A small number of abnormal brain connections predicts adult autism spectrum disorder

MHNet: Multi-view High-Order Network for Diagnosing Neurodevelopmental Disorders Using Resting-State fMRI

Deep learning models have shown promise in diagnosing neurodevelopmental disorders (NDD) like ASD and ADHD. However, many models either use graph neural networks (GNN) to construct single-level brain functional networks (BFNs) or employ spatial convolution filtering for local information extraction from rs-fMRI data, often neglecting high-order features crucial for NDD classification. We introduce a Multi-view High-order Network (MHNet) to capture hierarchical and high-order features from multi-view BFNs derived from rs-fMRI data for NDD prediction. MHNet has two branches: the Euclidean Space Features Extraction (ESFE) module and the Non-Euclidean Space Features Extraction (Non-ESFE) module, followed by a Feature Fusion-based Classification (FFC) module for NDD identification. ESFE includes a Functional Connectivity Generation (FCG) module and a High-order Convolutional Neural Network (HCNN) module to extract local and high-order features from BFNs in Euclidean space. Non-ESFE comprises a Generic Internet-like Brain Hierarchical Network Generation (G-IBHN-G) module and a High-order Graph Neural Network (HGNN) module to capture topological and high-order features in non-Euclidean space. Experiments on three public datasets show that MHNet outperforms state-of-the-art methods using both AAL1 and Brainnetome Atlas templates. Extensive ablation studies confirm the superiority of MHNet and the effectiveness of using multi-view fMRI information and high-order features. Our study also offers atlas options for constructing more sophisticated hierarchical networks and explains the association between key brain regions and NDD. MHNet leverages multi-view feature learning from both Euclidean and non-Euclidean spaces, incorporating high-order information from BFNs to enhance NDD classification performance.

What is the best brain state to predict autistic traits?

Autism is a heterogeneous condition, and functional magnetic resonance imaging-based studies have advanced understanding of neurobiological correlates of autistic features. Nevertheless, little work has focused on the optimal brain states to reveal brain-phenotype relationships. In addition, there is a need to better understand the relevance of attentional abilities in mediating autistic features. Using connectome-based predictive modelling, we interrogate three datasets to determine scanning conditions that can boost prediction of clinically relevant phenotypes and assess generalizability. In dataset one, a sample of youth with autism and neurotypical participants, we find that a sustained attention task (the gradual onset continuous performance task) results in high prediction performance of autistic traits compared to a free-viewing social attention task and a resting-state condition. In dataset two, we observe the predictive network model of autistic traits generated from the sustained attention task generalizes to predict measures of attention in neurotypical adults. In dataset three, we show the same predictive network model of autistic traits from dataset one further generalizes to predict measures of social responsiveness in data from the Autism Brain Imaging Data Exchange. In sum, our data suggest that an in-scanner sustained attention challenge can help delineate robust markers of autistic traits and support the continued investigation of the optimal brain states under which to predict phenotypes in psychiatric conditions.

Enhancing prediction of human traits and behaviors through ensemble learning of traditional and novel resting-state fMRI connectivity analyses

Recent advances in cognitive neuroscience have focused on using resting-state functional connectivity (RSFC) data from fMRI scans to more accurately predict human traits and behaviors. Traditional approaches generally analyze RSFC by correlating averaged time-series data across regions of interest (ROIs) or networks, which may overlook important spatial signal patterns. To address this limitation, we introduced a novel linear regression technique that estimates RSFC by predicting spatial brain activity patterns in a target ROI from those in a seed ROI. We applied both traditional and our novel RSFC estimation methods to a large-scale dataset from the Human Connectome Project and the Brain Genomics Superstruct Project, analyzing resting-state fMRI data to predict sex, age, personality traits, and psychological task performance. To enhance prediction accuracy, we developed an ensemble learner that combines these qualitatively different methods using a weighted average approach. Our findings revealed that hierarchical clustering of RSFC patterns using our novel method displays distinct whole-brain grouping patterns compared to the traditional approach. Importantly, the ensemble model, integrating these diverse weak learners, outperformed the traditional RSFC method in predicting human traits and behaviors. Notably, the predictions from the traditional and novel methods showed relatively low similarity, indicating that our novel approach captures unique and previously undetected information about human traits and behaviors through fine-grained local spatial patterns of neural activation. These results highlight the potential of combining traditional and innovative RSFC analysis techniques to enrich our understanding of the neural basis of human traits and behaviors.

Generalizable and transportable resting-state neural signatures characterized by functional networks, neurotransmitters, and clinical symptoms in autism

Autism spectrum disorder (ASD) is a lifelong condition with elusive biological mechanisms. The complexity of factors, including inter-site and developmental differences, hinders the development of a generalizable neuroimaging classifier for ASD. Here, we developed a classifier for ASD using a large-scale, multisite resting-state fMRI dataset of 730 Japanese adults, aiming to capture neural signatures that reflect pathophysiology at the functional network level, neurotransmitters, and clinical symptoms of the autistic brain. Our adult ASD classifier was successfully generalized to adults in the United States, Belgium, and Japan. The classifier further demonstrated its successful transportability to children and adolescents. The classifier contained 141 functional connections (FCs) that were important for discriminating individuals with ASD from typically developing controls. These FCs and their terminal brain regions were associated with difficulties in social interaction and dopamine and serotonin, respectively. Finally, we mapped attention-deficit/hyperactivity disorder (ADHD), schizophrenia (SCZ), and major depressive disorder (MDD) onto the biological axis defined by the ASD classifier. ADHD and SCZ, but not MDD, were located proximate to ASD on the biological dimensions. Our results revealed functional signatures of the ASD brain, grounded in molecular characteristics and clinical symptoms, achieving generalizability and transportability applicable to the evaluation of the biological continuity of related diseases.

A survey of brain functional network extraction methods using fMRI data

Functional network (FN) analyses play a pivotal role in uncovering insights into brain function and understanding the pathophysiology of various brain disorders. This paper focuses on classical and advanced methods for deriving brain FNs from functional magnetic resonance imaging (fMRI) data. We systematically review their foundational principles, advantages, shortcomings, and interrelations, encompassing both static and dynamic FN extraction approaches. In the context of static FN extraction, we present hypothesis-driven methods such as region of interest (ROI)-based approaches as well as data-driven methods including matrix decomposition, clustering, and deep learning. For dynamic FN extraction, both window-based and windowless methods are surveyed with respect to the estimation of time-varying FN and the subsequent computation of FN states. We also discuss the scope of application of the various methods and avenues for future improvements.

