Differences in atypical resting-state effective connectivity distinguish autism from schizophrenia

A review of studies on constructing classification models to identify mental illness using brain effective connectivity

Brain effective connectivity (EC) is a functional measurement that reflects the causal effects and topological relationships of neural activities. Recent research has increasingly focused on the classification for mental illnesses and healthy controls using brain EC; however, no comprehensive reviews have synthesized these studies. Therefore, the aim of this review is to thoroughly examine the existing literature on constructing diagnosis model for mental illnesses using brain EC. We first conducted a systematical literature search and thirty-five papers met the inclusion criteria. Subsequently, we summarized the approaches for estimating EC, the classification and validation methods used, the accuracies of models, and the main findings. Finally, we discussed the limitations of current research and the challenges in future research. These summaries and discussion provide references for future research on mental illnesses identification based on brain EC.

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.

Altered temporal lobe connectivity is associated with psychotic symptoms in drug-naïve adolescent patients with first-episode schizophrenia

Research on individuals with a younger onset age of schizophrenia is important for identifying neurobiological processes derived from the interaction of genes and the environment that lead to the manifestation of schizophrenia. Schizophrenia has long been recognized as a disorder of dysconnectivity, but it is largely unknown how brain connectivity changes are associated with psychotic symptoms. Twenty-one adolescent-onset schizophrenia (AOS) patients and 21 matched healthy controls (HCs) were recruited and underwent resting-state functional magnetic resonance imaging. Regional homogeneity (ReHo) was used to investigate local brain connectivity alterations in AOS. Regions with significant ReHo changes in patients were selected as "seeds" for further functional connectivity (FC) analysis and Granger causality analysis (GCA), and associations of the obtained functional brain measures with psychotic symptoms in patients with AOS were examined. Compared with HCs, AOS patients showed significantly increased ReHo in the right middle temporal gyrus (MTG), which was positively correlated with PANSS-positive scores, PSYRATS-delusion scores and auditory hallucination scores. With the MTG as the seed, lower connectivity with the bilateral postcentral gyrus (PCG) and higher connectivity with the right precuneus were observed in patients. The reduced FC between the right MTG and bilateral PCG was significantly and positively correlated with hallucination scores. GCA indicated decreased Granger causality from the right MTG to the left middle frontal gyrus (MFG) and from the right MFG to the right MTG in AOS patients, but such effects did not significantly associate with psychotic symptoms. Abnormalities in the connectivity within the MTG and its connectivity with other networks were identified and were significantly correlated with hallucination and delusion ratings. This region may be a key neural substrate of psychotic symptoms in AOS.

Exploring Brain Effective Connectivity Networks Through Spatiotemporal Graph Convolutional Models

Learning brain effective connectivity networks (ECN) from functional magnetic resonance imaging (fMRI) data has gained much attention in recent years. With the successful applications of deep learning in numerous fields, several brain ECN learning methods based on deep learning have been reported in the literature. However, current methods ignore the deep temporal features of fMRI data and fail to fully employ the spatial topological relationship between brain regions. In this article, we propose a novel method for learning brain ECN based on spatiotemporal graph convolutional models (STGCM), named STGCMEC, in which we first adopt the temporal convolutional network to extract the deep temporal features of fMRI data and utilize the graph convolutional network to update the spatial features of each brain region by aggregating information from neighborhoods, which makes the features of brain regions more discriminative. Then, based on such features of brain regions, we design a joint loss function to guide STGCMEC to learn the brain ECN, which includes a task prediction loss and a graph regularization loss. The experimental results on a simulated dataset and a real Alzheimer's disease neuroimaging initiative (ADNI) dataset show that the proposed STGCMEC is able to better learn brain ECN compared with some state-of-the-art methods.

Searching Reproducible Brain Features using NeuroMark: Templates for Different Age Populations and Imaging Modalities

A primary challenge to the data-driven analysis is the balance between poor generalizability of population-based research and characterizing more subject-, study- and population-specific variability. We previously introduced a fully automated spatially constrained independent component analysis (ICA) framework called NeuroMark and its functional MRI (fMRI) template. NeuroMark has been successfully applied in numerous studies, identifying brain markers reproducible across datasets and disorders. The first NeuroMark template was constructed based on young adult cohorts. We recently expanded on this initiative by creating a standardized normative multi-spatial-scale functional template using over 100,000 subjects, aiming to improve generalizability and comparability across studies involving diverse cohorts. While a unified template across the lifespan is desirable, a comprehensive investigation of the similarities and differences between components from different age populations might help systematically transform our understanding of the human brain by revealing the most well-replicated and variable network features throughout the lifespan. In this work, we introduced two significant expansions of NeuroMark templates first by generating replicable fMRI templates for infants, adolescents, and aging cohorts, and second by incorporating structural MRI (sMRI) and diffusion MRI (dMRI) modalities. Specifically, we built spatiotemporal fMRI templates based on 6,000 resting-state scans from four datasets. This is the first attempt to create robust ICA templates covering dynamic brain development across the lifespan. For the sMRI and dMRI data, we used two large publicly available datasets including more than 30,000 scans to build reliable templates. We employed a spatial similarity analysis to identify replicable templates and investigate the degree to which unique and similar patterns are reflective in different age populations. Our results suggest remarkably high similarity of the resulting adapted components, even across extreme age differences. With the new templates, the NeuroMark framework allows us to perform age-specific adaptations and to capture features adaptable to each modality, therefore facilitating biomarker identification across brain disorders. In sum, the present work demonstrates the generalizability of NeuroMark templates and suggests the potential of new templates to boost accuracy in mental health research and advance our understanding of lifespan and cross-modal alterations.

