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Schielen SJC, Pilmeyer J, Aldenkamp AP, Zinger S. The diagnosis of ASD with MRI: a systematic review and meta-analysis. Transl Psychiatry 2024; 14:318. [PMID: 39095368 PMCID: PMC11297045 DOI: 10.1038/s41398-024-03024-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 06/25/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024] Open
Abstract
While diagnosing autism spectrum disorder (ASD) based on an objective test is desired, the current diagnostic practice involves observation-based criteria. This study is a systematic review and meta-analysis of studies that aim to diagnose ASD using magnetic resonance imaging (MRI). The main objective is to describe the state of the art of diagnosing ASD using MRI in terms of performance metrics and interpretation. Furthermore, subgroups, including different MRI modalities and statistical heterogeneity, are analyzed. Studies that dichotomously diagnose individuals with ASD and healthy controls by analyses progressing from magnetic resonance imaging obtained in a resting state were systematically selected by two independent reviewers. Studies were sought on Web of Science and PubMed, which were last accessed on February 24, 2023. The included studies were assessed on quality and risk of bias using the revised Quality Assessment of Diagnostic Accuracy Studies tool. A bivariate random-effects model was used for syntheses. One hundred and thirty-four studies were included comprising 159 eligible experiments. Despite the overlap in the studied samples, an estimated 4982 unique participants consisting of 2439 individuals with ASD and 2543 healthy controls were included. The pooled summary estimates of diagnostic performance are 76.0% sensitivity (95% CI 74.1-77.8), 75.7% specificity (95% CI 74.0-77.4), and an area under curve of 0.823, but uncertainty in the study assessments limits confidence. The main limitations are heterogeneity and uncertainty about the generalization of diagnostic performance. Therefore, comparisons between subgroups were considered inappropriate. Despite the current limitations, methods progressing from MRI approach the diagnostic performance needed for clinical practice. The state of the art has obstacles but shows potential for future clinical application.
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Affiliation(s)
- Sjir J C Schielen
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands.
| | - Jesper Pilmeyer
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Albert P Aldenkamp
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
- Department of Behavioral Sciences, Epilepsy Center Kempenhaeghe, Heeze, the Netherlands
| | - Svitlana Zinger
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
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2
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Battistella E, Ghiassian D, Barabási AL. Improving the performance and interpretability on medical datasets using graphical ensemble feature selection. Bioinformatics 2024; 40:btae341. [PMID: 38837347 PMCID: PMC11187494 DOI: 10.1093/bioinformatics/btae341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/19/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
MOTIVATION A major hindrance towards using Machine Learning (ML) on medical datasets is the discrepancy between a large number of variables and small sample sizes. While multiple feature selection techniques have been proposed to avoid the resulting overfitting, overall ensemble techniques offer the best selection robustness. Yet, current methods designed to combine different algorithms generally fail to leverage the dependencies identified by their components. Here, we propose Graphical Ensembling (GE), a graph-theory-based ensemble feature selection technique designed to improve the stability and relevance of the selected features. RESULTS Relying on four datasets, we show that GE increases classification performance with fewer selected features. For example, on rheumatoid arthritis patient stratification, GE outperforms the baseline methods by 9% Balanced Accuracy while relying on fewer features. We use data on sub-cellular networks to show that the selected features (proteins) are closer to the known disease genes, and the uncovered biological mechanisms are more diversified. By successfully tackling the complex correlations between biological variables, we anticipate that GE will improve the medical applications of ML. AVAILABILITY AND IMPLEMENTATION https://github.com/ebattistella/auto_machine_learning.