Brain age monotonicity and functional connectivity differences of healthy subjects

Alterations in the brain's connectivity or the interactions among brain regions have been studied with the aid of resting state (rs)fMRI data attained from large numbers of healthy subjects of various demographics. This has been instrumental in providing insight into how a phenotype as fundamental as age affects the brain. Although machine learning (ML) techniques have already been deployed in such studies, novel questions are investigated in this work. We study whether young brains develop properties that progressively resemble those of aged brains, and if the aging dynamics of older brains provide information about the aging trajectory in young subjects. The degree of a prospective monotonic relationship will be quantified, and hypotheses of brain aging trajectories will be tested via ML. Furthermore, the degree of functional connectivity across the age spectrum of three datasets will be compared at a population level and across sexes. The findings scrutinize similarities and differences among the male and female subjects at greater detail than previously performed.

[The neural basis of face-to-face communication: exploring transmission and sharing through neuroimaging]

Effective human communication is a complex process that involves transmitting and sharing information, ideas, and attitudes between two or more individuals. Researchers need to explore both transmission and sharing concepts to understand the neural basis of communication. Face-to-face communication refers to changing someone's mental state by sharing information, ideas, or attitudes. This type of communication is characterized by "mutual predictability." Scientists are working to clarify the neural basis of communication by studying how inter-individual synchronization of behavior and neural activity occurs during face-to-face communication.

Behavior can be decoded across the cortex when individual differences are considered

Group-level analyses have typically associated behavioral signatures with a constrained set of brain areas. Here we show that two behavioral metrics - reaction time (RT) and confidence - can be decoded across the cortex when each individual is considered separately. Subjects (N=50) completed a perceptual decision-making task with confidence. We built models decoding trial-level RT and confidence separately for each subject using the activation patterns in one brain area at a time after splitting the entire cortex into 200 regions of interest (ROIs). At the group level, we replicated previous results by showing that both RT and confidence could be decoded from a small number of ROIs (12.0% and 3.5%, respectively). Critically, at the level of the individual, both RT and confidence could be decoded from most brain regions even after Bonferroni correction (90.0% and 72.5%, respectively). Surprisingly, we observed that many brain regions exhibited opposite brain-behavior relationships across individuals, such that, for example, higher activations predicted fast RTs in some subjects but slow RTs in others. These results were further replicated in a second dataset. Lastly, we developed a simple test to determine the robustness of decoding performance, which showed that several hundred trials per subject are required for robust decoding. These results show that behavioral signatures can be decoded from a much broader range of cortical areas than previously recognized and suggest the need to study the brain-behavior relationship at both the group and the individual level.

Delineating Transdiagnostic Subtypes in Neurodevelopmental Disorders via Contrastive Graph Machine Learning of Brain Connectivity Patterns

Neurodevelopmental disorders, such as Attention Deficit/Hyperactivity Disorder (ADHD) and Autism Spectrum Disorder (ASD), are characterized by comorbidity and heterogeneity. Identifying distinct subtypes within these disorders can illuminate the underlying neurobiological and clinical characteristics, paving the way for more tailored treatments. We adopted a novel transdiagnostic approach across ADHD and ASD, using cutting-edge contrastive graph machine learning to determine subtypes based on brain network connectivity as revealed by resting-state functional magnetic resonance imaging. Our approach identified two generalizable subtypes characterized by robust and distinct functional connectivity patterns, prominently within the frontoparietal control network and the somatomotor network. These subtypes exhibited pronounced differences in major cognitive and behavioural measures. We further demonstrated the generalizability of these subtypes using data collected from independent study sites. Our data-driven approach provides a novel solution for parsing biological heterogeneity in neurodevelopmental disorders.

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.

Imaging-based chemogenetics for dissecting neural circuits in nonhuman primates

Nonhuman primates, particularly macaque and marmoset monkeys, serve as invaluable models for studying complex brain functions and behavior. However, the lack of suitable genetic neuromodulation tools has constrained research at the network level. This review examines the application of a chemogenetic technology, specifically, designer receptors exclusively activated by designer drugs (DREADDs), to nonhuman primates. DREADDs offer a means of reversibly controlling neuronal activity within a specific cell type or neural pathway, effectively targeting multiple brain regions simultaneously. The combination of DREADDs with imaging techniques, such as positron emission tomography and magnetic resonance imaging, has significantly enhanced nonhuman primate research, facilitating the precise visualization and manipulation of specific brain circuits and enabling the detailed monitoring of changes in network activity, which can then be correlated with altered behavior. This review outlines these technological advances and considers their potential for enhancing our understanding of primate brain circuit function and developing novel therapeutic approaches for treating brain diseases.

Systematic bibliometric and visualized analysis of research hotspots and trends in artificial intelligence in autism spectrum disorder

Background

Artificial intelligence (AI) has been the subject of studies in autism spectrum disorder (ASD) and may affect its identification, diagnosis, intervention, and other medical practices in the future. Although previous studies have used bibliometric techniques to analyze and investigate AI, there has been little research on the adoption of AI in ASD. This study aimed to explore the broad applications and research frontiers of AI used in ASD.

Methods

Citation data were retrieved from the Web of Science Core Collection (WoSCC) database to assess the extent to which AI is used in ASD. CiteSpace.5.8. R3 and VOSviewer, two online tools for literature metrology analysis, were used to analyze the data.

Results

A total of 776 publications from 291 countries and regions were analyzed; of these, 256 publications were from the United States and 173 publications were from China, and England had the largest centrality of 0.33; Stanford University had the highest H-index of 17; and the largest cluster label of co-cited references was machine learning. In addition, keywords with a high number of occurrences in this field were autism spectrum disorder (295), children (255), classification (156) and diagnosis (77). The burst keywords from 2021 to 2023 were infants and feature selection, and from 2022 to 2023, the burst keyword was corpus callosum.

Conclusion

This research provides a systematic analysis of the literature concerning AI used in ASD, presenting an overall demonstration in this field. In this area, the United States and China have the largest number of publications, England has the greatest influence, and Stanford University is the most influential. In addition, the research on AI used in ASD mostly focuses on classification and diagnosis, and "infants, feature selection, and corpus callosum are at the forefront, providing directions for future research. However, the use of AI technologies to identify ASD will require further research.

Assessing Predictive Ability of Dynamic Time Warping Functional Connectivity for ASD Classification

Functional connectivity MRI (fcMRI) is a technique used to study the functional connectedness of distinct regions of the brain by measuring the temporal correlation between their blood oxygen level-dependent (BOLD) signals. fcMRI is typically measured with the Pearson correlation (PC), which assumes that there is no lag between time series. Dynamic time warping (DTW) is an alternative measure of similarity between time series that is robust to such time lags. We used PC fcMRI data and DTW fcMRI data as predictors in machine learning models for classifying autism spectrum disorder (ASD). When combined with dimension reduction techniques, such as principal component analysis, functional connectivity estimated with DTW showed greater predictive ability than functional connectivity estimated with PC. Our results suggest that DTW fcMRI can be a suitable alternative measure that may be characterizing fcMRI in a different, but complementary, way to PC fcMRI that is worth continued investigation. In studying different variants of cross validation (CV), our results suggest that, when it is necessary to tune model hyperparameters and assess model performance at the same time, a K-fold CV nested within leave-one-out CV may be a competitive contender in terms of performance and computational speed, especially when sample size is not large.