Distinct Symptom Network Structure and Shared Central Social Communication Symptomatology in Autism and Schizophrenia: A Bayesian Network Analysis

Autism (ASD) and schizophrenia spectrum disorders (SCZ) are neurodevelopmental conditions with overlapping and interrelated symptoms. A network analysis approach that represents clinical conditions as a set of "nodes" (symptoms) connected by "edges" (relations among symptoms) was used to compare symptom organization in the two conditions. Gaussian graphical models were estimated using Bayesian methods to model separate symptom networks for adults with confirmed ASD or SCZ diagnoses. Though overall symptom organization differed by diagnostic group, both symptom networks demonstrated high centrality of social communication difficulties. Autism-relevant restricted and repetitive behaviors and schizophrenia-related cognitive-perceptual symptoms were uniquely central to the ASD and SCZ networks, respectively. Results offer recommendations to improve differential diagnosis and highlight potential treatment targets in ASD and SCZ.

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

BACKGROUND

The development of machine learning models for aiding in the diagnosis of mental disorder is recognized as a significant breakthrough in the field of psychiatry. However, clinical practice of such models remains a challenge, with poor generalizability being a major limitation.

METHODS

Here, we conducted a pre-registered meta-research assessment on neuroimaging-based models in the psychiatric literature, quantitatively examining global and regional sampling issues over recent decades, from a view that has been relatively underexplored. A total of 476 studies (n = 118,137) were included in the current assessment. Based on these findings, we built a comprehensive 5-star rating system to quantitatively evaluate the quality of existing machine learning models for psychiatric diagnoses.

RESULTS

A global sampling inequality in these models was revealed quantitatively (sampling Gini coefficient (G) = 0.81, p < .01), varying across different countries (regions) (e.g., China, G = 0.47; the USA, G = 0.58; Germany, G = 0.78; the UK, G = 0.87). Furthermore, the severity of this sampling inequality was significantly predicted by national economic levels (β =  - 2.75, p < .001, R²_adj = 0.40; r =  - .84, 95% CI: - .41 to - .97), and was plausibly predictable for model performance, with higher sampling inequality for reporting higher classification accuracy. Further analyses showed that lack of independent testing (84.24% of models, 95% CI: 81.0-87.5%), improper cross-validation (51.68% of models, 95% CI: 47.2-56.2%), and poor technical transparency (87.8% of models, 95% CI: 84.9-90.8%)/availability (80.88% of models, 95% CI: 77.3-84.4%) are prevailing in current diagnostic classifiers despite improvements over time. Relating to these observations, model performances were found decreased in studies with independent cross-country sampling validations (all p < .001, BF₁₀ > 15). In light of this, we proposed a purpose-built quantitative assessment checklist, which demonstrated that the overall ratings of these models increased by publication year but were negatively associated with model performance.

CONCLUSIONS

Together, improving sampling economic equality and hence the quality of machine learning models may be a crucial facet to plausibly translating neuroimaging-based diagnostic classifiers into clinical practice.

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

IMPORTANCE

Neuroimaging-based artificial intelligence (AI) diagnostic models have proliferated in psychiatry. However, their clinical applicability and reporting quality (ie, feasibility) for clinical practice have not been systematically evaluated.

OBJECTIVE

To systematically assess the risk of bias (ROB) and reporting quality of neuroimaging-based AI models for psychiatric diagnosis.

EVIDENCE REVIEW

PubMed was searched for peer-reviewed, full-length articles published between January 1, 1990, and March 16, 2022. Studies aimed at developing or validating neuroimaging-based AI models for clinical diagnosis of psychiatric disorders were included. Reference lists were further searched for suitable original studies. Data extraction followed the CHARMS (Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modeling Studies) and PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines. A closed-loop cross-sequential design was used for quality control. The PROBAST (Prediction Model Risk of Bias Assessment Tool) and modified CLEAR (Checklist for Evaluation of Image-Based Artificial Intelligence Reports) benchmarks were used to systematically evaluate ROB and reporting quality.

FINDINGS

A total of 517 studies presenting 555 AI models were included and evaluated. Of these models, 461 (83.1%; 95% CI, 80.0%-86.2%) were rated as having a high overall ROB based on the PROBAST. The ROB was particular high in the analysis domain, including inadequate sample size (398 of 555 models [71.7%; 95% CI, 68.0%-75.6%]), poor model performance examination (with 100% of models lacking calibration examination), and lack of handling data complexity (550 of 555 models [99.1%; 95% CI, 98.3%-99.9%]). None of the AI models was perceived to be applicable to clinical practices. Overall reporting completeness (ie, number of reported items/number of total items) for the AI models was 61.2% (95% CI, 60.6%-61.8%), and the completeness was poorest for the technical assessment domain with 39.9% (95% CI, 38.8%-41.1%).

CONCLUSIONS AND RELEVANCE

This systematic review found that the clinical applicability and feasibility of neuroimaging-based AI models for psychiatric diagnosis were challenged by a high ROB and poor reporting quality. Particularly in the analysis domain, ROB in AI diagnostic models should be addressed before clinical application.

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.

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.

Neuroimaging correlates of insight in non-affective psychosis: A systematic review and meta-analysis

OBJECTIVE

Neurological correlates of impaired insight in non-affective psychosis remain unclear. This study aimed to review and meta-analyze the studies assessing the grey matter volumetric correlates of impaired insight in non-affective psychosis.