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Affiliation(s)
- Enzo Battistella
- Network Science Institute, Northeastern University, Boston, MA 02115, United States
| | | | - Albert-László Barabási
- Network Science Institute, Northeastern University, Boston, MA 02115, United States
- Department of Data and Network Science, Central Eastern University, Budapest 1051, Hungary
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States
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3
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Guan Z, Yu J, Shi Z, Liu X, Yu R, Lai T, Yang C, Dong H, Chen R, Wei L. Dynamic graph transformer network via dual-view connectivity for autism spectrum disorder identification. Comput Biol Med 2024; 174:108415. [PMID: 38599070 DOI: 10.1016/j.compbiomed.2024.108415] [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: 09/10/2023] [Revised: 03/17/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder that requires objective and accurate identification methods for effective early intervention. Previous population-based methods via functional connectivity (FC) analysis ignore the differences between positive and negative FCs, which provide the potential information complementarity. And they also require additional information to construct a pre-defined graph. Meanwhile, two challenging demand attentions are the imbalance of performance caused by the class distribution and the inherent heterogeneity of multi-site data. In this paper, we propose a novel dynamic graph Transformer network based on dual-view connectivity for ASD Identification. It is based on the Autoencoders, which regard the input feature as individual feature and without any inductive bias. First, a dual-view feature extractor is designed to extract individual and complementary information from positive and negative connectivity. Then Graph Transformer network is innovated with a hot plugging K-Nearest Neighbor (KNN) algorithm module which constructs a dynamic population graph without any additional information. Additionally, we introduce the PolyLoss function and the Vrex method to address the class imbalance and improve the model's generalizability. The evaluation experiment on 1102 subjects from the ABIDE I dataset demonstrates our method can achieve superior performance over several state-of-the-art methods and satisfying generalizability for ASD identification.
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Affiliation(s)
- Zihao Guan
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Digital Fujian Research Institute of Big Data for Agriculture and Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiaming Yu
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Digital Fujian Research Institute of Big Data for Agriculture and Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenshan Shi
- Department of Radiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350002, China
| | - Xiumei Liu
- Developmental and Behavior Pediatrics Department, Fujian Children's Hospital - Fujian Branch of Shanghai Children's Medical Center, Fuzhou, 350002, China; College of Clinical Medicine for Obstetrics Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350012, China
| | - Renping Yu
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Taotao Lai
- College of Computer and Control Engineering, Minjiang University, Fuzhou, 350108, China
| | - Changcai Yang
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Digital Fujian Research Institute of Big Data for Agriculture and Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Heng Dong
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Digital Fujian Research Institute of Big Data for Agriculture and Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Riqing Chen
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Digital Fujian Research Institute of Big Data for Agriculture and Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lifang Wei
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Digital Fujian Research Institute of Big Data for Agriculture and Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Tekkesinoglu S, Pudas S. Explaining graph convolutional network predictions for clinicians-An explainable AI approach to Alzheimer's disease classification. Front Artif Intell 2024; 6:1334613. [PMID: 38259822 PMCID: PMC10801225 DOI: 10.3389/frai.2023.1334613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Graph-based representations are becoming more common in the medical domain, where each node defines a patient, and the edges signify associations between patients, relating individuals with disease and symptoms in a node classification task. In this study, a Graph Convolutional Networks (GCN) model was utilized to capture differences in neurocognitive, genetic, and brain atrophy patterns that can predict cognitive status, ranging from Normal Cognition (NC) to Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD), on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Elucidating model predictions is vital in medical applications to promote clinical adoption and establish physician trust. Therefore, we introduce a decomposition-based explanation method for individual patient classification. Methods Our method involves analyzing the output variations resulting from decomposing input values, which allows us to determine the degree of impact on the prediction. Through this process, we gain insight into how each feature from various modalities, both at the individual and group levels, contributes to the diagnostic result. Given that graph data contains critical information in edges, we studied relational data by silencing all the edges of a particular class, thereby obtaining explanations at the neighborhood level. Results Our functional evaluation showed that the explanations remain stable with minor changes in input values, specifically for edge weights exceeding 0.80. Additionally, our comparative analysis against SHAP values yielded comparable results with significantly reduced computational time. To further validate the model's explanations, we conducted a survey study with 11 domain experts. The majority (71%) of the responses confirmed the correctness of the explanations, with a rating of above six on a 10-point scale for the understandability of the explanations. Discussion Strategies to overcome perceived limitations, such as the GCN's overreliance on demographic information, were discussed to facilitate future adoption into clinical practice and gain clinicians' trust as a diagnostic decision support system.
