Sparse brain network recovery under compressed sensing

Optimizing functional brain network analysis by incorporating nonlinear factors and frequency band selection with machine learning models

The accurate assessment of the brain's functional network is seen as crucial for the understanding of complex relationships between different brain regions. Hidden information within different frequency bands, which is often overlooked by traditional linear correlation-based methods such as Pearson correlation (PC) and partial correlation, fails to be revealed, leading to the neglect of more intricate nonlinear factors. These limitations were aimed to be overcome in this study by the combination of fast continuous wavelet transform and normalized mutual information (NMI) to develop a novel approach. Original time-domain signals from resting-state functional magnetic resonance imaging were decomposed into different frequency domains using fast continuous wavelet transform, and adjacency matrices were constructed to enhance feature separation across brain regions. Both linear and nonlinear aspects between brain regions were comprehensively considered through the integration of complex correlation coefficient and NMI. The construction of functional brain networks was enabled by the adaptive selection of optimal frequency band combinations. The construction of the model was facilitated by feature extraction using tree models with extreme gradient boosting. It was demonstrated through comparative analysis that the method outperformed baseline methods such as PC and NMI, achieving an area under the curve of 0.9054. The introduction of nonlinear factors was found to increase precision by 14.25% and recall by 17.14%. Importantly, the approach optimized the original data without significantly altering the feature topology. Overall, this innovation advances the understanding of brain function, offering more accurate potential for future research and clinical applications.

Sensory and motor cortices parcellations estimated via distance-weighted sparse representation with application to autism spectrum disorder

BACKGROUND

Motor impairments and sensory processing abnormalities are prevalent in autism spectrum disorder (ASD), closely related to the core functions of the primary motor cortex (M1) and the primary somatosensory cortex (S1). Currently, there is limited knowledge about potential therapeutic targets in the subregions of M1 and S1 in ASD patients. This study aims to map clinically significant functional subregions of M1 and S1.

METHODS

Resting-state functional magnetic resonance imaging data (NTD = 266) from Autism Brain Imaging Data Exchange (ABIDE) were used for subregion modeling. We proposed a distance-weighted sparse representation algorithm to construct brain functional networks. Functional subregions of M1 and S1 were identified through consensus clustering at the group level. Differences in the characteristics of functional subregions were analyzed, along with their correlation with clinical scores.

RESULTS

We observed symmetrical and continuous subregion organization from dorsal to ventral aspects in M1 and S1, with M1 subregions conforming to the functional pattern of the motor homunculus. Significant intergroup differences and clinical correlations were found in the dorsal and ventral aspects of M1 (p < 0.05/3, Bonferroni correction) and the ventromedial BA3 of S1 (p < 0.05/5). These functional characteristics were positively correlated with autism severity. All subregions showed significant results in the ROI-to-ROI intergroup differential analysis (p < 0.05/80).

LIMITATIONS

The generalizability of the segmentation model requires further evaluation.

CONCLUSIONS

This study highlights the significance of M1 and S1 in ASD treatment and may provide new insights into brain parcellation and the identification of therapeutic targets for ASD.

Learning functional brain networks with heterogeneous connectivities for brain disease identification

Functional brain networks (FBNs), which are used to portray interactions between different brain regions, have been widely used to identify potential biomarkers of neurological and mental disorders. The FBNs estimated using current methods tend to be homogeneous, indicating that different brain regions exhibit the same type of correlation. This homogeneity limits our ability to accurately encode complex interactions within the brain. Therefore, to the best of our knowledge, in the present study, for the first time, we propose the existence of heterogeneous FBNs and introduce a novel FBN estimation model that adaptively assigns heterogeneous connections to different pairs of brain regions, thereby effectively encoding the complex interaction patterns in the brain. Specifically, we first construct multiple types of candidate correlations from different views or based on different methods and then develop an improved orthogonal matching pursuit algorithm to select at most one correlation for each brain region pair under the guidance of label information. These adaptively estimated heterogeneous FBNs were then used to distinguish subjects with neurological/mental disorders from healthy controls and identify potential biomarkers related to these disorders. Experimental results on real datasets show that the proposed scheme improves classification performance by 7.07% and 7.58% at the two sites, respectively, compared with the baseline approaches. This emphasizes the plausibility of the heterogeneity hypothesis and effectiveness of the heterogeneous connection assignment algorithm.

Jointly constrained group sparse connectivity representation improves early diagnosis of Alzheimer's disease on routinely acquired T1-weighted imaging-based brain network

Background

Radiomics-based morphological brain networks (radMBN) constructed from routinely acquired structural MRI (sMRI) data have gained attention in Alzheimer's disease (AD). However, the radMBN suffers from limited characterization of AD because sMRI only characterizes anatomical changes and is not a direct measure of neuronal pathology or brain activity.

Purpose

To establish a group sparse representation of the radMBN under a joint constraint of group-level white matter fiber connectivity and individual-level sMRI regional similarity (JCGS-radMBN).

Methods

Two publicly available datasets were adopted, including 120 subjects from ADNI with both T1-weighted image (T1WI) and diffusion MRI (dMRI) for JCGS-radMBN construction, 818 subjects from ADNI and 200 subjects solely with T1WI from AIBL for validation in early AD diagnosis. Specifically, the JCGS-radMBN was conducted by jointly estimating non-zero connections among subjects, with the regularization term constrained by group-level white matter fiber connectivity and individual-level sMRI regional similarity. Then, a triplet graph convolutional network was adopted for early AD diagnosis. The discriminative brain connections were identified using a two-sample t-test, and the neurobiological interpretation was validated by correlating the discriminative brain connections with cognitive scores.

Results

The JCGS-radMBN exhibited superior classification performance over five brain network construction methods. For the typical NC vs. AD classification, the JCGS-radMBN increased by 1-30% in accuracy over the alternatives on ADNI and AIBL. The discriminative brain connections exhibited a strong connectivity to hippocampus, parahippocampal gyrus, and basal ganglia, and had significant correlation with MMSE scores.

Conclusion

The proposed JCGS-radMBN facilitated the AD characterization of brain network established on routinely acquired imaging modality of sMRI.

Supplementary Information

The online version of this article (10.1007/s13755-023-00269-0) contains supplementary material, which is available to authorized users.

Neighborhood structure-guided brain functional networks estimation for mild cognitive impairment identification

The adoption and growth of functional magnetic resonance imaging (fMRI) technology, especially through the use of Pearson's correlation (PC) for constructing brain functional networks (BFN), has significantly advanced brain disease diagnostics by uncovering the brain's operational mechanisms and offering biomarkers for early detection. However, the PC always tends to make for a dense BFN, which violates the biological prior. Therefore, in practice, researchers use hard-threshold to remove weak connection edges or introduce l 1-norm as a regularization term to obtain sparse BFNs. However, these approaches neglect the spatial neighborhood information between regions of interest (ROIs), and ROI with closer distances has higher connectivity prospects than ROI with farther distances due to the principle of simple wiring costs in resent studies. Thus, we propose a neighborhood structure-guided BFN estimation method in this article. In detail, we figure the ROIs' Euclidean distances and sort them. Then, we apply the K-nearest neighbor (KNN) to find out the top K neighbors closest to the current ROIs, where each ROI's K neighbors are independent of each other. We establish the connection relationship between the ROIs and these K neighbors and construct the global topology adjacency matrix according to the binary network. Connect ROI nodes with k nearest neighbors using edges to generate an adjacency graph, forming an adjacency matrix. Based on adjacency matrix, PC calculates the correlation coefficient between ROIs connected by edges, and generates the BFN. With the purpose of evaluating the performance of the introduced method, we utilize the estimated BFN for distinguishing individuals with mild cognitive impairment (MCI) from the healthy ones. Experimental outcomes imply this method attains better classification performance than the baselines. Additionally, we compared it with the most commonly used time series methods in deep learning. Results of the performance of K-nearest neighbor-Pearson's correlation (K-PC) has some advantage over deep learning.

