latent representation and its trajectory represent the spatiotemporal characteristics of rsfMRI activity. The latent variables reflect the principal gradients of the latent trajectory and drive activity changes in cortical networks. Representational geometry captured as covariance or correlation between latent variables, rather than cortical connectivity, can be used as a more reliable feature to accurately identify subjects from a large group, even if only a short period of data is available in each subject. Our results demonstrate that VAE is a valuable addition to existing tools, particularly suited for unsupervised representation learning of resting state fMRI activity.
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Affiliation(s)
- Jung-Hoon Kim
- Department of Biomedical Engineering, University of Michigan, United States; Weldon School of Biomedical Engineering, Purdue University, United States
| | - Yizhen Zhang
- Department of Electrical Engineering and Computer Science, University of Michigan, United States
| | - Kuan Han
- Department of Electrical Engineering and Computer Science, University of Michigan, United States
| | - Zheyu Wen
- Department of Electrical Engineering and Computer Science, University of Michigan, United States
| | - Minkyu Choi
- Department of Electrical Engineering and Computer Science, University of Michigan, United States
| | - Zhongming Liu
- Department of Biomedical Engineering, University of Michigan, United States; Department of Electrical Engineering and Computer Science, University of Michigan, United States.
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23
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Azizi S, Hier DB, Wunsch DC. Schizophrenia Classification Using Resting State EEG Functional Connectivity: Source Level Outperforms Sensor Level. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:1770-1773. [PMID: 34891630 DOI: 10.1109/embc46164.2021.9630713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Disrupted functional and structural connectivity measures have been used to distinguish schizophrenia patients from healthy controls. Classification methods based on functional connectivity derived from EEG signals are limited by the volume conduction problem. Recorded time series at scalp electrodes capture a mixture of common sources signals, resulting in spurious connections. We have transformed sensor level resting state EEG times series to source level EEG signals utilizing a source reconstruction method. Functional connectivity networks were calculated by computing phase lag values between brain regions at both the sensor and source level. Brain complex network analysis was used to extract features and the best features were selected by a feature selection method. A logistic regression classifier was used to distinguish schizophrenia patients from healthy controls at five different frequency bands. The best classifier performance was based on connectivity measures derived from the source space and the theta band.The transformation of scalp EEG signals to source signals combined with functional connectivity analysis may provide superior features for machine learning applications.
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24
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Shi L, Liu X, Wu K, Sun K, Lin C, Li Z, Zhao S, Fan X. Surface values, volumetric measurements and radiomics of structural MRI for the diagnosis and subtyping of attention-deficit/hyperactivity disorder. Eur J Neurosci 2021; 54:7654-7667. [PMID: 34614247 DOI: 10.1111/ejn.15485] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 08/22/2021] [Accepted: 10/03/2021] [Indexed: 11/28/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is diagnosed subjectively based on an individual's behaviour and performance. The clinical community has no objective biomarker to inform the diagnosis and subtyping of ADHD. This study aimed to explore the potential diagnostic biomarkers of ADHD among surface values, volumetric metrics and radiomic features that were extracted from structural MRI images. Public data of New York University and Peking University were downloaded from the ADHD-200 Consortium. MRI T1-weighted images were pre-processed using CAT12. We calculated surface values based on the Desikan-Killiany atlas. The volumetric metrics (mean grey matter volume and mean white matter volume) and radiomic features within each automated anatomical labelling (AAL) brain area were calculated using DPABI and IBEX, respectively. The differences among three groups of participants were tested using ANOVA or Kruskal-Wallis test depending on the normality of the data. We selected discriminative features and classified typically developing controls (TDCs) and ADHD patients as well as two ADHD subtypes using least absolute shrinkage and selection operator and support vector machine algorithms. Our results showed that the radiomics-based model outperformed the others in discriminating ADHD from TDC and classifying ADHD subtypes (area under the curve [AUC]: 0.78 and 0.94 in training test; 0.79 and 0.85 in testing set). Combining grey matter volumes, surface values and clinical factors with radiomic features can improve the performance for classifying ADHD patients and TDCs with training and testing AUCs of 0.82 and 0.83, respectively. This study demonstrates that MRI T1-weighted features, especially radiomic features, are potential diagnostic biomarkers of ADHD.
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Affiliation(s)
- Liting Shi
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Department of Medical Imaging, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, China
| | - Xuechun Liu
- Medical Engineering and Technology Research Center; Department of Radiology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Keqing Wu
- Department of Medical Imaging, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, China.,School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Kui Sun
- Medical Engineering and Technology Research Center; Department of Radiology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Chunsen Lin
- Department of Radiology, Taian Disabled Soldiers' Hospital of Shandong Province, Tai'an, China
| | - Zhengmei Li
- Medical Engineering and Technology Research Center; Department of Radiology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Shuying Zhao
- Medical Engineering and Technology Research Center; Department of Radiology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China.,The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Xiuqin Fan
- Laboratory of Nutrition and Development, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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25
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Csukly G, Szabó Á, Polgár P, Farkas K, Gyebnár G, Kozák LR, Stefanics G. Fronto-thalamic structural and effective connectivity and delusions in schizophrenia: a combined DTI/DCM study. Psychol Med 2021; 51:2083-2093. [PMID: 32329710 PMCID: PMC8426148 DOI: 10.1017/s0033291720000859] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 02/07/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Schizophrenia (SZ) is a complex disorder characterized by a range of behavioral and cognitive symptoms as well as structural and functional alterations in multiple cortical and subcortical structures. SZ is associated with reduced functional network connectivity involving core regions such as the anterior cingulate cortex (ACC) and the thalamus. However, little is known whether effective coupling, the directed influence of one structure over the other, is altered during rest in the ACC-thalamus network. METHODS We collected resting-state fMRI and diffusion-weighted MRI data from 18 patients and 20 healthy controls. We analyzed fronto-thalamic effective connectivity using dynamic causal modeling for cross-spectral densities in a network consisting of the ACC and the left and right medio-dorsal thalamic regions. We studied structural connectivity using fractional anisotropy (FA). RESULTS We found decreased coupling strength from the right thalamus to the ACC and from the right thalamus to the left thalamus, as well as increased inhibitory intrinsic connectivity in the right thalamus in patients relative to controls. ACC-to-left thalamus coupling strength correlated with the Positive and Negative Syndrome Scale (PANSS) total positive syndrome score and with delusion score. Whole-brain structural analysis revealed several tracts with reduced FA in patients, with a maximum decrease in white matter tracts containing fronto-thalamic and cingulo-thalamic fibers. CONCLUSIONS We found altered effective and structural connectivity within the ACC-thalamus network in SZ. Our results indicate that ACC-thalamus network activity at rest is characterized by reduced thalamus-to-ACC coupling. We suggest that positive symptoms may arise as a consequence of compensatory measures to imbalanced fronto-thalamic coupling.