Graph fusion prediction of autism based on attentional mechanisms

Autism spectrum disorder (ASD) is a pervasive developmental disorder, and the earlier detection and timely intervention for treatment positively affect the prognosis of patients. Deep learning algorithms based on graph structure have achieved good results in autism prediction in recent years. However, there are problems with standardized operations in extracting features and combining neighborhood node features with the structure of the graph dependent, which limits the generalization ability of the trained model to other graph structures. In this paper, we propose a graph fusion autism prediction model based on attentional mechanisms(AGF) to address the above problems. The AGF model represents the overall population (patients or healthy controls) as a sparse graph, where nodes are subjects, and non-imaging features are integrated as edge weights. Different weights can be defined for different nodes in the neighborhood through the attention mechanism without relying on prior knowledge of the graph structure. The model is also able to dynamically fuse multiple sparse graphs obtained from different non-imaging features by way of training weight assignment. Its performance is also compared with several other models (e.g., S-AGF, GCN, etc.), and the results show that it has superior prediction accuracy compared to the baseline model. The results show that this improvement of graph fusion works better on the ABIDE databases, and the classification accuracy can reach 73.9%. The datasets and source code are freely available at https://github.com/chengyu-github1012/Graph-Fusion.git. Strengths and limitations of this study: graph fusion; disease prediction; noise.

A heterogeneous graph convolutional attention network method for classification of autism spectrum disorder

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.

A face image classification method of autistic children based on the two-phase transfer learning

Autism spectrum disorder (ASD) is a neurodevelopmental disorder, which seriously affects children's normal life. Screening potential autistic children before professional diagnose is helpful to early detection and early intervention. Autistic children have some different facial features from non-autistic children, so the potential autistic children can be screened by taking children's facial images and analyzing them with a mobile phone. The area under curve (AUC) is a more robust metrics than accuracy in evaluating the performance of a model used to carry out the two-category classification, and the AUC of the deep learning model suitable for the mobile terminal in the existing research can be further improved. Moreover, the size of an input image is large, which is not fit for a mobile phone. A deep transfer learning method is proposed in this research, which can use images with smaller size and improve the AUC of existing studies. The proposed transfer method uses the two-phase transfer learning mode and the multi-classifier integration mode. For MobileNetV2 and MobileNetV3-Large that are suitable for a mobile phone, the two-phase transfer learning mode is used to improve their classification performance, and then the multi-classifier integration mode is used to integrate them to further improve the classification performance. A multi-classifier integrating calculation method is also proposed to calculate the final classification results according to the classifying results of the participating models. The experimental results show that compared with the one-phase transfer learning, the two-phase transfer learning can significantly improve the classification performance of MobileNetV2 and MobileNetV3-Large, and the classification performance of the integrated classifier is better than that of any participating classifiers. The accuracy of the integrated classifier in this research is 90.5%, and the AUC is 96.32%, which is 3.51% greater than the AUC (92.81%) of the previous studies.

Perspective of artificial intelligence in healthcare data management: A journey towards precision medicine

Mounting evidence has highlighted the implementation of big data handling and management in the healthcare industry to improve the clinical services. Various private and public companies have generated, stored, and analyzed different types of big healthcare data, such as omics data, clinical data, electronic health records, personal health records, and sensing data with the aim to move in the direction of precision medicine. Additionally, with the advancement in technologies, researchers are curious to extract the potential involvement of artificial intelligence and machine learning on big healthcare data to enhance the quality of patient's lives. However, seeking solutions from big healthcare data requires proper management, storage, and analysis, which imposes hinderances associated with big data handling. Herein, we briefly discuss the implication of big data handling and the role of artificial intelligence in precision medicine. Further, we also highlighted the potential of artificial intelligence in integrating and analyzing the big data that offer personalized treatment. In addition, we briefly discuss the applications of artificial intelligence in personalized treatment, especially in neurological diseases. Lastly, we discuss the challenges and limitations imposed by artificial intelligence in big data management and analysis to hinder precision medicine.

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.

Are sleep disturbances a cause or consequence of autism spectrum disorder?

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by core symptoms such as atypical social communication, stereotyped behaviors, and restricted interests. One of the comorbid symptoms of individuals with ASD is sleep disturbance. There are two major hypotheses regarding the neural mechanism underlying ASD, i.e., the excitation/inhibition (E/I) imbalance and the altered neuroplasticity hypotheses. However, the pathology of ASD remains unclear due to inconsistent research results. This paper argues that sleep is a confounding factor, thus, must be considered when examining the pathology of ASD because sleep plays an important role in modulating the E/I balance and neuroplasticity in the human brain. Investigation of the E/I balance and neuroplasticity during sleep might enhance our understanding of the neural mechanisms of ASD. It may also lead to the development of neurobiologically informed interventions to supplement existing psychosocial therapies.

Resting-state functional connectivity disruption between the left and right pallidum as a biomarker for subthreshold depression

Although the identification of late adolescents with subthreshold depression (StD) may provide a basis for developing effective interventions that could lead to a reduction in the prevalence of StD and prevent the development of major depressive disorder, knowledge about the neural basis of StD remains limited. The purpose of this study was to develop a generalizable classifier for StD and to shed light on the underlying neural mechanisms of StD in late adolescents. Resting-state functional magnetic resonance imaging data of 91 individuals (30 StD subjects, 61 healthy controls) were included to build an StD classifier, and eight functional connections were selected by using the combination of two machine learning algorithms. We applied this biomarker to an independent cohort (n = 43) and confirmed that it showed generalization performance (area under the curve = 0.84/0.75 for the training/test datasets). Moreover, the most important functional connection was between the left and right pallidum, which may be related to clinically important dysfunctions in subjects with StD such as anhedonia and hyposensitivity to rewards. Investigation of whether modulation of the identified functional connections can be an effective treatment for StD may be an important topic of future research.

Molecular and network-level mechanisms explaining individual differences in autism spectrum disorder

The mechanisms underlying phenotypic heterogeneity in autism spectrum disorder (ASD) are not well understood. Using a large neuroimaging dataset, we identified three latent dimensions of functional brain network connectivity that predicted individual differences in ASD behaviors and were stable in cross-validation. Clustering along these three dimensions revealed four reproducible ASD subgroups with distinct functional connectivity alterations in ASD-related networks and clinical symptom profiles that were reproducible in an independent sample. By integrating neuroimaging data with normative gene expression data from two independent transcriptomic atlases, we found that within each subgroup, ASD-related functional connectivity was explained by regional differences in the expression of distinct ASD-related gene sets. These gene sets were differentially associated with distinct molecular signaling pathways involving immune and synapse function, G-protein-coupled receptor signaling, protein synthesis and other processes. Collectively, our findings delineate atypical connectivity patterns underlying different forms of ASD that implicate distinct molecular signaling mechanisms.