Towards an accurate autism spectrum disorder diagnosis: multiple connectome views from fMRI data

Functional connectome has revealed remarkable potential in the diagnosis of neurological disorders, e.g. autism spectrum disorder. However, existing studies have primarily focused on a single connectivity pattern, such as full correlation, partial correlation, or causality. Such an approach fails in discovering the potential complementary topology information of FCNs at different connection patterns, resulting in lower diagnostic performance. Consequently, toward an accurate autism spectrum disorder diagnosis, a straightforward ambition is to combine the multiple connectivity patterns for the diagnosis of neurological disorders. To this end, we conduct functional magnetic resonance imaging data to construct multiple brain networks with different connectivity patterns and employ kernel combination techniques to fuse information from different brain connectivity patterns for autism diagnosis. To verify the effectiveness of our approach, we assess the performance of the proposed method on the Autism Brain Imaging Data Exchange dataset for diagnosing autism spectrum disorder. The experimental findings demonstrate that our method achieves precise autism spectrum disorder diagnosis with exceptional accuracy (91.30%), sensitivity (91.48%), and specificity (91.11%).

Wavelet transform-based frequency self-adaptive model for functional brain network

The accurate estimation of functional brain networks is essential for comprehending the intricate relationships between different brain regions. Conventional methods such as Pearson Correlation and Sparse Representation often fail to uncover concealed information within diverse frequency bands. To address this limitation, we introduce a novel frequency-adaptive model based on wavelet transform, enabling selective capture of highly correlated frequency band sequences. Our approach involves decomposing the original time-domain signal from resting-state functional magnetic resonance imaging into distinct frequency domains, thus constructing an adjacency matrix that offers enhanced separation of features across brain regions. Comparative analysis demonstrates the superior performance of our proposed model over conventional techniques, showcasing improved clarity and distinctiveness. Notably, we achieved the highest accuracy rate of 89.01% using Sparse Representation based on Wavelet Transform, outperforming Pearson Correlation based on Wavelet Transform with an accuracy of 81.32%. Importantly, our method optimizes raw data without significantly altering feature topology, rendering it adaptable to various functional brain network estimation approaches. Overall, this innovation holds the potential to advance the understanding of brain function and furnish more accurate samples for future research and clinical applications.

Autism spectrum disorder diagnosis based on deep unrolling-based spatial constraint representation

Accurate diagnosis of autism spectrum disorder (ASD) is crucial for effective treatment and prognosis. Functional brain networks (FBNs) constructed from functional magnetic resonance imaging (fMRI) have become a popular tool for ASD diagnosis. However, existing model-driven approaches used to construct FBNs lack the ability to capture potential non-linear relationships between data and labels. Moreover, most existing studies treat the FBNs construction and disease classification as separate steps, leading to large inter-subject variability in the estimated FBNs and reducing the statistical power of subsequent group comparison. To address these limitations, we propose a new approach to FBNs construction called the deep unrolling-based spatial constraint representation (DUSCR) model and integrate it with a convolutional classifier to create an end-to-end framework for ASD recognition. Specifically, the model spatial constraint representation (SCR) is solved using a proximal gradient descent algorithm, and we unroll it into deep networks using the deep unrolling algorithm. Classification is then performed using a convolutional prototype learning model. We evaluated the effectiveness of the proposed method on the ABIDE I dataset and observed a significant improvement in model performance and classification accuracy. The resting state fMRI images are preprocessed into time series data and 3D coordinates of each region of interest. The data are fed into the DUSCR model, a model for building functional brain networks using deep learning instead of traditional models, that we propose, and then the outputs are fed into the convolutional classifier with prototype learning to determine whether the patient has ASD disease.

Functional Connectivity Networks with Latent Distributions for Mild Cognitive Impairment Identification

This work presents a novel approach to estimate brain functional connectivity networks via generative learning. Due to the complexity and variability of rs-fMRI signal, we consider it as a random variable, and utilize variational autoencoder networks to encode it as a confidence distribution in the latent space rather than as a fixed vector, so as to establish the relationship between them. First, the mean time series of each brain region of interest is mapped into a multivariate Gaussian distribution. The correlation between two brain regions is measured by the Jensen-Shannon divergence that describes the statistical similarity between two probability distributions, and then the adjacency matrix is created to indicate the functional connectivity strength of pairwise brain regions. Meanwhile, our findings show that the adjacency matrices obtained at VAE latent spaces of different dimensionalities have good complementarity for MCI identification in precision and recall, and the classification performance can be further boosted by an efficient cascade of classifiers. This proposal constructs brain functional networks from a statistical modeling standpoint, improving the statistical ability of population data and the generalization ability of observation data variability. We evaluate the proposed framework over the task of identifying subjects with MCI from normal controls, and the experimental results on the public dataset show that our method significantly outperforms both the baseline and current state-of-the-art methods.

Learning to Fuse Multiple Brain Functional Networks for Automated Autism Identification

Functional connectivity network (FCN) has become a popular tool to identify potential biomarkers for brain dysfunction, such as autism spectrum disorder (ASD). Due to its importance, researchers have proposed many methods to estimate FCNs from resting-state functional MRI (rs-fMRI) data. However, the existing FCN estimation methods usually only capture a single relationship between brain regions of interest (ROIs), e.g., linear correlation, nonlinear correlation, or higher-order correlation, thus failing to model the complex interaction among ROIs in the brain. Additionally, such traditional methods estimate FCNs in an unsupervised way, and the estimation process is independent of the downstream tasks, which makes it difficult to guarantee the optimal performance for ASD identification. To address these issues, in this paper, we propose a multi-FCN fusion framework for rs-fMRI-based ASD classification. Specifically, for each subject, we first estimate multiple FCNs using different methods to encode rich interactions among ROIs from different perspectives. Then, we use the label information (ASD vs. healthy control (HC)) to learn a set of fusion weights for measuring the importance/discrimination of those estimated FCNs. Finally, we apply the adaptively weighted fused FCN on the ABIDE dataset to identify subjects with ASD from HCs. The proposed FCN fusion framework is straightforward to implement and can significantly improve diagnostic accuracy compared to traditional and state-of-the-art methods.

Fused Brain Functional Connectivity Network and Edge-attention Graph Convolution Network for Fibromyalgia Syndrome Diagnosis

Fibromyalgia syndrome (FMS) is a type of rheumatology that seriously affects the normal life of patients. Due to the complex clinical manifestations of FMS, it is challenging to detect FMS. Therefore, an automatic FMS diagnosis model is urgently needed to assist physicians. Brain functional connectivity networks (BFCNs) constructed by resting-state functional magnetic resonance imaging (rs-fMRI) to describe brain functions have been widely used to identify individuals with relevant diseases from normal control (NC). Therefore, we propose a novel model based on BFCN and graph convolutional network (GCN) for automatic FMS diagnosis. Firstly, a novel fused BFCN method is proposed by fusing Pearson's correlation (PC) and low-rank (LR) BFCN, which retains information and reduces data redundancy to construct BFCN. Then we combine the feature of BFCN with non-image information of subjects to obtain nodes and adjacency matrices, which builds a graph with edge attention. Finally, the graph is sent to the GCN layer for FMS diagnosis. Our model is evaluated on the in-house FMS dataset to achieve 82.48% accuracy. The experimental results show that our method outperforms the state-of-the-art competing methods.

