arXiv subjects

Anuj Srivastava

Publications and source records attributed to Anuj Srivastava.

At least 55 records · Page 3Linked to original sources

arXiv2020

Agent-Level Pandemic Simulation (ALPS) for Analyzing Effects of Lockdown Measures

This paper develops an agent-level simulation model, termed ALPS, for simulating the spread of an infectious disease in a confined community. The mechanism of transmission is agent-to-agent contact, using parameters reported for Corona COVID-19 pandemic. The main goal of the ALPS simulation is analyze effects of preventive measures -- imposition and lifting of lockdown norms -- on the rates of infections, fatalities and recoveries. The model assumptions and choices represent a balance between competing demands of being realistic and being efficient for real-time inferences. The model provides quantification of gains in reducing casualties by imposition and maintenance of restrictive measures in place.

physics.soc-ph↗

arXiv2019

Statistical Analysis and Modeling of the Geometry and Topology of Plant Roots

The root is an important organ of a plant since it is responsible for water and nutrient uptake. Analyzing and modelling variabilities in the geometry and topology of roots can help in assessing the plant's health, understanding its growth patterns, and modeling relations between plant species and between plants and their environment. In this article, we develop a framework for the statistical analysis and modeling of the geometry and topology of plant roots. We represent root structures as points in a tree-shape space equipped with a metric that quantifies geometric and topological differences between pairs of roots. We then use these building blocks to compute geodesics, i.e., optimal deformations under the metric between root structures, and to perform statistical analysis on root populations. We demonstrate the utility of the proposed framework through an application to a dataset of wheat roots grown in different environmental conditions. We also show that the framework can be used in various applications including classification and regression.

cs.GR↗

arXiv2019

Intensity Estimation for Poisson Process with Compositional Noise

Intensity estimation for Poisson processes is a classical problem and has been extensively studied over the past few decades. Practical observations, however, often contain compositional noise, i.e. a nonlinear shift along the time axis, which makes standard methods not directly applicable. The key challenge is that these observations are not "aligned", and registration procedures are required for successful estimation. In this paper, we propose an alignment-based framework for positive intensity estimation. We first show that the intensity function is area-preserved with respect to compositional noise. Such a property implies that the time warping is only encoded in the normalized intensity, or density, function. Then, we decompose the estimation of the intensity by the product of the estimated total intensity and estimated density. The estimation of the density relies on a metric which measures the phase difference between two density functions. An asymptotic study shows that the proposed estimation algorithm provides a consistent estimator for the normalized intensity. We then extend the framework to estimating non-negative intensity functions. The success of the proposed estimation algorithms is illustrated using two simulations. Finally, we apply the new framework in a real data set of neural spike trains, and find that the newly estimated intensities provide better classification accuracy than previous methods.

stat.ME↗

arXiv2019

Analyzing Dynamical Brain Functional Connectivity As Trajectories on Space of Covariance Matrices

Human brain functional connectivity (FC) is often measured as the similarity of functional MRI responses across brain regions when a brain is either resting or performing a task. This paper aims to statistically analyze the dynamic nature of FC by representing the collective time-series data, over a set of brain regions, as a trajectory on the space of covariance matrices, or symmetric-positive definite matrices (SPDMs). We use a recently developed metric on the space of SPDMs for quantifying differences across FC observations, and for clustering and classification of FC trajectories. To facilitate large scale and high-dimensional data analysis, we propose a novel, metric-based dimensionality reduction technique to reduce data from large SPDMs to small SPDMs. We illustrate this comprehensive framework using data from the Human Connectome Project (HCP) database for multiple subjects and tasks, with task classification rates that match or outperform state-of-the-art techniques.

cs.CV↗

arXiv2019

Discovering Common Change-Point Patterns in Functional Connectivity Across Subjects