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Affiliation(s)
- Gábor Csukly
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Ádám Szabó
- Magnetic Resonance Research Centre, Semmelweis University, Budapest, Hungary
| | - Patrícia Polgár
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Kinga Farkas
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Gyula Gyebnár
- Magnetic Resonance Research Centre, Semmelweis University, Budapest, Hungary
| | - Lajos R. Kozák
- Magnetic Resonance Research Centre, Semmelweis University, Budapest, Hungary
| | - Gábor Stefanics
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, Wilfriedstrasse 6, 8032, Zurich, Switzerland
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26
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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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27
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Intrinsic functional connectivity of the frontoparietal network predicts inter-individual differences in the propensity for costly third-party punishment. COGNITIVE AFFECTIVE & BEHAVIORAL NEUROSCIENCE 2021; 21:1222-1232. [PMID: 34331267 DOI: 10.3758/s13415-021-00927-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
Humans are motivated to give norm violators their just deserts through costly punishment even as unaffected third parties (i.e., third-party punishment, TPP). A great deal of individual variability exists in costly punishment; however, how this variability particularly in TPP is represented by the brain's intrinsic network architecture remains elusive. Here, we examined whether inter-individual differences in the propensity for TPP can be predicted based on resting-state functional connectivity (RSFC) combining an economic TPP game with task-free functional neuroimaging and a multivariate prediction framework. Our behavioral results revealed that TPP punishment increased with the severity of unfairness for offers. People with higher TPP propensity punished more harshly across norm-violating scenarios. Our neuroimaging findings showed RSFC within the frontoparietal network predicted individual differences in TPP propensity. Our findings contribute to understanding the neural fingerprint for an individual's propensity to costly punish strangers, and shed some light on how social norm enforcement behaviors are represented by the brain's intrinsic network architecture.
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28
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Cui LB, Zhang YJ, Lu HL, Liu L, Zhang HJ, Fu YF, Wu XS, Xu YQ, Li XS, Qiao YT, Qin W, Yin H, Cao F. Thalamus Radiomics-Based Disease Identification and Prediction of Early Treatment Response for Schizophrenia. Front Neurosci 2021; 15:682777. [PMID: 34290581 PMCID: PMC8289251 DOI: 10.3389/fnins.2021.682777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/31/2021] [Indexed: 12/15/2022] Open
Abstract
Background Emerging evidence suggests structural and functional disruptions of the thalamus in schizophrenia, but whether thalamus abnormalities are able to be used for disease identification and prediction of early treatment response in schizophrenia remains to be determined. This study aims at developing and validating a method of disease identification and prediction of treatment response by multi-dimensional thalamic features derived from magnetic resonance imaging in schizophrenia patients using radiomics approaches. Methods A total of 390 subjects, including patients with schizophrenia and healthy controls, participated in this study, among which 109 out of 191 patients had clinical characteristics of early outcome (61 responders and 48 non-responders). Thalamus-based radiomics features were extracted and selected. The diagnostic and predictive capacity of multi-dimensional thalamic features was evaluated using radiomics approach. Results Using radiomics features, the classifier accurately discriminated patients from healthy controls, with an accuracy of 68%. The features were further confirmed in prediction and random forest of treatment response, with an accuracy of 75%. Conclusion Our study demonstrates a radiomics approach by multiple thalamic features to identify schizophrenia and predict early treatment response. Thalamus-based classification could be promising to apply in schizophrenia definition and treatment selection.
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Affiliation(s)
- Long-Biao Cui
- The Second Medical Center, Chinese PLA General Hospital, Beijing, China.,Department of Clinical Psychology, Fourth Military Medical University, Xi'an, China
| | - Ya-Juan Zhang
- Military Medical Psychology School, Fourth Military Medical University, Xi'an, China
| | - Hong-Liang Lu
- Military Medical Psychology School, Fourth Military Medical University, Xi'an, China
| | - Lin Liu
- School of Life Sciences and Technology, Xidian University, Xi'an, China.,Peking University Sixth Hospital/Institute of Mental Health and Key Laboratory of Mental Health, Peking University, Beijing, China
| | - Hai-Jun Zhang
- Department of Clinical Aerospace Medicine, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, China
| | - Yu-Fei Fu
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xu-Sha Wu
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yong-Qiang Xu
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiao-Sa Li
- Department of Psychiatry, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yu-Ting Qiao
- Department of Psychiatry, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wei Qin
- School of Life Sciences and Technology, Xidian University, Xi'an, China
| | - Hong Yin
- Department of Radiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Feng Cao
- The Second Medical Center, Chinese PLA General Hospital, Beijing, China
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29
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Lai JW, Ang CKE, Acharya UR, Cheong KH. Schizophrenia: A Survey of Artificial Intelligence Techniques Applied to Detection and Classification. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:6099. [PMID: 34198829 PMCID: PMC8201065 DOI: 10.3390/ijerph18116099] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023]
Abstract
Artificial Intelligence in healthcare employs machine learning algorithms to emulate human cognition in the analysis of complicated or large sets of data. Specifically, artificial intelligence taps on the ability of computer algorithms and software with allowable thresholds to make deterministic approximate conclusions. In comparison to traditional technologies in healthcare, artificial intelligence enhances the process of data analysis without the need for human input, producing nearly equally reliable, well defined output. Schizophrenia is a chronic mental health condition that affects millions worldwide, with impairment in thinking and behaviour that may be significantly disabling to daily living. Multiple artificial intelligence and machine learning algorithms have been utilized to analyze the different components of schizophrenia, such as in prediction of disease, and assessment of current prevention methods. These are carried out in hope of assisting with diagnosis and provision of viable options for individuals affected. In this paper, we review the progress of the use of artificial intelligence in schizophrenia.
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Affiliation(s)
- Joel Weijia Lai
- Science, Mathematics and Technology, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore; (J.W.L.); (C.K.E.A.)
| | - Candice Ke En Ang
- Science, Mathematics and Technology, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore; (J.W.L.); (C.K.E.A.)
- MOH Holdings Pte Ltd, 1 Maritime Square, Singapore 099253, Singapore
| | - U. Rajendra Acharya
- Department of Electronics and Computer Engineering, Ngee Ann Polytechnic, Clementi 599489, Singapore;
- Department of Biomedical Engineering, School of Science and Technology, Singapore University of Social Sciences, Clementi 599491, Singapore
- Department of Biomedical Informatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
| | - Kang Hao Cheong
- Science, Mathematics and Technology, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore; (J.W.L.); (C.K.E.A.)
