arXiv subjects

Hernando Ombao

Publications and source records attributed to Hernando Ombao.

At least 55 records · Page 3Linked to original sources

arXiv2024

Dynamic MRI reconstruction using low-rank plus sparse decomposition with smoothness regularization

The low-rank plus sparse (L+S) decomposition model has enabled better reconstruction of dynamic magnetic resonance imaging (dMRI) with separation into background (L) and dynamic (S) component. However, use of low-rank prior alone may not fully explain the slow variations or smoothness of the background part at the local scale. In this paper, we propose a smoothness-regularized L+S (SR-L+S) model for dMRI reconstruction from highly undersampled k-t-space data. We exploit joint low-rank and smooth priors on the background component of dMRI to better capture both its global and local temporal correlated structures. Extending the L+S formulation, the low-rank property is encoded by the nuclear norm, while the smoothness by a general \ell_{p}-norm penalty on the local differences of the columns of L. The additional smoothness regularizer can promote piecewise local consistency between neighboring frames. By smoothing out the noise and dynamic activities, it allows accurate recovery of the background part, and subsequently more robust dMRI reconstruction. Extensive experiments on multi-coil cardiac and synthetic data shows that the SR-L+S model outp

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arXiv2023

Dynamic Topological Data Analysis of Functional Human Brain Networks

Developing reliable methods to discriminate different transient brain states that change over time is a key neuroscientific challenge in brain imaging studies. Topological data analysis (TDA), a novel framework based on algebraic topology, can handle such a challenge. However, existing TDA has been somewhat limited to capturing the static summary of dynamically changing brain networks. We propose a novel dynamic-TDA framework that builds persistent homology over a time series of brain networks. We construct a Wasserstein distance based inference procedure to discriminate between time series of networks. The method is applied to the resting-state functional magnetic resonance images of human brain. We demonstrate that our proposed dynamic-TDA approach can distinctly discriminate between the topological patterns of male and female brain networks. MATLAB code for implementing this method is available at https://github.com/laplcebeltrami/PH-STAT.

q-bio.NC↗

arXiv2023

Statistical Inference for Modulation Index in Phase-Amplitude Coupling

Phase-amplitude coupling is a phenomenon observed in several neurological processes, where the phase of one signal modulates the amplitude of another signal with a distinct frequency. The modulation index (MI) is a common technique used to quantify this interaction by assessing the Kullback-Leibler divergence between a uniform distribution and the empirical conditional distribution of amplitudes with respect to the phases of the observed signals. The uniform distribution is an ideal representation that is expected to appear under the absence of coupling. However, it does not reflect the statistical properties of coupling values caused by random chance. In this paper, we propose a statistical framework for evaluating the significance of an observed MI value based on a null hypothesis that a MI value can be entirely explained by chance. Significance is obtained by comparing the value with a reference distribution derived under the null hypothesis of independence (i.e., no coupling) between signals. We derived a closed-form distribution of this null model, resulting in a scaled beta distribution. To validate the efficacy of our proposed framework, we conducted comprehensive Monte Carlo simulations, assessing the significance of MI values under various experimental scenarios, including amplitude modulation, trains of spikes, and sequences of high-frequency oscillations. Furthermore, we corroborated the reliability of our model by comparing its statistical significance thresholds with reported values from other research studies conducted under different experimental settings. Our method offers several advantages such as meta-analysis reliability, simplicity and computational efficiency, as it provides p-values and significance levels without resorting to generating surrogate data through sampling procedures.

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arXiv2023

Stylized Projected GAN: A Novel Architecture for Fast and Realistic Image Generation

Generative Adversarial Networks are used for generating the data using a generator and a discriminator, GANs usually produce high-quality images, but training GANs in an adversarial setting is a difficult task. GANs require high computation power and hyper-parameter regularization for converging. Projected GANs tackle the training difficulty of GANs by using transfer learning to project the generated and real samples into a pre-trained feature space. Projected GANs improve the training time and convergence but produce artifacts in the generated images which reduce the quality of the generated samples, we propose an optimized architecture called Stylized Projected GANs which integrates the mapping network of the Style GANs with Skip Layer Excitation of Fast GAN. The integrated modules are incorporated within the generator architecture of the Fast GAN to mitigate the problem of artifacts in the generated images.