METHODS

This study consisted of a systematic review of 23 studies, and a meta-analysis with SDM-PSI of the 11 studies that were whole-brain and reported maps or peaks of correlation of studies investigating the grey matter volumetric correlates of insight assessments of non-affective psychosis, PubMed and OVID datasets were independently reviewed for articles reporting neuroimaging correlates of insight in non-affective psychosis. Quality assessment was realized following previous methodological approaches for the ABC quality assessment test of imaging studies, based on two main criteria: the statistical power and the multidimensional assessment of insight. Study peaks of correlation between grey matter volume and insight were used to recreate brain correlation maps.

RESULTS

A total of 418 records were identified through database searching. Of these records, twenty-three magnetic resonance imaging (MRI) studies that used different insight scales were included. The quality of the evidence was high in 11 studies, moderate in nine, and low in three. Patients with reduced insight showed decreases in the frontal, temporal (specifically in superior temporal gyrus), precuneus, cingulate, insula, and occipital lobes cortical grey matter volume. The meta-analysis indicated a positive correlation between grey matter volume and insight in the right insula (i.e., the smaller the grey matter, the lower the insight).

CONCLUSION

Several brain areas might be involved in impaired insight in patients with non-affective psychoses. The methodologies employed, such as the applied insight scales, may have contributed to the considerable discrepancies in the findings.

Autism spectrum disorder and schizophrenia: An updated conceptual review

Autism spectrum disorder (ASD) and schizophrenia (SCZ) are separate disorders, with distinct clinical profiles and natural histories. ASD, typically diagnosed in childhood, is characterized by restricted or repetitive interests or behaviors and impaired social communication, and it tends to have a stable course. SCZ, typically diagnosed in adolescence or adulthood, is characterized by hallucinations and delusions, and tends to be associated with declining function. However, youth with ASD are three to six times more likely to develop SCZ than their neurotypical counterparts, and increasingly, research has shown that ASD and SCZ converge at several levels. We conducted a systematic review of studies since 2013 relevant to understanding this convergence, and present here a narrative synthesis of key findings, which we have organized into four broad categories: symptoms and behavior, perception and cognition, biomarkers, and genetic and environmental risk. We then discuss opportunities for future research into the phenomenology and neurobiology of overlap between ASD and SCZ. Understanding this overlap will allow for researchers, and eventually clinicians, to understand the factors that may make a child with ASD vulnerable to developing SCZ. LAY SUMMARY: Autism spectrum disorder and schizophrenia are distinct diagnoses, but people with autism and people with schizophrena share several characteristics. We review recent studies that have examined these areas of overlap, and discuss the kinds of studies we will need to better understand how these disorders are related. Understanding this will be important to help us identify which autistic children are at risk of developing schizophrenia.

Abnormal causal connectivity of left superior temporal gyrus in drug-naïve first- episode adolescent-onset schizophrenia: A resting-state fMRI study

This study aimed to investigate the alterations of causal connectivity between the brain regions in Adolescent-onset schizophrenia (AOS) patients. Thirty-two first-episode drug-naïve AOS patients and 27 healthy controls (HC) were recruited for resting-state functional MRI scanning. The brain region with the between-group difference in regional homogeneity (ReHo) values was chosen as a seed to perform the Granger causality analysis (GCA) and further detect the alterations of causal connectivity in AOS. AOS patients exhibited increased ReHo values in left superior temporal gyrus (STG) compared with HCs. Significantly decreased values of outgoing Granger causality from left STG to right superior frontal gyrus and right angular gyrus were observed in GC mapping for AOS. Significantly stronger causal outflow from left STG to right insula and stronger causal inflow from right middle occipital gyrus (MOG) to left STG were also observed in AOS patients. Based on assessments of the two strengthened causal connectivity of the left STG with insula and MOG, a discriminant model could identify all patients from controls with 94.9% accuracy. This study indicated that alterations of directional connections in left STG may play an important role in the pathogenesis of AOS and serve as potential biomarkers for the disease.

Evidence of shared and distinct functional and structural brain signatures in schizophrenia and autism spectrum disorder

Schizophrenia (SZ) and autism spectrum disorder (ASD) share considerable clinical features and intertwined historical roots. It is greatly needed to explore their similarities and differences in pathophysiologic mechanisms. We assembled a large sample size of neuroimaging data (about 600 SZ patients, 1000 ASD patients, and 1700 healthy controls) to study the shared and unique brain abnormality of the two illnesses. We analyzed multi-scale brain functional connectivity among functional networks and brain regions, intra-network connectivity, and cerebral gray matter density and volume. Both SZ and ASD showed lower functional integration within default mode and sensorimotor domains, but increased interaction between cognitive control and default mode domains. The shared abnormalties in intra-network connectivity involved default mode, sensorimotor, and cognitive control networks. Reduced gray matter volume and density in the occipital gyrus and cerebellum were observed in both illnesses. Interestingly, ASD had overall weaker changes than SZ in the shared abnormalities. Interaction between visual and cognitive regions showed disorder-unique deficits. In summary, we provide strong neuroimaging evidence of the convergent and divergent changes in SZ and ASD that correlated with clinical features.

Neuroimaging correlates of insight in non-affective psychosis: A systematic review and meta-analysis

OBJECTIVE

Neurological correlates of impaired insight in non-affective psychosis remain unclear. This study aimed to review and meta-analyze the studies assessing the grey matter volumetric correlates of impaired insight in non-affective psychosis.