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30
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Zhang T, Gao JS, Çukur T, Gallant JL. Voxel-Based State Space Modeling Recovers Task-Related Cognitive States in Naturalistic fMRI Experiments. Front Neurosci 2021; 14:565976. [PMID: 34045937 PMCID: PMC8145286 DOI: 10.3389/fnins.2020.565976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/24/2020] [Indexed: 11/23/2022] Open
Abstract
Complex natural tasks likely recruit many different functional brain networks, but it is difficult to predict how such tasks will be represented across cortical areas and networks. Previous electrophysiology studies suggest that task variables are represented in a low-dimensional subspace within the activity space of neural populations. Here we develop a voxel-based state space modeling method for recovering task-related state spaces from human fMRI data. We apply this method to data acquired in a controlled visual attention task and a video game task. We find that each task induces distinct brain states that can be embedded in a low-dimensional state space that reflects task parameters, and that attention increases state separation in the task-related subspace. Our results demonstrate that the state space framework offers a powerful approach for modeling human brain activity elicited by complex natural tasks.
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Affiliation(s)
- Tianjiao Zhang
- Program in Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - James S Gao
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Tolga Çukur
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey.,National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara, Turkey.,Neuroscience Program, Sabuncu Brain Research Center, Bilkent University, Ankara, Turkey
| | - Jack L Gallant
- Program in Bioengineering, University of California, Berkeley, Berkeley, CA, United States.,Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States.,Department of Psychology, University of California, Berkeley, Berkeley, CA, United States
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31
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Lin Y, Du P, Sun H, Liang Y, Wang Z, Cui Y, Chen K, Xia Y, Yao D, Yu L, Guo D. Identifying Refractory Epilepsy Without Structural Abnormalities by Fusing the Common Spatial Patterns of Functional and Effective EEG Networks. IEEE Trans Neural Syst Rehabil Eng 2021; 29:708-717. [PMID: 33830925 DOI: 10.1109/tnsre.2021.3071785] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Drug refractory epilepsy (RE) is believed to be associated with structural lesions, but some RE patients show no significant structural abnormalities (RE-no-SA) on conventional magnetic resonance imaging scans. Since most of the medically controlled epilepsy (MCE) patients also do not exhibit structural abnormalities, a reliable assessment needs to be developed to differentiate RE-no-SA patients and MCE patients to avoid misdiagnosis and inappropriate treatment. Using resting-state scalp electroencephalogram (EEG) datasets, we extracted the spatial pattern of network (SPN) features from the functional and effective EEG networks of both RE-no-SA patients and MCE patients. Compared to the performance of traditional resting-state EEG network properties, the SPN features exhibited remarkable superiority in classifying these two groups of epilepsy patients, and accuracy values of 90.00% and 80.00% were obtained for the SPN features of the functional and effective EEG networks, respectively. By further fusing the SPN features of functional and effective networks, we demonstrated that the highest accuracy value of 96.67% could be reached, with a sensitivity of 100% and specificity of 92.86%. Overall, these findings not only indicate that the fused functional and effective SPN features are promising as reliable measurements for distinguishing RE-no-SA patients and MCE patients but also may provide a new perspective to explore the complex neurophysiology of refractory epilepsy.
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32
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Luo Z, Zeng LL, Qin J, Hou C, Shen H, Hu D. Functional Parcellation of Human Brain Precuneus Using Density-Based Clustering. Cereb Cortex 2021; 30:269-282. [PMID: 31044223 DOI: 10.1093/cercor/bhz086] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/12/2019] [Accepted: 03/29/2019] [Indexed: 12/22/2022] Open
Abstract
The human precuneus is involved in many high-level cognitive functions, which strongly suggests the existence of biologically meaningful subdivisions. However, the functional parcellation of the precuneus needs much to be investigated. In this study, we developed an eigen clustering (EIC) approach for the parcellation using precuneus-cortical functional connectivity from fMRI data of the Human Connectome Project. The EIC approach is robust to noise and can automatically determine the cluster number. It is consistently demonstrated that the human precuneus can be subdivided into six symmetrical and connected parcels. The anterior and posterior precuneus participate in sensorimotor and visual functions, respectively. The central precuneus with four subregions indicates a media role in the interaction of the default mode, dorsal attention, and frontoparietal control networks. The EIC-based functional parcellation is free of the spatial distance constraint and is more functionally coherent than parcellation using typical clustering algorithms. The precuneus subregions had high accordance with cortical morphology and revealed good functional segregation and integration characteristics in functional task-evoked activations. This study may shed new light on the human precuneus function at a delicate level and offer an alternative scheme for human brain parcellation.
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Affiliation(s)
- Zhiguo Luo
- College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, China
| | - Ling-Li Zeng
- College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, China
| | - Jian Qin
- College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, China
| | - Chenping Hou
- College of Science, National University of Defense Technology, Changsha, Hunan, China
| | - Hui Shen
- College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, China
| | - Dewen Hu
- College of Mechatronics and Automation, National University of Defense Technology, Changsha, Hunan, China
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33
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Saha DK, Damaraju E, Rashid B, Abrol A, Plis SM, Calhoun VD. A Classification-Based Approach to Estimate the Number of Resting Functional Magnetic Resonance Imaging Dynamic Functional Connectivity States. Brain Connect 2021; 11:132-145. [PMID: 33317408 DOI: 10.1089/brain.2020.0794] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aim: To determine the optimal number of connectivity states in dynamic functional connectivity analysis. Introduction: Recent work has focused on the study of dynamic (vs. static) brain connectivity in resting functional magnetic resonance imaging data. In this work, we focus on temporal correlation between time courses extracted from coherent networks called functional network connectivity (FNC). Dynamic FNC is most commonly estimated using a sliding window-based approach to capture short periods of FNC change. These data are then clustered to estimate transient connectivity patterns or states. Determining the number of states is a challenging problem. The elbow criterion is one of the widely used approaches to determine the connectivity states. Materials and Methods: In our work, we present an alternative approach that evaluates classification (e.g., healthy controls [HCs] vs. patients) as a measure to select the optimal number of states (clusters). We apply different classification strategies to perform classification between HCs and patients with schizophrenia for different numbers of states (i.e., varying the model order in the clustering algorithm). We compute cross-validated accuracy for different model orders to evaluate the classification performance. Results: Our results are consistent with our earlier work which shows that overall accuracy improves when dynamic connectivity measures are used separately or in combination with static connectivity measures. Results also show that the optimal model order for classification is different from that using the standard k-means model selection method, and that such optimization improves cross-validated accuracy. The optimal model order obtained from the proposed approach also gives significantly improved classification performance over the traditional model selection method. Conclusion: The observed results suggest that if one's goal is to perform classification, using the proposed approach as a criterion for selecting the optimal number of states in dynamic connectivity analysis leads to improved accuracy in hold-out data.