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Affiliation(s)
| | - Sara Pudas
- Department of Integrative Medical Biology (IMB), Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
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Wang M, Ma Z, Wang Y, Liu J, Guo J. A multi-view convolutional neural network method combining attention mechanism for diagnosing autism spectrum disorder. PLoS One 2023; 18:e0295621. [PMID: 38064474 PMCID: PMC10707567 DOI: 10.1371/journal.pone.0295621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental condition whose current psychiatric diagnostic process is subjective and behavior-based. In contrast, functional magnetic resonance imaging (fMRI) can objectively measure brain activity and is useful for identifying brain disorders. However, the ASD diagnostic models employed to date have not reached satisfactory levels of accuracy. This study proposes the use of MAACNN, a method that utilizes multi-view convolutional neural networks (CNNs) in conjunction with attention mechanisms for identifying ASD in multi-scale fMRI. The proposed algorithm effectively combines unsupervised and supervised learning. In the initial stage, we employ stacked denoising autoencoders, an unsupervised learning method for feature extraction, which provides different nodes to adapt to multi-scale data. In the subsequent stage, we perform supervised learning by employing multi-view CNNs for classification and obtain the final results. Finally, multi-scale data fusion is achieved by using the attention fusion mechanism. The ABIDE dataset is used to evaluate the model we proposed., and the experimental results show that MAACNN achieves superior performance with 75.12% accuracy and 0.79 AUC on ABIDE-I, and 72.88% accuracy and 0.76 AUC on ABIDE-II. The proposed method significantly contributes to the clinical diagnosis of ASD.
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Affiliation(s)
- Mingzhi Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, China
| | - Zhiqiang Ma
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, China
| | - Yongjie Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, China
| | - Jing Liu
- College of Computer Science and Engineering, Guilin University of Aerospace Technology, Guilin, China
| | - Jifeng Guo
- College of Computer Science and Engineering, Guilin University of Aerospace Technology, Guilin, China
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Shao L, Fu C, Chen X. A heterogeneous graph convolutional attention network method for classification of autism spectrum disorder. BMC Bioinformatics 2023; 24:363. [PMID: 37759189 PMCID: PMC10536734 DOI: 10.1186/s12859-023-05495-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a serious developmental disorder of the brain. Recently, various deep learning methods based on functional magnetic resonance imaging (fMRI) data have been developed for the classification of ASD. Among them, graph neural networks, which generalize deep neural network models to graph structured data, have shown great advantages. However, in graph neural methods, because the graphs constructed are homogeneous, the phenotype information of the subjects cannot be fully utilized. This affects the improvement of the classification performance. METHODS To fully utilize the phenotype information, this paper proposes a heterogeneous graph convolutional attention network (HCAN) model to classify ASD. By combining an attention mechanism and a heterogeneous graph convolutional network, important aggregated features can be extracted in the HCAN. The model consists of a multilayer HCAN feature extractor and a multilayer perceptron (MLP) classifier. First, a heterogeneous population graph was constructed based on the fMRI and phenotypic data. Then, a multilayer HCAN is used to mine graph-based features from the heterogeneous graph. Finally, the extracted features are fed into an MLP for the final classification. RESULTS The proposed method is assessed on the autism brain imaging data exchange (ABIDE) repository. In total, 871 subjects in the ABIDE I dataset are used for the classification task. The best classification accuracy of 82.9% is achieved. Compared to the other methods using exactly the same subjects in the literature, the proposed method achieves superior performance to the best reported result. CONCLUSIONS The proposed method can effectively integrate heterogeneous graph convolutional networks with a semantic attention mechanism so that the phenotype features of the subjects can be fully utilized. Moreover, it shows great potential in the diagnosis of brain functional disorders with fMRI data.
