Modelling cognitive loads in schizophrenia by means of new functional dynamic indexes

A new directionality index based on high-resolution joint symbolic dynamics to assess information transfer in multivariate networks

The detection and quantification of coupling strength and direction are important aspects for achieving a deeper understanding of physiological regulatory processes in the field of network physiology. Due to the limitations of established approaches, we developed directionality indices based on simple mathematical symbolization principles and simple computational procedures that allow a quick and comprehensive understanding of the underlying couplings. We introduced a new directionality index (D HRJSD) derived from the pattern family density matrix of the High-Resolution Joint Symbolic Dynamics (HRJSD) approach and its multivariate version (mHRJSD) to determine coupling direction and driver-response relationships. The mHRJSD approach contains the multivariate directionality index D mHRJSD (D mHRJSD(x,y|z), D mHRJSD(x,z|y), and D mHRJSD(y,z|x)), allowing us to determine the primary driver **D mHRJSD, the secondary driver *D mHRJSD, and the dominant responder - D mHRJSD in multivariate systems that are at least weakly coupled. Different linear and non-linear bi- and multivariate coupled systems (Gaussian autoregressive models) with different mutual influences were generated to validate these indices. The simulation results showed that D HRJSD was able to correctly detect the dominant coupling direction in linear bivariate coupled systems but was partly able to detect the dominant coupling direction in non-linear bivariate coupled systems. The proposed directionality index D mHRJSD derived from the mHRJSD approach is able to correctly detect the driver-responder relationships in linear coupled systems. The main advantages of the newly introduced directionality indices include their insensitivity to non-stationary time series, their ability to capture couplings through a simple, fast, and easy-to-implement symbolization procedure, and their scale invariance. Additionally, they are independent of time series length, model order selection, and the procedure for determining their significance level.

Resolving heterogeneity in dynamics of synchronization stability within the salience network in autism spectrum disorder

BACKGROUND

Heterogeneity in resting-state functional connectivity (FC) are one of the characteristics of autism spectrum disorder (ASD). Traditional resting-state FC primarily focuses on linear correlations, ignoring the nonlinear properties involved in synchronization between networks or brain regions.

METHODS

In the present study, the cross-recurrence quantification analysis, a nonlinear method based on dynamical systems, was utilized to quantify the synchronization stability between brain regions within the salience network (SN) of ASD. Using the resting-state functional magnetic resonance imaging data of 207 children (ASD/typically-developing controls (TC): 105/102) in Autism Brain Imaging Data Exchange database, we analyzed the laminarity and trapping time differences of the synchronization stability between the ASD subtype derived by a K-means clustering analysis and the TC group, and examined the relationship between synchronization stability and the severity of clinical symptoms of the ASD subtypes.

RESULTS

Based on the synchronization stability within the SN of ASD, we identified two subtypes that showed opposite changes in synchronization stability relative to the TC group. In addition, the synchronization stability of ASD subtypes 1 and 2 can predict the social interaction and communication impairments, respectively.

CONCLUSIONS

These findings reveal that ASD subgroups with different patterns of synchronization stability within the SN appear distinct clinical symptoms, and highlight the importance of exploring the potential neural mechanism of ASD from a nonlinear perspective.

Unveiling the potential of machine learning in schizophrenia diagnosis: A meta-analytic study of task-based neuroimaging data

