A Novel Sparse Dictionary Learning Separation (SDLS) Model With Adaptive Dictionary Mutual Incoherence Constraint for fMRI Data Analysis

By finding broader temporal and spatial patterns of brain activity, dictionary learning and sparse coding techniques circumvent the constraints of typical voxel-level studies of task-based functional magnetic resonance imaging (fMRI) data. Prior applications of these algorithms to task-related fMRI data, on the other hand, have not been tuned to simultaneously uncover temporal patterns of activity that change in tandem with changes in task circumstances and spatial patterns that exploit existing neuroscience knowledge. This work, presents a sparse dictionary learning method that decomposes fMRI data into temporal patterns of signals that loosely differ between task conditions and sparse spatial patterns that are at least partially similar to known functional network hubs, based on prior knowledge of the temporal pattern of task conditions and the locations of brain regions hypothesized to be involved in the task. To over come the a major drawback of the prior work in terms being constrained to provide an equal number of spatial and temporal patterns, even when the data was more accurately represented by a larger number spatial than temporal patterns (or vice versa), this work also propose a constrained decoupled dictionary learning method that uses prior knowledge related to task paradigms and the spatial locations of task-related brain regions to estimate decoupled spatial and temporal patterns that represent the fMRI data. The utility of sparse dictionary learning methods applied to task fMRI data is increased by simultaneously exploiting the task's known temporal structure and biasing solutions towards putative network hubs. The method identifies a high percentage of the spatial and temporal patterns programmed into simulated fMRI data. The temporal and spatial patterns are identified using an effective on-line optimization methodology. The technique detects geographical and temporal patterns in synthetic task fMRI data. When applied to two real-world fMRI data sets, the method: 1. automatically identifies temporal and spatial patterns that were known by neuroscientists to be task-related a priori but were not provided as inputs to the method; 2. provides measurements that differ significantly between differing tasks. When applied to real fMRI data from 100 participants two different studies, the suggested method also identifies geographic regions known a priori to be engaged by the Attention Network Task (ANT), AX-Continuous Performance Task (AX-CPT) and Stroop Task more thoroughly than competing methods. Using task information to partially constrain dictionary learning allowed this method to identify task related networks in real and synthetic fMRI data.

THINGS-data reflects three large-scale neuroimaging and behavioral datasets of object processing in humans, comprising densely sampled functional MRI and magnetoencephalographic recordings, as well as 4.70 million similarity judgments in response to thousands of photographic images for up to 1854 objects.

[1] Sparse geologic dictionaries provide a novel approach for subsurface flow model representation and calibration. Learning sparse dictionaries from prior training data sets is an effective approach to describe complex geologic connectivity patterns in subsurface imaging applications. However, the computational cost of sparse learning algorithms becomes prohibitive for large models. Performing the sparse dictionary learning process on smaller image patches (segments) provides a simple approach to address this problem in image processing applications. However, in underdetermined subsurface flow model calibration inverse problems, reconstruction of a segmented image can introduce significant structural distortion and discontinuity at the boundaries of the segments. This paper proposes an alternative sparse learning approach where the sparse dictionaries are learned from low-rank representations of the large-scale training data set in spectral domains (e.g., frequency domain). The objective is to develop a computationally efficient dictionary learning approach that emphasizes large-scale spatial connectivity patterns. This is achieved by removing the strong spatial correlations in the training data, thereby eliminating a large number of insignificant components from the sparse learning computation. In addition to improving the computational complexity, sparse learning from low-rank training data sets suppresses the small-scale details from entering the reconstruction of large-scale connectivity patterns, thereby providing a regularization effect in solving the resulting ill-posed inverse problems. We apply the proposed approach to travel-time tomography inversion and nonlinear subsurface flow model calibration inverse problems to demonstrate its effectiveness and practicality.

Identification of module structure in brain functional networks is a promising way to obtain novel insights into neural information processing, as modules correspond to delineated brain regions in which interactions are strongly increased. Tracking of network modules in time-varying brain functional networks is not yet commonly considered in neuroscience despite its potential for gaining an understanding of the time evolution of functional interaction patterns and associated changing degrees of functional segregation and integration. We introduce a general computational framework for extracting consensus partitions from defined time windows in sequences of weighted directed edge-complete networks and show how the temporal reorganization of the module structure can be tracked and visualized. Part of the framework is a new approach for computing edge weight thresholds for individual networks based on multiobjective optimization of module structure quality criteria as well as an approach for matching modules across time steps. By testing our framework using synthetic network sequences and applying it to brain functional networks computed from electroencephalographic recordings of healthy subjects that were exposed to a major balance perturbation, we demonstrate the framework's potential for gaining meaningful insights into dynamic brain function in the form of evolving network modules. The precise chronology of the neural processing inferred with our framework and its interpretation helps to improve the currently incomplete understanding of the cortical contribution for the compensation of such balance perturbations.