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Affiliation(s)
- Lizhen Shao
- Beijing Engineering Research Center of Industrial Spectrum Imaging, School of Automation and Electrical Engineering, Beijing, 100083, China.
- Lancaster University, Lancaster, LA1 4YX, UK.
| | - Cong Fu
- Beijing Engineering Research Center of Industrial Spectrum Imaging, School of Automation and Electrical Engineering, Beijing, 100083, China
- Shunde Graduate School, University of Science and Technology Beijing, Foshan, 528399, China
| | - Xunying Chen
- Beijing Engineering Research Center of Industrial Spectrum Imaging, School of Automation and Electrical Engineering, Beijing, 100083, China
- Shunde Graduate School, University of Science and Technology Beijing, Foshan, 528399, China
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7
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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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Zaripova K, Cosmo L, Kazi A, Ahmadi SA, Bronstein MM, Navab N. Graph-in-Graph (GiG): Learning interpretable latent graphs in non-Euclidean domain for biological and healthcare applications. Med Image Anal 2023; 88:102839. [PMID: 37263109 DOI: 10.1016/j.media.2023.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 06/03/2023]
Abstract
Graphs are a powerful tool for representing and analyzing unstructured, non-Euclidean data ubiquitous in the healthcare domain. Two prominent examples are molecule property prediction and brain connectome analysis. Importantly, recent works have shown that considering relationships between input data samples has a positive regularizing effect on the downstream task in healthcare applications. These relationships are naturally modeled by a (possibly unknown) graph structure between input samples. In this work, we propose Graph-in-Graph (GiG), a neural network architecture for protein classification and brain imaging applications that exploits the graph representation of the input data samples and their latent relation. We assume an initially unknown latent-graph structure between graph-valued input data and propose to learn a parametric model for message passing within and across input graph samples, end-to-end along with the latent structure connecting the input graphs. Further, we introduce a Node Degree Distribution Loss (NDDL) that regularizes the predicted latent relationships structure. This regularization can significantly improve the downstream task. Moreover, the obtained latent graph can represent patient population models or networks of molecule clusters, providing a level of interpretability and knowledge discovery in the input domain, which is of particular value in healthcare.
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Affiliation(s)
- Kamilia Zaripova
- Department of Computer Science, Technical University of Munich, Munich, Germany.
| | - Luca Cosmo
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy; Informatics Department, USI University of Lugano, Lugano, Switzerland
| | - Anees Kazi
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | | | | | - Nassir Navab
- Department of Computer Science, Technical University of Munich, Munich, Germany; Whiting School of Engineering, Johns Hopkins University, Baltimore, USA
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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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Abbas SQ, Chi L, Chen YPP. DeepMNF: Deep Multimodal Neuroimaging Framework for Diagnosing Autism Spectrum Disorder. Artif Intell Med 2023; 136:102475. [PMID: 36710063 DOI: 10.1016/j.artmed.2022.102475] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 10/24/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
The growing prevalence of neurological disorders, e.g., Autism Spectrum Disorder (ASD), demands robust computer-aided diagnosis (CAD) due to the diverse symptoms which require early intervention, particularly in young children. The absence of a benchmark neuroimaging diagnostics paves the way to study transitions in the brain's anatomical structure and neurological patterns associated with ASD. The existing CADs take advantage of the large-scale baseline dataset from the Autism Brain Imaging Data Exchange (ABIDE) repository to improve diagnostic performance, but the involvement of multisite data also amplifies the variabilities and heterogeneities that hinder satisfactory results. To resolve this problem, we propose a Deep Multimodal Neuroimaging Framework (DeepMNF) that employs Functional Magnetic Resonance Imaging (fMRI) and Structural Magnetic Resonance Imaging (sMRI) to integrate cross-modality spatiotemporal information by exploiting 2-dimensional time-series data along with 3-dimensional images. The purpose is to fuse complementary information that increases group differences and homogeneities. To the best of our knowledge, our DeepMNF achieves superior validation performance than the best reported result on the ABIDE-1 repository involving datasets from all available screening sites. In this work, we also demonstrate the performance of the studied modalities in a single model as well as their possible combinations to develop the multimodal framework.