The emergence of machine learning (ML) techniques has opened up new avenues for identifying biomarkers associated with schizophrenia (SCZ) using task-related fMRI (t-fMRI) designs. To evaluate the effectiveness of this approach, we conducted a comprehensive meta-analysis of 31 t-fMRI studies using a bivariate model. Our findings revealed a high overall sensitivity of 0.83 and specificity of 0.82 for t-fMRI studies. Notably, neuropsychological domains modulated the classification performance, with selective attention demonstrating a significantly higher specificity than working memory (β = 0.98, z = 2.11, P = 0.04). Studies involving older, chronic patients with SCZ reported higher sensitivity (P <0.015) and specificity (P <0.001) than those involving younger, first-episode patients or high-risk individuals for psychosis. Additionally, we found that the severity of negative symptoms was positively associated with the specificity of the classification model (β = 7.19, z = 2.20, P = 0.03). Taken together, these results support the potential of using task-based fMRI data in combination with machine learning techniques to identify biomarkers related to symptom outcomes in SCZ, providing a promising avenue for improving diagnostic accuracy and treatment efficacy. Future attempts to deploy ML classification should consider the factors of algorithm choice, data quality and quantity, as well as issues related to generalization.

A miR-137-Related Biological Pathway of Risk for Schizophrenia Is Associated With Human Brain Emotion Processing

BACKGROUND

miR-137 is a microRNA involved in brain development, regulating neurogenesis and neuronal maturation. Genome-wide association studies have implicated miR-137 in schizophrenia risk but do not explain its involvement in brain function and underlying biology. Polygenic risk for schizophrenia mediated by miR-137 targets is associated with working memory, although other evidence points to emotion processing. We characterized the functional brain correlates of miR-137 target genes associated with schizophrenia while disentangling previously reported associations of miR-137 targets with working memory and emotion processing.

METHODS

Using RNA sequencing data from postmortem prefrontal cortex (N = 522), we identified a coexpression gene set enriched for miR-137 targets and schizophrenia risk genes. We validated the relationship of this set to miR-137 in vitro by manipulating miR-137 expression in neuroblastoma cells. We translated this gene set into polygenic scores of coexpression prediction and associated them with functional magnetic resonance imaging activation in healthy volunteers (n1 = 214; n2 = 136; n3 = 2075; n4 = 1800) and with short-term treatment response in patients with schizophrenia (N = 427).

RESULTS

In 4652 human participants, we found that 1) schizophrenia risk genes were coexpressed in a biologically validated set enriched for miR-137 targets; 2) increased expression of miR-137 target risk genes was mediated by low prefrontal miR-137 expression; 3) alleles that predict greater gene set coexpression were associated with greater prefrontal activation during emotion processing in 3 independent healthy cohorts (n1, n2, n3) in interaction with age (n4); and 4) these alleles predicted less improvement in negative symptoms following antipsychotic treatment in patients with schizophrenia.

CONCLUSIONS

The functional translation of miR-137 target gene expression linked with schizophrenia involves the neural substrates of emotion processing.

A robust framework to investigate the reliability and stability of explainable artificial intelligence markers of Mild Cognitive Impairment and Alzheimer's Disease

In clinical practice, several standardized neuropsychological tests have been designed to assess and monitor the neurocognitive status of patients with neurodegenerative diseases such as Alzheimer's disease. Important research efforts have been devoted so far to the development of multivariate machine learning models that combine the different test indexes to predict the diagnosis and prognosis of cognitive decline with remarkable results. However, less attention has been devoted to the explainability of these models. In this work, we present a robust framework to (i) perform a threefold classification between healthy control subjects, individuals with cognitive impairment, and subjects with dementia using different cognitive indexes and (ii) analyze the variability of the explainability SHAP values associated with the decisions taken by the predictive models. We demonstrate that the SHAP values can accurately characterize how each index affects a patient's cognitive status. Furthermore, we show that a longitudinal analysis of SHAP values can provide effective information on Alzheimer's disease progression.