Multiple measurement analysis of resting-state fMRI for ADHD classification in adolescent brain from the ABCD study

Attention deficit hyperactivity disorder (ADHD) is one of the most common psychiatric disorders in school-aged children. Its accurate diagnosis looks after patients' interests well with effective treatment, which is important to them and their family. Resting-state functional magnetic resonance imaging (rsfMRI) has been widely used to characterize the abnormal brain function by computing the voxel-wise measures and Pearson's correlation (PC)-based functional connectivity (FC) for ADHD diagnosis. However, exploring the powerful measures of rsfMRI to improve ADHD diagnosis remains a particular challenge. To this end, this paper proposes an automated ADHD classification framework by fusion of multiple measures of rsfMRI in adolescent brain. First, we extract the voxel-wise measures and ROI-wise time series from the brain regions of rsfMRI after preprocessing. Then, to extract the multiple functional connectivities, we compute the PC-derived FCs including the topographical information-based high-order FC (tHOFC) and dynamics-based high-order FC (dHOFC), the sparse representation (SR)-derived FCs including the group SR (GSR), the strength and similarity guided GSR (SSGSR), and sparse low-rank (SLR). Finally, these measures are combined with multiple kernel learning (MKL) model for ADHD classification. The proposed method is applied to the Adolescent Brain and Cognitive Development (ABCD) dataset. The results show that the FCs of dHOFC and SLR perform better than the others. Fusing multiple measures achieves the best classification performance (AUC = 0.740, accuracy = 0.6916), superior to those from the single measure and the previous studies. We have identified the most discriminative FCs and brain regions for ADHD diagnosis, which are consistent with those of published literature.

Fusing Multiview Functional Brain Networks by Joint Embedding for Brain Disease Identification

Background: Functional brain networks (FBNs) derived from resting-state functional MRI (rs-fMRI) have shown great potential in identifying brain disorders, such as autistic spectrum disorder (ASD). Therefore, many FBN estimation methods have been proposed in recent years. Most existing methods only model the functional connections between brain regions of interest (ROIs) from a single view (e.g., by estimating FBNs through a specific strategy), failing to capture the complex interactions among ROIs in the brain. Methods: To address this problem, we propose fusion of multiview FBNs through joint embedding, which can make full use of the common information of multiview FBNs estimated by different strategies. More specifically, we first stack the adjacency matrices of FBNs estimated by different methods into a tensor and use tensor factorization to learn the joint embedding (i.e., a common factor of all FBNs) for each ROI. Then, we use Pearson's correlation to calculate the connections between each embedded ROI in order to reconstruct a new FBN. Results: Experimental results obtained on the public ABIDE dataset with rs-fMRI data reveal that our method is superior to several state-of-the-art methods in automated ASD diagnosis. Moreover, by exploring FBN "features" that contributed most to ASD identification, we discovered potential biomarkers for ASD diagnosis. The proposed framework achieves an accuracy of 74.46%, which is generally better than the compared individual FBN methods. In addition, our method achieves the best performance compared to other multinetwork methods, i.e., an accuracy improvement of at least 2.72%. Conclusions: We present a multiview FBN fusion strategy through joint embedding for fMRI-based ASD identification. The proposed fusion method has an elegant theoretical explanation from the perspective of eigenvector centrality.

Joint selection of brain network nodes and edges for MCI identification

BACKGROUND AND OBJECTIVE

Functional brain graph (FBG), by describing the interactions between different brain regions, provides an effective representation of fMRI data for identifying mild cognitive impairment (MCI), an early stage of Alzheimer's Disease (AD). Prior to the identification task, selecting features from the estimated FBG is a necessary step for reducing computational cost, alleviating the risk of overfitting, and finding potential biomarkers of brain diseases. In practice, either node-based features (e.g., local clustering coefficients) or edge-based features (e.g., adjacency weights) are generally considered in current studies. Despite their popularity, these schemes can only capture one granularity (node or edge) of information in the FBG, which might be insufficient for the classification task and the interpretation of the classification result.

METHODS

To address this issue, in this paper, we propose to jointly select nodes and edges from the estimated FBGs. Specifically, we first assign the edges to different node groups. Then, sparse group least absolute shrinkage and selection operator (sgLASSO) is used to select groups (nodes) and edges in the groups towards a better classification performance. Such a technique enables us to simultaneously locate discriminative brain regions, as well as connections between these brain regions, making the classification results more interpretable.

RESULTS

Experimental results show that the proposed method achieves better classification performance than state-of-the-art methods. Moreover, by exploring brain network "features" that contributed most to MCI identification, we discover potential biomarkers for MCI diagnosis.

CONCLUSION

A novel method for jointly selecting nodes and edges from the estimated functional brain graphs (FBGs) is proposed.

Human-Guided Functional Connectivity Network Estimation for Chronic Tinnitus Identification: A Modularity View

The functional connectivity network (FCN) has been used to achieve several remarkable advancements in the diagnosis of neuro-degenerative disorders. Therefore, it is imperative to accurately estimate biologically meaningful FCNs. Several efforts have been dedicated to this purpose by encoding biological priors. However, owing to the high complexity of the human brain, the estimation of an 'ideal' FCN remains an open problem. To the best of our knowledge, almost all existing studies lack the integration of domain expert knowledge, which limits their performance. In this study, we focused on incorporating domain expert knowledge into the FCN estimation from a modularity perspective. To achieve this, we presented a human-guided modular representation (MR) FCN estimation framework. Specifically, we designed an adversarial low-rank constraint to describe the module structure of FCNs under the guidance of domain expert knowledge (i.e., a predefined participant index). The chronic tinnitus (TIN) identification task based on the estimated FCNs was conducted to examine the proposed MR methods. Remarkably, MR significantly outperformed the baseline and state-of-the-art(SOTA) methods, achieving an accuracy of 92.11%. Moreover, post-hoc analysis revealed that the FCNs estimated by the proposed MR could highlight more biologically meaningful connections, which is beneficial for exploring the underlying mechanisms of TIN and diagnosing early TIN.

A Deep Spatiotemporal Attention Network for Mild Cognitive Impairment Identification

Mild cognitive impairment (MCI) is a nervous system disease, and its clinical status can be used as an early warning of Alzheimer's disease (AD). Subtle and slow changes in brain structure between patients with MCI and normal controls (NCs) deprive them of effective diagnostic methods. Therefore, the identification of MCI is a challenging task. The current functional brain network (FBN) analysis to predict human brain tissue structure is a new method emerging in recent years, which provides sensitive and effective medical biomarkers for the diagnosis of neurological diseases. Therefore, to address this challenge, we propose a novel Deep Spatiotemporal Attention Network (DSTAN) framework for MCI recognition based on brain functional networks. Specifically, we first extract spatiotemporal features between brain functional signals and FBNs by designing a spatiotemporal convolution strategy (ST-CONV). Then, on this basis, we introduce a learned attention mechanism to further capture brain nodes strongly correlated with MCI. Finally, we fuse spatiotemporal features for MCI recognition. The entire network is trained in an end-to-end fashion. Extensive experiments show that our proposed method significantly outperforms current baselines and state-of-the-art methods, with a classification accuracy of 84.21%.