Generalizable neuromarker for autism spectrum disorder across imaging sites and developmental stages: A multi-site study

Autism spectrum disorder (ASD) is a lifelong condition, and its underlying biological mechanisms remain elusive. The complexity of various factors, including inter-site and development-related differences, makes it challenging to develop generalizable neuroimaging-based biomarkers for ASD. This study used a large-scale, multi-site dataset of 730 Japanese adults to develop a generalizable neuromarker for ASD across independent sites (U.S., Belgium, and Japan) and different developmental stages (children and adolescents). Our adult ASD neuromarker achieved successful generalization for the US and Belgium adults (area under the curve [AUC] = 0.70) and Japanese adults (AUC = 0.81). The neuromarker demonstrated significant generalization for children (AUC = 0.66) and adolescents (AUC = 0.71; all P < 0.05 , family-wise-error corrected). We identified 141 functional connections (FCs) important for discriminating individuals with ASD from TDCs. These FCs largely centered on social brain regions such as the amygdala, hippocampus, dorsomedial and ventromedial prefrontal cortices, and temporal cortices. Finally, we mapped schizophrenia (SCZ) and major depressive disorder (MDD) onto the biological axis defined by the neuromarker and explored the biological continuity of ASD with SCZ and MDD. We observed that SCZ, but not MDD, was located proximate to ASD on the biological dimension defined by the ASD neuromarker. The successful generalization in multifarious datasets and the observed relations of ASD with SCZ on the biological dimensions provide new insights for a deeper understanding of ASD.

Prediction of Needle Physiological Traits Using UAV Imagery for Breeding Selection of Slash Pine

Leaf nitrogen (N) content and nonstructural carbohydrate (NSC) content are 2 important physiological indicators that reflect the growth state of trees. Rapid and accurate measurement of these 2 traits multitemporally enables dynamic monitoring of tree growth and efficient tree breeding selection. Traditional methods to monitor N and NSC are time-consuming, are mostly used on a small scale, and are nonrepeatable. In this paper, the performance of unmanned aerial vehicle multispectral imaging was evaluated over 11 months of 2021 on the estimation of canopy N and NSC contents from 383 slash pine trees. Four machine learning methods were compared to generate the optimal model for N and NSC prediction. In addition, the temporal scale of heritable variation for N and NSC was evaluated. The results show that the gradient boosting machine model yields the best prediction results on N and NSC, with R ² values of 0.60 and 0.65 on the validation set (20%), respectively. The heritability (h ²) of all traits in 11 months ranged from 0 to 0.49, with the highest h ² for N and NSC found in July and March (0.26 and 0.49, respectively). Finally, 5 families with high N and NSC breeding values were selected. To the best of our knowledge, this is the first study to predict N and NSC contents in trees using time-series unmanned aerial vehicle multispectral imaging and estimating the genetic variation of N and NSC along a temporal scale, which provides more reliable information about the overall performance of families in a breeding program.

The foundation and architecture of precision medicine in neurology and psychiatry

Neurological and psychiatric diseases have high degrees of genetic and pathophysiological heterogeneity, irrespective of clinical manifestations. Traditional medical paradigms have focused on late-stage syndromic aspects of these diseases, with little consideration of the underlying biology. Advances in disease modeling and methodological design have paved the way for the development of precision medicine (PM), an established concept in oncology with growing attention from other medical specialties. We propose a PM architecture for central nervous system diseases built on four converging pillars: multimodal biomarkers, systems medicine, digital health technologies, and data science. We discuss Alzheimer's disease (AD), an area of significant unmet medical need, as a case-in-point for the proposed framework. AD can be seen as one of the most advanced PM-oriented disease models and as a compelling catalyzer towards PM-oriented neuroscience drug development and advanced healthcare 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.

BrainGB: A Benchmark for Brain Network Analysis With Graph Neural Networks

Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neural Networks (GNNs) motivated from geometric deep learning have attracted broad interest due to their established power for modeling complex networked data. Despite their superior performance in many fields, there has not yet been a systematic study of how to design effective GNNs for brain network analysis. To bridge this gap, we present BrainGB, a benchmark for brain network analysis with GNNs. BrainGB standardizes the process by (1) summarizing brain network construction pipelines for both functional and structural neuroimaging modalities and (2) modularizing the implementation of GNN designs. We conduct extensive experiments on datasets across cohorts and modalities and recommend a set of general recipes for effective GNN designs on brain networks. To support open and reproducible research on GNN-based brain network analysis, we host the BrainGB website at https://braingb.us with models, tutorials, examples, as well as an out-of-box Python package. We hope that this work will provide useful empirical evidence and offer insights for future research in this novel and promising direction.

Classification of Brain Disorders in rs-fMRI via Local-to-Global Graph Neural Networks

Recently, functional brain network has been used for the classification of brain disorders, such as Autism Spectrum Disorder (ASD) and Alzheimer's disease (AD). Existing methods either ignore the non-imaging information associated with the subjects and the relationship between the subjects, or cannot identify and analyze disease-related local brain regions and biomarkers, leading to inaccurate classification results. This paper proposes a local-to-global graph neural network (LG-GNN) to address this issue. A local ROI-GNN is designed to learn feature embeddings of local brain regions and identify biomarkers, and a global Subject-GNN is then established to learn the relationship between the subjects with the embeddings generated by the local ROI-GNN and the non-imaging information. The local ROI-GNN contains a self-attention based pooling module to preserve the embeddings most important for the classification. The global Subject-GNN contains an adaptive weight aggregation block to generate the multi-scale feature embedding corresponding to each subject. The proposed LG-GNN is thoroughly validated using two public datasets for ASD and AD classification. The experimental results demonstrated that it achieves the state-of-the-art performance in terms of various evaluation metrics.

Geometric learning of functional brain network on the correlation manifold

The correlation matrix is a typical representation of node interactions in functional brain network analysis. The analysis of the correlation matrix to characterize brain networks observed in several neuroimaging modalities has been conducted predominantly in the Euclidean space by assuming that pairwise interactions are mutually independent. One way to take account of all interactions in the network as a whole is to analyze the correlation matrix under some geometric structure. Recent studies have focused on the space of correlation matrices as a strict subset of symmetric positive definite (SPD) matrices, which form a unique mathematical structure known as the Riemannian manifold. However, mathematical operations of the correlation matrix under the SPD geometry may not necessarily be coherent (i.e., the structure of the correlation matrix may not be preserved), necessitating a post-hoc normalization. The contribution of the current paper is twofold: (1) to devise a set of inferential methods on the correlation manifold and (2) to demonstrate its applicability in functional network analysis. We present several algorithms on the correlation manifold, including measures of central tendency, cluster analysis, hypothesis testing, and low-dimensional embedding. Simulation and real data analysis support the application of the proposed framework for brain network analysis.