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Affiliation(s)
- Debbrata K Saha
- Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, USA
| | - Eswar Damaraju
- Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, USA
| | | | - Anees Abrol
- Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, USA
| | - Sergey M Plis
- Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, USA
| | - Vince D Calhoun
- Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, USA
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34
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Dilernia A, Quevedo K, Camchong J, Lim K, Pan W, Zhang L. Penalized model-based clustering of fMRI data. Biostatistics 2021; 23:825-843. [PMID: 33527998 DOI: 10.1093/biostatistics/kxaa061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
Functional magnetic resonance imaging (fMRI) data have become increasingly available and are useful for describing functional connectivity (FC), the relatedness of neuronal activity in regions of the brain. This FC of the brain provides insight into certain neurodegenerative diseases and psychiatric disorders, and thus is of clinical importance. To help inform physicians regarding patient diagnoses, unsupervised clustering of subjects based on FC is desired, allowing the data to inform us of groupings of patients based on shared features of connectivity. Since heterogeneity in FC is present even between patients within the same group, it is important to allow subject-level differences in connectivity, while still pooling information across patients within each group to describe group-level FC. To this end, we propose a random covariance clustering model (RCCM) to concurrently cluster subjects based on their FC networks, estimate the unique FC networks of each subject, and to infer shared network features. Although current methods exist for estimating FC or clustering subjects using fMRI data, our novel contribution is to cluster or group subjects based on similar FC of the brain while simultaneously providing group- and subject-level FC network estimates. The competitive performance of RCCM relative to other methods is demonstrated through simulations in various settings, achieving both improved clustering of subjects and estimation of FC networks. Utility of the proposed method is demonstrated with application to a resting-state fMRI data set collected on 43 healthy controls and 61 participants diagnosed with schizophrenia.
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Affiliation(s)
- Andrew Dilernia
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Karina Quevedo
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Jazmin Camchong
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Kelvin Lim
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Wei Pan
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Lin Zhang
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
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35
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Jiang W, Zhang H, Zeng L, Shen H, Qin J, Thung K, Yap P, Liu H, Hu D, Wang W, Shen D. Dynamic neural circuit disruptions associated with antisocial behaviors. Hum Brain Mapp 2021; 42:329-344. [PMID: 33064332 PMCID: PMC7776000 DOI: 10.1002/hbm.25225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 08/28/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
Antisocial behavior (ASB) is believed to have neural substrates; however, the association between ASB and functional brain networks remains unclear. The temporal variability of the functional connectivity (or dynamic FC) derived from resting-state functional MRI has been suggested as a useful metric for studying abnormal behaviors including ASB. This is the first study using low-frequency fluctuations of the dynamic FC to unravel potential system-level neural correlates with ASB. Specifically, we individually associated the dynamic FC patterns with the ASB scores (measured by Antisocial Process Screening Device) of the male offenders (age: 23.29 ± 3.36 years) based on machine learning. Results showed that the dynamic FCs were associated with individual ASB scores. Moreover, we found that it was mainly the inter-network dynamic FCs that were negatively associated with the ASB severity. Three major high-order cognitive functional networks and the sensorimotor network were found to be more associated with ASB. We further found that impaired behavior in the ASB subjects was mainly associated with decreased FC dynamics in these networks, which may explain why ASB subjects usually have impaired executive control and emotional processing functions. Our study shows that temporal variation of the FC could be a promising tool for ASB assessment, treatment, and prevention.
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Affiliation(s)
- Weixiong Jiang
- Department of Radiology and BRICUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Department of Information Science and EngineeringHunan First Normal UniversityChangshaHunanChina
| | - Han Zhang
- Department of Radiology and BRICUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Ling‐Li Zeng
- College of Intelligence Science and TechnologyNational University of Defense TechnologyChangshaHunanChina
| | - Hui Shen
- College of Intelligence Science and TechnologyNational University of Defense TechnologyChangshaHunanChina
| | - Jian Qin
- College of Intelligence Science and TechnologyNational University of Defense TechnologyChangshaHunanChina
| | - Kim‐Han Thung
- Department of Radiology and BRICUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Pew‐Thian Yap
- Department of Radiology and BRICUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Huasheng Liu
- Department of Radiology, The Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Dewen Hu
- College of Intelligence Science and TechnologyNational University of Defense TechnologyChangshaHunanChina
| | - Wei Wang
- Department of Radiology, The Third Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Dinggang Shen
- Department of Radiology and BRICUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Department of Artificial IntelligenceKorea UniversitySeoulSouth Korea
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36
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Zhu J, Cao J. Distributional representation of resting-state fMRI for functional brain connectivity analysis. Neurocomputing 2021. [DOI: 10.1016/j.neucom.2020.07.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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37
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Najafpour Z, Fatemi A, Goudarzi Z, Goudarzi R, Shayanfard K, Noorizadeh F. Cost-effectiveness of neuroimaging technologies in management of psychiatric and insomnia disorders: A meta-analysis and prospective cost analysis. J Neuroradiol 2021; 48:348-358. [PMID: 33383065 DOI: 10.1016/j.neurad.2020.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND The optimal diagnostic strategy for patients with psychiatric and insomnia disorders has not been established yet. PURPOSE The purpose of this study was to perform cost-effectiveness analysis of six neuroimaging technologies in diagnosis of patients with psychiatric and insomnia disorders. METHODS An economic evaluation study was conducted in three parts, including a systematic review for determining diagnostic accuracy, a descriptive cross-sectional study with Activity-Based Costing (ABC) technique for tracing resource consumption, and a cost-effectiveness analysis using a short-term decision-analytic model. RESULTS In the first phase, 93 diagnostic accuracy studies were included in the systematic review. The accumulated results (meta-analysis) showed that the highest diagnostic accuracy for psychiatric and insomnia disorders was attributed to PET (sensitivity of 90% and specificity of 80%) and MRI (sensitivity of 76% and specificity of 78%) respectively. In the second phase of the study, we calculated the cost of each technology. The results showed that MRI has the lowest cost. Based on the results in the model of cost-effectiveness sMRI ($ 50.08 per accurate diagnosis) and MRI ($ 58.54 per accurate diagnosis) were more cost-effective neuroimaging technologies. CONCLUSION In psychiatric disorders, no single strategy was characterized by both low cost and high accuracy. However, MRI and PET scan had lower cost and higher accuracy for psychiatric disorders, respectively. MRI was the least costly with the highest diagnostic accuracy in insomnia disorders. Based on our model, sMRI in psychiatric disorders and MRI in insomnia disorders were the most cost-effective technologies.
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Affiliation(s)
- Zhila Najafpour
- Department of Health Care Management, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Asieh Fatemi
- Dpartment of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Faculty of Paramedical sciences, Rafsanjan University of Medical Sciences, Iran.
| | - Zahra Goudarzi
- Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Reza Goudarzi
- Health Services Management Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran.
| | | | - Farsad Noorizadeh
- Basir Eye Health Research Center, Exceptional Talents Development Center, Tehran University of Medical Sciences, Tehran, Iran.
