arXiv subjects

Nicole A. Lazar

Publications and source records attributed to Nicole A. Lazar.

7 recordsLinked to original sources

arXiv2026

An MCMC-Based Method for Dynamic Causal Modeling of Effective Connectivity in Functional MRI

Effective connectivity analysis in functional magnetic resonance imaging (fMRI) studies directional interactions among brain regions and experimental stimuli. Dynamic causal modeling (DCM) is a widely used method to estimate effective connectivity, based on a state-space representation consisting of a latent neural signal model and an observation model transforming the neural signal into the observed blood-oxygen-level-dependent (BOLD) response. A standard DCM combines ordinary differential equation (ODE) dynamics for the latent signal with a complex neural-hemodynamic system for the observation model, and typically uses variational Bayes for parameter estimation. While physically well-motivated, this approach can lead to practical challenges such as inexact solutions and underestimated uncertainty. We introduce Canonical DCM (CDCM), a Markov chain Monte Carlo (MCMC)-based method that adopts a simpler observation model and the No-U-Turn Sampler for posterior sampling. The simpler observation model admits a piecewise analytic solution to the neural ODE, increasing computational efficiency and enabling explicit derivation of sufficient conditions for parameter identifiability. The results indicate that CDCM provides reliable uncertainty quantification and consistent estimation of parameters related to experimental inputs for simulated and real data. We use publicly available data from the Wellcome Centre for Human Neuroimaging and the Human Connectome Project (HCP) to benchmark CDCM against standard DCM methods and examine replicability of estimated connectivity patterns in small- and large-scale neuroimaging settings.

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arXiv2024

Scale Reliant Inference

Many scientific fields, including human gut microbiome science, collect multivariate count data where the sum of the counts is unrelated to the scale of the underlying system being measured (e.g., total microbial load in a subject's colon). This disconnect complicates downstream analyses such as differential analysis in case-control studies. This article is motivated by a novel study of in vitro human gut microbiome models. Popular tools for analyzing these data led to dramatically elevated rates of both false positives and false negatives. To understand those failures, we provide a formal problem statement that frames these challenges of scale in terms of the classical theory of identifiability. We call this the problem of Scale Reliant Inference (SRI). We use this formulation to prove fundamental limits on SRI in terms of criteria such as consistency and type-I error control. We show that the failures of existing methods stem from a fundamental failure to properly quantify uncertainty in the system scale. We demonstrate that a particular type of Bayesian model called a Bayesian Partially Identified Model (PIMs) can correctly quantify uncertainty in SRI. We introduce Scale Simulation Random Variables (SSRVs) as a flexible and efficient approach to specifying and inferring Bayesian PIMs. In the context of both real and simulated data, we find SSRVs drastically decrease type-I and type-II error rates.

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arXiv2023

Hypothesis Testing for Shapes using Vectorized Persistence Diagrams

Topological data analysis involves the statistical characterization of the shape of data. Persistent homology is a primary tool of topological data analysis, which can be used to analyze topological features and perform statistical inference. In this paper, we present a two-stage hypothesis test for vectorized persistence diagrams. The first stage filters vector elements in the vectorized persistence diagrams to enhance the power of the test. The second stage consists of multiple hypothesis tests, with false positives controlled by false discovery rates. We demonstrate the flexibility of our method by applying it to a variety of simulated and real-world data types. Our results show that the proposed hypothesis test enables accurate and informative inferences on the shape of data compared to the existing hypothesis testing methods for persistent homology.

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arXiv2019

Method of Moments Histograms

Uniform bin width histograms are widely used so this data graphic should represent data as correctly as possible. Method of moments based on familiar mean, variance and Fisher-Pearson skewness cure this problem.

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arXiv2017

Persistence Terrace for Topological Inference of Point Cloud Data

Topological data analysis (TDA) is a rapidly developing collection of methods for studying the shape of point cloud and other data types. One popular approach, designed to be robust to noise and outliers, is to first use a smoothing function to convert the point cloud into a manifold and then apply persistent homology to a Morse filtration. A significant challenge is that this smoothing process involves the choice of a parameter and persistent homology is highly sensitive to that choice; moreover, important scale information is lost. We propose a novel topological summary plot, called a persistence terrace, that incorporates a wide range of smoothing parameters and is robust, multi-scale, and parameter-free. This plot allows one to isolate distinct topological signals that may have merged for any fixed value of the smoothing parameter, and it also allows one to infer the size and point density of the topological features. We illustrate our method in some simple settings where noise is a serious issue for existing frameworks and then we apply it to a real data set by counting muscle fibers in a cross-sectional image.

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arXiv2017

A Bayesian Generalized CAR Model for Correlated Signal Detection

Over the last decade, large-scale multiple testing has found itself at the forefront of modern data analysis. In many applications data are correlated, so that the observed test statistic used for detecting a non-null case, or signal, at each location in a dataset carries some information about the chances of a true signal at other locations. Brown, Lazar, Datta, Jang, and McDowell (2014) proposed in the neuroimaging context a Bayesian multiple testing model that accounts for the dependence of each volume element on the behavior of its neighbors through a conditional autoregressive (CAR) model. Here, we propose a generalized CAR model that allows for inclusion of points with no neighbors at all, something that is not possible under conventional CAR models. We consider also neighborhoods based on criteria other than physical location, such as genetic pathways in microarray determined from existing biological knowledge. This generalization provides a unified framework for the simultaneous modeling of dependent and independent cases, resulting in stronger Bayesian learning in the posterior and increased precision in the estimates of interesting signals. We justify the selected prior distribution and prove that the resulting posterior distribution is proper. We illustrate the effectiveness and applicability of our proposed model by using it to analyze both simulated and real microarray data in which the genes exhibit dependence that is determined by physical adjacency on a chromosome or predefined gene pathways.

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arXiv2013

Regression shrinkage and grouping of highly correlated predictors with HORSES

Identifying homogeneous subgroups of variables can be challenging in high dimensional data analysis with highly correlated predictors. We propose a new method called Hexagonal Operator for Regression with Shrinkage and Equality Selection, HORSES for short, that simultaneously selects positively correlated variables and identifies them as predictive clusters. This is achieved via a constrained least-squares problem with regularization that consists of a linear combination of an L_1 penalty for the coefficients and another L_1 penalty for pairwise differences of the coefficients. This specification of the penalty function encourages grouping of positively correlated predictors combined with a sparsity solution. We construct an efficient algorithm to implement the HORSES procedure. We show via simulation that the proposed method outperforms other variable selection methods in terms of prediction error and parsimony. The technique is demonstrated on two data sets, a small data set from analysis of soil in Appalachia, and a high dimensional data set from a near infrared (NIR) spectroscopy study, showing the flexibility of the methodology.

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