Functional Connectome-Based Predictive Modeling in Autism

Autism is a heterogeneous neurodevelopmental condition, and functional magnetic resonance imaging-based studies have helped advance our understanding of its effects on brain network activity. We review how predictive modeling, using measures of functional connectivity and symptoms, has helped reveal key insights into this condition. We discuss how different prediction frameworks can further our understanding of the brain-based features that underlie complex autism symptomatology and consider how predictive models may be used in clinical settings. Throughout, we highlight aspects of study interpretation, such as data decay and sampling biases, that require consideration within the context of this condition. We close by suggesting exciting future directions for predictive modeling in autism.

Assessing Multi-Site rs-fMRI-Based Connectomic Harmonization Using Information Theory

Several harmonization techniques have recently been proposed for connectomics/networks derived from resting-state functional magnetic resonance imaging (rs-fMRI) acquired at multiple sites. These techniques have the objective of mitigating site-specific biases that complicate its subsequent analysis and, therefore, compromise the quality of the results when these images are analyzed together. Thus, harmonization is indispensable when large cohorts are required in which the data obtained must be independent of the particular condition of each resonator, its make and model, its calibration, and other features or artifacts that may affect the significance of the acquisition. To date, no assessment of the actual efficacy of these harmonization techniques has been proposed. In this work, we apply recently introduced Information Theory tools to analyze the effectiveness of these techniques, developing a methodology that allows us to compare different harmonization models. We demonstrate the usefulness of this methodology by applying it to some of the most widespread harmonization frameworks and datasets. As a result, we are able to show that some of these techniques are indeed ineffective since the acquisition site can still be determined from the fMRI data after the processing.

A new multimodality fusion classification approach to explore the uniqueness of schizophrenia and autism spectrum disorder

Schizophrenia (SZ) and autism spectrum disorder (ASD) sharing overlapping symptoms have a long history of diagnostic confusion. It is unclear what their differences at a brain level are. Here, we propose a multimodality fusion classification approach to investigate their divergence in brain function and structure. Using brain functional network connectivity (FNC) calculated from resting-state fMRI data and gray matter volume (GMV) estimated from sMRI data, we classify the two disorders using the main data (335 SZ and 380 ASD patients) via an unbiased 10-fold cross-validation pipeline, and also validate the classification generalization ability on an independent cohort (120 SZ and 349 ASD patients). The classification accuracy reached up to 83.08% for the testing data and 72.10% for the independent data, significantly better than the results from using the single-modality features. The discriminative FNCs that were automatically selected primarily involved the sub-cortical, default mode, and visual domains. Interestingly, all discriminative FNCs relating to the default mode network showed an intermediate strength in healthy controls (HCs) between SZ and ASD patients. Their GMV differences were mainly driven by the frontal gyrus, temporal gyrus, and insula. Regarding these regions, the mean GMV of HC fell intermediate between that of SZ and ASD, and ASD showed the highest GMV. The middle frontal gyrus was associated with both functional and structural differences. In summary, our work reveals the unique neuroimaging characteristics of SZ and ASD that can achieve high and generalizable classification accuracy, supporting their potential as disorder-specific neural substrates of the two entwined disorders.

A cognitive neurogenetic approach to uncovering the structure of executive functions

One central mission of cognitive neuroscience is to understand the ontology of complex cognitive functions. We addressed this question with a cognitive neurogenetic approach using a large-scale dataset of executive functions (EFs), whole-brain resting-state functional connectivity, and genetic polymorphisms. We found that the bifactor model with common and shifting-specific components not only was parsimonious but also showed maximal dissociations among the EF components at behavioral, neural, and genetic levels. In particular, the genes with enhanced expression in the middle frontal gyrus (MFG) and the subcallosal cingulate gyrus (SCG) showed enrichment for the common and shifting-specific component, respectively. Finally, High-dimensional mediation models further revealed that the functional connectivity patterns significantly mediated the genetic effect on the common EF component. Our study not only reveals insights into the ontology of EFs and their neurogenetic basis, but also provides useful tools to uncover the structure of complex constructs of human cognition.

Sparse Hierarchical Representation Learning on Functional Brain Networks for Prediction of Autism Severity Levels

Machine learning algorithms have been widely applied in diagnostic tools for autism spectrum disorder (ASD), revealing an altered brain connectivity. However, little is known about whether an magnetic resonance imaging (MRI)-based brain network is related to the severity of ASD symptoms in a large-scale cohort. We propose a graph convolution neural network-based framework that can generate sparse hierarchical graph representations for functional brain connectivity. Instead of assigning initial features for each node, we utilized a feature extractor to derive node features and the extracted representations can be fed to a hierarchical graph self-attention framework to effectively represent the entire graph. By incorporating connectivity embeddings in the feature extractor, we propose adjacency embedding networks to characterize the heterogeneous representations of the brain connectivity. Our proposed model variants outperform the benchmarking model with different configurations of adjacency embedding networks and types of functional connectivity matrices. Using this approach with the best configuration (SHEN atlas for node definition, Tikhonov correlation for connectivity estimation, and identity-adjacency embedding), we were able to predict individual ASD severity levels with a meaningful accuracy: the mean absolute error (MAE) and correlation between predicted and observed ASD severity scores resulted in 0.96, and r = 0.61 (P < 0.0001), respectively. To obtain a better understanding on how to generate better representations, we investigate the relationships between the extracted feature embeddings and the graph theory-based nodal measurements using canonical correlation analysis. Finally, we visualized the model to identify the most contributive functional connections for predicting ASD severity scores.

Development of a classifier for gambling disorder based on functional connections between brain regions

AIM

Recently, a machine-learning (ML) technique has been used to create generalizable classifiers for psychiatric disorders based on information of functional connections (FCs) between brain regions at resting state. These classifiers predict diagnostic labels by a weighted linear sum (WLS) of the correlation values of a small number of selected FCs. We aimed to develop a generalizable classifier for gambling disorder (GD) from the information of FCs using the ML technique and examine relationships between WLS and clinical data.

METHODS

As a training dataset for ML, data from 71 GD patients and 90 healthy controls (HCs) were obtained from two magnetic resonance imaging sites. We used an ML algorithm consisting of a cascade of an L1-regularized sparse canonical correlation analysis and a sparse logistic regression to create the classifier. The generalizability of the classifier was verified using an external dataset. This external dataset consisted of six GD patients and 14 HCs, and was collected at a different site from the sites of the training dataset. Correlations between WLS and South Oaks Gambling Screen (SOGS) and duration of illness were examined.