One of human brain's remarkable traits lies in its capacity to dynamically coordinate the activities of multiple brain regions or networks, adapting to an externally changing environment. Studying the dynamic functional brain networks (DFNs) and their role in perception, assessment, and action can significantly advance our comprehension of how the brain responds to patterns of sensory input. Movies provide a valuable tool for studying DFNs, as they offer a naturalistic paradigm that can evoke complex cognitive and emotional experiences through rich multimodal and dynamic stimuli. However, most previous research on DFNs have predominantly concentrated on the resting-state paradigm, investigating the topological structure of temporal dynamic brain networks generated via chosen templates. The dynamic spatial configurations of the functional networks elicited by naturalistic stimuli demand further exploration. In this study, we employed an unsupervised dictionary learning and sparse coding method combing with a sliding window strategy to map and quantify the dynamic spatial patterns of functional brain networks (FBNs) present in naturalistic functional magnetic resonance imaging (NfMRI) data, and further evaluated whether the temporal dynamics of distinct FBNs are aligned to the sensory, cognitive, and affective processes involved in the subjective perception of the movie. The results revealed that movie viewing can evoke complex FBNs, and these FBNs were time-varying with the movie storylines and were correlated with the movie annotations and the subjective ratings of viewing experience. The reliability of DFNs was also validated by assessing the Intra-class coefficient (ICC) among two scanning sessions under the same naturalistic paradigm with a three-month interval. Our findings offer novel insight into comprehending the dynamic properties of FBNs in response to naturalistic stimuli, which could potentially deepen our understanding of the neural mechanisms underlying the brain's dynamic changes during the processing of visual and auditory stimuli.

Resting-state brain functional networks (BFNs) give information about spatio-temporal interactions in the brain when the subject is at rest or not performing any task. Investigations with resting-state functional Magnetic Resonance Imaging (rs-fMRI) data have shown that the BFN possesses a modular architecture. However, the nodal degree distributions within the modules of BFN, over a large population of subjects, have not thus far been investigated. The aim of this work is to assign modular memberships to brain functional regions and study nodal degree distributions of brain functional modules. We fit different models of nodal degree distributions for brain functional modules such as default mode, visual, sensory/somatomotor hand, and fronto-parietal task control networks by using power-law, exponential, and stretched-exponential distributions. Our analysis shows nodal degree distributions in the complete BFN and individual brain modules follow stretched exponential probability distribution. This suggests a uniform trend in functional connection formation across the BFN where connections follow neither random nor the preferential attachment model. Experiments have been performed on data gathered from rs-fMRI scans of 627 subjects from the Human Connectome Project (HCP).

Task-based fMRI (tfMRI) has been widely used to study functional brain networks. Modeling tfMRI data is challenging due to at least two problems: the lack of the ground truth of underlying neural activity and the intrinsic structure of tfMRI data is highly complex. To better understand brain networks based on fMRI data, data-driven approaches were proposed, for instance, Independent Component Analysis (ICA) and Sparse Dictionary Learning (SDL). However, both ICA and SDL only build shallow models, and they are under the strong assumption that original fMRI signal could be linearly decomposed into time series components with their corresponding spatial maps. As growing evidence shows that human brain function is hierarchically organized, new approaches that can infer and model the hierarchical structure of brain networks are widely called for. Recently, deep convolutional neural network (CNN) has drawn much attention, in that deep CNN has been proven to be a powerful method for learning high-level and mid-level abstractions from low-level raw data. Inspired by the power of deep CNN, in this study, we developed a new neural network structure based on CNN, called Deep Convolutional Auto-Encoder (DCAE), in order to take the advantages of both data-driven approach and CNN’s hierarchical feature abstraction ability for the purpose of learning mid-level and high-level features from complex tfMRI time series in an unsupervised manner. The DCAE has been applied and tested on the publicly available human connectome project (HCP) tfMRI datasets, and promising results are achieved.

Sparse dictionary learning by block proximal gradient with global convergence

A two-step super-Gaussian independent component analysis approach for fMRI data

BGCSL: An unsupervised framework reveals the underlying structure of large-scale whole-brain functional connectivity networks.