cs.CV↗

arXiv2023

Topological Data Analysis for Directed Dependence Networks of Multivariate Time Series Data

Topological data analysis (TDA) approaches are becoming increasingly popular for studying the dependence patterns in multivariate time series data. In particular, various dependence patterns in brain networks may be linked to specific tasks and cognitive processes, which can be altered by various neurological impairments such as epileptic seizures. Existing TDA approaches rely on the notion of distance between data points that is symmetric by definition for building graph filtrations. For brain dependence networks, this is a major limitation that constrains practitioners to using only symmetric dependence measures, such as correlations or coherence. However, it is known that the brain dependence network may be very complex and can contain a directed flow of information from one brain region to another. Such dependence networks are usually captured by more advanced measures of dependence such as partial directed coherence, which is a Granger causality based dependence measure. These dependence measures will result in a non-symmetric distance function, especially during epileptic seizures. In this paper we propose to solve this limitation by decomposing the weighted connectivity network into its symmetric and anti-symmetric components using matrix decomposition and comparing the anti-symmetric component prior to and post seizure. Our analysis of epileptic seizure EEG data shows promising results.

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arXiv2023

An MCMC Approach to Bayesian Image Analysis in Fourier Space

Bayesian methods are commonly applied to solve image analysis problems such as noise-reduction, feature enhancement and object detection. A primary limitation of these approaches is the computational complexity due to the interdependence of neighboring pixels which limits the ability to perform full posterior sampling through Markov chain Monte Carlo (MCMC). To alleviate this problem, we develop a new posterior sampling method that is based on modeling the prior and likelihood in the space of the Fourier transform of the image. One advantage of Fourier-based methods is that many spatially correlated processes in image space can be represented via independent processes over Fourier space. A recent approach known as Bayesian Image Analysis in Fourier Space (or BIFS), has introduced parameter functions to describe prior expectations about image properties in Fourier space. To date BIFS has relied on Maximum a Posteriori (MAP) estimation for generating posterior estimates; providing just a single point estimate. The work presented here develops a posterior sampling approach for BIFS that can explore the full posterior distribution while continuing to take advantage of the independence modeling over Fourier space. As a result computational efficiency is improved over that for conventional Bayesian image analysis and mixing concerns that commonly have to be dealt with in high dimensional Markov chain Monte Carlo sampling problems are avoided. Implementation results and details are provided using simulated data.

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arXiv2023

Bayesian Nonparametric Multivariate Mixture of Autoregressive Processes: With Application to Brain Signals

One of the goals of neuroscience is to study interactions between different brain regions during rest and while performing specific cognitive tasks. The Multivariate Bayesian Autoregressive Decomposition (MBMARD) is proposed as an intuitive and novel Bayesian non-parametric model to represent high-dimensional signals as a low-dimensional mixture of univariate uncorrelated latent oscillations. Each latent oscillation captures a specific underlying oscillatory activity and hence will be modeled as a unique second-order autoregressive process due to a compelling property that its spectral density has a shape characterized by a unique frequency peak and bandwidth, which are parameterized by a location and a scale parameter. The posterior distributions of the parameters of the latent oscillations are computed via a metropolis-within-Gibbs algorithm. One of the advantages of MBMARD is its robustness against misspecification of standard models which is demonstrated in simulation studies. The main scientific questions addressed by MBMARD are the effects of long-term abuse of alcohol consumption on memory by analyzing EEG records of alcoholic and non-alcoholic subjects performing a visual recognition experiment. The MBMARD model exhibited novel interesting findings including identifying subject-specific clusters of low and high-frequency oscillations among different brain regions.

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arXiv2023

An Improved Unbiased Particle Filter

In this paper we consider the filtering of partially observed multi-dimensional diffusion processes that are observed regularly at discrete times. We assume that, for numerical reasons, one has to time-discretize the diffusion process which typically leads to filtering that is subject to discretization bias. The approach in [16] establishes that when only having access to the time-discretized diffusion it is possible to remove the discretization bias with an estimator of finite variance. We improve on the method in [16] by introducing a modified estimator based on the recent work of [17]. We show that this new estimator is unbiased and has finite variance. Moreover, we conjecture and verify in numerical simulations that substantial gains are obtained. That is, for a given mean square error (MSE) and a particular class of multi-dimensional diffusion, the cost to achieve the said MSE falls.