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Affiliation(s)
- S Qasim Abbas
- Department of Computer Science and Information Technology, La Trobe University, Melbourne, VIC 3086, Australia.
| | - Lianhua Chi
- Department of Computer Science and Information Technology, La Trobe University, Melbourne, VIC 3086, Australia.
| | - Yi-Ping Phoebe Chen
- Department of Computer Science and Information Technology, La Trobe University, Melbourne, VIC 3086, Australia.
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Liu Y, Li H, Luo T, Zhang C, Xiao Z, Wei Y, Gao Y, Shi F, Shan F, Shen D. Structural Attention Graph Neural Network for Diagnosis and Prediction of COVID-19 Severity. IEEE TRANSACTIONS ON MEDICAL IMAGING 2023; 42:557-567. [PMID: 36459600 DOI: 10.1109/tmi.2022.3226575] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
With rapid worldwide spread of Coronavirus Disease 2019 (COVID-19), jointly identifying severe COVID-19 cases from mild ones and predicting the conversion time (from mild to severe) is essential to optimize the workflow and reduce the clinician's workload. In this study, we propose a novel framework for COVID-19 diagnosis, termed as Structural Attention Graph Neural Network (SAGNN), which can combine the multi-source information including features extracted from chest CT, latent lung structural distribution, and non-imaging patient information to conduct diagnosis of COVID-19 severity and predict the conversion time from mild to severe. Specifically, we first construct a graph to incorporate structural information of the lung and adopt graph attention network to iteratively update representations of lung segments. To distinguish different infection degrees of left and right lungs, we further introduce a structural attention mechanism. Finally, we introduce demographic information and develop a multi-task learning framework to jointly perform both tasks of classification and regression. Experiments are conducted on a real dataset with 1687 chest CT scans, which includes 1328 mild cases and 359 severe cases. Experimental results show that our method achieves the best classification (e.g., 86.86% in terms of Area Under Curve) and regression (e.g., 0.58 in terms of Correlation Coefficient) performance, compared with other comparison methods.
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12
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Hejazi S, Karwowski W, Farahani FV, Marek T, Hancock PA. Graph-Based Analysis of Brain Connectivity in Multiple Sclerosis Using Functional MRI: A Systematic Review. Brain Sci 2023; 13:brainsci13020246. [PMID: 36831789 PMCID: PMC9953947 DOI: 10.3390/brainsci13020246] [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: 12/06/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
(1) Background: Multiple sclerosis (MS) is an immune system disease in which myelin in the nervous system is affected. This abnormal immune system mechanism causes physical disabilities and cognitive impairment. Functional magnetic resonance imaging (fMRI) is a common neuroimaging technique used in studying MS. Computational methods have recently been applied for disease detection, notably graph theory, which helps researchers understand the entire brain network and functional connectivity. (2) Methods: Relevant databases were searched to identify articles published since 2000 that applied graph theory to study functional brain connectivity in patients with MS based on fMRI. (3) Results: A total of 24 articles were included in the review. In recent years, the application of graph theory in the MS field received increased attention from computational scientists. The graph-theoretical approach was frequently combined with fMRI in studies of functional brain connectivity in MS. Lower EDSSs of MS stage were the criteria for most of the studies (4) Conclusions: This review provides insights into the role of graph theory as a computational method for studying functional brain connectivity in MS. Graph theory is useful in the detection and prediction of MS and can play a significant role in identifying cognitive impairment associated with MS.
