Dynamic Functional Magnetic Resonance Imaging Connectivity Tensor Decomposition: A New Approach to Analyze and Interpret Dynamic Brain Connectivity

Dynamic functional network connectivity analysis in schizophrenia based on a spatiotemporal CPD framework

Objective.Dynamic functional network connectivity (dFNC), based on data-driven group independent component (IC) analysis, is an important avenue for investigating underlying patterns of certain brain diseases such as schizophrenia. Canonical polyadic decomposition (CPD) of a higher-way dynamic functional connectivity tensor, can offer an innovative spatiotemporal framework to accurately characterize potential dynamic spatial and temporal fluctuations. Since multi-subject dFNC data from sliding-window analysis are also naturally a higher-order tensor, we propose an innovative sparse and low-rank CPD (SLRCPD) for the three-way dFNC tensor to excavate significant dynamic spatiotemporal aberrant changes in schizophrenia.Approach.The proposed SLRCPD approach imposes two constraints. First, the L1regularization on spatial modules is applied to extract sparse but significant dynamic connectivity and avoid overfitting the model. Second, low-rank constraint is added on time-varying weights to enhance the temporal state clustering quality. Shared dynamic spatial modules, group-specific dynamic spatial modules and time-varying weights can be extracted by SLRCPD. The strength of connections within- and between-IC networks and connection contribution are proposed to inspect the spatial modules. K-means clustering and classification are further conducted to explore temporal group difference.Main results.82 subject resting-state functional magnetic resonance imaging (fMRI) dataset and opening Center for Biomedical Research Excellence (COBRE) schizophrenia dataset both containing schizophrenia patients (SZs) and healthy controls (HCs) were utilized in our work. Three typical dFNC patterns between different brain functional regions were obtained. Compared to the spatial modules of HCs, the aberrant connections among auditory network, somatomotor, visual, cognitive control and cerebellar networks in 82 subject dataset and COBRE dataset were detected. Four temporal states reveal significant differences between SZs and HCs for these two datasets. Additionally, the accuracy values for SZs and HCs classification based on time-varying weights are larger than 0.96.Significance.This study significantly excavates spatio-temporal patterns for schizophrenia disease.

Kernel-based joint independence tests for multivariate stationary and non-stationary time series

Multivariate time-series data that capture the temporal evolution of interconnected systems are ubiquitous in diverse areas. Understanding the complex relationships and potential dependencies among co-observed variables is crucial for the accurate statistical modelling and analysis of such systems. Here, we introduce kernel-based statistical tests of joint independence in multivariate time series by extending the d-variable Hilbert-Schmidt independence criterion to encompass both stationary and non-stationary processes, thus allowing broader real-world applications. By leveraging resampling techniques tailored for both single- and multiple-realization time series, we show how the method robustly uncovers significant higher-order dependencies in synthetic examples, including frequency mixing data and logic gates, as well as real-world climate, neuroscience and socio-economic data. Our method adds to the mathematical toolbox for the analysis of multivariate time series and can aid in uncovering high-order interactions in data.

A semi-supervised classification RBM with an improved fMRI representation algorithm

BACKGROUND AND OBJECTIVE

Training an effective and robust supervised learning classifier is not easy due to the limitations of acquiring and labeling considerable human functional magnetic resonance imaging (fMRI) data. Semi-supervised learning uses unlabeled data for feature learning and combines them into labeled data to build better classification models.

METHODS

Since no premises or assumptions are required, a restricted Boltzmann machine (RBM) is suitable for learning data representation of neuroimages. In our study, an improved fMRI representation algorithm with a hybrid L1/L2 regularization method (HRBM) was proposed to optimize the original model for sparsity. Different from common semi-supervised classification models that treat feature learning and classification as two separate training steps, we then constructed a new semi-supervised classification RBM based on a joint training algorithm with HRBM, named Semi-HRBM. This joint training algorithm jointly trains the objective function of feature learning and classification process, so that the learned features can effectively represent the original fMRI data and adapt to the classification tasks.

RESULTS

This study uses fMRI data to identify categories of visual stimuli. In the fMRI data classification task under four visual stimuli (house, face, car, and cat), our HRBM has satisfactory feature representation capabilities and better performance for multiple classification tasks. Taking the supervised RBM (sup-RBM) as an example, our Semi-HRBM classification model improves the average accuracy of the four-classification task by 7.68%, and improves the average F1 score of each visual stimulus task by 8.90%. In addition, the generalization ability of the model was also improved.

CONCLUSION

This research might contribute to enrich solutions for insufficiently labeled neuroimaging samples, which could help to identify complex brain states under different stimuli or tasks.