Multiview Feature Learning With Multiatlas-Based Functional Connectivity Networks for MCI Diagnosis

Functional connectivity (FC) networks built from resting-state functional magnetic resonance imaging (rs-fMRI) has shown promising results for the diagnosis of Alzheimer's disease and its prodromal stage, that is, mild cognitive impairment (MCI). FC is usually estimated as a temporal correlation of regional mean rs-fMRI signals between any pair of brain regions, and these regions are traditionally parcellated with a particular brain atlas. Most existing studies have adopted a predefined brain atlas for all subjects. However, the constructed FC networks inevitably ignore the potentially important subject-specific information, particularly, the subject-specific brain parcellation. Similar to the drawback of the "single view" (versus the "multiview" learning) in medical image-based classification, FC networks constructed based on a single atlas may not be sufficient to reveal the underlying complicated differences between normal controls and disease-affected patients due to the potential bias from that particular atlas. In this study, we propose a multiview feature learning method with multiatlas-based FC networks to improve MCI diagnosis. Specifically, a three-step transformation is implemented to generate multiple individually specified atlases from the standard automated anatomical labeling template, from which a set of atlas exemplars is selected. Multiple FC networks are constructed based on these preselected atlas exemplars, providing multiple views of the FC network-based feature representations for each subject. We then devise a multitask learning algorithm for joint feature selection from the constructed multiple FC networks. The selected features are jointly fed into a support vector machine classifier for multiatlas-based MCI diagnosis. Extensive experimental comparisons are carried out between the proposed method and other competing approaches, including the traditional single-atlas-based method. The results indicate that our method significantly improves the MCI classification, demonstrating its promise in the brain connectome-based individualized diagnosis of brain diseases.

Estimating High-Order Brain Functional Networks in Bayesian View for Autism Spectrum Disorder Identification

Brain functional network (BFN) has become an increasingly important tool to understand the inherent organization of the brain and explore informative biomarkers of neurological disorders. Pearson’s correlation (PC) is the most widely accepted method for constructing BFNs and provides a basis for designing new BFN estimation schemes. Particularly, a recent study proposes to use two sequential PC operations, namely, correlation’s correlation (CC), for constructing the high-order BFN. Despite its empirical effectiveness in identifying neurological disorders and detecting subtle changes of connections in different subject groups, CC is defined intuitively without a solid and sustainable theoretical foundation. For understanding CC more rigorously and providing a systematic BFN learning framework, in this paper, we reformulate it in the Bayesian view with a prior of matrix-variate normal distribution. As a result, we obtain a probabilistic explanation of CC. In addition, we develop a Bayesian high-order method (BHM) to automatically and simultaneously estimate the high- and low-order BFN based on the probabilistic framework. An efficient optimization algorithm is also proposed. Finally, we evaluate BHM in identifying subjects with autism spectrum disorder (ASD) from typical controls based on the estimated BFNs. Experimental results suggest that the automatically learned high- and low-order BFNs yield a superior performance over the artificially defined BFNs via conventional CC and PC.

Positron Emission Tomography in the Neuroimaging of Autism Spectrum Disorder: A Review

Autism spectrum disorder (ASD) is a basket term for neurodevelopmental disorders characterized by marked impairments in social interactions, repetitive and stereotypical behaviors, and restricted interests and activities. Subtypes include (A) disorders with known genetic abnormalities including fragile X syndrome, Rett syndrome, and tuberous sclerosis and (B) idiopathic ASD, conditions with unknown etiologies. Positron emission tomography (PET) is a molecular imaging technology that can be utilized in vivo for dynamic and quantitative research, and is a valuable tool for exploring pathophysiological mechanisms, evaluating therapeutic efficacy, and accelerating drug development in ASD. Recently, several imaging studies on ASD have been published and physiological changes during ASD progression was disclosed by PET. This paper reviews the specific radioligands for PET imaging of critical biomarkers in ASD, and summarizes and discusses the similar and different discoveries in outcomes of previous studies. It is of great importance to identify general physiological changes in cerebral glucose metabolism, cerebral blood flow perfusion, abnormalities in neurotransmitter systems, and inflammation in the central nervous system in ASD, which may provide excellent points for further ASD research.

Extracting BOLD signals based on time-constrained multiset canonical correlation analysis for brain functional network estimation and classification

Brain functional network (BFN), usually estimated from blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI), has been proven to be a powerful tool to study the organization of the brain and discover biomarkers for diagnosis of brain disorders. Prior to BFN estimation and classification, extracting representative BOLD signals from brain regions of interest (ROIs) is a critical step. Traditional extraction methods include averaging, peaking operation and dimensionality reduction, often leading to signal cancellation and information loss. In this paper, we propose a novel method, namely time-constrained multiset canonical correlation analysis (TMCCA), to extract representative BOLD signals for subsequent BFN estimation and classification. Different from traditional methods that equally treat all BOLD signals in a ROI, the proposed method assigns weights to different BOLD signals, and learns the optimal weights to make the extracted representative signals jointly maximize the multiple correlations between ROIs. Importantly, time-constraint is incorporated into our proposed method, which can effectively encode nonlinear relationship among BOLD signals. To evaluate the effectiveness of the proposed method, the extracted BOLD signals is used to estimate BFN and, in turn, identify brain disorders, including mild cognitive impairment (MCI) and autistic spectrum disorder (ASD). Experimental results demonstrate that our proposed TMCCA can lead to better performance than traditional methods.

Adaptive noise depression for functional brain network estimation

Autism spectrum disorder (ASD) is one common psychiatric illness that manifests in neurological and developmental disorders, which can last throughout a person's life and cause challenges in social interaction, communication, and behavior. Since the standard ASD diagnosis is highly based on the symptoms of the disease, it is difficult to make an early diagnosis to take the best cure opportunity. Compared to the standard methods, functional brain network (FBN) could reveal the statistical dependence among neural architectures in brains and provide potential biomarkers for the early neuro-disease diagnosis and treatment of some neurological disorders. However, there are few FBN estimation methods that take into account the noise during the data acquiring process, resulting in poor quality of FBN and thus poor diagnosis results. To address such issues, we provide a brand-new approach for estimating FBNs under a noise modeling framework. In particular, we introduce a noise term to model the representation errors and impose a regularizer to incorporate noise prior into FBNs estimation. More importantly, the proposed method can be formulated as conducting traditional FBN estimation based on transformed fMRI data, which means the traditional methods can be elegantly modified to support noise modeling. That is, we provide a plug-and-play noise module capable of being embedded into different methods and adjusted according to different noise priors. In the end, we conduct abundant experiments to identify ASD from normal controls (NCs) based on the constructed FBNs to illustrate the effectiveness and flexibility of the proposed method. Consequently, we achieved up to 13.04% classification accuracy improvement compared with the baseline methods.

Analyzing Complex Problem Solving by Dynamic Brain Networks

Complex problem solving is a high level cognitive task of the human brain, which has been studied over the last decade. Tower of London (TOL) is a game that has been widely used to study complex problem solving. In this paper, we aim to explore the underlying cognitive network structure among anatomical regions of complex problem solving and its subtasks, namely planning and execution. A new computational model for estimating a brain network at each time instant of fMRI recordings is proposed. The suggested method models the brain network as an Artificial Neural Network, where the weights correspond to the relationships among the brain anatomic regions. The first step of the model is preprocessing that manages to decrease the spatial redundancy while increasing the temporal resolution of the fMRI recordings. Then, dynamic brain networks are estimated using the preprocessed fMRI signal to train the Artificial Neural Network. The properties of the estimated brain networks are studied in order to identify regions of interest, such as hubs and subgroups of densely connected brain regions. The representation power of the suggested brain network is shown by decoding the planning and execution subtasks of complex problem solving. Our findings are consistent with the previous results of experimental psychology. Furthermore, it is observed that there are more hubs during the planning phase compared to the execution phase, and the clusters are more strongly connected during planning compared to execution.