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Affiliation(s)
- Sara Hejazi
- Computational Neuroergonomics Laboratory, Department of Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL 32816, USA
- Correspondence:
| | - Waldemar Karwowski
- Computational Neuroergonomics Laboratory, Department of Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL 32816, USA
| | - Farzad V. Farahani
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tadeusz Marek
- Department of Cognitive Neuroscience and Neuroergonomics, Institute of Applied Psychology, Jagiellonian University, 30-348 Kraków, Poland
| | - P. A. Hancock
- Department of Psychology, University of Central Florida, Orlando, FL 32816, USA
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Qin C, Zhu X, Ye L, Peng L, Li L, Wang J, Ma J, Liu T. Autism detection based on multiple time scale model. J Neural Eng 2022; 19. [PMID: 35985297 DOI: 10.1088/1741-2552/ac8b39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/19/2022] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Current autism clinical detection relies on doctor observation and filling of clinical scales, which is subjective and easily misdetection. Existing autism research of functional magnetic resonance imaging (fMRI) over-compresses the time-scale information and has poor generalization ability. This study extracts multiple time scale brain features of fMRI, providing objective detection. APPROACH We first use least absolute shrinkage and selection operator (LASSO) to build a sparse network and extract features with a time scale of 1. Then, we use hidden markov model (HMM) to extract features that describe the dynamic changes of the brain, with a time scale of 2. Additionally, to analyze the features of the potential network activity of autism from a higher time scale, we use long short-term memory (LSTM) to construct an auto-encoder to re-encode the original data and extract the features of the at a higher time scale, with a time scale of T, and T is the time length of fMRI. We use Recursive Feature Elimination (RFE) for feature selection for three different time scale features, merge them into multiple time scale features, and finally use one-dimensional convolution neural network (1DCNN) for classification. MAIN RESULTS Compared with well-established models, our method has achieved better results. The accuracy of our method is 76.0%, and the area under the roc curve is 0.83, tested on the completely independent data, so our method has better generalization ability. SIGNIFICANCE This research analyzes fMRI sequences from multiple time scale to detect autism, and it also provides a new framework and research ideas for subsequent fMRI analysis.
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Affiliation(s)
- Chi Qin
- Xi'an Jiaotong University, School of Life Science and Technology, Xi'an, 710049, CHINA
| | - Xiaofei Zhu
- Tangdu Hospital Fourth Military Medical University, Department of Radiology, Xi'an, Shaanxi, 710038, CHINA
| | - Lin Ye
- Xi'an Jiaotong University, School of Life Science and Technology, Xi'an, 710049, CHINA
| | - Li Peng
- Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Department of Radiology, Wuhan, Hubei, 430030, CHINA
| | - Long Li
- Xi'an Jiaotong University, School of Life Science and Technology, Xi'an, 710049, CHINA
| | - Jue Wang
- Xi'an Jiaotong University, School of Life Science and Technology, Xi'an, 710049, CHINA
| | - Jin Ma
- Air Force Medical University, School of Aerospace Medicine, Xi'an, 710032, CHINA
| | - Tian Liu
- Xi'an Jiaotong University, School of Life Science and Technology, Xi'an, 710049, CHINA
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Melillo R, Leisman G, Machado C, Machado-Ferrer Y, Chinchilla-Acosta M, Kamgang S, Melillo T, Carmeli E. Retained Primitive Reflexes and Potential for Intervention in Autistic Spectrum Disorders. Front Neurol 2022; 13:922322. [PMID: 35873782 PMCID: PMC9301367 DOI: 10.3389/fneur.2022.922322] [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: 04/17/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
We provide evidence to support the contention that many aspects of Autistic Spectrum Disorder (ASD) are related to interregional brain functional disconnectivity associated with maturational delays in the development of brain networks. We think a delay in brain maturation in some networks may result in an increase in cortical maturation and development in other networks, leading to a developmental asynchrony and an unevenness of functional skills and symptoms. The paper supports the close relationship between retained primitive reflexes and cognitive and motor function in general and in ASD in particular provided to indicate that the inhibition of RPRs can effect positive change in ASD.
