Classifying ASD based on time-series fMRI using spatial-temporal transformer

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.

A review of the applications of generative adversarial networks to structural and functional MRI based diagnostic classification of brain disorders

Structural and functional MRI (magnetic resonance imaging) based diagnostic classification using machine learning has long held promise, but there are many roadblocks to achieving their potential. While traditional machine learning models suffered from their inability to capture the complex non-linear mapping, deep learning models tend to overfit the model. This is because there is data scarcity and imbalanced classes in neuroimaging; it is expensive to acquire data from human subjects and even more so in clinical populations. Due to their ability to augment data by learning underlying distributions, generative adversarial networks (GAN) provide a potential solution to this problem. Here, we provide a methodological primer on GANs and review the applications of GANs to classification of mental health disorders from neuroimaging data such as functional MRI and showcase the progress made thus far. We also highlight gaps in methodology as well as interpretability that are yet to be addressed. This provides directions about how the field can move forward. We suggest that since there are a range of methodological choices available to users, it is critical for users to interact with method developers so that the latter can tailor their development according to the users' needs. The field can be enriched by such synthesis between method developers and users in neuroimaging.

Effective hyper-connectivity network construction and learning: Application to major depressive disorder identification

Functional connectivity (FC) derived from resting-state fMRI (rs-fMRI) is a primary approach for identifying brain diseases, but it is limited to capturing the pairwise correlation between regions-of-interest (ROIs) in the brain. Thus, hyper-connectivity which describes the higher-order relationship among multiple ROIs is receiving increasing attention. However, most hyper-connectivity methods overlook the directionality of connections. The direction of information flow constitutes a pivotal factor in shaping brain activity and cognitive processes. Neglecting this directional aspect can lead to an incomplete understanding of high-order interactions within the brain. To this end, we propose a novel effective hyper-connectivity (EHC) network that integrates direction detection and hyper-connectivity modeling. It characterizes the high-order directional information flow among multiple ROIs, providing a more comprehensive understanding of brain activity. Then, we develop a directed hypergraph convolutional network (DHGCN) to acquire deep representations from EHC network and functional indicators of ROIs. In contrast to conventional hypergraph convolutional networks designed for undirected hypergraphs, DHGCN is specifically tailored to handle directed hypergraph data structures. Moreover, unlike existing methods that primarily focus on fMRI time series, our proposed DHGCN model also incorporates multiple functional indicators, providing a robust framework for feature learning. Finally, deep representations generated via DHGCN, combined with demographic factors, are used for major depressive disorder (MDD) identification. Experimental results demonstrate that the proposed framework outperforms both FC and undirected hyper-connectivity models, as well as surpassing other state-of-the-art methods. The identification of EHC abnormalities through our framework can enhance the analysis of brain function in individuals with MDD.

Classification of MDD using a Transformer classifier with large-scale multisite resting-state fMRI data

Major depressive disorder (MDD) is one of the most common psychiatric disorders worldwide with high recurrence rate. Identifying MDD patients, particularly those with recurrent episodes with resting-state fMRI, may reveal the relationship between MDD and brain function. We proposed a Transformer-Encoder model, which utilized functional connectivity extracted from large-scale multisite rs-fMRI datasets to classify MDD and HC. The model discarded the Transformer's Decoder part, reducing the model's complexity and decreasing the number of parameters to adapt to the limited sample size and it does not require a complex feature selection process and achieves end-to-end classification. Additionally, our model is suitable for classifying data combined from multiple brain atlases and has an optional unsupervised pre-training module to acquire optimal initial parameters and speed up the training process. The model's performance was tested on a large-scale multisite dataset and identified brain regions affected by MDD using the Grad-CAM method. After conducting five-fold cross-validation, our model achieved an average classification accuracy of 68.61% on a dataset consisting of 1611 samples. For the selected recurrent MDD dataset, the model reached an average classification accuracy of 78.11%. Abnormalities were detected in the frontal gyri and cerebral cortex of MDD patients in both datasets. Furthermore, the identified brain regions in the recurrent MDD dataset generally exhibited a higher contribution to the model's performance.

