Significant progress has been made using fMRI to characterize the brain changes that occur in ASD, a complex neuro-developmental disorder. However, due to the high dimensionality and low signal-to-noise ratio of fMRI, embedding informative and robust brain regional fMRI representations for both graph-level classification and region-level functional difference detection tasks between ASD and healthy control (HC) groups is difficult. Here, we model the whole brain fMRI as a graph, which preserves geometrical and temporal information and use a Graph Neural Network (GNN) to learn from the graph-structured fMRI data. We investigate the potential of including mutual information (MI) loss (Infomax), which is an unsupervised term encouraging large MI of each nodal representation and its corresponding graph-level summarized representation to learn a better graph embedding. Specifically, this work developed a pipeline including a GNN encoder, a classifier and a discriminator, which forces the encoded nodal representations to both benefit classification and reveal the common nodal patterns in a graph. We simultaneously optimize graph-level classification loss and Infomax. We demonstrated that Infomax graph embedding improves classification performance as a regularization term. Furthermore, we found separable nodal representations of ASD and HC groups in prefrontal cortex, cingulate cortex, visual regions, and other social, emotional and execution related brain regions. In contrast with GNN with classification loss only, the proposed pipeline can facilitate training more robust ASD classification models. Moreover, the separable nodal representations can detect the functional differences between the two groups and contribute to revealing new ASD biomarkers.
Diagnosis and Pathogenic Analysis of Autism Spectrum Disorder Using Fused Brain Connection Graph
Southwestern University of Finance and Economics（西南财经大学）；Osaka University（大阪大学）；West China Hospital of Sichuan University（四川大学华西医院）；The University of Hong Kong（香港大学）；General Hospital of Ningxia Medical University（宁夏医科大学总医院）
Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS)（神经影像与数据科学转化研究三机构中心（TReNDS））；Georgia State University（佐治亚州立大学）；Georgia Tech（佐治亚理工学院）；Emory（埃默里大学）
Discovering distinct features and their relations from data can help us uncover valuable knowledge crucial for various tasks, e.g., classification. In neuroimaging, these features could help to understand, classify, and possibly prevent brain disorders. Model introspection of highly performant overparameterized deep learning (DL) models could help find these features and relations. However, to achieve high-performance level DL models require numerous labeled training samples ($n$) rarely available in many fields. This paper presents a pre-training method involving graph convolutional/neural ne…
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁医学院）
Finding the biomarkers associated with ASD is helpful for understanding the underlying roots of the disorder and can lead to earlier diagnosis and more targeted treatment. A promising approach to identify biomarkers is using Graph Neural Networks (GNNs), which can be used to analyze graph structured data, i.e. brain networks constructed by fMRI. One way to interpret important features is through looking at how the classification probability changes if the features are occluded or replaced. The major limitation of this approach is that replacing values may change the distribution of the data an…
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁大学医学院）；Facebook AI Research（Facebook人工智能研究院）
Understanding how certain brain regions relate to a specific neurological disorder has been an important area of neuroimaging research. A promising approach to identify the salient regions is using Graph Neural Networks (GNNs), which can be used to analyze graph structured data, e.g. brain networks constructed by functional magnetic resonance imaging (fMRI). We propose an interpretable GNN framework with a novel salient region selection mechanism to determine neurological brain biomarkers associated with disorders. Specifically, we design novel regularized pooling layers that highlight salient…
JARA-Brain Institute II（JARA脑科学第二研究所）；RWTH Aachen University（亚琛工业大学）；Research Centre Juelich（于利希研究中心）；University Medical Center Göttingen（哥廷根大学医学中心）；Leibniz ScienceCampus Primate Cognition（莱布尼茨灵长类认知科学园区）
Research in machine learning for autism spectrum disorder (ASD) classification bears the promise to improve clinical diagnoses. However, recent studies in clinical imaging have shown the limited generalization of biomarkers across and beyond benchmark datasets. Despite increasing model complexity and sample size in neuroimaging, the classification performance of ASD remains far away from clinical application. This raises the question of how we can overcome these barriers to develop early biomarkers for ASD. One approach might be to rethink how we operationalize the theoretical basis of this di…