Exploring the Alterations in the Distribution of Neural Network Weights in Dementia Due to Alzheimer's Disease

Alzheimer's disease (AD) is a neurodegenerative disorder which has become an outstanding social problem. The main objective of this study was to evaluate the alterations that dementia due to AD elicits in the distribution of functional network weights. Functional connectivity networks were obtained using the orthogonalized Amplitude Envelope Correlation (AEC), computed from source-reconstructed resting-state eletroencephalographic (EEG) data in a population formed by 45 cognitive healthy elderly controls, 69 mild cognitive impaired (MCI) patients and 81 AD patients. Our results indicated that AD induces a progressive alteration of network weights distribution; specifically, the Shannon entropy (SE) of the weights distribution showed statistically significant between-group differences (p < 0.05, Kruskal-Wallis test, False Discovery Rate corrected). Furthermore, an in-depth analysis of network weights distributions was performed in delta, alpha, and beta-1 frequency bands to discriminate the weight ranges showing statistical differences in SE. Our results showed that lower and higher weights were more affected by the disease, whereas mid-range connections remained unchanged. These findings support the importance of performing detailed analyses of the network weights distribution to further understand the impact of AD progression on functional brain activity.

ISOMAP and machine learning algorithms for the construction of embedded functional connectivity networks of anatomically separated brain regions from resting state fMRI data of patients with Schizophrenia

We construct Functional Connectivity Networks (FCN) from resting state fMRI (rsfMRI) recordings towards the classification of brain activity between healthy and schizophrenic subjects using a publicly available dataset (the COBRE dataset) of 145 subjects (74 healthy controls and 71 schizophrenic subjects). First, we match the anatomy of the brain of each individual to the Desikan-Killiany brain atlas. Then, we use the conventional approach of correlating the parcellated time series to construct FCN and ISOMAP, a nonlinear manifold learning algorithm to produce low-dimensional embeddings of the correlation matrices. For the classification analysis, we computed five key local graph-theoretic measures of the FCN and used the LASSO and Random Forest (RF) algorithms for feature selection. For the classification we used standard linear Support Vector Machines. The classification performance is tested by a double cross-validation scheme (consisting of an outer and an inner loop of "Leave one out" cross-validation (LOOCV)). The standard cross-correlation methodology produced a classification rate of 73.1%, while ISOMAP resulted in 79.3%, thus providing a simpler model with a smaller number of features as chosen from LASSO and RF, namely the participation coefficient of the right thalamus and the strength of the right lingual gyrus.

Synergistic effects of HIV and marijuana use on functional brain network organization

HIV is associated with disruptions in cognition and brain function. Marijuana use is highly prevalent in HIV but its effects on resting brain function in HIV are unknown. Brain function can be characterized by brain activity that is correlated between regions over time, called functional connectivity. Neuropsychiatric disorders are increasingly being characterized by disruptions in such connectivity. We examined the synergistic effects of HIV and marijuana use on functional whole-brain network organization during resting state. Our sample included 78 adults who differed on HIV and marijuana status (19 with co-occurring HIV and marijuana use, 20 HIV-only, 17 marijuana-only, and 22 controls). We examined differences in local and long-range brain network organization using eight graph theoretical metrics: transitivity, local efficiency, within-module degree, modularity, global efficiency, strength, betweenness, and participation coefficient. Local and long-range connectivity were similar between the co-occurring HIV and marijuana use and control groups. In contrast, the HIV-only and marijuana-only groups were both associated with disruptions in brain network organization. These results suggest that marijuana use in HIV may normalize disruptions in brain network organization observed in persons with HIV. However, future work is needed to determine whether this normalization is suggestive of a beneficial or detrimental effect of marijuana on cognitive functioning in HIV.

Association between Structural Connectivity and Generalized Cognitive Spectrum in Alzheimer's Disease