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Fan L, Zhong Q, Qin J, Li N, Su J, Zeng LL, Hu D, Shen H. Brain parcellation driven by dynamic functional connectivity better capture intrinsic network dynamics. Hum Brain Mapp 2020; 42:1416-1433. [PMID: 33283954 PMCID: PMC7927310 DOI: 10.1002/hbm.25303] [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: 09/11/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 01/04/2023] Open
Abstract
Until now, dynamic functional connectivity (dFC) based on functional magnetic resonance imaging is typically estimated on a set of predefined regions of interest (ROIs) derived from an anatomical or static functional atlas which follows an implicit assumption of functional homogeneity within ROIs underlying temporal fluctuation of functional coupling, potentially leading to biases or underestimation of brain network dynamics. Here, we presented a novel computational method based on dynamic functional connectivity degree (dFCD) to derive meaningful brain parcellations that can capture functional homogeneous regions in temporal variance of functional connectivity. Several spatially distributed but functionally meaningful areas that are well consistent with known intrinsic connectivity networks were identified through independent component analysis (ICA) of time‐varying dFCD maps. Furthermore, a systematical comparison with commonly used brain atlases, including the Anatomical Automatic Labeling template, static ICA‐driven parcellation and random parcellation, demonstrated that the ROI‐definition strategy based on the proposed dFC‐driven parcellation could better capture the interindividual variability in dFC and predict observed individual cognitive performance (e.g., fluid intelligence, cognitive flexibility, and sustained attention) based on chronnectome. Together, our findings shed new light on the functional organization of resting brains at the timescale of seconds and emphasized the significance of a dFC‐driven and voxel‐wise functional homogeneous parcellation for network dynamics analyses in neuroscience.
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Affiliation(s)
- Liangwei Fan
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Qi Zhong
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Jian Qin
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Na Li
- Department of Radiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jianpo Su
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Ling-Li Zeng
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Dewen Hu
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
| | - Hui Shen
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, Hunan, China
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Perl YS, Bocaccio H, Pérez-Ipiña I, Zamberlán F, Piccinini J, Laufs H, Kringelbach M, Deco G, Tagliazucchi E. Generative Embeddings of Brain Collective Dynamics Using Variational Autoencoders. PHYSICAL REVIEW LETTERS 2020; 125:238101. [PMID: 33337222 DOI: 10.1103/physrevlett.125.238101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/29/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
We consider the problem of encoding pairwise correlations between coupled dynamical systems in a low-dimensional latent space based on few distinct observations. We use variational autoencoders (VAEs) to embed temporal correlations between coupled nonlinear oscillators that model brain states in the wake-sleep cycle into a two-dimensional manifold. Training a VAE with samples generated using two different parameter combinations results in an embedding that encodes the repertoire of collective dynamics, as well as the topology of the underlying connectivity network. We first follow this approach to infer the trajectory of brain states measured from wakefulness to deep sleep from the two end points of this trajectory; then, we show that the same architecture was capable of representing the pairwise correlations of generic Landau-Stuart oscillators coupled by complex network topology.
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Affiliation(s)
- Yonatan Sanz Perl
- Universidad de San Andrés, Buenos Aires 1644, Argentina
- Physics Department, University of Buenos Aires and Buenos Aires Physics Institute, Buenos Aires 1428, Argentina
- Center for Brain and Cognition, Computational Neuroscience Group, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Hernán Bocaccio
- Physics Department, University of Buenos Aires and Buenos Aires Physics Institute, Buenos Aires 1428, Argentina
| | - Ignacio Pérez-Ipiña
- Physics Department, University of Buenos Aires and Buenos Aires Physics Institute, Buenos Aires 1428, Argentina
| | - Federico Zamberlán
- Physics Department, University of Buenos Aires and Buenos Aires Physics Institute, Buenos Aires 1428, Argentina
| | - Juan Piccinini
- Physics Department, University of Buenos Aires and Buenos Aires Physics Institute, Buenos Aires 1428, Argentina
| | - Helmut Laufs
- Department of Neurology, Christian-Albrechts-University Kiel, Kiel 24118, Germany
| | - Morten Kringelbach
- Department of Psychiatry, University of Oxford, Oxford 2JD, United Kingdom
| | - Gustavo Deco
- Center for Brain and Cognition, Computational Neuroscience Group, Universitat Pompeu Fabra, Barcelona 08002, Spain
| | - Enzo Tagliazucchi
- Physics Department, University of Buenos Aires and Buenos Aires Physics Institute, Buenos Aires 1428, Argentina
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40
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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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41
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Clark SV, Tannahill A, Calhoun VD, Bernard JA, Bustillo J, Turner JA. Weaker Cerebellocortical Connectivity Within Sensorimotor and Executive Networks in Schizophrenia Compared to Healthy Controls: Relationships with Processing Speed. Brain Connect 2020; 10:490-503. [PMID: 32893675 PMCID: PMC7699013 DOI: 10.1089/brain.2020.0792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: The cognitive dysmetria theory of schizophrenia proposes that communication between the cerebellum and cerebral cortex is disrupted by structural and functional abnormalities, resulting in psychotic symptoms and cognitive deficits. Methods: Using publicly available data, resting-state functional connectivity (rsFC) was calculated from 20 hemispheric cerebellar lobules as seed regions of interest to the rest of the brain. Group differences in rsFC between individuals with schizophrenia (SZ) and healthy controls (HCs) were computed, and relationships between rsFC and symptom severity and cognitive functioning were explored. Results: HCs demonstrated stronger connectivity than SZ between several cerebellar lobules and cortical regions, most robustly between motor-related cerebellar lobules (V and VIIIa/b) and temporal and parietal cortices. In addition, seven of nine lobules in which reduced cerebellocortical connectivity was observed showed diagnosis × processing speed interactions; HC showed a positive relationship between connectivity and processing speed, whereas SZ did not show this relationship. Other cognitive domains and symptom severity did not show relationships with connectivity. Conclusions: These findings partially support the cognitive dysmetria theory, and suggest that disrupted cerebellocortical connectivity is associated with slowed processing speed in schizophrenia. Impact statement We show in this work that in chronic schizophrenia, there is weaker functional connectivity between previously unstudied inferior posterior cerebellar lobules and cortical association areas. These findings align and extend previous work showing abnormal connectivity of anterior cerebellar lobules. Further, we present a novel finding that these connectivity deficits are differentially associated with processing speed in the schizophrenia versus healthy control groups. Findings provide further evidence for cerebellocortical dysconnectivity and processing speed deficits as biomarkers of schizophrenia, which may have implications for downstream effects on higher order cognitive functions, in line with the cognitive dysmetria theory.