RESULTS

The classifier distinguished between the GD patients and HCs with high accuracy in leave-one-out cross-validation (area under curve (AUC = 0.89)). This performance was confirmed in the external dataset (AUC = 0.81). There was no correlation between WLS, and SOGS and duration of illness in the GD patients.

CONCLUSION

We developed a generalizable classifier for GD based on information of functional connections between brain regions at resting state.

Diagnosis-informed connectivity subtyping discovers subgroups of autism with reproducible symptom profiles

Clinical heterogeneity has been one of the main barriers to develop effective biomarkers and therapeutic strategies in autism spectrum disorder (ASD). Recognizing this challenge, much effort has been made in recent neuroimaging studies to find biologically more homogeneous subgroups (called 'neurosubtypes') in autism. However, most approaches have rarely evaluated how much the employed features in subtyping represent the core anomalies of ASD, obscuring its utility in actual clinical diagnosis. To address this, we combined two data-driven methods, 'connectome-based gradient' and 'functional random forest', collectively allowing to discover reproducible neurosubtypes based on resting-state functional connectivity profiles that are specific to ASD. Indeed, the former technique provides the features (as input for subtyping) that effectively summarize whole-brain connectome variations in both normal and ASD conditions, while the latter leverages a supervised random forest algorithm to inform diagnostic labels to clustering, which makes neurosubtyping driven by the features of ASD core anomalies. Applying this framework to the open-sharing Autism Brain Imaging Data Exchange repository data (discovery, n = 103/108 for ASD/typically developing [TD]; replication, n = 44/42 for ASD/TD), we found three dominant subtypes of functional gradients in ASD and three subtypes in TD. The subtypes in ASD revealed distinct connectome profiles in multiple brain areas, which are associated with different Neurosynth-derived cognitive functions previously implicated in autism studies. Moreover, these subtypes showed different symptom severity, which degree co-varies with the extent of functional gradient changes observed across the groups. The subtypes in the discovery and replication datasets showed similar symptom profiles in social interaction and communication domains, confirming a largely reproducible brain-behavior relationship. Finally, the connectome gradients in ASD subtypes present both common and distinct patterns compared to those in TD, reflecting their potential overlap and divergence in terms of developmental mechanisms involved in the manifestation of large-scale functional networks. Our study demonstrated a potential of the diagnosis-informed subtyping approach in developing a clinically useful brain-based classification system for future ASD research.

rs-fMRI and machine learning for ASD diagnosis: a systematic review and meta-analysis

Autism Spectrum Disorder (ASD) diagnosis is still based on behavioral criteria through a lengthy and time-consuming process. Much effort is being made to identify brain imaging biomarkers and develop tools that could facilitate its diagnosis. In particular, using Machine Learning classifiers based on resting-state fMRI (rs-fMRI) data is promising, but there is an ongoing need for further research on their accuracy and reliability. Therefore, we conducted a systematic review and meta-analysis to summarize the available evidence in the literature so far. A bivariate random-effects meta-analytic model was implemented to investigate the sensitivity and specificity across the 55 studies that offered sufficient information for quantitative analysis. Our results indicated overall summary sensitivity and specificity estimates of 73.8% and 74.8%, respectively. SVM stood out as the most used classifier, presenting summary estimates above 76%. Studies with bigger samples tended to obtain worse accuracies, except in the subgroup analysis for ANN classifiers. The use of other brain imaging or phenotypic data to complement rs-fMRI information seems promising, achieving higher sensitivities when compared to rs-fMRI data alone (84.7% versus 72.8%). Finally, our analysis showed AUC values between acceptable and excellent. Still, given the many limitations indicated in our study, further well-designed studies are warranted to extend the potential use of those classification algorithms to clinical settings.

Using graph convolutional network to characterize individuals with major depressive disorder across multiple imaging sites

BACKGROUND

Establishing objective and quantitative neuroimaging biomarkers at individual level can assist in early and accurate diagnosis of major depressive disorder (MDD). However, most previous studies using machine learning to identify MDD were based on small sample size and did not account for the brain connectome that is associated with the pathophysiology of MDD. Here, we addressed these limitations by applying graph convolutional network (GCN) in a large multi-site MDD dataset.

METHODS

Resting-state functional MRI scans of 1586 participants (821 MDD vs. 765 controls) across 16 sites of Rest-meta-MDD consortium were collected. GCN model was trained with individual whole-brain functional network to identify MDD patients from controls, characterize the most salient regions contributing to classification, and explore the relationship between topological characteristics of salient regions and clinical measures.

FINDINGS

GCN achieved an accuracy of 81·5% (95%CI: 80·5-82·5%, AUC: 0·865), which was higher than other common machine learning classifiers. The most salient regions contributing to classification were primarily identified within the default mode, fronto-parietal, and cingulo-opercular networks. Nodal topologies of the left inferior parietal lobule and left dorsolateral prefrontal cortex were associated with depressive severity and illness duration, respectively.

INTERPRETATION

These findings based on a large, multi-site dataset support the feasibility and effectiveness of GCN in characterizing MDD, and also illustrate the potential utility of GCN for enhancing understanding of the neurobiology of MDD by detecting clinically-relevant disruption in functional network topology.

FUNDING

This study was supported by the National Natural Science Foundation of China (Grant Nos. 81621003, 82027808, 81820108018).

Depressive symptoms reduce when dorsolateral prefrontal cortex-precuneus connectivity normalizes after functional connectivity neurofeedback

Depressive disorders contribute heavily to global disease burden; This is possibly because patients are often treated homogeneously, despite having heterogeneous symptoms with differing underlying neural mechanisms. A novel treatment that can directly influence the neural circuit relevant to an individual patient's subset of symptoms might more precisely and thus effectively aid in the alleviation of their specific symptoms. We tested this hypothesis in a proof-of-concept study using fMRI functional connectivity neurofeedback. We targeted connectivity between the left dorsolateral prefrontal cortex/middle frontal gyrus and the left precuneus/posterior cingulate cortex, because this connection has been well-established as relating to a specific subset of depressive symptoms. Specifically, this connectivity has been shown in a data-driven manner to be less anticorrelated in patients with melancholic depression than in healthy controls. Furthermore, a posterior cingulate dominant state-which results in a loss of this anticorrelation-is expected to specifically relate to an increase in rumination symptoms such as brooding. In line with predictions, we found that, with neurofeedback training, the more a participant normalized this connectivity (restored the anticorrelation), the more related (depressive and brooding symptoms), but not unrelated (trait anxiety), symptoms were reduced. Because these results look promising, this paradigm next needs to be examined with a greater sample size and with better controls. Nonetheless, here we provide preliminary evidence for a correlation between the normalization of a neural network and a reduction in related symptoms. Showing their reproducibility, these results were found in two experiments that took place several years apart by different experimenters. Indicative of its potential clinical utility, effects of this treatment remained one-two months later.Clinical trial registration: Both experiments reported here were registered clinical trials (UMIN000015249, jRCTs052180169).