Modeling disease progression through the cognitive scores has become an attractive challenge in the field of computational neuroscience due to its importance for early diagnosis of Alzheimer's disease (AD). Several scores such as Alzheimer's Disease Assessment Scale cognitive total score, Mini Mental State Exam score and Rey Auditory Verbal Learning Test provide a quantitative assessment of the cognitive conditions of the patients and are commonly used as objective criteria for clinical diagnosis of dementia and mild cognitive impairment (MCI). On the other hand, connectivity patterns extracted from diffusion tensor imaging (DTI) have been successfully used to classify AD and MCI subjects with machine learning algorithms proving their potential application in the clinical setting. In this work, we carried out a pilot study to investigate the strength of association between DTI structural connectivity of a mixed ADNI cohort and cognitive spectrum in AD. We developed a machine learning framework to find a generalized cognitive score that summarizes the different functional domains reflected by each cognitive clinical index and to identify the connectivity biomarkers more significantly associated with the score. The results indicate that the efficiency and the centrality of some regions can effectively track cognitive impairment in AD showing a significant correlation with the generalized cognitive score (R = 0.7).

Predicting brain age with complex networks: From adolescence to adulthood

In recent years, several studies have demonstrated that machine learning and deep learning systems can be very useful to accurately predict brain age. In this work, we propose a novel approach based on complex networks using 1016 T1-weighted MRI brain scans (in the age range 7-64years). We introduce a structural connectivity model of the human brain: MRI scans are divided in rectangular boxes and Pearson's correlation is measured among them in order to obtain a complex network model. Brain connectivity is then characterized through few and easy-to-interpret centrality measures; finally, brain age is predicted by feeding a compact deep neural network. The proposed approach is accurate, robust and computationally efficient, despite the large and heterogeneous dataset used. Age prediction accuracy, in terms of correlation between predicted and actual age r=0.89and Mean Absolute Error MAE =2.19years, compares favorably with results from state-of-the-art approaches. On an independent test set including 262 subjects, whose scans were acquired with different scanners and protocols we found MAE =2.52. The only imaging analysis steps required in the proposed framework are brain extraction and linear registration, hence robust results are obtained with a low computational cost. In addition, the network model provides a novel insight on aging patterns within the brain and specific information about anatomical districts displaying relevant changes with aging.

Multifractal and Entropy-Based Analysis of Delta Band Neural Activity Reveals Altered Functional Connectivity Dynamics in Schizophrenia

Dynamic functional connectivity (DFC) was established in the past decade as a potent approach to reveal non-trivial, time-varying properties of neural interactions – such as their multifractality or information content –, that otherwise remain hidden from conventional static methods. Several neuropsychiatric disorders were shown to be associated with altered DFC, with schizophrenia (SZ) being one of the most intensely studied among such conditions. Here we analyzed resting-state electroencephalography recordings of 14 SZ patients and 14 age- and gender-matched healthy controls (HC). We reconstructed dynamic functional networks from delta band (0.5–4 Hz) neural activity and captured their spatiotemporal dynamics in various global network topological measures. The acquired network measure time series were made subject to dynamic analyses including multifractal analysis and entropy estimation. Besides group-level comparisons, we built a classifier to explore the potential of DFC features in classifying individual cases. We found stronger delta-band connectivity, as well as increased variance of DFC in SZ patients. Surrogate data testing verified the true multifractal nature of DFC in SZ, with patients expressing stronger long-range autocorrelation and degree of multifractality when compared to controls. Entropy analysis indicated reduced temporal complexity of DFC in SZ. When using these indices as features, an overall cross-validation accuracy surpassing 89% could be achieved in classifying individual cases. Our results imply that dynamic features of DFC such as its multifractal properties and entropy are potent markers of altered neural dynamics in SZ and carry significant potential not only in better understanding its pathophysiology but also in improving its diagnosis. The proposed framework is readily applicable for neuropsychiatric disorders other than schizophrenia.

