Large-Scale Brain Functional Network Integration for Discrimination of Autism Using a 3-D Deep Learning Model

Atypical hierarchical brain connectivity in autism: Insights from stepwise causal analysis using Liang information flow

Autism spectrum disorder (ASD) is associated with atypical brain connectivity, yet its hierarchical organization remains underexplored. In this study, we applied the Liang information flow method to analyze stepwise causal functional connectivity in ASD, offering a novel approach to understanding how different brain networks interact. Using resting-state fMRI data from ASD individuals and healthy controls, we observed significant alterations in both positive and negative causal connections across the ventral attention network, limbic network, frontal-parietal network, and default mode network. These disruptions were detected at multiple hierarchical levels, indicating changes in communication patterns across brain regions. By leveraging features of hierarchical causal connectivity, we achieved high classification accuracy between ASD and healthy individuals. Additionally, changes in network node degrees were found to correlate with ASD clinical symptoms, particularly social and communication behaviors. Our findings provide new insights into disrupted hierarchical brain connectivity in ASD and demonstrate the potential of this approach for distinguishing ASD from typical development.

Language networks in Autism Spectrum Disorder: A systematic review of connectivity-based fMRI studies

Autism Spectrum Disorder (ASD) is a heterogeneous condition associated with differences in functional neural connectivity relative to neurotypical (NT) peers. Language-based functional connectivity represents an ideal context in which to characterize connectivity because language is heterogeneous and linked to core features in ASD, and NT language networks are well-defined. We conducted a systematic review of language-related functional connectivity literature on individuals with ASD using PubMed, PsychInfo, Scopus, ProQuest, and Google Scholar, yielding 96 studies. Language-task studies indicated local over-connectivity within the language network and global under-connectivity of language with out-of-network regions in ASD. Resting-state studies showed mixed patterns, and connectivity was associated ASD symptomology and language skills. This evidence indicates language-task elicited local over-connectivity and global under-connectivity in ASD, but not a local versus global distinction of resting-state language-related connectivity. Associations with behavior suggest that local over-connectivity and global under-connectivity characterize ASD, and heightened language-related connectivity may support social function.

Investigation of Electrical Signals in the Brain of People with Autism Using Effective Connectivity Network

Unlike other functional integration methods that examine the relationship and correlation between two channels, effective connection reports the direct effect of one channel on another and expresses their causal relationship. In this article, we investigate and classify electroencephalographic (EEG) signals based on effective connectivity. In this study, we leverage the Granger causality (GC) relationship, a method for measuring effective connectivity, to analyze EEG signals from both healthy individuals and those with autism. The EEG signals examined in this article were recorded during the presentation of abstract images. Given the nonstationary nature of EEG signals, a vector autoregression model has been employed to model the relationships between signals across different channels. GC is then used to quantify the influence of these channels on one another. Selecting regions of interest (ROI) is a critical step, as the quality of the time periods under consideration significantly impacts the outcomes of the connectivity analysis among the electrodes. By comparing these effects in the ROI and various areas, we have distinguished healthy subjects from those suffering from autism. Furthermore, through statistical analysis, we have compared the results between healthy individuals and those with autism. It has been observed that the causal relationship between these two hemispheres is significantly weaker in healthy individuals compared to those with autism.

The diagnosis of ASD with MRI: a systematic review and meta-analysis

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.

Delineating a Pathway for the Discovery of Functional Connectome Biomarkers of Autism

The promise of individually tailored care for autism has driven efforts to establish biomarkers. This chapter appraises the state of precision-medicine research focused on biomarkers based on the functional brain connectome. This work is grounded on abundant evidence supporting the brain dysconnection model of autism and the advantages of resting-state functional MRI (R-fMRI) for studying the brain in vivo. After considering biomarker requirements of consistency and clinical relevance, we provide a scoping review of R-fMRI studies of individual prediction in autism. In the past 10 years, responding to the availability of open data through the Autism Brain Imaging Data Exchange, machine learning studies have surged. Nearly all have focused on diagnostic label classification. These efforts have shown that autism prediction is feasible using functional connectome markers, with accuracy reported well above chance. In parallel, emerging approaches more directly addressing autism heterogeneity are paving the way for much-needed biomarkers of longitudinal outcome and treatment response. We conclude with key challenges to be addressed by the next generation of studies.