Multiple Connection Pattern Combination From Single-Mode Data for Mild Cognitive Impairment Identification

Mild cognitive impairment (MCI) is generally considered to be a key indicator for predicting the early progression of Alzheimer’s disease (AD). Currently, the brain connection (BC) estimated by fMRI data has been validated to be an effective diagnostic biomarker for MCI. Existing studies mainly focused on the single connection pattern for the neuro-disease diagnosis. Thus, such approaches are commonly insufficient to reveal the underlying changes between groups of MCI patients and normal controls (NCs), thereby limiting their performance. In this context, the information associated with multiple patterns (e.g., functional connectivity or effective connectivity) from single-mode data are considered for the MCI diagnosis. In this paper, we provide a novel multiple connection pattern combination (MCPC) approach to combine different patterns based on the kernel combination trick to identify MCI from NCs. In particular, sixty-three MCI cases and sixty-four NC cases from the ADNI dataset are conducted for the validation of the proposed MCPC method. The proposed method achieves 87.40% classification accuracy and significantly outperforms methods that use a single pattern.

Detecting synaptic connections in neural systems using compressive sensing

Revealing synaptic connections between neurons is of great significance and practical value to biomedicine and bio-neurology. We present a general approach to reconstruct neuronal synapses, which is based on compressive sensing and special data processing. And this approach is more suitable for nervous system with peak time series. Numerical simulations illustrate the feasibility and effectiveness of the proposed approach. Moreover, this approach not only adapts to the asymmetry of neural connections and the diversity of coupling strength, but also adapts to the excitability and inhibition of neural node classification. In addition, the effects of the factors on the synaptic connection identification performance and their optimal states for the synaptic connection recovery are discussed. Besides, it is of great practical significance to control the order of Taylor expansion to improve the performance of synaptic connection recognition.

Autism spectrum disorder diagnosis using graph attention network based on spatial-constrained sparse functional brain networks

The accurate diagnosis of autism spectrum disorder (ASD), a common mental disease in children, has always been an important task in clinical practice. In recent years, the use of graph neural network (GNN) based on functional brain network (FBN) has shown powerful performance for disease diagnosis. The challenge to construct "ideal" FBN from resting-state fMRI data remained. Moreover, it remains unclear whether and to what extent the non-Euclidean structure of different FBNs affect the performance of GNN-based disease classification. In this paper, we proposed a new method named Pearson's correlation-based Spatial Constraints Representation (PSCR) to estimate the FBN structures that were transformed to brain graphs and then fed into a graph attention network (GAT) to diagnose ASD. Extensive experiments on comparing different FBN construction methods and classification frameworks were conducted on the ABIDE I dataset (n = 871). The results demonstrated the superiority of our PSCR method and the influence of different FBNs on the GNN-based classification results. The proposed PSCR and GAT framework achieved promising classification results for ASD (accuracy: 72.40%), which significantly outperformed competing methods. This will help facilitate patient-control separation, and provide a promising solution for future disease diagnosis based on the FBN and GNN framework.

Brain Function Network: Higher Order vs. More Discrimination

Brain functional network (BFN) has become an increasingly important tool to explore individual differences and identify neurological/mental diseases. For estimating a "good" BFN (with more discriminative information for example), researchers have developed various methods, in which the most popular and simplest is Pearson's correlation (PC). Despite its empirical effectiveness, PC only encodes the low-order (second-order) statistics between brain regions. To model high-order statistics, researchers recently proposed to estimate BFN by conducting two sequential PCs (denoted as PC ² in this paper), and found that PC ²-based BFN can provide additional information for group difference analysis. This inspires us to think about (1) what will happen if continuing the correlation operation to construct much higher-order BFN by PC ⁿ (n>2), and (2) whether the higher-order correlation will result in stronger discriminative ability. To answer these questions, we use PC ⁿ -based BFNs to predict individual differences (Female vs. Male) as well as identify subjects with mild cognitive impairment (MCI) from healthy controls (HCs). Through experiments, we have the following findings: (1) with the increase of n, the discriminative ability of PC ⁿ -based BFNs tends to decrease; (2) fusing the PC ⁿ -based BFNs (n>1) with the PC ¹-based BFN can generally improve the sensitivity for MCI identification, but fail to help the classification accuracy. In addition, we empirically find that the sequence of BFN adjacency matrices estimated by PC ⁿ (n = 1,2,3,⋯ ) will converge to a binary matrix with elements of ± 1.

Distribution-guided Network Thresholding for Functional Connectivity Analysis in fMRI-based Brain Disorder Identification

Brain functional connectivity (FC) networks derived from resting-state functional magnetic resonance imaging (rs-fMRI) have been widely applied to automated identification of brain disorders, such as Alzheimer's disease (AD) and attention deficit hyperactivity disorder (ADHD). To generate compact representations of FC networks, various thresholding strategies have been developed to analyze brain FC networks. However, existing studies usually employ predefined thresholds or percentages of connections to threshold FC networks, thus ignoring the diversity of temporal correlation (particularly strong associations) among brain regions in same/different subject groups. Also, it is usually challenging to decide the optimal threshold or connection percentage in practice. To this end, in this paper, we propose a distribution-guided network thresholding (DNT) method for functional connectivity analysis in brain disorder identification with rs-fMRI. Specifically, for each functional connectivity of a pair of brain regions, we proposed to compute its specific threshold based on the distribution of connection strength (i.e., temporal correlation) between subject groups (e.g., patients and normal controls). The proposed DNT can adaptively yield FC-specific threshold for each connection in brain networks, thus preserving the diversity of temporal correlation among brain regions. Experiment results on both ADNI and ADHD-200 datasets demonstrate the effectiveness of our proposed DNT method in fMRI-based identification of AD and ADHD.

Learning Brain Functional Networks with Latent Temporal Dependency for MCI Identification

AbstractResting-state functional magnetic resonance imaging (rs-fMRI) has become a popular non-invasive way of diagnosing neurological disorders or their early stages by probing functional connectivity between different brain regions of interest (ROIs) across subjects. In the past decades, researchers have proposed many methods to estimate brain functional networks (BFNs) based on blood-oxygen-level-dependent (BOLD) signals captured by rs-fMRI. However, most of the existing methods estimate BFNs under the assumption that signals are independently sampled, which ignores the temporal dependency and sequential order of different time points (or volumes). To address this problem, in this paper, we first propose a novel BFN estimation model by introducing a latent variable to control the sequence of volumes for encoding the temporal dependency and sequential information of signals into the estimated BFNs. Then, we develop an efficient learning algorithm to solve the proposed model by the alternating optimization scheme. To verify the effectiveness of the proposed method, the estimated BFNs are used to identify subjects with mild cognitive impairment (MCIs) from normal controls (NCs). Experimental results show that our method outperforms the baseline methods in the sense of classification performance.

Decomposition of individual-specific and individual-shared components from resting-state functional connectivity using a multi-task machine learning method

Resting-state functional connectivity (RSFC) can be used for mapping large-scale human brain networks during rest. There is considerable interest in distinguishing the individual-shared and individual-specific components in RSFC for the better identification of individuals and prediction of behavior. Therefore, we propose a multi-task learning based sparse convex alternating structure optimization (MTL-sCASO) method to decompose RSFC into individual-specific connectivity and individual-shared connectivity. We used synthetic data to validate the efficacy of the MTL-sCASO method. In addition, we verified that individual-specific connectivity achieves higher identification rates than the Pearson correlation (PC) method, and the individual-specific components observed in 886 individuals from the Human Connectome Project (HCP) examined in two sessions over two consecutive days might serve as individual fingerprints. Individual-specific connectivity has low inter-subject similarity (-0.005±0.023), while individual-shared connectivity has high inter-subject similarity (0.822±0.061). We also determined the anatomical locations (region or subsystem) related to individual attributes and common features. We find that individual-specific connectivity exhibits low degree centrality in the sensorimotor processing system but high degree centrality in the control system. Importantly, the individual-specific connectivity estimated by the MTL-sCASO method accurately predicts behavioral scores (improved by 9.4% compared to the PC method) in the cognitive dimension. The decomposition of individual-specific and individual-shared components from RSFC provides a new approach for tracing individual traits and group analysis using functional brain networks.