Combining Radiomics and Machine Learning Approaches for Objective ASD Diagnosis: Verifying White Matter Associations with ASD
School of Control Science and Engineering, Shandong University（山东大学控制科学与工程学院）；Department of Pediatric, Qilu Hospital of Shandong University（山东大学齐鲁医院儿科）；Department of Radiology, Qilu Hospital of Shandong University（山东大学齐鲁医院放射科）；Cheeloo College of Medicine, Shandong University（山东大学齐鲁医学院）
Michigan State University（密歇根州立大学）；Florida International University（佛罗里达国际大学）
Mental disorders such as Autism Spectrum Disorders (ASD) are heterogeneous disorders that are notoriously difficult to diagnose, especially in children. The current psychiatric diagnostic process is based purely on the behavioural observation of symptomology (DSM-5/ICD-10) and may be prone to over-prescribing of drugs due to misdiagnosis. In order to move the field towards more quantitative fashion, we need advanced and scalable machine learning infrastructure that will allow us to identify reliable biomarkers of mental health disorders. In this paper, we propose a framework called ASD-DiagNet…
Indian Institute of Technology Mandi（印度理工学院曼迪分校）；Indian Institute of Technology Jodhpur（印度理工学院焦特布尔分校）
Resting-state fMRI is commonly used for diagnosing Autism Spectrum Disorder (ASD) by using network-based functional connectivity. It has been shown that ASD is associated with brain regions and their inter-connections. However, discriminating based on connectivity patterns among imaging data of the control population and that of ASD patients' brains is a non-trivial task. In order to tackle said classification task, we propose a novel deep learning architecture (MHATC) consisting of multi-head attention and temporal consolidation modules for classifying an individual as a patient of ASD. The d…
Lawrence Livermore National Laboratory（劳伦斯利弗莫尔国家实验室）
Using predictive models to identify patterns that can act as biomarkers for different neuropathoglogical conditions is becoming highly prevalent. In this paper, we consider the problem of Autism Spectrum Disorder (ASD) classification where previous work has shown that it can be beneficial to incorporate a wide variety of meta features, such as socio-cultural traits, into predictive modeling. A graph-based approach naturally suits these scenarios, where a contextual graph captures traits that characterize a population, while the specific brain activity patterns are utilized as a multivariate si…
The autism dataset is studied to identify the differences between autistic and healthy groups. For this, the resting-state Functional Magnetic Resonance Imaging (rs-fMRI) data of the two groups are analyzed, and networks of connections between brain regions were created. Several classification frameworks are developed to distinguish the connectivity patterns between the groups. The best models for statistical inference and precision were compared, and the tradeoff between precision and model interpretability was analyzed. Finally, the classification accuracy measures were reported to justify t…
Amrita School of Engineering（阿姆里塔工程学院）；Amrita Vishwa Vidyapeetham（阿姆里塔大学）；Inception Institute of Artificial Intelligence（起源人工智能研究院）；University of Canberra（堪培拉大学）
Diagnosis of Autism Spectrum Disorder (ASD) using clinical evaluation (cognitive tests) is challenging due to wide variations amongst individuals. Since no effective treatment exists, prompt and reliable ASD diagnosis can enable the effective preparation of treatment regimens. This paper proposes structural Magnetic Resonance Imaging (sMRI)-based ASD diagnosis via an outlier detection approach. To learn Spatio-temporal patterns in structural brain connectivity, a Generative Adversarial Network (GAN) is trained exclusively with sMRI scans of healthy subjects. Given a stack of three adjacent sli…
Lebanese American University（黎巴嫩美国大学）；Zayed University（扎耶德大学）；New York University（纽约大学）
Autism Spectrum Disorder (ASD) is a neuro-developmental syndrome resulting from alterations in the embryological brain before birth. This disorder distinguishes its patients by special socially restricted and repetitive behavior in addition to specific behavioral traits. Hence, this would possibly deteriorate their social behavior among other individuals, as well as their overall interaction within their community. Moreover, medical research has proved that ASD also affects the facial characteristics of its patients, making the syndrome recognizable from distinctive signs within an individual'…