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arXiv2023

Antithetic Multilevel Particle Filters

In this paper we consider the filtering of partially observed multi-dimensional diffusion processes that are observed regularly at discrete times. This is a challenging problem which requires the use of advanced numerical schemes based upon time-discretization of the diffusion process and then the application of particle filters. Perhaps the state-of-the-art method for moderate dimensional problems is the multilevel particle filter of \cite{mlpf}. This is a method that combines multilevel Monte Carlo and particle filters. The approach in that article is based intrinsically upon an Euler discretization method. We develop a new particle filter based upon the antithetic truncated Milstein scheme of \cite{ml_anti}. We show that for a class of diffusion problems, for $ε>0$ given, that the cost to produce a mean square error (MSE) in estimation of the filter, of $\mathcal{O}(ε^2)$ is $\mathcal{O}(ε^{-2}\log(ε)^2)$. In the case of multidimensional diffusions with non-constant diffusion coefficient, the method of \cite{mlpf} has a cost of $\mathcal{O}(ε^{-2.5})$ to achieve the same MSE. We support our theory with numerical results in several examples.

math.NA↗

arXiv2022

Graph-Regularized Manifold-Aware Conditional Wasserstein GAN for Brain Functional Connectivity Generation

Common measures of brain functional connectivity (FC) including covariance and correlation matrices are semi-positive definite (SPD) matrices residing on a cone-shape Riemannian manifold. Despite its remarkable success for Euclidean-valued data generation, use of standard generative adversarial networks (GANs) to generate manifold-valued FC data neglects its inherent SPD structure and hence the inter-relatedness of edges in real FC. We propose a novel graph-regularized manifold-aware conditional Wasserstein GAN (GR-SPD-GAN) for FC data generation on the SPD manifold that can preserve the global FC structure. Specifically, we optimize a generalized Wasserstein distance between the real and generated SPD data under an adversarial training, conditioned on the class labels. The resulting generator can synthesize new SPD-valued FC matrices associated with different classes of brain networks, e.g., brain disorder or healthy control. Furthermore, we introduce additional population graph-based regularization terms on both the SPD manifold and its tangent space to encourage the generator to respect the inter-subject similarity of FC patterns in the real data. This also helps in avoiding mode collapse and produces more stable GAN training. Evaluated on resting-state functional magnetic resonance imaging (fMRI) data of major depressive disorder (MDD), qualitative and quantitative results show that the proposed GR-SPD-GAN clearly outperforms several state-of-the-art GANs in generating more realistic fMRI-based FC samples. When applied to FC data augmentation for MDD identification, classification models trained on augmented data generated by our approach achieved the largest margin of improvement in classification accuracy among the competing GANs over baselines without data augmentation.

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arXiv2022

Filtrated Common Functional Principal Components for Multivariate Functional data

Local field potentials (LFPs) are signals that measure electrical activity in localized cortical regions from implanted tetrodes in the human or animal brain. The LFP signals are curves observed at multiple tetrodes which are implanted across a patch on the surface of the cortex. Hence, they can be treated as multi-group functional data, where the trajectories collected across temporal epochs from one tetrode are viewed as a group of functions. In many cases, multi-tetrode LFP trajectories contain both global variation patterns (which are shared in common to all groups, due to signal synchrony) and isolated variation patterns (common only to a small subset of groups), and such structure is very informative to the analysis of such data. Therefore, one goal in this paper is to develop an efficient procedure that is able to capture and quantify both global and isolated features. We propose a novel tree-structured functional principal components (filt-fPC) analysis through finite-dimensional functional representation - specifically via filtration. A major advantage of the proposed filt-fPC method is the ability to extract the components that are common to multiple groups (or tetrodes) in a flexible "multi-resolution" manner and simultaneously preserve the idiosyncratic individual components of different tetrodes. The proposed filt-fPC approach is highly data-driven and no "ground-truth" model pre-specification is needed, making it a suitable approach for analyzing multi-group functional data that is complex. In addition, the filt-fPC method is able to produce a parsimonious, interpretable, and efficient low dimensional representation of multi-group functional data with orthonormal basis functions. Here, the proposed filt-fPCA method is employed to study the impact of a shock (induced stroke) on the synchrony structure of the rat brain.