Constructing Dynamic Functional Networks via Weighted Regularization and Tensor Low-Rank Approximation for Early Mild Cognitive Impairment Classification

Brain functional networks constructed via regularization has been widely used in early mild cognitive impairment (eMCI) classification. However, few methods can properly reflect the similarities and differences of functional connections among different people. Most methods ignore some topological attributes, such as connection strength, which may delete strong functional connections in brain functional networks. To overcome these limitations, we propose a novel method to construct dynamic functional networks (DFN) based on weighted regularization (WR) and tensor low-rank approximation (TLA), and apply it to identify eMCI subjects from normal subjects. First, we introduce the WR term into the DFN construction and obtain WR-based DFNs (WRDFN). Then, we combine the WRDFNs of all subjects into a third-order tensor for TLA processing, and obtain the DFN based on WR and TLA (WRTDFN) of each subject in the tensor. We calculate the weighted-graph local clustering coefficient of each region in each WRTDFN as the effective feature, and use the t-test for feature selection. Finally, we train a linear support vector machine (SVM) classifier to classify the WRTDFNs of all subjects. Experimental results demonstrate that the proposed method can obtain DFNs with the scale-free property, and that the classification accuracy (ACC), the sensitivity (SEN), the specificity (SPE), and the area under curve (AUC) reach 87.0662% ± 0.3202%, 83.4363% ± 0.5076%, 90.6961% ± 0.3250% and 0.9431 ± 0.0023, respectively. We also achieve the best classification results compared with other comparable methods. This work can effectively improve the classification performance of DFNs constructed by existing methods for eMCI and has certain reference value for the early diagnosis of Alzheimer’s disease (AD).

Inter-Subject Analysis: A Partial Gaussian Graphical Model Approach

Different from traditional intra-subject analysis, the goal of inter-subject analysis (ISA) is to explore the dependency structure between different subjects with the intra-subject dependency as nuisance. ISA has important applications in neuroscience to study the functional connectivity between brain regions under natural stimuli. We propose a modeling framework for ISA that is based on Gaussian graphical models, under which ISA can be converted to the problem of estimation and inference of a partial Gaussian graphical model. The main statistical challenge is that we do not impose sparsity constraints on the whole precision matrix and we only assume the inter-subject part is sparse. For estimation, we propose to estimate an alternative parameter to get around the nonsparse issue and it can achieve asymptotic consistency even if the intra-subject dependency is dense. For inference, we propose an "untangle and chord" procedure to de-bias our estimator. It is valid without the sparsity assumption on the inverse Hessian of the log-likelihood function. This inferential method is general and can be applied to many other statistical problems, thus it is of independent theoretical interest. Numerical experiments on both simulated and brain imaging data validate our methods and theory. Supplementary materials for this article are available online.

Estimating sparse functional connectivity networks via hyperparameter-free learning model

Functional connectivity networks (FCNs) provide a potential way for understanding the brain organizational patterns and diagnosing neurological diseases. Currently, researchers have proposed many methods for FCN construction, among which the most classic example is Pearson's correlation (PC). Despite its simplicity and popularity, PC always results in dense FCNs, and thus a thresholding strategy is usually needed in practice to sparsify the estimated FCNs prior to the network analysis, which undoubtedly causes the problem of threshold parameter selection. As an alternative to PC, sparse representation (SR) can directly generate sparse FCNs due to the l₁ regularizer in the estimation model. However, similar to the thresholding scheme used in PC, it is also challenging to determine suitable values for the regularization parameter in SR. To circumvent the difficulty of parameter selection involved in these traditional methods, we propose a hyperparameter-free method for FCN construction based on the global representation among fMRI time courses. Interestingly, the proposed method can automatically generate sparse FCNs, without any thresholding or regularization parameters. To verify the effectiveness of the proposed method, we conduct experiments to identify subjects with mild cognitive impairment (MCI) and Autism spectrum disorder (ASD) from normal controls (NCs) based on the estimated FCNs. Experimental results on two benchmark databases demonstrate that the achieved classification performance of our proposed scheme is comparable to four conventional methods.

Fusion of ULS Group Constrained High- and Low-Order Sparse Functional Connectivity Networks for MCI Classification

Functional connectivity networks, derived from resting-state fMRI data, have been found as effective biomarkers for identifying mild cognitive impairment (MCI) from healthy elderly. However, the traditional functional connectivity network is essentially a low-order network with the assumption that the brain activity is static over the entire scanning period, ignoring temporal variations among the correlations derived from brain region pairs. To overcome this limitation, we proposed a new type of sparse functional connectivity network to precisely describe the relationship of temporal correlations among brain regions. Specifically, instead of using the simple pairwise Pearson's correlation coefficient as connectivity, we first estimate the temporal low-order functional connectivity for each region pair based on an ULS Group constrained-UOLS regression algorithm, where a combination of ultra-least squares (ULS) criterion with a Group constrained topology structure detection algorithm is applied to detect the topology of functional connectivity networks, aided by an Ultra-Orthogonal Least Squares (UOLS) algorithm to estimate connectivity strength. Compared to the classical least squares criterion which only measures the discrepancy between the observed signals and the model prediction function, the ULS criterion takes into consideration the discrepancy between the weak derivatives of the observed signals and the model prediction function and thus avoids the overfitting problem. By using a similar approach, we then estimate the high-order functional connectivity from the low-order connectivity to characterize signal flows among the brain regions. We finally fuse the low-order and the high-order networks using two decision trees for MCI classification. Experimental results demonstrate the effectiveness of the proposed method on MCI classification.

Functional connectivity network estimation with an inter-similarity prior for mild cognitive impairment classification

Functional connectivity network (FCN) analysis is an effective technique for modeling human brain patterns and diagnosing neurological disorders such as Alzheimer's disease (AD) and its early stage, Mild Cognitive Impairment. However, accurately estimating biologically meaningful and discriminative FCNs remains challenging due to the poor quality of functional magnetic resonance imaging (fMRI) data and our limited understanding of the human brain. Inspired by the inter-similarity nature of FCNs, similar regions of interest tend to share similar connection patterns. Here, we propose a functional brain network modeling scheme by encoding Inter-similarity prior into a graph-regularization term, which can be easily solved with an efficient optimization algorithm. To illustrate its effectiveness, we conducted experiments to distinguish Mild Cognitive Impairment from normal controls based on their respective FCNs. Our method outperformed the baseline and state-of-the-art methods by achieving an 88.19% classification accuracy. Furthermore, post hoc inspection of the informative features showed that our method yielded more biologically meaningful functional brain connectivity.