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Affiliation(s)
- Sarah V. Clark
- Department of Psychology, Georgia State University, Atlanta, Georgia, USA
| | - Amber Tannahill
- Department of Psychology, Georgia State University, Atlanta, Georgia, USA
| | - Vince D. Calhoun
- Department of Psychology, Georgia State University, Atlanta, Georgia, USA
- Department of Neuroscience, Georgia State University, Atlanta, Georgia, USA
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, USA
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, New Mexico, USA
- The Mind Research Network, Albuquerque, New Mexico, USA
| | - Jessica A. Bernard
- Department of Psychological and Brain Sciences and Texas A&M Institute for Neuroscience, Texas A&M University, College Station, Texas, USA
| | - Juan Bustillo
- Department of Psychiatry, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jessica A. Turner
- Department of Psychology, Georgia State University, Atlanta, Georgia, USA
- Department of Neuroscience, Georgia State University, Atlanta, Georgia, USA
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, USA
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42
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Wang M, Hao X, Huang J, Wang K, Shen L, Xu X, Zhang D, Liu M. Hierarchical Structured Sparse Learning for Schizophrenia Identification. Neuroinformatics 2020; 18:43-57. [PMID: 31016571 DOI: 10.1007/s12021-019-09423-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fractional amplitude of low-frequency fluctuation (fALFF) has been widely used for resting-state functional magnetic resonance imaging (rs-fMRI) based schizophrenia (SZ) diagnosis. However, previous studies usually measure the fALFF within low-frequency fluctuation (from 0.01 to 0.08Hz), which cannot fully cover the complex neural activity pattern in the resting-state brain. In addition, existing studies usually ignore the fact that each specific frequency band can delineate the unique spontaneous fluctuations of neural activities in the brain. Accordingly, in this paper, we propose a novel hierarchical structured sparse learning method to sufficiently utilize the specificity and complementary structure information across four different frequency bands (from 0.01Hz to 0.25Hz) for SZ diagnosis. The proposed method can help preserve the partial group structures among multiple frequency bands and the specific characters in each frequency band. We further develop an efficient optimization algorithm to solve the proposed objective function. We validate the efficacy of our proposed method on a real SZ dataset. Also, to demonstrate the generality of the method, we apply our proposed method on a subset of Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Experimental results on both datasets demonstrate that our proposed method achieves promising performance in brain disease classification, compared with several state-of-the-art methods.
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Affiliation(s)
- Mingliang Wang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China.,The State Key Laboratory of Integrated Services Networks, Xidian University, Xi'an, Shaanxi, China
| | - Xiaoke Hao
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| | - Jiashuang Huang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| | - Kangcheng Wang
- Department of Psychology, Southwest University, Chongqing, China
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xijia Xu
- Department of Psychiatry, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China.
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China.
| | - Mingxia Liu
- Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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43
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Li Y, Liu J, Tang Z, Lei B. Deep Spatial-Temporal Feature Fusion From Adaptive Dynamic Functional Connectivity for MCI Identification. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:2818-2830. [PMID: 32112678 DOI: 10.1109/tmi.2020.2976825] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Dynamic functional connectivity (dFC) analysis using resting-state functional Magnetic Resonance Imaging (rs-fMRI) is currently an advanced technique for capturing the dynamic changes of neural activities in brain disease identification. Most existing dFC modeling methods extract dynamic interaction information by using the sliding window-based correlation, whose performance is very sensitive to window parameters. Because few studies can convincingly identify the optimal combination of window parameters, sliding window-based correlation may not be the optimal way to capture the temporal variability of brain activity. In this paper, we propose a novel adaptive dFC model, aided by a deep spatial-temporal feature fusion method, for mild cognitive impairment (MCI) identification. Specifically, we adopt an adaptive Ultra-weighted-lasso recursive least squares algorithm to estimate the adaptive dFC, which effectively alleviates the problem of parameter optimization. Then, we extract temporal and spatial features from the adaptive dFC. In order to generate coarser multi-domain representations for subsequent classification, the temporal and spatial features are further mapped into comprehensive fused features with a deep feature fusion method. Experimental results show that the classification accuracy of our proposed method is reached to 87.7%, which is at least 5.5% improvement than the state-of-the-art methods. These results elucidate the superiority of the proposed method for MCI classification, indicating its effectiveness in the early identification of brain abnormalities.
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44
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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: 65] [Impact Index Per Article: 16.3] [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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45
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Matsubara T, Kusano K, Tashiro T, Ukai K, Uehara K. Deep Generative Model of Individual Variability in fMRI Images of Psychiatric Patients. IEEE Trans Biomed Eng 2020; 68:592-605. [PMID: 32746057 DOI: 10.1109/tbme.2020.3008707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Neuroimaging techniques, such as the resting-state functional magnetic resonance imaging (fMRI), have been investigated to find objective biomarkers of neuro-logical and psychiatric disorders. Objective biomarkers potentially provide a refined diagnosis and quantitative measurements of the effects of treatment. However, fMRI images are sensitive to individual variability, such as functional topography and personal attributes. Suppressing the irrelevant individual variability is crucial for finding objective biomarkers for multiple subjects. Herein, we propose a structured generative model based on deep learning (i.e., a deep generative model) that considers such individual variability. The proposed model builds a joint distribution of (preprocessed) fMRI images, state (with or without a disorder), and individual variability. It can thereby discriminate individual variability from the subject's state. Experimental results demonstrate that the proposed model can diagnose unknown subjects with greater accuracy than conventional approaches. Moreover, the diagnosis is fairer to gender and state, because the proposed model extracts subject attributes (age, gender, and scan site) in an unsupervised manner.
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46
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Lei D, Pinaya WHL, van Amelsvoort T, Marcelis M, Donohoe G, Mothersill DO, Corvin A, Gill M, Vieira S, Huang X, Lui S, Scarpazza C, Young J, Arango C, Bullmore E, Qiyong G, McGuire P, Mechelli A. Detecting schizophrenia at the level of the individual: relative diagnostic value of whole-brain images, connectome-wide functional connectivity and graph-based metrics. Psychol Med 2020; 50:1852-1861. [PMID: 31391132 PMCID: PMC7477363 DOI: 10.1017/s0033291719001934] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 06/25/2019] [Accepted: 07/11/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Previous studies using resting-state functional neuroimaging have revealed alterations in whole-brain images, connectome-wide functional connectivity and graph-based metrics in groups of patients with schizophrenia relative to groups of healthy controls. However, it is unclear which of these measures best captures the neural correlates of this disorder at the level of the individual patient. METHODS Here we investigated the relative diagnostic value of these measures. A total of 295 patients with schizophrenia and 452 healthy controls were investigated using resting-state functional Magnetic Resonance Imaging at five research centres. Connectome-wide functional networks were constructed by thresholding correlation matrices of 90 brain regions, and their topological properties were analyzed using graph theory-based methods. Single-subject classification was performed using three machine learning (ML) approaches associated with varying degrees of complexity and abstraction, namely logistic regression, support vector machine and deep learning technology. RESULTS Connectome-wide functional connectivity allowed single-subject classification of patients and controls with higher accuracy (average: 81%) than both whole-brain images (average: 53%) and graph-based metrics (average: 69%). Classification based on connectome-wide functional connectivity was driven by a distributed bilateral network including the thalamus and temporal regions. CONCLUSION These results were replicated across the three employed ML approaches. Connectome-wide functional connectivity permits differentiation of patients with schizophrenia from healthy controls at single-subject level with greater accuracy; this pattern of results is consistent with the 'dysconnectivity hypothesis' of schizophrenia, which states that the neural basis of the disorder is best understood in terms of system-level functional connectivity alterations.