METHODS

This study consisted of a systematic review of 23 studies, and a meta-analysis with SDM-PSI of the 11 studies that were whole-brain and reported maps or peaks of correlation of studies investigating the grey matter volumetric correlates of insight assessments of non-affective psychosis, PubMed and OVID datasets were independently reviewed for articles reporting neuroimaging correlates of insight in non-affective psychosis. Quality assessment was realized following previous methodological approaches for the ABC quality assessment test of imaging studies, based on two main criteria: the statistical power and the multidimensional assessment of insight. Study peaks of correlation between grey matter volume and insight were used to recreate brain correlation maps.

RESULTS

A total of 418 records were identified through database searching. Of these records, twenty-three magnetic resonance imaging (MRI) studies that used different insight scales were included. The quality of the evidence was high in 11 studies, moderate in nine, and low in three. Patients with reduced insight showed decreases in the frontal, temporal (specifically in superior temporal gyrus), precuneus, cingulate, insula, and occipital lobes cortical grey matter volume. The meta-analysis indicated a positive correlation between grey matter volume and insight in the right insula (i.e., the smaller the grey matter, the lower the insight).

CONCLUSION

Several brain areas might be involved in impaired insight in patients with non-affective psychoses. The methodologies employed, such as the applied insight scales, may have contributed to the considerable discrepancies in the findings.

Graph-Based Deep Learning for Medical Diagnosis and Analysis: Past, Present and Future

With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered, which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interacting nodes connected by edges whose weights can be determined by either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure, and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.

Structurally constrained effective brain connectivity

The relationship between structure and function is of interest in many research fields involving the study of complex biological processes. In neuroscience in particular, the fusion of structural and functional data can help to understand the underlying principles of the operational networks in the brain. To address this issue, this paper proposes a constrained autoregressive model leading to a representation of effective connectivity that can be used to better understand how the structure modulates the function. Or simply, it can be used to find novel biomarkers characterizing groups of subjects. In practice, an initial structural connectivity representation is re-weighted to explain the functional co-activations. This is obtained by minimizing the reconstruction error of an autoregressive model constrained by the structural connectivity prior. The model has been designed to also include indirect connections, allowing to split direct and indirect components in the functional connectivity, and it can be used with raw and deconvoluted BOLD signal. The derived representation of dependencies was compared to the well known dynamic causal model, giving results closer to known ground-truth. Further evaluation of the proposed effective network was performed on two typical tasks. In a first experiment the direct functional dependencies were tested on a community detection problem, where the brain was partitioned using the effective networks across multiple subjects. In a second experiment the model was validated in a case-control task, which aimed at differentiating healthy subjects from individuals with autism spectrum disorder. Results showed that using effective connectivity leads to clusters better describing the functional interactions in the community detection task, while maintaining the original structural organization, and obtaining a better discrimination in the case-control classification task.

Statistical and Machine Learning Link Selection Methods for Brain Functional Networks: Review and Comparison

Network-based representations have introduced a revolution in neuroscience, expanding the understanding of the brain from the activity of individual regions to the interactions between them. This augmented network view comes at the cost of high dimensionality, which hinders both our capacity of deciphering the main mechanisms behind pathologies, and the significance of any statistical and/or machine learning task used in processing this data. A link selection method, allowing to remove irrelevant connections in a given scenario, is an obvious solution that provides improved utilization of these network representations. In this contribution we review a large set of statistical and machine learning link selection methods and evaluate them on real brain functional networks. Results indicate that most methods perform in a qualitatively similar way, with NBS (Network Based Statistics) winning in terms of quantity of retained information, AnovaNet in terms of stability and ExT (Extra Trees) in terms of lower computational cost. While machine learning methods are conceptually more complex than statistical ones, they do not yield a clear advantage. At the same time, the high heterogeneity in the set of links retained by each method suggests that they are offering complementary views to the data. The implications of these results in neuroscience tasks are finally discussed.

Performance of machine learning classification models of autism using resting-state fMRI is contingent on sample heterogeneity

Autism spectrum disorders (ASDs) are heterogeneous neurodevelopmental conditions. In fMRI studies, including most machine learning studies seeking to distinguish ASD from typical developing (TD) samples, cohorts differing in gender and symptom severity composition are often treated statistically as one "ASD group". Using resting-state functional connectivity (FC) data, we implemented random forest to build diagnostic classifiers in 4 ASD samples including a total of 656 participants (N_ASD = 306, N_TD = 350, ages 6-18). Groups were manipulated to titrate heterogeneity of gender and symptom severity and partially overlapped. Each sample differed on inclusionary criteria: (1) all genders, unrestricted severity range; (2) only male participants, unrestricted severity; (3) all genders, higher severity only; (4) only male participants, higher severity. Each set consisted of 200 participants per group (ASD, TD; matched on age and head motion), 160 for training and 40 for validation. FMRI time series from 237 regions of interest (ROIs) were Pearson correlated in a 237×237 FC matrix and classifiers were built using random forest in training samples. Classification accuracies in validation samples were 62.5%, 65%, 70% and 73.75%, respectively for samples 1-4. Connectivity within cingulo-opercular task control (COTC) network, and between COTC ROIs and default mode and dorsal attention network contributed overall most informative features, but features differed across sets. Findings suggest that diagnostic classifiers vary depending on ASD sample composition. Specifically, greater homogeneity of samples regarding gender and symptom severity enhances classifier performance. However, given the true heterogeneity of ASDs, performance metrics alone may not adequately reflect classifier utility.

