scholarly journals Beyond linear dynamic functional connectivity: a vine copula change point model

2021 ◽  
Author(s):  
Xin Xiong ◽  
Ivor Cribben
Keyword(s):  
Functional Connectivity ◽  
Change Point ◽  
Sliding Window ◽  
Brain Regions ◽  
Change Points ◽  
Fmri Data ◽  
Data Sets ◽  
Dynamic Functional Connectivity ◽  
Vine Copula ◽  
Vine Copulas

To estimate dynamic functional connectivity for functional magnetic resonance imaging (fMRI) data, two approaches have dominated: sliding window and change point methods. While computationally feasible, the sliding window approach has several limitations. In addition, the existing change point methods assume a Gaussian distribution for and linear dependencies between the fMRI time series. In this work, we introduce a new methodology called Vine Copula Change Point (VCCP) to estimate change points in the functional connectivity network structure between brain regions. It uses vine copulas, various state-of-the-art segmentation methods to identify multiple change points, and a likelihood ratio test or the stationary bootstrap for inference. The vine copulas allow for various forms of dependence between brain regions including tail, symmetric and asymmetric dependence, which has not been explored before in the analysis of neuroimaging data. We apply VCCP to various simulation data sets and to two fMRI data sets: a reading task and an anxiety inducing experiment. In particular, for the former data set, we illustrate the complexity of textual changes during the reading of Chapter 9 in Harry Potter and the Sorcerer's Stone and find that change points across subjects are related to changes in more than one type of textual attributes. Further, the graphs created by the vine copulas indicate the importance of working beyond Gaussianity and linear dependence. Finally, the R package vccp implementing the methodology from the paper is available from CRAN.

scholarly journals Cross-covariance isolate detect: a new change-point method for estimating dynamic functional connectivity

2020 ◽  
Author(s):  
Andreas Anastasiou ◽  
Ivor Cribben ◽  
Piotr Fryzlewicz
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Change Point ◽  
Sliding Window ◽  
Resting State Fmri ◽  
Change Point Detection ◽  
Change Points ◽  
Fmri Data ◽  
Cross Covariance ◽  
Window Approach

Evidence of the non stationary behavior of functional connectivity (FC) networks has been observed in task based functional magnetic resonance imaging (fMRI) experiments and even prominently in resting state fMRI data. This has led to the development of several new statistical methods for estimating this time-varying connectivity, with the majority of the methods utilizing a sliding window approach. While computationally feasible, the sliding window approach has several limitations. In this paper, we circumvent the sliding window, by introducing a statistical method that finds change-points in FC networks where the number and location of change-points are unknown a priori. The new method, called cross-covariance isolate detect (CCID), detects multiple change-points in the second-order (cross-covariance or network) structure of multivariate, possibly high-dimensional time series. CCID allows for change-point detection in the presence of frequent changes of possibly small magnitudes, can assign change-points to one or multiple brain regions, and is computationally fast. In addition, CCID is particularly suited to task based data, where the subject alternates between task and rest, as it firstly attempts isolation of each of the change-points within subintervals, and secondly their detection therein. Furthermore, we also propose a new information criterion for CCID to identify the change-points. We apply CCID to several simulated data sets and to task based and resting state fMRI data and compare it to recent change-point methods. CCID is also applicable to electroencephalography (EEG), magentoencephalography (MEG) and electrocorticography (ECoG) data. Similar to other biological networks, understanding the complex network organization and functional dynamics of the brain can lead to profound clinical implications. Finally, the R package ccid implementing the method from the paper is available from GitHub.

scholarly journals A Novel Unit-Based Personalized Fingerprint Feature Selection Strategy for Dynamic Functional Connectivity Networks

2021 ◽  
Vol 15 ◽  
Author(s):  
Feng Zhao ◽  
Zhiyuan Chen ◽  
Islem Rekik ◽  
Peiqiang Liu ◽  
Ning Mao ◽  
...  
Keyword(s):  
Feature Selection ◽  
Functional Connectivity ◽  
Evaluation Method ◽  
Brain Regions ◽  
Autism Spectrum ◽  
Superior Performance ◽  
Selection Strategy ◽  
Dynamic Functional Connectivity ◽  
Discriminative Feature ◽  
Fingerprint Feature