At rest, human brain functional networks display striking modular architecture in which coherent clusters of brain regions are activated. The modular account of brain function is pervasive, reliable, and reproducible. Yet, a complementary perspective posits a core–periphery or rich-club account of brain function, where hubs are densely interconnected with one another, allowing for integrative processing. Unifying these two perspectives has remained difficult due to the fact that the methodological tools to identify modules are entirely distinct from the methodological tools to identify core–periphery structure. Here, we leverage a recently-developed model-based approach—the weighted stochastic block model—that simultaneously uncovers modular and core–periphery structure, and we apply it to functional magnetic resonance imaging data acquired at rest in 872 youth of the Philadelphia Neurodevelopmental Cohort. We demonstrate that functional brain networks display rich mesoscale organization beyond that sought by modularity maximization techniques. Moreover, we show that this mesoscale organization changes appreciably over the course of neurodevelopment, and that individual differences in this organization predict individual differences in cognition more accurately than module organization alone. Broadly, our study provides a unified assessment of modular and core–periphery structure in functional brain networks, offering novel insights into their development and implications for behavior.

High dimensionality data have become common in neuroimaging fields, especially group‐level functional magnetic resonance imaging (fMRI) datasets. fMRI connectivity analysis is a widely used, powerful technique for studying functional brain networks to probe underlying mechanisms of brain function and neuropsychological disorders. However, data‐driven technique like independent components analysis (ICA), can yield unstable and inconsistent results, confounding the true effects of interest and hindering the understanding of brain functionality and connectivity. A key contributing factor to this instability is the information loss that occurs during fMRI data reduction. Data reduction of high dimensionality fMRI data in the temporal domain to identify the important information within group datasets is necessary for such analyses and is crucial to ensure the accuracy and stability of the outputs. In this study, we describe an fMRI data reduction strategy based on an adapted neighborhood preserving embedding (NPE) algorithm. Both simulated and real data results indicate that, compared with the widely used data reduction method, principal component analysis, the NPE‐based data reduction method (a) shows superior performance on efficient data reduction, while enhancing group‐level information, (b) develops a unique stratagem for selecting components based on an adjacency graph of eigenvectors, (c) generates more reliable and reproducible brain networks under different model orders when the outputs of NPE are used for ICA, (d) is more sensitive to revealing task‐evoked activation for task fMRI, and (e) is extremely attractive and powerful for the increasingly popular fast fMRI and very large datasets.

Aiming to study the local functional structure of brain function network in resting state, the Fuzzy C-means (FCM) algorithm is adapted to modular the brain functional network. Then the nodes in module are connected into a network using correlation between the time series extracted from Functional Magnetic Resonance Imaging (fMRI) data. Afterwards node degree, clustering coefficient and shortest path length are used to analyse the functional characteristics of networks. Finally, the differences in activation between patients and normal controls’ brain regions are compared through Amplitude of Low Frequency Fluctuation (ALFF). Experimental results demonstrate that, the shortest path length of the patient is smaller than that of the normal human, so the information transmission rate increases. Clustering coefficient is higher than the normal, and the degree of grouping of network is enhanced. The correlation between the patient nodes is generally greater than the normal, and there is a weakened situation in the local area. It also found that the proportion of region for the activation level higher than the average of the whole brain in normal with more than the patient. In particular, the activation level of the Precentral gyrus (PreCG) and other regions in patient has a large degree decline. And the activation level in left Caudate nucleus (CAU.L), the lenticular nucleus, Putamen (PUT) and the lenticular nucleus, Palladium (PAL) and other regions is increased for patient. The research results verify the feasibility of modularization analysis of brain functional network using algorithm and correlation in resting state.

Investigating the enhancement of template-free activation detection of event-related fMRI data using wavelet shrinkage and figures of merit

The central nervous system, specifically the brain, is implicated in the development of exertional fatigue under a hot environment. Diverse neuroimaging techniques have been used to visualize the brain activity during or after exercise. Notably, the use of magnetic resonance imaging (MRI) has become prevalent due to its excellent spatial resolution and versatility. This review evaluates the significance and limitations of various brain MRI techniques in exercise studies-brain volumetric analysis, functional MRI, functional connectivity MRI, and arterial spin labeling. The review aims to provide a summary on the neural basis of exertional fatigue and proposes future directions for brain MRI studies. A systematic literature search was performed where a total of thirty-seven brain MRI studies associated with exercise, fatigue, or related physiological factors were reviewed. The findings suggest that with moderate dehydration, there is a decrease in total brain volume accompanied with expansion of ventricular volume. With exercise fatigue, there is increased activation of sensorimotor and cognitive brain areas, increased thalamo-insular activation and decreased interhemispheric connectivity in motor cortex. Under passive hyperthermia, there are regional changes in cerebral perfusion, a reduction in local connectivity in functional brain networks and an impairment to executive function. Current literature suggests that the brain structure and function are influenced by exercise, fatigue, and related physiological perturbations. However, there is still a dearth of knowledge and it is hoped that through understanding of MRI advantages and limitations, future studies will shed light on the central origin of exertional fatigue in the heat.