Estimating sparse functional brain networks with spatial constraints for MCI identification

Functional brain network (FBN), estimated with functional magnetic resonance imaging (fMRI), has become a potentially useful way of diagnosing neurological disorders in their early stages by comparing the connectivity patterns between different brain regions across subjects. However, this depends, to a great extent, on the quality of the estimated FBNs, indicating that FBN estimation is a key step for the subsequent task of disorder identification. In the past decades, researchers have developed many methods to estimate FBNs, including Pearson’s correlation and (regularized) partial correlation, etc. Despite their widespread applications in current studies, most of the existing methods estimate FBNs only based on the dependency between the measured blood oxygen level dependent (BOLD) signals, which ignores spatial relationship of signals associated with different brain regions. Due to the space and material parsimony principle of our brain, we believe that the spatial distance between brain regions has an important influence on FBN topology. Therefore, in this paper, we assume that spatially neighboring brain regions tend to have stronger connections and/or share similar connections with others; based on this assumption, we propose two novel methods to estimate FBNs by incorporating the information of brain region distance into the estimation model. To validate the effectiveness of the proposed methods, we use the estimated FBNs to identify subjects with mild cognitive impairment (MCI) from normal controls (NCs). Experimental results show that the proposed methods are better than the baseline methods in the sense of MCI identification accuracy.

A Brain Network Constructed on an L1-Norm Regression Model Is More Sensitive in Detecting Small World Network Changes in Early AD

Most previous imaging studies have used traditional Pearson correlation analysis to construct brain networks. This approach fails to adequately and completely account for the interaction between adjacent brain regions. In this study, we used the L1-norm linear regression model to test the small-world attributes of the brain networks of three groups of patients, namely, those with mild cognitive impairment (MCI), Alzheimer's disease (AD), and healthy controls (HCs); we attempted to identify the method that may detect minor differences in MCI and AD patients. Twenty-four AD patients, 33 MCI patients, and 27 HC elderly subjects were subjected to functional MRI (fMRI). We applied traditional Pearson correlation and the L1-norm to construct the brain networks and then tested the small-world attributes by calculating the following parameters: clustering coefficient (Cp), path length (Lp), global efficiency (Eg), and local efficiency (Eloc). As expected, L1 could detect slight changes, mainly in MCI patients expressing higher Cp and Eloc; however, no statistical differences were found between MCI patients and HCs in terms of Cp, Lp, Eg, and Eloc, using Pearson correlation. Compared with HCs, AD patients expressed a lower Cp, Eloc, and Lp and an increased Eg using both connectivity metrics. The statistical differences between the groups indicated the brain networks constructed by the L1-norm were more sensitive to detect slight small-world network changes in early stages of AD.

Self-weighted adaptive structure learning for ASD diagnosis via multi-template multi-center representation

As a kind of neurodevelopmental disease, autism spectrum disorder (ASD) can cause severe social, communication, interaction, and behavioral challenges. To date, many imaging-based machine learning techniques have been proposed to address ASD diagnosis issues. However, most of these techniques are restricted to a single template or dataset from one imaging center. In this paper, we propose a novel multi-template multi-center ensemble classification scheme for automatic ASD diagnosis. Specifically, based on different pre-defined templates, we construct multiple functional connectivity (FC) brain networks for each subject based on our proposed Pearson's correlation-based sparse low-rank representation. After extracting features from these FC networks, informative features to learn optimal similarity matrix are then selected by our self-weighted adaptive structure learning (SASL) model. For each template, the SASL method automatically assigns an optimal weight learned from the structural information without additional weights and parameters. Finally, an ensemble strategy based on the multi- template multi-center representations is applied to derive the final diagnosis results. Extensive experiments are conducted on the publicly available Autism Brain Imaging Data Exchange (ABIDE) database to demonstrate the efficacy of our proposed method. Experimental results verify that our proposed method boosts ASD diagnosis performance and outperforms state-of-the-art methods.

Toward a Better Estimation of Functional Brain Network for Mild Cognitive Impairment Identification: A Transfer Learning View

Mild cognitive impairment (MCI) is an intermediate stage of brain cognitive decline, associated with increasing risk of developing Alzheimer's disease (AD). It is believed that early treatment of MCI could slow down the progression of AD, and functional brain network (FBN) could provide potential imaging biomarkers for MCI diagnosis and response to treatment. However, there are still some challenges to estimate a "good" FBN, particularly due to the poor quality and limited quantity of functional magnetic resonance imaging (fMRI) data from the target domain (i.e., MCI study). Inspired by the idea of transfer learning, we attempt to transfer information in high-quality data from source domain (e.g., human connectome project in this paper) into the target domain towards a better FBN estimation, and propose a novel method, namely NERTL (Network Estimation via Regularized Transfer Learning). Specifically, we first construct a high-quality network "template" based on the source data, and then use the template to guide or constrain the target of FBN estimation by a weighted l1-norm regularizer. Finally, we conduct experiments to identify subjects with MCI from normal controls (NCs) based on the estimated FBNs. Despite its simplicity, our proposed method is more effective than the baseline methods in modeling discriminative FBNs, as demonstrated by the superior MCI classification accuracy of 82.4% and the area under curve (AUC) of 0.910.

Group Similarity Constraint Functional Brain Network Estimation for Mild Cognitive Impairment Classification

Functional brain network (FBN) provides an effective biomarker for understanding brain activation patterns and a diagnostic criterion for neurodegenerative diseases detections. Unfortunately, it remains challenges to estimate the biologically meaningful or discriminative FBNs accurately, because of the poor quality of functional magnetic resonance imaging data or our limited understanding of human brain. In this study, a novel FBN estimation model based on group similarity prior was proposed. In particular, we extended the FBN estimation model to tensor form and incorporated the tensor trace-norm regularizer to formulate the group similarity constraint. To verify the proposed method, we conducted experiments on identifying mild cognitive impairments (MCIs) from normal controls (NCs) based on the estimated FBNs. Experimental results illustrated that our method is effective in modeling FBNs. Consequently, we achieved 91.97% classification accuracy, outperforming the state-of-the-art methods. The post hoc analysis further demonstrated that more biologically meaningful functional brain connections were obtained using our proposed method.

Hypernetwork Construction and Feature Fusion Analysis Based on Sparse Group Lasso Method on fMRI Dataset

Recent works have shown that the resting-state brain functional connectivity hypernetwork, where multiple nodes can be connected, are an effective technique for brain disease diagnosis and classification research. The lasso method was used to construct hypernetworks by solving sparse linear regression models in previous research. But, constructing a hypernetwork based on the lasso method simply selects a single variable, in that it lacks the ability to interpret the grouping effect. Considering the group structure problem, the previous study proposed to create a hypernetwork based on the elastic net and the group lasso methods, and the results showed that the former method had the best classification performance. However, the highly correlated variables selected by the elastic net method were not necessarily in the active set in the group. Therefore, we extended our research to address this issue. Herein, we propose a new method that introduces the sparse group lasso method to improve the construction of the hypernetwork by solving the group structure problem of the brain regions. We used the traditional lasso, group lasso method, and sparse group lasso method to construct a hypernetwork in patients with depression and normal subjects. Meanwhile, other clustering coefficients (clustering coefficients based on pairs of nodes) were also introduced to extract features with traditional clustering coefficients. Two types of features with significant differences obtained after feature selection were subjected to multi-kernel learning for feature fusion and classification using each method, respectively. The network topology results revealed differences among the three networks, where hypernetwork using the lasso method was the strictest; the group lasso, most lenient; and the sgLasso method, moderate. The network topology of the sparse group lasso method was similar to that of the group lasso method but different from the lasso method. The classification results show that the sparse group lasso method achieves the best classification accuracy by using multi-kernel learning, which indicates that better classification performance can be achieved when the group structure exists and is properly extended.