Impact of Machine Learning Pipeline Choices in Autism Prediction From Functional Connectivity Data

Autism Spectrum Disorder (ASD) is a largely prevalent neurodevelopmental condition with a big social and economical impact affecting the entire life of families. There is an intense search for biomarkers that can be assessed as early as possible in order to initiate treatment and preparation of the family to deal with the challenges imposed by the condition. Brain imaging biomarkers have special interest. Specifically, functional connectivity data extracted from resting state functional magnetic resonance imaging (rs-fMRI) should allow to detect brain connectivity alterations. Machine learning pipelines encompass the estimation of the functional connectivity matrix from brain parcellations, feature extraction, and building classification models for ASD prediction. The works reported in the literature are very heterogeneous from the computational and methodological point of view. In this paper, we carry out a comprehensive computational exploration of the impact of the choices involved while building these machine learning pipelines. Specifically, we consider six brain parcellation definitions, five methods for functional connectivity matrix construction, six feature extraction/selection approaches, and nine classifier building algorithms. We report the prediction performance sensitivity to each of these choices, as well as the best results that are comparable with the state of the art.

Dynamic functional network reconfiguration underlying the pathophysiology of schizophrenia and autism spectrum disorder

The dynamics of the human brain span multiple spatial scales, from connectivity associated with a specific region/network to the global organization, each representing different brain mechanisms. Yet brain reconfigurations at different spatial scales are seldom explored and whether they are associated with the neural aspects of brain disorders is far from understood. In this study, we introduced a dynamic measure called step-wise functional network reconfiguration (sFNR) to characterize how brain configuration rewires at different spatial scales. We applied sFNR to two independent datasets, one includes 160 healthy controls (HCs) and 151 patients with schizophrenia (SZ) and the other one includes 314 HCs and 255 individuals with autism spectrum disorder (ASD). We found that both SZ and ASD have increased whole-brain sFNR and sFNR between cerebellar and subcortical/sensorimotor domains. At the ICN level, the abnormalities in SZ are mainly located in ICNs within subcortical, sensory, and cerebellar domains, while the abnormalities in ASD are more widespread across domains. Interestingly, the overlap SZ-ASD abnormality in sFNR between cerebellar and sensorimotor domains was correlated with the reasoning-problem-solving performance in SZ (r = -.1652, p = .0058) as well as the Autism Diagnostic Observation Schedule in ASD (r = .1853, p = .0077). Our findings suggest that dynamic reconfiguration deficits may represent a key intersecting point for SZ and ASD. The investigation of brain dynamics at different spatial scales can provide comprehensive insights into the functional reconfiguration, which might advance our knowledge of cognitive decline and other pathophysiology in brain disorders.

Diagnostic classification of autism using resting-state fMRI data improves with full correlation functional brain connectivity compared to partial correlation

BACKGROUND

Autism Spectrum Disorder (ASD) is a neurodevelopmental disability with altered connectivity in brain networks.

NEW METHOD

In this study, brain connections in Resting-state functional Magnetic Resonance Imaging (Rs-fMRI) of ASD and Typical Developing (TD) are analyzed by partial and full correlation methods such as Gaussian Graphical Least Absolute Shrinkage and Selection Operator (GLASSO), Max-Det Matrix Completion (MDMC), and Pearson Correlation Co-Efficient (PCCE). We investigated Functional Connectivity (FC) of ASD and TD brain from 238 functionally defined regions of interest. Furthermore, we constructed a series of feature sets by applying conditional random forests and conditional permutation importance. We built classifier models by Random Forest (RF), Oblique RF (ORF), Support Vector Machine (SVM), and Convolutional Neural Network (CNN) for each feature set. FC features are ranked based on p-value and we analyzed the top 20 FC features.

RESULTS

We achieved a single-trial test accuracy of 72.5 %, though MDMC-SVM and PCCE-CNN pipelines. Further, PCCE-CNN pipeline gives better average test accuracy (70.31 %) and area under the curve (0.73) compared to other pipelines. We found that top-20 PCCE based FC features are from networks such as Dorsal Attention (DA), Cingulo-Opercular Task Control (COTC), somatosensory motor hand and subcortical. In addition, among top 20 PCCE features, many FC links are found between COTC and DA (4 connections) which helped to discriminate the ASD and TD.

COMPARISON WITH EXISTING METHODS AND CONCLUSIONS

The generalized classifier models built in our study for highly heterogeneous participants perform better than previous studies with similar data sets and diagnostic groups.

Altered empathy-related resting-state functional connectivity in adolescents with early-onset schizophrenia and autism spectrum disorders

Empathy refers to the ability to understand other people's feelings and reacting emotionally to others. Impaired empathy has been reported in both individuals with schizophrenia and autism spectrum disorders (ASD). Despite overlaps, few studies have directly examined the neural mechanisms of impaired empathy in these two clinical groups. We used resting-state fMRI to investigate the neural correlates of empathic functioning in adolescents with ASD (N = 11), early-onset schizophrenia (EOS) (N = 20), and typically developing (TD) controls (N = 26). Their parents completed the Griffith Empathy Measure (GEM) to assess the adolescents' empathic capacity. We found that EOS and ASD participants both exhibited impaired empathy as measured by the GEM, especially in cognitive empathy (post-hoc ps < 0.05). Regions-of-interest-based functional connectivity revealed decreased connectivity between the salience network (SN) (i.e., the anterior insula and the anterior cingulate cortex) and core regions of the mentalizing network (e.g., the temporal-parietal junction and the precuneus), and among the SN and the bilateral superior temporal gyri (STG) and the left cerebellum in EOS participants. Subsequent comparisons revealed reduced grey matter volume in the STG bilaterally in both clinical groups. Increased resting-state functional connectivity within the social brain network was correlated with higher parent-reported scores of empathic capacity in TD adolescents, but such a brain-phenotype relationship was absent in the two clinical groups. These findings indicate that structural alterations and disturbed resting-state functional connectivity in the core empathy network may be the neural correlates of social cognitive deficits in individuals with EOS and ASD.