Resting-state brain activity can predict target-independent aptitude in fMRI-neurofeedback training

Neurofeedback (NF) aptitude, which refers to an individual's ability to change brain activity through NF training, has been reported to vary significantly from person to person. The prediction of individual NF aptitudes is critical in clinical applications to screen patients suitable for NF treatment. In the present study, we extracted the resting-state functional brain connectivity (FC) markers of NF aptitude, independent of NF-targeting brain regions. We combined the data from fMRI-NF studies targeting four different brain regions at two independent sites (obtained from 59 healthy adults and six patients with major depressive disorder) to collect resting-state fMRI data associated with aptitude scores in subsequent fMRI-NF training. We then trained the multiple regression models to predict the individual NF aptitude scores from the resting-state fMRI data using a discovery dataset from one site and identified six resting-state FCs that predicted NF aptitude. Subsequently, the reproducibility of the prediction model was validated using independent test data from another site. The identified FC model revealed that the posterior cingulate cortex was the functional hub among the brain regions and formed predictive resting-state FCs, suggesting that NF aptitude may be involved in the attentional mode-orientation modulation system's characteristics in task-free resting-state brain activity.

Classification of ASD based on fMRI data with deep learning

Autism spectrum disorder (ASD) is a neuro-developmental disorder that affects the social abilities of patients. Studies have shown that a small number of abnormal functional connections (FCs) exist in the cerebral hemisphere of ASD patients. The identification of these abnormal FCs provides a biological ground for the diagnosis of ASD. In this paper, we propose a combined deep feature selection (DFS) and graph convolutional network method to classify ASD. Firstly, in the DFS process, a sparse one-to-one layer is added between the input and the first hidden layer of a multilayer perceptron, thus each functional connection (FC) feature can be weighted and a subset of FC features can be selected accordingly. Then based on the selected FCs and the phenotypic information of subjects, a graph convolutional network is constructed to classify ASD and typically developed controls. Finally, we test our proposed method on the ABIDE database and compare it with some other methods in the literature. Experimental results indicate that the DFS can effectively select critical FC features for classification according to the weights of input FC features. With DFS, the performance of GCN classifier can be improved dramatically. The proposed method achieves state-of-the-art performance with an accuracy of 79.5% and an area under the receiver operating characteristic curve (AUC) of 0.85 on the preprocessed ABIDE dataset; it is superior to the other methods. Further studies on the top-ranked thirty FCs obtained by DFS show that these FCs are widespread over the cerebral hemisphere, and the ASD group appears a significantly higher number of weak connections compared to the typically developed group.

Dimensional distribution of cortical abnormality across antipsychotics treatment-resistant and responsive schizophrenia

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Different etiology is assumed in treatment-resistant and responsive schizophrenia.

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Patients with treatment-resistant schizophrenia were classified from controls.

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Patients with non-treatment-resistant schizophrenia were classified from controls.

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Two classifications reached area under the curve as high as 0.69 and 0.85.

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Area under the curve remained as high as 0.69 when two classifiers were swapped.

Background

One-third of patients with schizophrenia are treatment-resistant to non-clozapine antipsychotics (TRS), while the rest respond (NTRS). Examining whether TRS and NTRS represent different pathophysiologies is an important step toward precision medicine.

Methods

Focusing on cortical thickness (CT), we analyzed international multi-site cross-sectional datasets of magnetic resonance imaging comprising 110 patients with schizophrenia (NTRS = 46, TRS = 64) and 52 healthy controls (HCs). We utilized a logistic regression with L1-norm regularization to find brain regions related to either NTRS or TRS. We conducted nested 10-fold cross-validation and computed the accuracy and area under the curve (AUC). Then, we applied the NTRS classifier to patients with TRS, and vice versa.

Results

Patients with NTRS and TRS were classified from HCs with 65% and 78% accuracies and with the AUC of 0.69 and 0.85 (p = 0.014 and < 0.001, corrected), respectively. The left planum temporale (PT) and left anterior insula/inferior frontal gyrus (IFG) contributed to both NTRS and TRS classifiers. The left supramarginal gyrus only contributed to NTRS and right superior temporal sulcus and right lateral orbitofrontal cortex only to the TRS. The NTRS classifiers successfully distinguished those with TRS from HCs with the AUC of 0.78 (p < 0.001), while the TRS classifiers classified those with NTRS from HCs with the AUC of 0.69 (p = 0.015).

Conclusion

Both NTRS and TRS could be distinguished from HCs on the basis of CT. The CT pathological basis of NTRS and TRS has commonalities, and TRS presents unique CT features.

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.

A multi-site, multi-disorder resting-state magnetic resonance image database

Machine learning classifiers for psychiatric disorders using resting-state functional magnetic resonance imaging (rs-fMRI) have recently attracted attention as a method for directly examining relationships between neural circuits and psychiatric disorders. To develop accurate and generalizable classifiers, we compiled a large-scale, multi-site, multi-disorder neuroimaging database. The database comprises resting-state fMRI and structural images of the brain from 993 patients and 1,421 healthy individuals, as well as demographic information such as age, sex, and clinical rating scales. To harmonize the multi-site data, nine healthy participants (“traveling subjects”) visited the sites from which the above datasets were obtained and underwent neuroimaging with 12 scanners. All participants consented to having their data shared and analyzed at multiple medical and research institutions participating in the project, and 706 patients and 1,122 healthy individuals consented to having their data disclosed. Finally, we have published four datasets: 1) the SRPBS Multi-disorder Connectivity Dataset 2), the SRPBS Multi-disorder MRI Dataset (restricted), 3) the SRPBS Multi-disorder MRI Dataset (unrestricted), and 4) the SRPBS Traveling Subject MRI Dataset.