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Affiliation(s)
- Du Lei
- Departments of Radiology, Huaxi MR Research Center (HMRRC), 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
- Center of Mathematics, Computation, and Cognition, Universidade Federal do ABC, Santo André, Brazil
| | - Therese van Amelsvoort
- Department of Psychiatry and Neuropsychology, School of Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherland
| | - Machteld Marcelis
- Department of Psychiatry and Neuropsychology, School of Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherland
- 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
| | - Michael Gill
- 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
- Departments of Radiology, Huaxi MR Research Center (HMRRC), West China Hospital of Sichuan University, Chengdu, China
| | - Su Lui
- Departments of Radiology, Huaxi MR Research Center (HMRRC), 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
| | - Jonathan Young
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, De Crespigny Park, London, UK
- IXICO plc, London, UK
| | - Celso Arango
- Hospital General Universitario Gregorio Marañon. School of Medicine, Universidad Complutense Madrid. IiSGM, CIBERSAM, Madrid, Spain
| | - Edward Bullmore
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Gong Qiyong
- Departments of Radiology, Huaxi MR Research Center (HMRRC), West China Hospital of Sichuan University, Chengdu, China
- Psychoradiology Research Unit of the Chinese Academy of Medical Sciences (2018RU011), West China Hospital of Sichuan University, Chengdu, Sichuan, 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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Duarte Neto JMW, Wanderley MCDA, da Silva TAF, Marques DAV, da Silva GR, Gurgel JF, Oliveira JDP, Porto ALF. Bacillus thuringiensis endotoxin production: a systematic review of the past 10 years. World J Microbiol Biotechnol 2020; 36:128. [PMID: 32712871 DOI: 10.1007/s11274-020-02904-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/14/2020] [Indexed: 12/16/2022]
Abstract
Bacillus thuringiensis (Bt) is one of the most promising biological control agents used commercially. Its products can contribute to reducing ecological and environmental problems associated with the use of chemical pesticides. Among the limiting factors of using Bt as bioinsecticide are the costs and ensuring its biological activity, which may vary according to the strain and culture conditions. This systematic review aimed to collect state-of-the-art information on the production of Bt endotoxins and to score the methodological feasibility of the data obtained, thus highlighting possible incoherencies. In order to consolidate recent findings and guide future studies, a total of 47 original articles from the last 10 years was analysed, with special attention being given to corroborating data, identifying inconsistencies and suggesting future adjustments so as to increase data reliability. With a maximum score of 8 points, three production parameters were classified on the following scale: preferable (score: 2), adequate (score: 1) and inadequate (score: 0), and another two parameter were classified as adequate (score: 1) or inadequate (score: 0). No article scored more than 6 out of the maximum of 8, thus reflecting the need for more detailed studies regarding Bt endotoxin production. The lack of standardization of methods and units of measurement also have made a comparison of results and an overall analysis difficult. Standards are suggested in the present study. The inclusion of bioassays and quantifying toxin via alkaline dilution are strongly recommended for studies of this nature, along with LC50 expressed in mg/L. Sixteen articles (34%) did not use either of these suggested methods, which indicates the need for further supporting studies. These findings reinforce the need for robust studies in this area, which could include the development of more affordable and effective bioinsecticides, thus increasing their competitiveness against insecticides derived from unsustainable sources.
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Affiliation(s)
- José Manoel W Duarte Neto
- Biotechnology Laboratory, Agronomic Institute of Pernambuco, IPA, Av. General San Martin, Recife, PE, 137150761-000, Brazil.,Bioactives Technology Laboratory (LABTECBIO), Animal Morphology and Physiology Department, Federal Rural University of Pernambuco, UFRPE, Av. Dom Manoel de Medeiros, n/nr, Recife, PE, 52171-900, Brazil.,Keizo Asami Immunopathology Laboratory (LIKA), Federal University of Pernambuco, UFPE, Av. Prof. Moraes Lins Do Rego, n/nr, Recife, PE, 50670-901, Brazil
| | - Maria Carolina de A Wanderley
- Bioactives Technology Laboratory (LABTECBIO), Animal Morphology and Physiology Department, Federal Rural University of Pernambuco, UFRPE, Av. Dom Manoel de Medeiros, n/nr, Recife, PE, 52171-900, Brazil.,Keizo Asami Immunopathology Laboratory (LIKA), Federal University of Pernambuco, UFPE, Av. Prof. Moraes Lins Do Rego, n/nr, Recife, PE, 50670-901, Brazil
| | - Túlio Alexandre F da Silva
- Bioactives Technology Laboratory (LABTECBIO), Animal Morphology and Physiology Department, Federal Rural University of Pernambuco, UFRPE, Av. Dom Manoel de Medeiros, n/nr, Recife, PE, 52171-900, Brazil
| | - Daniela A Viana Marques
- University of Pernambuco (UPE), Serra Talhada Campus, Av. Afonso Magalhães, n/nr, Serra Talhada, PE, Brazil
| | - Gilvanda R da Silva
- Biotechnology Laboratory, Agronomic Institute of Pernambuco, IPA, Av. General San Martin, Recife, PE, 137150761-000, Brazil
| | - Josimar Fernandes Gurgel
- Biotechnology Laboratory, Agronomic Institute of Pernambuco, IPA, Av. General San Martin, Recife, PE, 137150761-000, Brazil
| | - José de Paula Oliveira
- Biotechnology Laboratory, Agronomic Institute of Pernambuco, IPA, Av. General San Martin, Recife, PE, 137150761-000, Brazil
| | - Ana Lúcia F Porto
- Biotechnology Laboratory, Agronomic Institute of Pernambuco, IPA, Av. General San Martin, Recife, PE, 137150761-000, Brazil. .,Bioactives Technology Laboratory (LABTECBIO), Animal Morphology and Physiology Department, Federal Rural University of Pernambuco, UFRPE, Av. Dom Manoel de Medeiros, n/nr, Recife, PE, 52171-900, Brazil. .,Keizo Asami Immunopathology Laboratory (LIKA), Federal University of Pernambuco, UFPE, Av. Prof. Moraes Lins Do Rego, n/nr, Recife, PE, 50670-901, Brazil.