Autism spectrum disorder (ASD) is associated with behavioral and communication problems. Often, functional magnetic resonance imaging (fMRI) is used to detect and characterize brain changes related to the disorder. Recently, machine learning methods have been employed to reveal new patterns by trying to classify ASD from spatio-temporal fMRI images. Typically, these methods have either focused on temporal or spatial information processing. Instead, we propose a 4D spatio-temporal deep learning approach for ASD classification where we jointly learn from spatial and temporal data. We employ 4D c…
STARFormer: A Novel Spatio-Temporal Aggregation Reorganization Transformer of FMRI for Brain Disorder Diagnosis
Laboratory of Digital Image and Intelligent Computation, College of Information Engineering, Shanghai Maritime University（数字图像与智能计算实验室，信息工程学院，上海 Maritime 大学）；Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University（中英双语研究部，香港理工大学）；Department of Neurology, Affiliated Lianyungang Hospital of Xuzhou Medical University（神经科，徐州医学院附属连云港医院）
针对 fMRI 脑疾病分类忽略时空依赖的问题，提出 STARFormer，通过 ROI 空间重组、时间特征重组和时空融合三个模块，在 ASD 和 ADHD 数据集上达到最先进性能。
Middle Tennessee State University（中田纳西州立大学）；St. Ambrose University（圣安布罗斯大学）
The objective of this study is to derive functional networks for the autism spectrum disorder (ASD) population using the group ICA and dictionary learning model together and to classify ASD and typically developing (TD) participants using the functional connectivity calculated from the derived functional networks. In our experiments, the ASD functional networks were derived from resting-state functional magnetic resonance imaging (rs-fMRI) data. We downloaded a total of 120 training samples, including 58 ASD and 62 TD participants, which were obtained from the public repository: Autism Brain I…
University of Mons（蒙斯大学）；Fund for Scientific Research - FNRS (F.R.S.-FNRS)（比利时科学研究基金）；Swiss Data Science Center, EPFL and ETH Zürich（瑞士数据科学中心，洛桑联邦理工学院和苏黎世联邦理工学院）
While the prevalence of Autism Spectrum Disorder (ASD) is increasing, research continues in an effort to identify common etiological and pathophysiological bases. In this regard, modern machine learning and network science pave the way for a better understanding of the neuropathology and the development of diagnosis aid systems. The present work addresses the classification of neurotypical and ASD subjects by combining knowledge about both the structure and the functional activity of the brain. In particular, we model the brain structure as a graph, and the resting-state functional MRI (rs-fMR…
Islamic Azad University（伊斯兰阿扎德大学）；Ferdowsi University of Mashhad（马什哈德菲尔多西大学）；Semnan University（塞姆南大学）；Qatar Biomedical Research Institute（卡塔尔生物医学研究所）；Hamad Bin Khalifa University（哈马德·本·哈利法大学）；University of Granada（格拉纳达大学）；Deakin University（迪肯大学）；University of Technology Sydney（悉尼科技大学）；University of Turku（图尔库大学）；Effat University（埃法特大学）；Ngee Ann Polytechnic（义安理工学院）；Asia University（亚洲大学）；Singapore University of Social Sciences（新加坡社会科学大学）
Autism spectrum disorder (ASD) is a brain condition characterized by diverse signs and symptoms that appear in early childhood. ASD is also associated with communication deficits and repetitive behavior in affected individuals. Various ASD detection methods have been developed, including neuroimaging modalities and psychological tests. Among these methods, magnetic resonance imaging (MRI) imaging modalities are of paramount importance to physicians. Clinicians rely on MRI modalities to diagnose ASD accurately. The MRI modalities are non-invasive methods that include functional (fMRI) and struc…
For machine learning applications in medical imaging, the availability of training data is often limited, which hampers the design of radiological classifiers for subtle conditions such as autism spectrum disorder (ASD). Transfer learning is one method to counter this problem of low training data regimes. Here we explore the use of meta-learning for very low data regimes in the context of having prior data from multiple sites - an approach we term site-agnostic meta-learning. Inspired by the effectiveness of meta-learning for optimizing a model across multiple tasks, here we propose a framewor…
A Privacy-Preserving Domain Adversarial Federated learning for multi-site brain functional connectivity analysis
School of Energy and Electrical Engineering, Chang'an University（长安大学能源与电气工程学院）；Tulane University（杜兰大学）；School of Data Science, University of Virginia（弗吉尼亚大学数据科学学院）；Georgia State University（佐治亚州立大学）；Georgia Institute of Technology（佐治亚理工学院）；Emory University（埃默里大学）
Southern University of Science and Technology（南方科技大学）；Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；Central South University（中南大学）
The development of noninvasive brain imaging such as resting-state functional magnetic resonance imaging (rs-fMRI) and its combination with AI algorithm provides a promising solution for the early diagnosis of Autism spectrum disorder (ASD). However, the performance of the current ASD classification based on rs-fMRI still needs to be improved. This paper introduces a classification framework to aid ASD diagnosis based on rs-fMRI. In the framework, we proposed a novel filter feature selection method based on the difference between step distribution curves (DSDC) to select remarkable functional …