Measurement(s)	mental or behavioural disorder • brain measurement • Demographic Data
Technology Type(s)	functional magnetic resonance imaging • magnetic resonance imaging • Resting State Functional Connectivity Magnetic Resonance Imaging
Factor Type(s)	age • sex • site • disorder
Sample Characteristic - Organism	Homo sapiens

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14716329

The Contribution of White Matter Diffusion and Cortical Perfusion Pathology to Vascular Cognitive Impairment: A Multimode Imaging-Based Machine Learning Study

Widespread impairments in white matter and cerebrovascular integrity have been consistently implicated in the pathophysiology of patients with small vessel disease (SVD). However, the neural circuit mechanisms that underlie the developing progress of clinical cognitive symptoms remain largely elusive. Here, we conducted cross-modal MRI scanning including diffusion tensor imaging and arterial spin labeling in a cohort of 113 patients with SVD, which included 74 patients with vascular mild cognitive impairment (vMCI) and 39 patients without vMCI symptoms, and hence developed multimode imaging-based machine learning models to identify markers that discriminated SVD subtypes. Diffusion and perfusion features, respectively, extracted from individual white matter and gray matter regions were used to train three sets of classifiers in a nested 10-fold fashion: diffusion-based, perfusion-based, and combined diffusion-perfusion-based classifiers. We found that the diffusion-perfusion combined classifier achieved the highest accuracy of 72.57% with leave-one-out cross-validation, with the diffusion features largely spanning the capsular lateral pathway of the cholinergic tracts, and the perfusion features mainly distributed in the frontal-subcortical-limbic areas. Furthermore, diffusion-based features within vMCI group were associated with performance on executive function tests. We demonstrated the superior accuracy of using diffusion-perfusion combined multimode imaging features for classifying vMCI subtype out of a cohort of patients with SVD. Disruption of white matter integrity might play a critical role in the progression of cognitive impairment in patients with SVD, while malregulation of coritcal perfusion needs further study.

Machine learning with neuroimaging data to identify autism spectrum disorder: a systematic review and meta-analysis

PURPOSE

Autism Spectrum Disorder (ASD) is diagnosed through observation or interview assessments, which is time-consuming, subjective, and with questionable validity and reliability. Thus, we aimed to evaluate the role of machine learning (ML) with neuroimaging data to provide a reliable classification of ASD.

METHODS

A systematic search of PubMed, Scopus, and Embase was conducted to identify relevant publications. Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) was used to assess the studies' quality. A bivariate random-effects model meta-analysis was employed to evaluate the pooled sensitivity, the pooled specificity, and the diagnostic performance through the hierarchical summary receiver operating characteristic (HSROC) curve of ML with neuroimaging data in classifying ASD. Meta-regression was also performed.

RESULTS

Forty-four studies (5697 ASD and 6013 typically developing individuals [TD] in total) were included in the quantitative analysis. The pooled sensitivity for differentiating ASD from TD individuals was 86.25 95% confidence interval [CI] (81.24, 90.08), while the pooled specificity was 83.31 95% CI (78.12, 87.48) with a combined area under the HSROC (AUC) of 0.889. Higgins I² (> 90%) and Cochran's Q (p < 0.0001) suggest a high degree of heterogeneity. In the bivariate model meta-regression, a higher pooled specificity was observed in studies not using a brain atlas (90.91 95% CI [80.67, 96.00], p = 0.032). In addition, a greater pooled sensitivity was seen in studies recruiting both males and females (89.04 95% CI [83.84, 92.72], p = 0.021), and combining imaging modalities (94.12 95% [85.43, 97.76], p = 0.036).

CONCLUSION

ML with neuroimaging data is an exciting prospect in detecting individuals with ASD but further studies are required to improve its reliability for usage in clinical practice.

Overlapping and specific neural correlates for empathizing, affective mentalizing, and cognitive mentalizing: A coordinate-based meta-analytic study

While the discussion on the foundations of social understanding mainly revolves around the notions of empathy, affective mentalizing, and cognitive mentalizing, their degree of overlap versus specificity is still unclear. We took a meta-analytic approach to unveil the neural bases of cognitive mentalizing, affective mentalizing, and empathy, both in healthy individuals and pathological conditions characterized by social deficits such as schizophrenia and autism. We observed partially overlapping networks for cognitive and affective mentalizing in the medial prefrontal, posterior cingulate, and lateral temporal cortex, while empathy mainly engaged fronto-insular, somatosensory, and anterior cingulate cortex. Adjacent process-specific regions in the posterior lateral temporal, ventrolateral, and dorsomedial prefrontal cortex might underpin a transition from abstract representations of cognitive mental states detached from sensory facets to emotionally-charged representations of affective mental states. Altered mentalizing-related activity involved distinct sectors of the posterior lateral temporal cortex in schizophrenia and autism, while only the latter group displayed abnormal empathy related activity in the amygdala. These data might inform the design of rehabilitative treatments for social cognitive deficits.

Intergenerational transmission of the patterns of functional and structural brain networks

There is clear evidence of intergenerational transmission of life values, cognitive traits, psychiatric disorders, and even aspects of daily decision making. To investigate biological substrates of this phenomenon, the brain has received increasing attention as a measurable biomarker and potential target for intervention. However, no previous study has quantitatively and comprehensively investigated the effects of intergenerational transmission on functional and structural brain networks. Here, by employing an unusually large cohort dataset (N = 84 parent-child dyads; 45 sons, 39 daughters, 81 mothers, and 3 fathers), we show that patterns of functional and structural brain networks are preserved over a generation. We also demonstrate that several demographic factors and behavioral/physiological phenotypes have a relationship with brain similarity. Collectively, our results provide a comprehensive picture of neurobiological substrates of intergenerational transmission and demonstrate the usability of our dataset for investigating the neurobiological substrates of intergenerational transmission.

Engrailed 2 deficiency and chronic stress alter avoidance and motivation behaviors

Autism spectrum disorder (ASD) is a pervasive neurodevelopmental disorder characterized by impairments in social interaction, cognition, and communication, as well as the presence of repetitive or stereotyped behaviors and interests. ASD is most often studied as a neurodevelopmental disease, but it is a lifelong disorder. Adults with ASD experience more stressful life events and greater perceived stress, and frequently have comorbid mood disorders such as anxiety and depression. It remains unclear whether adult exposure to chronic stress can exacerbate the behavioral and neurodevelopmental phenotypes associated with ASD. To address this issue, we first investigated whether adult male and female Engrailed-2 deficient (En2-KO, En2-/-) mice, which display behavioral disturbances in avoidance tasks and dysregulated monoaminergic neurotransmitter levels, also display impairments in instrumental behaviors associated with motivation, such as the progressive ratio task. We then exposed adult En2-KO mice to chronic environmental stress (CSDS, chronic social defeat stress), to determine if stress exacerbated the behavioral and neuroanatomical effects of En2 deletion. En2-/- mice showed impaired instrumental acquisition and significantly lower breakpoints in a progressive ratio test, demonstrating En2 deficiency decreases motivation to exert effort for reward. Furthermore, adult CSDS exposure increased avoidance behaviors in En2-KO mice. Interestingly, adult CSDS exposure also exacerbated the deleterious effects of En2 deficiency on forebrain-projecting monoaminergic fibers. Our findings thus suggest that adult exposure to stress may exacerbate behavioral and neuroanatomical phenotypes associated with developmental effects of genetic En2 deficiency.