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Affiliation(s)
- Robert Melillo
- Movement and Cognition Laboratory, Department of Physical Therapy, University of Haifa, Haifa, Israel
| | - Gerry Leisman
- Movement and Cognition Laboratory, Department of Physical Therapy, University of Haifa, Haifa, Israel
- Department of Neurology, University of the Medical Sciences of Havana, Havana, Cuba
| | - Calixto Machado
- Department of Clinical Neurophysiology, Institute for Neurology and Neurosurgery, Havana, Cuba
| | - Yanin Machado-Ferrer
- Department of Clinical Neurophysiology, Institute for Neurology and Neurosurgery, Havana, Cuba
| | | | - Shanine Kamgang
- Department of Neuroscience, Carleton University, Ottawa, ON, Canada
| | - Ty Melillo
- Northeast College of the Health Sciences, Seneca Falls, New York, NY, United States
| | - Eli Carmeli
- Movement and Cognition Laboratory, Department of Physical Therapy, University of Haifa, Haifa, Israel
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15
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Ahmed ZAT, Aldhyani THH, Jadhav ME, Alzahrani MY, Alzahrani ME, Althobaiti MM, Alassery F, Alshaflut A, Alzahrani NM, Al-madani AM. Facial Features Detection System To Identify Children With Autism Spectrum Disorder: Deep Learning Models. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3941049. [PMID: 35419082 PMCID: PMC9001065 DOI: 10.1155/2022/3941049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 12/04/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder associated with brain development that subsequently affects the physical appearance of the face. Autistic children have different patterns of facial features, which set them distinctively apart from typically developed (TD) children. This study is aimed at helping families and psychiatrists diagnose autism using an easy technique, viz., a deep learning-based web application for detecting autism based on experimentally tested facial features using a convolutional neural network with transfer learning and a flask framework. MobileNet, Xception, and InceptionV3 were the pretrained models used for classification. The facial images were taken from a publicly available dataset on Kaggle, which consists of 3,014 facial images of a heterogeneous group of children, i.e., 1,507 autistic children and 1,507 nonautistic children. Given the accuracy of the classification results for the validation data, MobileNet reached 95% accuracy, Xception achieved 94%, and InceptionV3 attained 0.89%.
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Affiliation(s)
- Zeyad A. T. Ahmed
- Department of Computer Science, Dr. Babasaheb Ambedkar Marathwada University, India
| | - Theyazn H. H. Aldhyani
- Applied College in Abqaiq, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Mukti E. Jadhav
- Shri Shivaji Science & Arts College, Chikhli Dist. Buldana, India
| | - Mohammed Y. Alzahrani
- Department of Computer Sciences and Information Technology, Albaha University, Albaha, P.O. Box 1988, Saudi Arabia
| | - Mohammad Eid Alzahrani
- Department of Engineering and Computer Science, Al Baha University, Albaha, P.O. Box 1988, Saudi Arabia
| | - Maha M. Althobaiti
- Department of Computer Science, College of Computing and Information technology, Taif University, P.O.Box 11099, Taif 21944, Saudi Arabia
| | - Fawaz Alassery
- Department of Computer Engineering, College of Computers and Information Technology, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Alshaflut
- College of Computer Science and Information Technology, Albaha University, Albaha, P.O. Box 1988, Saudi Arabia
| | - Nouf Matar Alzahrani
- College of Computer Science and Information Technology, Albaha University, Albaha, P.O. Box 1988, Saudi Arabia
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16
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Rakhimberdina Z, Jodelet Q, Liu X, Murata T. Natural Image Reconstruction From fMRI Using Deep Learning: A Survey. Front Neurosci 2021; 15:795488. [PMID: 34987359 PMCID: PMC8722107 DOI: 10.3389/fnins.2021.795488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022] Open
Abstract
With the advent of brain imaging techniques and machine learning tools, much effort has been devoted to building computational models to capture the encoding of visual information in the human brain. One of the most challenging brain decoding tasks is the accurate reconstruction of the perceived natural images from brain activities measured by functional magnetic resonance imaging (fMRI). In this work, we survey the most recent deep learning methods for natural image reconstruction from fMRI. We examine these methods in terms of architectural design, benchmark datasets, and evaluation metrics and present a fair performance evaluation across standardized evaluation metrics. Finally, we discuss the strengths and limitations of existing studies and present potential future directions.