Autism Spectrum Disorder Detection by Hybrid Convolutional Recurrent Neural Networks from Structural and Resting State Functional MRI Images

This study aims to increase the accuracy of autism spectrum disorder (ASD) diagnosis based on cognitive and behavioral phenotypes through multiple neuroimaging modalities. We apply machine learning (ML) algorithms to classify ASD patients and healthy control (HC) participants using structural magnetic resonance imaging (s-MRI) together with resting state functional MRI (rs-f-MRI and f-MRI) data from the large multisite data repository ABIDE (autism brain imaging data exchange) and identify important brain connectivity features. The 2D f-MRI images were converted into 3D s-MRI images, and datasets were preprocessed using the Montreal Neurological Institute (MNI) atlas. The data were then denoised to remove any confounding factors. We show, by using three fusion strategies such as early fusion, late fusion, and cross fusion, that, in this implementation, hybrid convolutional recurrent neural networks achieve better performance in comparison to either convolutional neural networks (CNNs) or recurrent neural networks (RNNs). The proposed model classifies subjects as autistic or not according to how functional and anatomical connectivity metrics provide an overall diagnosis based on the autism diagnostic observation schedule (ADOS) standard. Our hybrid network achieved an accuracy of 96% by fusing s-MRI and f-MRI together, which outperforms the methods used in previous studies.

Diagnosis of Autism Spectrum Disorder (ASD) Using Recursive Feature Elimination-Graph Neural Network (RFE-GNN) and Phenotypic Feature Extractor (PFE)

Autism spectrum disorder (ASD) poses as a multifaceted neurodevelopmental condition, significantly impacting children's social, behavioral, and communicative capacities. Despite extensive research, the precise etiological origins of ASD remain elusive, with observable connections to brain activity. In this study, we propose a novel framework for ASD detection, extracting the characteristics of functional magnetic resonance imaging (fMRI) data and phenotypic data, respectively. Specifically, we employ recursive feature elimination (RFE) for feature selection of fMRI data and subsequently apply graph neural networks (GNN) to extract informative features from the chosen data. Moreover, we devise a phenotypic feature extractor (PFE) to extract phenotypic features effectively. We then, synergistically fuse the features and validate them on the ABIDE dataset, achieving 78.7% and 80.6% accuracy, respectively, thereby showcasing competitive performance compared to state-of-the-art methods. The proposed framework provides a promising direction for the development of effective diagnostic tools for ASD.

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.

An Umbrella Review of the Fusion of fMRI and AI in Autism

The role of functional magnetic resonance imaging (fMRI) is assuming an increasingly central role in autism diagnosis. The integration of Artificial Intelligence (AI) into the realm of applications further contributes to its development. This study's objective is to analyze emerging themes in this domain through an umbrella review, encompassing systematic reviews. The research methodology was based on a structured process for conducting a literature narrative review, using an umbrella review in PubMed and Scopus. Rigorous criteria, a standard checklist, and a qualification process were meticulously applied. The findings include 20 systematic reviews that underscore key themes in autism research, particularly emphasizing the significance of technological integration, including the pivotal roles of fMRI and AI. This study also highlights the enigmatic role of oxytocin. While acknowledging the immense potential in this field, the outcome does not evade acknowledging the significant challenges and limitations. Intriguingly, there is a growing emphasis on research and innovation in AI, whereas aspects related to the integration of healthcare processes, such as regulation, acceptance, informed consent, and data security, receive comparatively less attention. Additionally, the integration of these findings into Personalized Medicine (PM) represents a promising yet relatively unexplored area within autism research. This study concludes by encouraging scholars to focus on the critical themes of health domain integration, vital for the routine implementation of these applications.