The sliding-window-based dynamic functional connectivity networks (SW-D-FCN) derive from resting-state functional Magnetic Resonance Imaging has become an increasingly useful tool in the diagnosis of various neurodegenerative diseases. However, it is still challenging to learn how to extract and select the most discriminative features from SW-D-FCN. Conventionally, existing methods opt to select a single discriminative feature set or concatenate a few more from the SW-D-FCN. However, such reductionist strategies may fail to fully capture the personalized discriminative characteristics contained in each functional connectivity (FC) sequence of the SW-D-FCN. To address this issue, we propose a unit-based personalized fingerprint feature selection (UPFFS) strategy to better capture the most discriminative feature associated with a target disease for each unit. Specifically, we regard the FC sequence between any pair of brain regions of interest (ROIs) is regarded as a unit. For each unit, the most discriminative feature is identified by a specific feature evaluation method and all the most discriminative features are then concatenated together as a feature set for the subsequent classification task. In such a way, the personalized fingerprint feature derived from each FC sequence can be fully mined and utilized in classification decision. To illustrate the effectiveness of the proposed strategy, we conduct experiments to distinguish subjects diagnosed with autism spectrum disorder from normal controls. Experimental results show that the proposed strategy can select relevant discriminative features and achieve superior performance to benchmark methods.

scholarly journals Single-scale time-dependent window-sizes in sliding-window dynamic functional connectivity analysis: A validation study

NeuroImage ◽  
2020 ◽  
Vol 220 ◽  
pp. 117111
Author(s):  
Xiaowei Zhuang ◽  
Zhengshi Yang ◽  
Virendra Mishra ◽  
Karthik Sreenivasan ◽  
Charles Bernick ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Validation Study ◽  
Sliding Window ◽  
Time Dependent ◽  
Connectivity Analysis ◽  
Dynamic Functional Connectivity ◽  
Functional Connectivity Analysis ◽  
Single Scale

scholarly journals A Universal Nonparametric Event Detection Framework for Neuropixels Data

2019 ◽  
Author(s):  
Hao Chen ◽  
Shizhe Chen ◽  
Xinyi Deng
Keyword(s):  
Change Point ◽  
Large Scale ◽  
Brain Regions ◽  
General Purpose ◽  
Electrophysiological Recording ◽  
Neural Population ◽  
Data Sets ◽  
Analysis Tool ◽  
Neural Activities ◽  
Spontaneous Behavior

SummaryNeuropixels probes present exciting new opportunities for neuroscience, but such large-scale high-density recordings also introduce unprecedented challenges in data analysis. Neuropixels data usually consist of hundreds or thousands of long stretches of sequential spiking activities that evolve non-stationarily over time and are often governed by complex, unknown dynamics. Extracting meaningful information from the Neuropixels recordings is a non-trial task. Here we introduce a general-purpose, graph-based statistical framework that, without imposing any parametric assumptions, detects points in time at which population spiking activity exhibits simultaneous changes as well as changes that only occur in a subset of the neural population, referred to as “change-points”. The sequence of change-point events can be interpreted as a footprint of neural population activities, which allows us to relate behavior to simultaneously recorded high-dimensional neural activities across multiple brain regions. We demonstrate the effectiveness of our method with an analysis of Neuropixels recordings during spontaneous behavior of an awake mouse in darkness. We observe that change-point dynamics in some brain regions display biologically interesting patterns that hint at functional pathways, as well as temporally-precise coordination with behavioral dynamics. We hypothesize that neural activities underlying spontaneous behavior, though distributed brainwide, show evidences for network modularity. Moreover, we envision the proposed framework to be a useful off-the-shelf analysis tool to the neuroscience community as new electrophysiological recording techniques continue to drive an explosive proliferation in the number and size of data sets.

scholarly journals The Relationship between Economic Growth, Small and Medium Enterprises and the Number of Employees in Malaysia using Vine Copula Approach

2021 ◽  
Vol 50 (8) ◽  
pp. 2455-2468
Author(s):  
Mazmira Adan ◽  
Saiful Izzuan Hussain
Keyword(s):  
Economic Growth ◽  
Small And Medium Enterprises ◽  
Value Added ◽  
Data Sets ◽  
Strong Positive Correlation ◽  
Copula Approach ◽  
Vine Copula ◽  
Medium Enterprises ◽  
The Relationship ◽  
Vine Copulas