Do it the transformer way: A comprehensive review of brain and vision transformers for autism spectrum disorder diagnosis and classification

Autism spectrum disorder (ASD) is a condition observed in children who display abnormal patterns of interaction, behavior, and communication with others. Despite extensive research efforts, the underlying causes of this neurodevelopmental disorder and its biomarkers remain unknown. However, advancements in artificial intelligence and machine learning have improved clinicians' ability to diagnose ASD. This review paper investigates various MRI modalities to identify distinct features that characterize individuals with ASD compared to typical control subjects. The review then moves on to explore deep learning models for ASD diagnosis, including convolutional neural networks (CNNs), autoencoders, graph convolutions, attention networks, and other models. CNNs and their variations are particularly effective due to their capacity to learn structured image representations and identify reliable biomarkers for brain disorders. Computer vision transformers often employ CNN architectures with transfer learning techniques like fine-tuning and layer freezing to enhance image classification performance, surpassing traditional machine learning models. This review paper contributes in three main ways. Firstly, it provides a comprehensive overview of a recommended architecture for using vision transformers in the systematic ASD diagnostic process. To this end, the paper investigates various pre-trained vision architectures such as VGG, ResNet, Inception, InceptionResNet, DenseNet, and Swin models that were fine-tuned for ASD diagnosis and classification. Secondly, it discusses the vision transformers of 2020th like BiT, ViT, MobileViT, and ConvNeXt, and applying transfer learning methods in relation to their prospective practicality in ASD classification. Thirdly, it explores brain transformers that are pre-trained on medically rich data and MRI neuroimaging datasets. The paper recommends a systematic architecture for ASD diagnosis using brain transformers. It also reviews recently developed brain transformer-based models, such as METAFormer, Com-BrainTF, Brain Network, ST-Transformer, STCAL, BolT, and BrainFormer, discussing their deep transfer learning architectures and results in ASD detection. Additionally, the paper summarizes and discusses brain-related transformers for various brain disorders, such as MSGTN, STAGIN, and MedTransformer, in relation to their potential usefulness in ASD. The study suggests that developing specialized transformer-based models, following the success of natural language processing (NLP), can offer new directions for image classification problems in ASD brain biomarkers learning and classification. By incorporating the attention mechanism, treating MRI modalities as sequence prediction tasks trained on brain disorder classification problems, and fine-tuned on ASD datasets, brain transformers can show a great promise in ASD diagnosis.

Multi-Slice Generation sMRI and fMRI for Autism Spectrum Disorder Diagnosis Using 3D-CNN and Vision Transformers

Researchers have explored various potential indicators of ASD, including changes in brain structure and activity, genetics, and immune system abnormalities, but no definitive indicator has been found yet. Therefore, this study aims to investigate ASD indicators using two types of magnetic resonance images (MRI), structural (sMRI) and functional (fMRI), and to address the issue of limited data availability. Transfer learning is a valuable technique when working with limited data, as it utilizes knowledge gained from a pre-trained model in a domain with abundant data. This study proposed the use of four vision transformers namely ConvNeXT, MobileNet, Swin, and ViT using sMRI modalities. The study also investigated the use of a 3D-CNN model with sMRI and fMRI modalities. Our experiments involved different methods of generating data and extracting slices from raw 3D sMRI and 4D fMRI scans along the axial, coronal, and sagittal brain planes. To evaluate our methods, we utilized a standard neuroimaging dataset called NYU from the ABIDE repository to classify ASD subjects from typical control subjects. The performance of our models was evaluated against several baselines including studies that implemented VGG and ResNet transfer learning models. Our experimental results validate the effectiveness of the proposed multi-slice generation with the 3D-CNN and transfer learning methods as they achieved state-of-the-art results. In particular, results from 50-middle slices from the fMRI and 3D-CNN showed a profound promise in ASD classifiability as it obtained a maximum accuracy of 0.8710 and F1-score of 0.8261 when using the mean of 4D images across the axial, coronal, and sagittal. Additionally, the use of the whole slices in fMRI except the beginnings and the ends of brain views helped to reduce irrelevant information and showed good performance of 0.8387 accuracy and 0.7727 F1-score. Lastly, the transfer learning with the ConvNeXt model achieved results higher than other transformers when using 50-middle slices sMRI along the axial, coronal, and sagittal planes.

Identification and analysis of autism spectrum disorder via large-scale dynamic functional network connectivity

Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder with severe cognitive impairment. Several studies have reported that brain functional network connectivity (FNC) has great potential for identifying ASD from healthy control (HC) and revealing the relationships between the brain and behaviors of ASD. However, few studies have explored dynamic large-scale FNC as a feature to identify individuals with ASD. This study used a time-sliding window method to study the dynamic FNC (dFNC) on the resting-state fMRI. To avoid arbitrarily determining the window length, we set a window length range of 10-75 TRs (TR = 2 s). We constructed linear support vector machine classifiers for all window length conditions. Using a nested 10-fold cross-validation framework, we obtained a grand average accuracy of 94.88% across window length conditions, which is higher than those reported in previous studies. In addition, we determined the optimal window length using the highest classification accuracy of 97.77%. Based on the optimal window length, we found that the dFNCs were located mainly in dorsal and ventral attention networks (DAN and VAN) and exhibited the highest weight in classification. Specifically, we found that the dFNC between DAN and temporal orbitofrontal network (TOFN) was significantly negatively correlated with social scores of ASD. Finally, using the dFNCs with high classification weights as features, we construct a model to predict the clinical score of ASD. Overall, our findings demonstrated that the dFNC could be a potential biomarker to identify ASD and provide new perspectives to detect cognitive changes in ASD.

Sampling inequalities affect generalization of neuroimaging-based diagnostic classifiers in psychiatry

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, R²_adj = 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.