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48
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Wang L, Li X, Zhu Y, Lin B, Bo Q, Li F, Wang C. Discriminative Analysis of Symptom Severity and Ultra-High Risk of Schizophrenia Using Intrinsic Functional Connectivity. Int J Neural Syst 2020; 30:2050047. [PMID: 32689843 DOI: 10.1142/s0129065720500471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Past studies have consistently shown functional dysconnectivity of large-scale brain networks in schizophrenia. In this study, we aimed to further assess whether multivariate pattern analysis (MVPA) could yield a sensitive predictor of patient symptoms, as well as identify ultra-high risk (UHR) stage of schizophrenia from intrinsic functional connectivity of whole-brain networks. We first combined rank-based feature selection and support vector machine methods to distinguish between 43 schizophrenia patients and 52 healthy controls. The constructed classifier was then applied to examine functional connectivity profiles of 18 UHR individuals. The classifier indicated reliable relationship between MVPA measures and symptom severity, with higher classification accuracy in more severely affected schizophrenia patients. The UHR subjects had classification scores falling between those of healthy controls and patients, suggesting an intermediate level of functional brain abnormalities. Moreover, UHR individuals with schizophrenia-like connectivity profiles at baseline presented higher rate of conversion to full-blown illness in the follow-up visits. Spatial maps of discriminative brain regions implicated increases of functional connectivity in the default mode network, whereas decreases of functional connectivity in the cerebellum, thalamus and visual areas in schizophrenia. The findings may have potential utility in the early diagnosis and intervention of schizophrenia.
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Affiliation(s)
- Lubin Wang
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, P. R. China
| | - Xianbin Li
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, P. R. China
| | - Yuyang Zhu
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, P. R. China
| | - Bei Lin
- Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences, Beijing 100850, P. R. China
| | - Qijing Bo
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, P. R. China
| | - Feng Li
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, P. R. China
| | - Chuanyue Wang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, P. R. China
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49
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Overton DJ, Bhagwat N, Viviano JD, Jacobs GR, Voineskos AN. Identifying psychosis spectrum youth using support vector machines and cerebral blood perfusion as measured by arterial spin labeled fMRI. NEUROIMAGE-CLINICAL 2020; 27:102304. [PMID: 32599552 PMCID: PMC7327868 DOI: 10.1016/j.nicl.2020.102304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/15/2020] [Accepted: 06/01/2020] [Indexed: 01/17/2023]
Abstract
Psychosis spectrum (PS) youth can be identified with support vector machines. Classification is improved when youth with psychiatric comorbidities are excluded. Cerebral blood flow (CBF) connectivity differences were noted between PS and non-PS.
Altered cerebral blood flow (CBF), as measured by arterial spin labelling (ASL), has been observed in several psychiatric conditions, but is a generally underutilized MRI technique, especially in the study of psychosis spectrum (PS) symptoms. We aimed to determine group differences in ASL resting state functional connectivity (rsFC) between PS and non-PS youth, and the reliability of a support vector machine (SVM) classifier trained on ASL rsFC features to differentiate PS and non-PS youth, especially compared to blood oxygen level dependent (BOLD) fMRI. 1146 youth aged 8–22 with ASL and BOLD data from the Philadelphia Neurodevelopmental Cohort were analyzed. Widespread ASL hyperconnectivity was found in the left cuneus, precuneus, and dorsolateral prefrontal cortex, and hypoconnectivity was found in the left cingulate cortex and orbitofrontal area (multiple linear regression, FDR corrected). An SVM trained on ASL and BOLD features outperformed either modality alone (AUCBOTH = 0.72 versus AUCASL = 0.68 and AUCBOLD = 0.67). Classification performance and precision improved when the non-PS group had no psychiatric comorbidities. The relative success of the classifier suggests ASL rsFC changes exist in PS individuals that differ from BOLD rsFC changes, and extends previous findings of CBF dysregulation in PS.
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Affiliation(s)
- Dawson J Overton
- Kimel Family Translational Imaging Genetics Research Laboratory, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Nikhil Bhagwat
- Kimel Family Translational Imaging Genetics Research Laboratory, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada; Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, Quebec, Canada; Department of Biological and Biomedical Engineering, McGill University, Montreal, Quebec, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Joseph D Viviano
- Kimel Family Translational Imaging Genetics Research Laboratory, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Grace R Jacobs
- Kimel Family Translational Imaging Genetics Research Laboratory, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Aristotle N Voineskos
- Kimel Family Translational Imaging Genetics Research Laboratory, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, The Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada.
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50
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Zhuang X, Yang Z, Mishra V, Sreenivasan K, Bernick C, Cordes D. Single-scale time-dependent window-sizes in sliding-window dynamic functional connectivity analysis: A validation study. Neuroimage 2020; 220:117111. [PMID: 32615255 PMCID: PMC7594665 DOI: 10.1016/j.neuroimage.2020.117111] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/19/2020] [Accepted: 06/26/2020] [Indexed: 12/16/2022] Open
Abstract
During the past ten years, dynamic functional connectivity (FC) has been extensively studied using the sliding-window method. A fixed window-size is usually selected heuristically, since no consensus exists yet on choice of the optimal window-size. Furthermore, without a known ground-truth, the validity of the computed dynamic FC remains unclear and questionable. In this study, we computed single-scale time-dependent (SSTD) window-sizes for the sliding-window method. SSTD window-sizes were based on the frequency content at every time point of a time series and were computed without any prior information. Therefore, they were time-dependent and data-driven. Using simulated sinusoidal time series with frequency shifts, we demonstrated that SSTD window-sizes captured the time-dependent period (inverse of frequency) information at every time point. We further validated the dynamic FC values computed with SSTD window-sizes with both a classification analysis using fMRI data with a low sampling rate and a regression analysis using fMRI data with a high sampling rate. Specifically, we achieved both a higher classification accuracy in predicting cognitive impairment status in fighters and a larger explained behavioral variance in healthy young adults when using dynamic FC matrices computed with SSTD window-sizes as features, as compared to using dynamic FC matrices computed with the conventional fixed window-sizes. Overall, our study computed and validated SSTD window-sizes in the sliding-window method for dynamic FC analysis. Our results demonstrate that dynamic FC matrices computed with SSTD window-sizes can capture more temporal dynamic information related to behavior and cognitive function.
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Affiliation(s)
- Xiaowei Zhuang
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, USA
| | - Zhengshi Yang
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, USA
| | - Virendra Mishra
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, USA
| | | | - Charles Bernick
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, USA; UW Medicine, Seattle, WA, USA
| | - Dietmar Cordes
- Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, USA; University of Colorado, Boulder, CO, USA; Department of Brain Health, University of Nevada, Las Vegas, NV, USA.
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