This paper investigates the dynamic linkages of dependency between economic growth, the development of small and medium enterprises (SMEs) in Malaysia represented by SMEs’ value-added, and the number of employees in Malaysia, shown by the total number of SMEs’ employees in Malaysia as an additional variable. A vine copula methods was used to assess the linkage between these three variables by utilizing the panel data sets from 1998-2017. The results confirmed that dependency modeling, using vine copulas, is useful for high dimensional distributions of binding affinity between these variables. Vine copulas provide a versatile and flexible approach to the study. The results show that there is a strong positive correlation among the variables. The dependence between the SMEs’ growth and the total number of employees is the strongest, followed by the dependence between SMEs’ growth and economic growth. This study also found that the interrelation among the variables and reliance structure is also influenced by the country’s economic system and situation.

scholarly journals Nuisance Effects and the Limitations of Nuisance Regression in Dynamic Functional Connectivity fMRI

2018 ◽  
Author(s):  
Alican Nalci ◽  
Bhaskar D. Rao ◽  
Thomas T. Liu
Keyword(s):  
Functional Connectivity ◽  
Resting State Fmri ◽  
Brain Regions ◽  
Blood Oxygenation ◽  
Dynamic Functional Connectivity ◽  
Temporal Fluctuations ◽  
Before And After ◽  
The Difference ◽  
Time Courses ◽  
The Relationship

AbstractIn resting-state fMRI, dynamic functional connectivity (DFC) measures are used to characterize temporal changes in the brain’s intrinsic functional connectivity. A widely used approach for DFC estimation is the computation of the sliding window correlation between blood oxygenation level dependent (BOLD) signals from different brain regions. Although the source of temporal fluctuations in DFC estimates remains largely unknown, there is growing evidence that they may reflect dynamic shifts between functional brain networks. At the same time, recent findings suggest that DFC estimates might be prone to the influence of nuisance factors such as the physiological modulation of the BOLD signal. Therefore, nuisance regression is used in many DFC studies to regress out the effects of nuisance terms prior to the computation of DFC estimates. In this work we examined the relationship between DFC estimates and nuisance factors. We found that DFC estimates were significantly correlated with temporal fluctuations in the magnitude (norm) of various nuisance regressors, with significant correlations observed in the majority (76%) of the cases examined. Significant correlations between the DFC estimates and nuisance regressor norms were found even when the underlying correlations between the nuisance and fMRI time courses were relatively small. We then show that nuisance regression does not eliminate the relationship between DFC estimates and nuisance norms, with significant correlations observed in the majority (71%) of the cases examined after nuisance regression. We present theoretical bounds on the difference between DFC estimates obtained before and after nuisance regression and relate these bounds to limitations in the efficacy of nuisance regression with regards to DFC estimates.

scholarly journals Multifractal and entropy analysis of resting-state electroencephalography reveals spatial organization in local dynamic functional connectivity

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Frigyes Samuel Racz ◽  
Orestis Stylianou ◽  
Peter Mukli ◽  
Andras Eke
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Spatial Organization ◽  
Brain Activity ◽  
Surrogate Data ◽  
Brain Regions ◽  
Local Dynamic ◽  
Dynamic Functional Connectivity ◽  
Multifractal Scaling ◽  
The Brain

Abstract Functional connectivity of the brain fluctuates even in resting-state condition. It has been reported recently that fluctuations of global functional network topology and those of individual connections between brain regions expressed multifractal scaling. To expand on these findings, in this study we investigated if multifractality was indeed an inherent property of dynamic functional connectivity (DFC) on the regional level as well. Furthermore, we explored if local DFC showed region-specific differences in its multifractal and entropy-related features. DFC analyses were performed on 62-channel, resting-state electroencephalography recordings of twelve young, healthy subjects. Surrogate data testing verified the true multifractal nature of regional DFC that could be attributed to the presumed nonlinear nature of the underlying processes. Moreover, we found a characteristic spatial distribution of local connectivity dynamics, in that frontal and occipital regions showed stronger long-range correlation and higher degree of multifractality, whereas the highest values of entropy were found over the central and temporal regions. The revealed topology reflected well the underlying resting-state network organization of the brain. The presented results and the proposed analysis framework could improve our understanding on how resting-state brain activity is spatio-temporally organized and may provide potential biomarkers for future clinical research.

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