A mixed-modeling framework for whole-brain dynamic network analysis

The emerging area of dynamic brain network analysis has gained considerable attention in recent years. However, development of multivariate statistical frameworks that allow for examining the associations between phenotypic traits and dynamic patterns of system-level properties of the brain, and drawing statistical inference about such associations, has largely lagged behind. To address this need we developed a mixed-modeling framework that allows for assessing the relationship between any desired phenotype and dynamic patterns of whole-brain connectivity and topology. This novel framework also allows for simulating dynamic brain networks with respect to desired covariates. Unlike current tools, which largely use data-driven methods, our model-based method enables aligning neuroscientific hypotheses with the analytic approach. We demonstrate the utility of this model in identifying the relationship between fluid intelligence and dynamic brain networks by using resting-state fMRI (rfMRI) data from 200 participants in the Human Connectome Project (HCP) study. We also demonstrate the utility of this model to simulate dynamic brain networks at both group and individual levels. To our knowledge, this approach provides the first model-based statistical method for examining dynamic patterns of system-level properties of the brain and their relationships to phenotypic traits as well as simulating dynamic brain networks.

In recent years, a growing body of studies have aimed at analyzing the brain as a complex dynamic system by using various neuroimaging data. This has opened new avenues to answer compelling questions about the brain function in health and disease. However, methods that allow for providing statistical inference about how the complex interactions of the brain are associated with desired phenotypes are to be developed for a more profound insight. This study introduces a promising regression-based model to relate dynamic brain networks to desired phenotypes and provide statistical inference. Moreover, it can be used for simulating dynamic brain networks with respect to desired phenotypes at the group and individual levels.

Predicting Biological Gender and Intelligence From fMRI via Dynamic Functional Connectivity

OBJECTIVE

This paper explores the predictive capability of dynamic functional connectivity extracted from functional magnetic resonance imaging (fMRI) of the human brain, in contrast to static connectivity used in past research.

METHODS

Several state-of-the-art features extracted from static functional connectivity of the brain are employed to predict biological gender and intelligence using publicly available Human Connectome Project (HCP) database. Next, a novel tensor parallel factor (PARAFAC) decomposition model is proposed to decompose sequence of dynamic connectivity matrices into common connectivity components that are orthonormal to each other, common time-courses, and corresponding distinct subject-wise weights. The subject-wise loading of the components are employed to predict biological gender and intelligence using a random forest classifier (respectively, regressor) using 5-fold cross-validation.

RESULTS

The results demonstrate that dynamic functional connectivity can indeed classify biological gender with a high accuracy (0.94, where male identification accuracy was 0.87 and female identification accuracy was 0.97). It can also predict intelligence with less normalized mean square error (0.139 for fluid intelligence and 0.031 for fluid ability metrics) compared with other functional connectivity measures (the nearest mean square error were 0.147 and 0.037 for fluid intelligence and fluid ability metrics, respectively, using static connectivity approaches).

CONCLUSION

Our work is an important milestone for the understanding of non-stationary behavior of hemodynamic blood-oxygen level dependent (BOLD) signal in brain and how they are associated with biological gender and intelligence.

SIGNIFICANCE

The paper demonstrates that dynamic behavior of brain can contribute substantially towards forming a fingerprint of biological gender and intelligence.

Characterizing Rapid Fluctuations of Resting State Functional Connectivity in Demyelinating, Neurodegenerative, and Psychiatric Conditions: From Static to Time-Varying Analysis

Functional magnetic resonance imaging (fMRI) at resting state (RS) has been widely used to characterize the main brain networks. Functional connectivity (FC) has been mostly assessed assuming that FC is static across the whole fMRI examination. However, FC is highly variable at a very fast time-scale, as demonstrated by neurophysiological techniques. Time-varying functional connectivity (TVC) is a novel approach that allows capturing reoccurring patterns of interaction among functional brain networks. Aim of this review is to provide a description of the methods currently used to assess TVC on RS fMRI data, and to summarize the main results of studies applying TVC in healthy controls and patients with multiple sclerosis (MS). An overview of the main results obtained in neurodegenerative and psychiatric conditions is also provided. The most popular TVC approach is based on the so-called “sliding windows,” in which the RS fMRI acquisition is divided in small temporal segments (windows). A window of fixed length is shifted over RS fMRI time courses, and data within each window are used to calculate FC and its variability over time. Sliding windows can be combined with clustering techniques to identify recurring FC states or used to assess global TVC properties of large-scale functional networks or specific brain regions. TVC studies have used heterogeneous methodologies so far. Despite this, similar results have been obtained across investigations. In healthy subjects, the default-mode network (DMN) exhibited the highest degree of connectivity dynamism. In MS patients, abnormal global TVC properties and TVC strengths were found mainly in sensorimotor, DMN and salience networks, and were associated with more severe structural MRI damage and with more severe physical and cognitive disability. Conversely, abnormal TVC measures of the temporal network were correlated with better cognitive performances and less severe fatigue. In patients with neurodegenerative and psychiatric conditions, TVC abnormalities of the DMN, attention and executive networks were associated to more severe clinical manifestations. TVC helps to provide novel insights into fundamental properties of functional networks, and improves the understanding of brain reorganization mechanisms. Future technical advances might help to clarify TVC association with disease prognosis and response to treatment.