stat.ME↗

arXiv2022

Bayesian Parameter Inference for Partially Observed SDEs driven by Fractional Brownian Motion

In this paper we consider Bayesian parameter inference for partially observed fractional Brownian motion (fBM) models. The approach we follow is to time-discretize the hidden process and then to design Markov chain Monte Carlo (MCMC) algorithms to sample from the posterior density on the parameters given data. We rely on a novel representation of the time discretization, which seeks to sample from an approximation of the posterior and then corrects via importance sampling; the approximation reduces the time (in terms of total observation time T) by O(T). This method is extended by using a multilevel MCMC method which can reduce the computational cost to achieve a given mean square error (MSE) versus using a single time discretization. Our methods are illustrated on simulated and real data.

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arXiv2022

Modeling and Simulating Dependence in Networks Using Topological Data Analysis

Topological data analysis (TDA) approaches are becoming increasingly popular for studying the dependence patterns in multivariate time series data. In particular, various dependence patterns in brain networks may be linked to specific tasks and cognitive processes, which can be altered by various neurological and cognitive impairments such as Alzheimer's and Parkinson's diseases, as well as attention deficit hyperactivity disorder (ADHD). Because there is no ground-truth with known dependence patterns in real brain signals, testing new TDA methods on multivariate time series is still a challenge. Simulations are crucial for evaluating the performance of proposed TDA methods and testing procedures as well as for creating computation-based confidence intervals. To our knowledge, there are no methods that simulate multivariate time series data with specific and manually imposed connectivity patterns. In this paper we present a novel approach to simulate multivariate time series with specific number of cycles/holes in its dependence network. Furthermore, we also provide a procedure for generating higher dimensional topological features.

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arXiv2022

Graph Autoencoders for Embedding Learning in Brain Networks and Major Depressive Disorder Identification

Brain functional connectivity (FC) reveals biomarkers for identification of various neuropsychiatric disorders. Recent application of deep neural networks (DNNs) to connectome-based classification mostly relies on traditional convolutional neural networks using input connectivity matrices on a regular Euclidean grid. We propose a graph deep learning framework to incorporate the non-Euclidean information about graph structure for classifying functional magnetic resonance imaging (fMRI)-derived brain networks in major depressive disorder (MDD). We design a novel graph autoencoder (GAE) architecture based on the graph convolutional networks (GCNs) to embed the topological structure and node content of large-sized fMRI networks into low-dimensional latent representations. In network construction, we employ the Ledoit-Wolf (LDW) shrinkage method to estimate the high-dimensional FC metrics efficiently from fMRI data. We consider both supervised and unsupervised approaches for the graph embedding learning. The learned embeddings are then used as feature inputs for a deep fully-connected neural network (FCNN) to discriminate MDD from healthy controls. Evaluated on two resting-state fMRI (rs-fMRI) MDD datasets, results show that the proposed GAE-FCNN model significantly outperforms several state-of-the-art methods for brain connectome classification, achieving the best accuracy using the LDW-FC edges as node features. The graph embeddings of fMRI FC networks learned by the GAE also reveal apparent group differences between MDD and HC. Our new framework demonstrates feasibility of learning graph embeddings on brain networks to provide discriminative information for diagnosis of brain disorders.

q-bio.NC↗

arXiv2022

Topological Data Analysis for Multivariate Time Series Data

Over the last two decades, topological data analysis (TDA) has emerged as a very powerful data analytic approach which can deal with various data modalities of varying complexities. One of the most commonly used tools in TDA is persistent homology (PH) which can extract topological properties from data at various scales. Our aim in this article is to introduce TDA concepts to a statistical audience and provide an approach to analyze multivariate time series data. The application focus will be on multivariate brain signals and brain connectivity networks. Finally, the paper concludes with an overview of some open problems and potential application of TDA to modeling directionality in a brain network as well as the casting of TDA in the context of mixed effects models to capture variations in the topological properties of data collected from multiple subjects

stat.ME↗

arXiv2022

Smooth Online Parameter Estimation for time varying VAR models with application to rat's LFP data