ShanghaiTech University（上海科技大学）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能医疗科技有限公司）
Functional connectivity network (FCN) data from functional magnetic resonance imaging (fMRI) is increasingly used for the diagnoses of brain disorders. However, state-of-the-art studies used to build the FCN using a single brain parcellation atlas at a certain spatial scale, which largely neglected functional interactions across different spatial scales in hierarchical manners. In this study, we propose a novel framework to perform multiscale FCN analysis for brain disorder diagnosis. We first use a set of well-defined multiscale atlases to compute multiscale FCNs. Then, we utilize biologicall…
University of Cambridge（剑桥大学）；University of Granada（格拉纳达大学）
Deep learning models for MRI classification face two recurring problems: they are typically limited by low sample size, and are abstracted by their own complexity (the "black box problem"). In this paper, we train a convolutional neural network (CNN) with the largest multi-source, functional MRI (fMRI) connectomic dataset ever compiled, consisting of 43,858 datapoints. We apply this model to a cross-sectional comparison of autism (ASD) vs typically developing (TD) controls that has proved difficult to characterise with inferential statistics. To contextualise these findings, we additionally pe…
Attention Deficit\Hyperactivity Disorder(ADHD) is considered a very common psychiatric disorder, but it is difficult to establish an accurate diagnostic method for ADHD. Recently, with the development of computing resources and machine learning methods, studies have been conducted to classify ADHD using resting-state functional magnetic resonance(rsfMRI) imaging data. However, most of them utilized all areas of the brain for training the models. In this study, as a different way from this approach, we conducted a study to classify ADHD by selecting areas that are essential for using a deep lea…
City University of Hong Kong（香港城市大学）；Yunnan University of Chinese Medicine（云南中医药大学）；City of Hope（希望之城）；Brown University（布朗大学）
Autism Spectrum Disorder(ASD) is a set of neurodevelopmental conditions that affect patients' social abilities. In recent years, many studies have employed deep learning to diagnose this brain dysfunction through functional MRI (fMRI). However, existing approaches solely focused on the abnormal brain functional connections but ignored the impact of regional activities. Due to this biased prior knowledge, previous diagnosis models suffered from inter-site measurement heterogeneity and inter-individual phenotypic differences. To address this issue, we propose a novel feature extraction method fo…
University of Amsterdam（阿姆斯特丹大学）；Amsterdam Neuroscience（阿姆斯特丹神经科学研究所）
Single-subject mapping of resting-state brain functional activity to non-imaging phenotypes is a major goal of neuroimaging. The large majority of learning approaches applied today rely either on static representations or on short-term temporal correlations. This is at odds with the nature of brain activity which is dynamic and exhibit both short- and long-range dependencies. Further, new sophisticated deep learning approaches have been developed and validated on single tasks/datasets. The application of these models for the study of a different targets typically require exhaustive hyperparame…
Background: Functional magnetic resonance imaging (fMRI) provides non-invasive measures of neuronal activity using an endogenous Blood Oxygenation-Level Dependent (BOLD) contrast. This article introduces a nonlinear dimensionality reduction (Locally Linear Embedding) to extract informative measures of the underlying neuronal activity from BOLD time-series. The method is validated using the Leave-One-Out-Cross-Validation (LOOCV) accuracy of classifying psychiatric diagnoses using resting-state and task-related fMRI. Methods: Locally Linear Embedding of BOLD time-series (into each voxel's respec…
University of Rochester（罗切斯特大学）；Ludwig Maximilian University（路德维希·马克西米利安大学）
We introduce large-scale Augmented Granger Causality (lsAGC) as a method for connectivity analysis in complex systems. The lsAGC algorithm combines dimension reduction with source time-series augmentation and uses predictive time-series modeling for estimating directed causal relationships among time-series. This method is a multivariate approach, since it is capable of identifying the influence of each time-series on any other time-series in the presence of all other time-series of the underlying dynamic system. We quantitatively evaluate the performance of lsAGC on synthetic directional time…