Altered dynamic effective connectivity of the default mode network in newly diagnosed drug-naïve juvenile myoclonic epilepsy

Juvenile myoclonic epilepsy (JME) has been repeatedly revealed to be associated with brain dysconnectivity in the default mode network (DMN). However, the implicit assumption of stationary and nondirectional functional connectivity (FC) in most previous resting-state fMRI studies raises an open question of JME-related aberrations in dynamic causal properties of FC. Here, we introduces an empirical method incorporating sliding-window approach and a multivariate Granger causality analysis to investigate, for the first time, the reorganization of dynamic effective connectivity (DEC) in DMN for patients with JME. DEC was obtained from resting-state fMRI of 34 patients with newly diagnosed and drug-naïve JME and 34 matched controls. Through clustering analysis, we found two distinct states that characterize the DEC patterns (i.e., a less frequent, strongly connected state (State 1) and a more frequent, weakly connected state (State 2)). Patients showed altered ECs within DMN subnetworks in the State 2, whereas abnormal ECs between DMN subnetworks were found in the State 1. Furthermore, we observed that the causal influence flows of the medial prefrontal cortex and angular gyrus were altered in a manner of state specificity, and associated with disease severity of patients. Overall, our findings extend the dysconnectivity hypothesis in JME from static to dynamic causal FC and demonstrate that aberrant DEC may underlie abnormal brain function in JME at early phase of illness.

A deep learning fusion model for brain disorder classification: Application to distinguishing schizophrenia and autism spectrum disorder

Deep learning has shown a great promise in classifying brain disorders due to its powerful ability in learning optimal features by nonlinear transformation. However, given the high-dimension property of neuroimaging data, how to jointly exploit complementary information from multimodal neuroimaging data in deep learning is difficult. In this paper, we propose a novel multilevel convolutional neural network (CNN) fusion method that can effectively combine different types of neuroimage-derived features. Importantly, we incorporate a sequential feature selection into the CNN model to increase the feature interpretability. To evaluate our method, we classified two symptom-related brain disorders using large-sample multi-site data from 335 schizophrenia (SZ) patients and 380 autism spectrum disorder (ASD) patients within a cross-validation procedure. Brain functional networks, functional network connectivity, and brain structural morphology were employed to provide possible features. As expected, our fusion method outperformed the CNN model using only single type of features, as our method yielded higher classification accuracy (with mean accuracy >85%) and was more reliable across multiple runs in differentiating the two groups. We found that the default mode, cognitive control, and subcortical regions contributed more in their distinction. Taken together, our method provides an effective means to fuse multimodal features for the diagnosis of different psychiatric and neurological disorders.

Measuring the Non-linear Directed Information Flow in Schizophrenia by Multivariate Transfer Entropy

People living with schizophrenia (SCZ) experience severe brain network deterioration. The brain is constantly fizzling with non-linear causal activities measured by electroencephalogram (EEG) and despite the variety of effective connectivity methods, only few approaches can quantify the direct non-linear causal interactions. To circumvent this problem, we are motivated to quantitatively measure the effective connectivity by multivariate transfer entropy (MTE) which has been demonstrated to be able to capture both linear and non-linear causal relationships effectively. In this work, we propose to construct the EEG effective network by MTE and further compare its performance with the Granger causal analysis (GCA) and Bivariate transfer entropy (BVTE). The simulation results quantitatively show that MTE outperformed GCA and BVTE under varied signal-to-noise conditions, edges recovered, sensitivity, and specificity. Moreover, its applications to the P300 task EEG of healthy controls (HC) and SCZ patients further clearly show the deteriorated network interactions of SCZ, compared to that of the HC. The MTE provides a novel tool to potentially deepen our knowledge of the brain network deterioration of the SCZ.

Accuracy of Machine Learning Algorithms for the Diagnosis of Autism Spectrum Disorder: Systematic Review and Meta-Analysis of Brain Magnetic Resonance Imaging Studies

BACKGROUND

In the recent years, machine learning algorithms have been more widely and increasingly applied in biomedical fields. In particular, their application has been drawing more attention in the field of psychiatry, for instance, as diagnostic tests/tools for autism spectrum disorder (ASD). However, given their complexity and potential clinical implications, there is an ongoing need for further research on their accuracy.

OBJECTIVE

This study aimed to perform a systematic review and meta-analysis to summarize the available evidence for the accuracy of machine learning algorithms in diagnosing ASD.