Extensive Evaluation of Morphological Statistical Harmonization for Brain Age Prediction

Characterizing both neurodevelopmental and aging brain structural trajectories is important for understanding normal biological processes and atypical patterns that are related to pathological phenomena. Initiatives to share open access morphological data contributed significantly to the advance in brain structure characterization. Indeed, such initiatives allow large brain morphology multi-site datasets to be shared, which increases the statistical sensitivity of the outcomes. However, using neuroimaging data from multi-site studies requires harmonizing data across the site to avoid bias. In this work we evaluated three different harmonization techniques on the Autism Brain Imaging Data Exchange (ABIDE) dataset for age prediction analysis in two groups of subjects (i.e., controls and autism spectrum disorder). We extracted the morphological features from T1-weighted images of a mixed cohort of 654 subjects acquired from 17 sites to predict the biological age of the subjects using three machine learning regression models. A machine learning framework was developed to quantify the effects of the different harmonization strategies on the final performance of the models and on the set of morphological features that are relevant to the age prediction problem in both the presence and absence of pathology. The results show that, even if two harmonization strategies exhibit similar accuracy of predictive models, a greater mismatch occurs between the sets of most age-related predictive regions for the Autism Spectrum Disorder (ASD) subjects. Thus, we propose to use a stability index to extract meaningful features for a robust clinical validation of the outcomes of multiple harmonization strategies.

Breath Analysis for Early Detection of Malignant Pleural Mesothelioma: Volatile Organic Compounds (VOCs) Determination and Possible Biochemical Pathways

Malignant pleural mesothelioma (MPM) is a rare neoplasm, mainly caused by asbestos exposure, with a high mortality rate. The management of patients with MPM is controversial due to a long latency period between exposure and diagnosis and because of non-specific symptoms generally appearing at advanced stage of the disease. Breath analysis, aimed at the identification of diagnostic Volatile Organic Compounds (VOCs) pattern in exhaled breath, is believed to improve early detection of MPM. Therefore, in this study, breath samples from 14 MPM patients and 20 healthy controls (HC) were collected and analyzed by Thermal Desorption-Gas Chromatography-Mass Spectrometry (TD-GC/MS). Nonparametric test allowed to identify the most weighting variables to discriminate between MPM and HC breath samples and multivariate statistics were applied. Considering that MPM is an aggressive neoplasm leading to a late diagnosis and thus the recruitment of patients is very difficult, a promising data mining approach was developed and validated in order to discriminate between MPM patients and healthy controls, even if no large population data are available. Three different machine learning algorithms were applied to perform the classification task with a leave-one-out cross-validation approach, leading to remarkable results (Area Under Curve AUC = 93%). Ten VOCs, such as ketones, alkanes and methylate derivates, as well as hydrocarbons, were able to discriminate between MPM patients and healthy controls and for each compound which resulted diagnostic for MPM, the metabolic pathway was studied in order to identify the link between VOC and the neoplasm. Moreover, five breath samples from asymptomatic asbestos-exposed persons (AEx) were exploratively analyzed, processed and tested by the validated statistical method as blinded samples in order to evaluate the performance for the early recognition of patients affected by MPM among asbestos-exposed persons. Good agreement was found between the information obtained by gold-standard diagnostic methods such as computed tomography CT and model output.

Machine Learning and DWI Brain Communicability Networks for Alzheimer’s Disease Detection

Signal processing and machine learning techniques are changing the clinical practice based on medical imaging from many perspectives. A major topic is related to (i) the development of computer aided diagnosis systems to provide clinicians with novel, non-invasive and low-cost support-tools, and (ii) to the development of new methodologies for the analysis of biomedical data for finding new disease biomarkers. Advancements have been recently achieved in the context of Alzheimer’s disease (AD) diagnosis through the use of diffusion weighted imaging (DWI) data. When combined with tractography algorithms, this imaging modality enables the reconstruction of the physical connections of the brain that can be subsequently investigated through a complex network-based approach. A graph metric particularly suited to describe the disruption of the brain connectivity due to AD is communicability. In this work, we develop a machine learning framework for the classification and feature importance analysis of AD based on communicability at the whole brain level. We fairly compare the performance of three state-of-the-art classification models, namely support vector machines, random forests and artificial neural networks, on the connectivity networks of a balanced cohort of healthy control subjects and AD patients from the ADNI database. Moreover, we clinically validate the information content of the communicability metric by performing a feature importance analysis. Both performance comparison and feature importance analysis provide evidence of the robustness of the method. The results obtained confirm that the whole brain structural communicability alterations due to AD are a valuable biomarker for the characterization and investigation of pathological conditions.