Multivariate time series data appear often as realizations of non-stationary processes where the covariance matrix or spectral matrix smoothly evolve over time. Most of the current approaches estimate the time-varying spectral properties only retrospectively - that is, after the entire data has been observed. Retrospective estimation is a major limitation in many adaptive control applications where it is important to estimate these properties and detect changes in the system as they happen in real-time. One major obstacle in online estimation is the computational cost due to the high-dimensionality of the parameters. Existing methods such as the Kalman filter or local least squares are feasible. However, they are not always suitable because they provide noisy estimates and can become prohibitively costly as the dimension of the time series increases. In our brain signal application, it is critical to develop a robust method that can estimate, in real-time, the properties of the underlying stochastic process, in particular, the spectral brain connectivity measures. For these reasons we propose a new smooth online parameter estimation approach (SOPE) that has the ability to control for the smoothness of the estimates with a reasonable computational complexity. Consequently, the models are fit in real-time even for high dimensional time series. We demonstrate that our proposed SOPE approach is as good as the Kalman filter in terms of mean-squared error for small dimensions. However, unlike the Kalman filter, the SOPE has lower computational cost and hence scalable for higher dimensions. Finally, we apply the SOPE method to a rat's local field potential data during a hippocampus-dependent sequence-memory task. As demonstrated in the video, the proposed SOPE method is able to capture the dynamics of the connectivity as the rat performs the sequence of non-spatial working memory tasks.

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arXiv2022

Poisson-Birnbaum-Saunders Regression Model for Clustered Count Data

The premise of independence among subjects in the same cluster/group often fails in practice, and models that rely on such untenable assumption can produce misleading results. To overcome this severe deficiency, we introduce a new regression model to handle overdispersed and correlated clustered counts. To account for correlation within clusters, we propose a Poisson regression model where the observations within the same cluster are driven by the same latent random effect that follows the Birnbaum-Saunders distribution with a parameter that controls the strength of dependence among the individuals. This novel multivariate count model is called Clustered Poisson Birnbaum-Saunders (CPBS) regression. As illustrated in this paper, the CPBS model is analytically tractable, and its moment structure can be explicitly obtained. Estimation of parameters is performed through the maximum likelihood method, and an Expectation-Maximization (EM) algorithm is also developed. Simulation results to evaluate the finite-sample performance of our proposed estimators are presented. We also discuss diagnostic tools for checking model adequacy. An empirical application concerning the number of inpatient admissions by individuals to hospital emergency rooms, from the Medical Expenditure Panel Survey (MEPS) conducted by the United States Agency for Health Research and Quality, illustrates the usefulness of our proposed methodology.

stat.ME↗

arXiv2022

Variation Pattern Classification of Functional Data

A new classification method for functional data is proposed in this paper. This work is motivated by the need to identify features that discriminate between neurological conditions on which local field potentials (LFPs) were recorded. Regardless of the condition, these local field potentials have zero mean and thus the first moments of these random processes do not have discriminating power. We propose the variation pattern classification (VPC) method {which employs the (auto-)covariance operators as the discriminating features} and uses the Hilbert-Schmidt norm to measure the discrepancy between the (auto-)covariance operators of different groups. The proposed VPC method is demonstrated to be sensitive to the discrepancy, {potentially leading to a higher rate of classification}. One important innovation lies in the dimension reduction where the VPC method data-adaptively determines the basis functions (discriminative feature functions) that account for the major discrepancy. In addition, the selected discriminative feature functions provide insights on the discrepancy between different groups because they reveal the features of variation pattern that differentiate groups. Consistency properties are established and, furthermore, simulation studies and the analysis of rat brain LFP trajectories empirically demonstrate the advantages and effectiveness of the proposed method.

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