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Affiliation(s)
- Zarina Rakhimberdina
- Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan
- AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory, Tokyo, Japan
| | - Quentin Jodelet
- Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan
- AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory, Tokyo, Japan
| | - Xin Liu
- AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory, Tokyo, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Digital Architecture Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Tsuyoshi Murata
- Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan
- AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory, Tokyo, Japan
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17
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Ahmedt-Aristizabal D, Armin MA, Denman S, Fookes C, Petersson L. Graph-Based Deep Learning for Medical Diagnosis and Analysis: Past, Present and Future. SENSORS (BASEL, SWITZERLAND) 2021; 21:4758. [PMID: 34300498 PMCID: PMC8309939 DOI: 10.3390/s21144758] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 01/17/2023]
Abstract
With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered, which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interacting nodes connected by edges whose weights can be determined by either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure, and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.
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Affiliation(s)
- David Ahmedt-Aristizabal
- Imaging and Computer Vision Group, CSIRO Data61, Canberra 2601, Australia; (M.A.A.); (L.P.)
- Signal Processing, Artificial Intelligence and Vision Technologies (SAIVT) Research Program, Queensland University of Technology, Brisbane 4000, Australia; (S.D.); (C.F.)
| | - Mohammad Ali Armin
- Imaging and Computer Vision Group, CSIRO Data61, Canberra 2601, Australia; (M.A.A.); (L.P.)
| | - Simon Denman
- Signal Processing, Artificial Intelligence and Vision Technologies (SAIVT) Research Program, Queensland University of Technology, Brisbane 4000, Australia; (S.D.); (C.F.)
| | - Clinton Fookes
- Signal Processing, Artificial Intelligence and Vision Technologies (SAIVT) Research Program, Queensland University of Technology, Brisbane 4000, Australia; (S.D.); (C.F.)
| | - Lars Petersson
- Imaging and Computer Vision Group, CSIRO Data61, Canberra 2601, Australia; (M.A.A.); (L.P.)
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18
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A Deep Learning Approach to Predict Autism Spectrum Disorder Using Multisite Resting-State fMRI. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11083636] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Autism spectrum disorder (ASD) is a complex and degenerative neuro-developmental disorder. Most of the existing methods utilize functional magnetic resonance imaging (fMRI) to detect ASD with a very limited dataset which provides high accuracy but results in poor generalization. To overcome this limitation and to enhance the performance of the automated autism diagnosis model, in this paper, we propose an ASD detection model using functional connectivity features of resting-state fMRI data. Our proposed model utilizes two commonly used brain atlases, Craddock 200 (CC200) and Automated Anatomical Labelling (AAL), and two rarely used atlases Bootstrap Analysis of Stable Clusters (BASC) and Power. A deep neural network (DNN) classifier is used to perform the classification task. Simulation results indicate that the proposed model outperforms state-of-the-art methods in terms of accuracy. The mean accuracy of the proposed model was 88%, whereas the mean accuracy of the state-of-the-art methods ranged from 67% to 85%. The sensitivity, F1-score, and area under receiver operating characteristic curve (AUC) score of the proposed model were 90%, 87%, and 96%, respectively. Comparative analysis on various scoring strategies show the superiority of BASC atlas over other aforementioned atlases in classifying ASD and control.
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