Directed EEG neural network analysis by LAPPS (p≤1) Penalized sparse Granger approach

The conventional multivariate Granger Analysis (GA) of directed interactions has been widely applied in brain network construction based on EEG recordings as well as fMRI. Nevertheless, EEG is usually inevitably contaminated by strong noise, which may cause network distortion due to the L2-norm used in GAs for directed network recovery. The Lp (p ≤1) norm has been shown to be more robust to outliers as compared to LASSO and L2-GAs. Motivated to construct the sparse brain networks under strong noise condition, we hereby introduce a new approach for GA analysis, termed LAPPS (Least Absolute LP (0<p<1) Penalized Solution). LAPPS utilizes the L1-loss function for the residual error to alleviate the effect of outliers, and another Lp-penalty term (p=0.5) to obtain the sparse connections while suppressing the spurious linkages in the networks. The simulation results reveal that LAPPS obtained the best performance under various noise conditions. In a real EEG data test when subjects performed the left and right hand Motor Imagery (MI) for brain network estimation, LAPPS also obtained a sparse network pattern with the hub at the contralateral brain primary motor areas consistent with the physiological basis of MI.

Functional Brain Network Estimation With Time Series Self-Scrubbing

Functional brain network (FBN) is becoming an increasingly important measurement for exploring cerebral mechanisms and mining informative biomarkers that assist diagnosis of some neurodegenerative disorders. Despite its effectiveness to discover valuable hidden patterns in the human brain, the estimated FBNs are often heavily influenced by the quality of the observed data (e.g., blood oxygen level dependent signal series). In practice, a preprocessing pipeline is usually employed for improving data quality. With this in mind, some data points (volumes or time course in the time series) are still not clean enough, due to artifacts including spurious resting-state processes (head movement, mind-wandering). Therefore, not all volumes in the fMRI time series can contribute to the subsequent FBN estimation. To address this issue, we propose a novel FBN estimation method by introducing a latent variable as an indicator of the data quality, and develop an alternating optimization algorithm for jointly scrubbing the data and estimating FBN simultaneously. To further illustrate the effectiveness of the proposed method, we conduct experiments on two public datasets to identify subjects with mild cognitive impairment from normal controls based on the estimated FBNs, and achieve improved accuracies than the baseline methods.

Estimating Functional Connectivity Networks via Low-Rank Tensor Approximation With Applications to MCI Identification

Functional connectivity network (FCN) has become an increasingly important approach to gain a better understanding of the brain, as well as discover informative biomarkers for diagnosis of neurodegenerative diseases. Due to its importance, many FCN estimation methods have been developed in the past decades, including methods based on the classical Pearson's correlation, (regularized) partial correlation, and some higher-order variants. However, most of the existing methods estimate one FCN at a time, thus ignoring the possibly shared structure among FCNs from different subjects. Recently, researchers introduce group constraints (or population priors) into FCN estimation by assuming that FCNs are topologically identical across subjects. Obviously, such a constraint/prior is too strong to be satisfied in practice, especially when both patients and healthy subjects are involved simultaneously in the group. To address this problem, we propose a novel FCN estimation approach based on an assumption that the involved FCNs have similar but not necessarily identical topology. More specifically, we implement this idea under a two-step learning framework. First, we independently estimate FCNs based on traditional methods, such as Pearson's correltion and sparse representation, making sure that each FCN captures the specific properties of the corresponding subject. Then, we stack the estimated FCNs (in fact, their adjacency matrices) into a tensor, and refine the stacked FCNs via low-rank tensor approximation. Finally, we apply the improved FCNs to identify subjects with mild cognitive impairment (MCI) from healthy controls, and achieve a higher classification accuracy.

Lasso Regression for the Prediction of Intermediate Outcomes Related to Cardiovascular Disease Prevention Using the TRANSIT Quality Indicators

BACKGROUND

Cardiovascular disease morbidity and mortality are largely influenced by poor control of hypertension, dyslipidemia, and diabetes. Process indicators are essential to monitor the effectiveness of quality improvement strategies. However, process indicators should be validated by demonstrating their ability to predict desirable outcomes. The objective of this study is to identify an effective method for building prediction models and to assess the predictive validity of the TRANSIT indicators.

METHODS

On the basis of blood pressure readings and laboratory test results at baseline, the TRANSIT study population was divided into 3 overlapping subpopulations: uncontrolled hypertension, uncontrolled dyslipidemia, and uncontrolled diabetes. A classic statistical method, a sparse machine learning technique, and a hybrid method combining both were used to build prediction models for whether a patient reached therapeutic targets for hypertension, dyslipidemia, and diabetes. The final models' performance for predicting these intermediate outcomes was established using cross-validated area under the curves (cvAUC).

RESULTS

At baseline, 320, 247, and 303 patients were uncontrolled for hypertension, dyslipidemia, and diabetes, respectively. Among the 3 techniques used to predict reaching therapeutic targets, the hybrid method had a better discriminative capacity (cvAUCs=0.73 for hypertension, 0.64 for dyslipidemia, and 0.79 for diabetes) and succeeded in identifying indicators with a better capacity for predicting intermediate outcomes related to cardiovascular disease prevention.

CONCLUSIONS

Even though this study was conducted in a complex population of patients, a set of 5 process indicators were found to have good predictive validity based on the hybrid method.

Weighted Graph Regularized Sparse Brain Network Construction for MCI Identification

Brain functional networks (BFNs) constructed from resting-state functional magnetic resonance imaging (rs-fMRI) have been widely applied to the analysis and diagnosis of brain diseases, such as Alzheimer's disease and its prodrome, namely mild cognitive impairment (MCI). Constructing a meaningful brain network based on, for example, sparse representation (SR) is the most essential step prior to the subsequent analysis or disease identification. However, the independent coding process of SR fails to capture the intrinsic locality and similarity characteristics in the data. To address this problem, we propose a novel weighted graph (Laplacian) regularized SR framework, based on which BFN can be optimized by considering both intrinsic correlation similarity and local manifold structure in the data, as well as sparsity prior of the brain connectivity. Additionally, the non-convergence of the graph Laplacian in the self-representation model has been solved properly. Combined with a pipeline of sparse feature selection and classification, the effectiveness of our proposed method is demonstrated by identifying MCI based on the constructed BFNs.

Novel Effective Connectivity Inference Using Ultra-Group Constrained Orthogonal Forward Regression and Elastic Multilayer Perceptron Classifier for MCI Identification

Mild cognitive impairment (MCI) detection is important, such that appropriate interventions can be imposed to delay or prevent its progression to severe stages, including Alzheimer's disease (AD). Brain connectivity network inferred from the functional magnetic resonance imaging data has been prevalently used to identify the individuals with MCI/AD from the normal controls. The capability to detect the causal or effective connectivity is highly desirable for understanding directed functional interactions between brain regions and further helping the detection of MCI. In this paper, we proposed a novel sparse constrained effective connectivity inference method and an elastic multilayer perceptron classifier for MCI identification. Specifically, a ultra-group constrained structure detection algorithm is first designed to identify the parsimonious topology of the effective connectivity network, in which the weak derivatives of the observable data are considered. Second, based on the identified topology structure, an effective connectivity network is then constructed by using an ultra-orthogonal forward regression algorithm to minimize the shrinking effect of the group constraint-based method. Finally, the effective connectivity network is validated in MCI identification using an elastic multilayer perceptron classifier, which extracts lower to higher level information from initial input features and hence improves the classification performance. Relatively high classification accuracy is achieved by the proposed method when compared with the state-of-the-art classification methods. Furthermore, the network analysis results demonstrate that MCI patients suffer a rich club effect loss and have decreased connectivity among several brain regions. These findings suggest that the proposed method not only improves the classification performance but also successfully discovers critical disease-related neuroimaging biomarkers.