Brain Age Prediction With Morphological Features Using Deep Neural Networks: Results From Predictive Analytic Competition 2019

Morphological changes in the brain over the lifespan have been successfully described by using structural magnetic resonance imaging (MRI) in conjunction with machine learning (ML) algorithms. International challenges and scientific initiatives to share open access imaging datasets also contributed significantly to the advance in brain structure characterization and brain age prediction methods. In this work, we present the results of the predictive model based on deep neural networks (DNN) proposed during the Predictive Analytic Competition 2019 for brain age prediction of 2638 healthy individuals. We used FreeSurfer software to extract some morphological descriptors from the raw MRI scans of the subjects collected from 17 sites. We compared the proposed DNN architecture with other ML algorithms commonly used in the literature (RF, SVR, Lasso). Our results highlight that the DNN models achieved the best performance with MAE = 4.6 on the hold-out test, outperforming the other ML strategies. We also propose a complete ML framework to perform a robust statistical evaluation of feature importance for the clinical interpretability of the results.

Altered Causal Coupling Pathways within the Central-Autonomic-Network in Patients Suffering from Schizophrenia

The multivariate analysis of coupling pathways within physiological (sub)systems focusing on identifying healthy and diseased conditions. In this study, we investigated a part of the central-autonomic-network (CAN) in 17 patients suffering from schizophrenia (SZO) compared to 17 age–gender matched healthy controls (CON) applying linear and nonlinear causal coupling approaches (normalized short time partial directed coherence, multivariate transfer entropy). Therefore, from all subjects continuous heart rate (successive beat-to-beat intervals, BBI), synchronized maximum successive systolic blood pressure amplitudes (SYS), synchronized calibrated respiratory inductive plethysmography signal (respiratory frequency, RESP), and the power P_EEG of frontal EEG activity were investigated for 15 min under resting conditions. The CAN revealed a bidirectional coupling structure, with central driving towards blood pressure (SYS), and respiratory driving towards P_EEG. The central-cardiac, central-vascular, and central-respiratory couplings are more dominated by linear regulatory mechanisms than nonlinear ones. The CAN showed significantly weaker nonlinear central-cardiovascular and central-cardiorespiratory coupling pathways, and significantly stronger linear central influence on the vascular system, and on the other hand significantly stronger linear respiratory and cardiac influences on central activity in SZO compared to CON, and thus, providing better understanding of the interrelationship of central and autonomic regulatory mechanisms in schizophrenia might be useful as a biomarker of this disease.

Communicability Characterization of Structural DWI Subcortical Networks in Alzheimer's Disease

In this paper, we investigate the connectivity alterations of the subcortical brain network due to Alzheimer’s disease (AD). Mostly, the literature investigated AD connectivity abnormalities at the whole brain level or at the cortex level, while very few studies focused on the sub-network composed only by the subcortical regions, especially using diffusion-weighted imaging (DWI) data. In this work, we examine a mixed cohort including 46 healthy controls (HC) and 40 AD patients from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) data set. We reconstruct the brain connectome through the use of state of the art tractography algorithms and we propose a method based on graph communicability to enhance the information content of subcortical brain regions in discriminating AD. We develop a classification framework, achieving 77% of area under the receiver operating characteristic (ROC) curve in the binary discrimination AD vs. HC only using a 12×12 subcortical features matrix. We find some interesting AD-related connectivity patterns highlighting that subcortical regions tend to increase their communicability through cortical regions to compensate the physical connectivity reduction between them due to AD. This study also suggests that AD connectivity alterations mostly regard the inter-connectivity between subcortical and cortical regions rather than the intra-subcortical connectivity.