Evaluation of Risk of Bias in Neuroimaging-Based Artificial Intelligence Models for Psychiatric Diagnosis: A Systematic Review

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.

Applications of Deep Learning to Neurodevelopment in Pediatric Imaging: Achievements and Challenges

Deep learning has achieved remarkable progress, particularly in neuroimaging analysis. Deep learning applications have also been extended from adult to pediatric medical images, and thus, this paper aims to present a systematic review of this recent research. We first introduce the commonly used deep learning methods and architectures in neuroimaging, such as convolutional neural networks, auto-encoders, and generative adversarial networks. A non-exhaustive list of commonly used publicly available pediatric neuroimaging datasets and repositories are included, followed by a categorical review of recent works in pediatric MRI-based deep learning studies in the past five years. These works are categorized into recognizing neurodevelopmental disorders, identifying brain and tissue structures, estimating brain age/maturity, predicting neurodevelopment outcomes, and optimizing MRI brain imaging and analysis. Finally, we also discuss the recent achievements and challenges on these applications of deep learning to pediatric neuroimaging.

Empirical Study of Autism Spectrum Disorder Diagnosis Using Facial Images by Improved Transfer Learning Approach

Autism spectrum disorder (ASD) is a neurological illness characterized by deficits in cognition, physical activities, and social skills. There is no specific medication to treat this illness; only early intervention can improve brain functionality. Since there is no medical test to identify ASD, a diagnosis might be challenging. In order to determine a diagnosis, doctors consider the child's behavior and developmental history. The human face can be used as a biomarker as it is one of the potential reflections of the brain and thus can be used as a simple and handy tool for early diagnosis. This study uses several deep convolutional neural network (CNN)-based transfer learning approaches to detect autistic children using the facial image. An empirical study is conducted to select the best optimizer and set of hyperparameters to achieve better prediction accuracy using the CNN model. After training and validating with the optimized setting, the modified Xception model demonstrates the best performance by achieving an accuracy of 95% on the test set, whereas the VGG19, ResNet50V2, MobileNetV2, and EfficientNetB0 achieved 86.5%, 94%, 92%, and 85.8%, accuracy, respectively. Our preliminary computational results demonstrate that our transfer learning approaches outperformed existing methods. Our modified model can be employed to assist doctors and practitioners in validating their initial screening to detect children with ASD disease.

Deep learning in neuroimaging data analysis: Applications, challenges, and solutions

Methods for the analysis of neuroimaging data have advanced significantly since the beginning of neuroscience as a scientific discipline. Today, sophisticated statistical procedures allow us to examine complex multivariate patterns, however most of them are still constrained by assuming inherent linearity of neural processes. Here, we discuss a group of machine learning methods, called deep learning, which have drawn much attention in and outside the field of neuroscience in recent years and hold the potential to surpass the mentioned limitations. Firstly, we describe and explain the essential concepts in deep learning: the structure and the computational operations that allow deep models to learn. After that, we move to the most common applications of deep learning in neuroimaging data analysis: prediction of outcome, interpretation of internal representations, generation of synthetic data and segmentation. In the next section we present issues that deep learning poses, which concerns multidimensionality and multimodality of data, overfitting and computational cost, and propose possible solutions. Lastly, we discuss the current reach of DL usage in all the common applications in neuroimaging data analysis, where we consider the promise of multimodality, capability of processing raw data, and advanced visualization strategies. We identify research gaps, such as focusing on a limited number of criterion variables and the lack of a well-defined strategy for choosing architecture and hyperparameters. Furthermore, we talk about the possibility of conducting research with constructs that have been ignored so far or/and moving toward frameworks, such as RDoC, the potential of transfer learning and generation of synthetic data.

Autism Spectrum Disorder Studies Using fMRI Data and Machine Learning: A Review

Machine learning methods have been frequently applied in the field of cognitive neuroscience in the last decade. A great deal of attention has been attracted to introduce machine learning methods to study the autism spectrum disorder (ASD) in order to find out its neurophysiological underpinnings. In this paper, we presented a comprehensive review about the previous studies since 2011, which applied machine learning methods to analyze the functional magnetic resonance imaging (fMRI) data of autistic individuals and the typical controls (TCs). The all-round process was covered, including feature construction from raw fMRI data, feature selection methods, machine learning methods, factors for high classification accuracy, and critical conclusions. Applying different machine learning methods and fMRI data acquired from different sites, classification accuracies were obtained ranging from 48.3% up to 97%, and informative brain regions and networks were located. Through thorough analysis, high classification accuracies were found to usually occur in the studies which involved task-based fMRI data, single dataset for some selection principle, effective feature selection methods, or advanced machine learning methods. Advanced deep learning together with the multi-site Autism Brain Imaging Data Exchange (ABIDE) dataset became research trends especially in the recent 4 years. In the future, advanced feature selection and machine learning methods combined with multi-site dataset or easily operated task-based fMRI data may appear to have the potentiality to serve as a promising diagnostic tool for ASD.