METHODS

The following databases were searched on November 28, 2018: MEDLINE, EMBASE, CINAHL Complete (with Open Dissertations), PsycINFO, and Institute of Electrical and Electronics Engineers Xplore Digital Library. Studies that used a machine learning algorithm partially or fully for distinguishing individuals with ASD from control subjects and provided accuracy measures were included in our analysis. The bivariate random effects model was applied to the pooled data in a meta-analysis. A subgroup analysis was used to investigate and resolve the source of heterogeneity between studies. True-positive, false-positive, false-negative, and true-negative values from individual studies were used to calculate the pooled sensitivity and specificity values, draw Summary Receiver Operating Characteristics curves, and obtain the area under the curve (AUC) and partial AUC (pAUC).

RESULTS

A total of 43 studies were included for the final analysis, of which a meta-analysis was performed on 40 studies (53 samples with 12,128 participants). A structural magnetic resonance imaging (sMRI) subgroup meta-analysis (12 samples with 1776 participants) showed a sensitivity of 0.83 (95% CI 0.76-0.89), a specificity of 0.84 (95% CI 0.74-0.91), and AUC/pAUC of 0.90/0.83. A functional magnetic resonance imaging/deep neural network subgroup meta-analysis (5 samples with 1345 participants) showed a sensitivity of 0.69 (95% CI 0.62-0.75), specificity of 0.66 (95% CI 0.61-0.70), and AUC/pAUC of 0.71/0.67.

CONCLUSIONS

The accuracy of machine learning algorithms for diagnosis of ASD was considered acceptable by few accuracy measures only in cases of sMRI use; however, given the many limitations indicated in our study, further well-designed studies are warranted to extend the potential use of machine learning algorithms to clinical settings.

TRIAL REGISTRATION

PROSPERO CRD42018117779; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=117779.

Learning Brain Effective Connectivity Network Structure Using Ant Colony Optimization Combining With Voxel Activation Information

Learning brain effective connectivity (EC) networks from functional magnetic resonance imaging (fMRI) data has become a new hot topic in the neuroinformatics field. However, how to accurately and efficiently learn brain EC networks is still a challenging problem. In this paper, we propose a new algorithm to learn the brain EC network structure using ant colony optimization (ACO) algorithm combining with voxel activation information, named as VACOEC. First, VACOEC uses the voxel activation information to measure the independence between each pair of brain regions and effectively restricts the space of candidate solutions, which makes many unnecessary searches of ants be avoided. Then, by combining the global score increase of a solution with the voxel activation information, a new heuristic function is designed to guide the process of ACO to search for the optimal solution. The experimental results on simulated datasets show that the proposed method can accurately and efficiently identify the directions of the brain EC networks. Moreover, the experimental results on real-world data show that patients with Alzheimers disease (AD) exhibit decreased effective connectivity not only in the intra-network within the default mode network (DMN) and salience network (SN), but also in the inter-network between DMN and SN, compared with normal control (NC) subjects. The experimental results demonstrate that VACOEC is promising for practical applications in the neuroimaging studies of geriatric subjects and neurological patients.

Application of Graph Theory for Identifying Connectivity Patterns in Human Brain Networks: A Systematic Review

Background: Analysis of the human connectome using functional magnetic resonance imaging (fMRI) started in the mid-1990s and attracted increasing attention in attempts to discover the neural underpinnings of human cognition and neurological disorders. In general, brain connectivity patterns from fMRI data are classified as statistical dependencies (functional connectivity) or causal interactions (effective connectivity) among various neural units. Computational methods, especially graph theory-based methods, have recently played a significant role in understanding brain connectivity architecture. Objectives: Thanks to the emergence of graph theoretical analysis, the main purpose of the current paper is to systematically review how brain properties can emerge through the interactions of distinct neuronal units in various cognitive and neurological applications using fMRI. Moreover, this article provides an overview of the existing functional and effective connectivity methods used to construct the brain network, along with their advantages and pitfalls. Methods: In this systematic review, the databases Science Direct, Scopus, arXiv, Google Scholar, IEEE Xplore, PsycINFO, PubMed, and SpringerLink are employed for exploring the evolution of computational methods in human brain connectivity from 1990 to the present, focusing on graph theory. The Cochrane Collaboration's tool was used to assess the risk of bias in individual studies. Results: Our results show that graph theory and its implications in cognitive neuroscience have attracted the attention of researchers since 2009 (as the Human Connectome Project launched), because of their prominent capability in characterizing the behavior of complex brain systems. Although graph theoretical approach can be generally applied to either functional or effective connectivity patterns during rest or task performance, to date, most articles have focused on the resting-state functional connectivity. Conclusions: This review provides an insight into how to utilize graph theoretical measures to make neurobiological inferences regarding the mechanisms underlying human cognition and behavior as well as different brain disorders.

Altered resting-state dynamics in autism spectrum disorder: Causal to the social impairment?

Autism spectrum disorder (ASD) is characterized by profound impairments in social abilities and by restricted interests and repetitive behaviors. Much work in the past decade has been dedicated to understanding the brain-bases of ASD, and in the context of resting-state functional connectivity fMRI in high-functioning adolescents and adults, the field has established a set of reliable findings: decreased cortico-cortical interactions among brain regions thought to be engaged in social processing, along with a simultaneous increase in thalamo-cortical and striato-cortical interactions. However, few studies have attempted to manipulate these altered patterns, leading to the question of whether such patterns are actually causally involved in producing the corresponding behavioral impairments. We discuss a few such recent attempts in the domains of fMRI neurofeedback and overt social interaction during scanning, and we conclude that the evidence of causal involvement is somewhat mixed. We highlight the potential role of the thalamus and striatum in ASD and emphasize the need for studies that directly compare scanning during multiple cognitive states in addition to the resting-state.

MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis

The analysis of the brain from a connectivity perspective is revealing novel insights into brain structure and function. Discovery is, however, hindered by the lack of prior knowledge used to make hypotheses. Additionally, exploratory data analysis is made complex by the high dimensionality of data. Indeed, to assess the effect of pathological states on brain networks, neuroscientists are often required to evaluate experimental effects in case-control studies, with hundreds of thousands of connections. In this paper, we propose an approach to identify the multivariate relationships in brain connections that characterize two distinct groups, hence permitting the investigators to immediately discover the subnetworks that contain information about the differences between experimental groups. In particular, we are interested in data discovery related to connectomics, where the connections that characterize differences between two groups of subjects are found. Nevertheless, those connections do not necessarily maximize the accuracy in classification since this does not guarantee reliable interpretation of specific differences between groups. In practice, our method exploits recent machine learning techniques employing sparsity to deal with weighted networks describing the whole-brain macro connectivity. We evaluated our technique on functional and structural connectomes from human and murine brain data. In our experiments, we automatically identified disease-relevant connections in datasets with supervised and unsupervised anatomy-driven parcellation approaches and by using high-dimensional datasets.

Application of Graph Theory for Identifying Connectivity Patterns in Human Brain Networks: A Systematic Review

Background: Analysis of the human connectome using functional magnetic resonance imaging (fMRI) started in the mid-1990s and attracted increasing attention in attempts to discover the neural underpinnings of human cognition and neurological disorders. In general, brain connectivity patterns from fMRI data are classified as statistical dependencies (functional connectivity) or causal interactions (effective connectivity) among various neural units. Computational methods, especially graph theory-based methods, have recently played a significant role in understanding brain connectivity architecture. Objectives: Thanks to the emergence of graph theoretical analysis, the main purpose of the current paper is to systematically review how brain properties can emerge through the interactions of distinct neuronal units in various cognitive and neurological applications using fMRI. Moreover, this article provides an overview of the existing functional and effective connectivity methods used to construct the brain network, along with their advantages and pitfalls. Methods: In this systematic review, the databases Science Direct, Scopus, arXiv, Google Scholar, IEEE Xplore, PsycINFO, PubMed, and SpringerLink are employed for exploring the evolution of computational methods in human brain connectivity from 1990 to the present, focusing on graph theory. The Cochrane Collaboration's tool was used to assess the risk of bias in individual studies. Results: Our results show that graph theory and its implications in cognitive neuroscience have attracted the attention of researchers since 2009 (as the Human Connectome Project launched), because of their prominent capability in characterizing the behavior of complex brain systems. Although graph theoretical approach can be generally applied to either functional or effective connectivity patterns during rest or task performance, to date, most articles have focused on the resting-state functional connectivity. Conclusions: This review provides an insight into how to utilize graph theoretical measures to make neurobiological inferences regarding the mechanisms underlying human cognition and behavior as well as different brain disorders.

Increased scale-free dynamics in salience network in adult high-functioning autism

Autism spectrum disorder (ASD) is clinically characterized by extremely slow and inflexible behavior. The neuronal mechanisms of these symptoms remain unclear though. Using fMRI, we investigate the resting state's temporal structure in the frequency domain (scale-free activity as measured with Power-Law Exponent, PLE, and Spectral Entropy, SE) and temporal variance (neural variability) in high-functioning, adult ASD comparing them with schizophrenic and neurotypical subjects. We show that ASD is characterized by high PLE in salience network, especially in dorsal anterior cingulate. This increase in PLE was 1) specific for salience network; 2) independent of other measures such as neuronal variability/SD and functional connectivity, which did not show any significant difference; 3) detected in two independent samples of ASD but not in the schizophrenia sample. Among salience network subregions, dorsal anterior cingulate cortex exhibited PLE differences between ASD and neurotypicals in both samples, showing high robustness in ROC curves values. Salience network abnormal temporal structure was confirmed by SE, which was strongly anticorrelated with PLE and thus decreased in ASD. Taken together, our findings show abnormal temporal structure (but normal temporal variance) in resting state salience network in adult high-functioning ASD. The abnormally high PLE indicates a relative predominance of slower over faster frequencies, which may underlie the slow adaptation to unexpected changes and the inflexible behavior observed in autistic individuals. The specificity of abnormal PLE in salience network suggests its potential utility as biomarker in ASD.

Leo Kanner and autism: a 75-year perspective

In 1943, Leo Kanner published the first systematic description of early infantile autism. He concluded that this was a neurodevelopmental disorder and that 'these children have come into the world with an innate inability to form the usual, biologically provided contact with people'. Moreover, his astute descriptions of parental behavior in his first publications were prescient and underlie later recognition of the importance of genetics. Our understanding has grown over the ensuing years with revisions in diagnostic classification, recognition of the broader autism phenotype in families, appreciation of the importance of developmental models, advances in genetic methodology, better understanding of the relationship to intellectual deficits, recognition of syndromic autism in neurogenetic sydromes, advances in neuroimaging, and advances in animal models, both mutant mouse models and transgenic non human primate models. Kanner recognized diagnostic heterogeneity and opined that the children had not read those diagnostic manuals and did not easily fall into clear cut categories. Such heterogeneity continues to confound our diagnostic efforts. Always an advocate for children, when reviewing the DSM III criteria in 1980, Kanner emphasized that no matter how well developed our criteria each child must be treated as a unique person.