This paper studies change-points in human brain functional connectivity (FC) and seeks patterns that are common across multiple subjects under identical external stimulus. FC relates to the similarity of fMRI responses across different brain regions when the brain is simply resting or performing a task. While the dynamic nature of FC is well accepted, this paper develops a formal statistical test for finding {\it change-points} in times series associated with FC. It represents short-term connectivity by a symmetric positive-definite matrix, and uses a Riemannian metric on this space to develop a graphical method for detecting change-points in a time series of such matrices. It also provides a graphical representation of estimated FC for stationary subintervals in between the detected change-points. Furthermore, it uses a temporal alignment of the test statistic, viewed as a real-valued function over time, to remove inter-subject variability and to discover common change-point patterns across subjects. This method is illustrated using data from Human Connectome Project (HCP) database for multiple subjects and tasks.

q-bio.NC↗

arXiv2018

Elastic Functional Principal Component Regression

We study regression using functional predictors in situations where these functions contain both phase and amplitude variability. In other words, the functions are misaligned due to errors in time measurements, and these errors can significantly degrade both model estimation and prediction performance. The current techniques either ignore the phase variability, or handle it via pre-processing, i.e., use an off-the-shelf technique for functional alignment and phase removal. We develop a functional principal component regression model which has comprehensive approach in handling phase and amplitude variability. The model utilizes a mathematical representation of the data known as the square-root slope function. These functions preserve the $\mathbf{L}^2$ norm under warping and are ideally suited for simultaneous estimation of regression and warping parameters. Using both simulated and real-world data sets, we demonstrate our approach and evaluate its prediction performance relative to current models. In addition, we propose an extension to functional logistic and multinomial logistic regression

stat.AP↗

arXiv2018

Robust Comparison of Kernel Densities on Spherical Domains

While spherical data arises in many contexts, including in directional statistics, the current tools for density estimation and population comparison on spheres are quite limited. Popular approaches for comparing populations (on Euclidean domains) mostly involvea two-step procedure: (1) estimate probability density functions (pdfs) from their respective samples, most commonly using the kernel density estimator, and, (2) compare pdfs using a metric such as the L2 norm. However, both the estimated pdfs and their differences depend heavily on the chosen kernels, bandwidths, and sample sizes. Here we develop a framework for comparing spherical populations that is robust to these choices. Essentially, we characterize pdfs on spherical domains by quantifying their smoothness. Our framework uses a spectral representation, with densities represented by their coefficients with respect to the eigenfunctions of the Laplacian operator on a sphere. The change in smoothness, akin to using different kernel bandwidths, is controlled by exponential decays in coefficient values. Then we derive a proper distance for comparing pdf coefficients while equalizing smoothness levels, negating influences of sample size and bandwidth. This signifies a fair and meaningful comparisons of populations, despite vastly different sample sizes, and leads to a robust and improved performance. We demonstrate this framework using examples of variables on S1 and S2, and evaluate its performance using a number of simulations and real data experiments.

stat.ME↗

arXiv2018

Shape-Constrained Univariate Density Estimation

While the problem of estimating a probability density function (pdf) from its observations is classical, the estimation under additional shape constraints is both important and challenging. We introduce an efficient, geometric approach for estimating pdfs given the number of its modes. This approach explores the space of constrained pdf's using an action of the diffeomorphism group that preserves their shapes. It starts with an initial template, with the desired number of modes and arbitrarily chosen heights at the critical points, and transforms it via: (1) composition by diffeomorphisms and (2) normalization to obtain the final density estimate. The search for optimal diffeomorphism is performed under the maximum-likelihood criterion and is accomplished by mapping diffeomorphisms to the tangent space of a Hilbert sphere, a vector space whose elements can be expressed using an orthogonal basis. This framework is first applied to shape-constrained univariate, unconditional pdf estimation and then extended to conditional pdf estimation. We derive asymptotic convergence rates of the estimator and demonstrate this approach using a synthetic dataset involving speed distribution for different traffic flow on Californian driveways.

stat.ME↗

arXiv2017

A Two-Step Geometric Framework For Density Modeling

We introduce a novel two-step approach for estimating a probability density function (pdf) given its samples, with the second and important step coming from a geometric formulation. The procedure involves obtaining an initial estimate of the pdf and then transforming it via a warping function to reach the final estimate. The initial estimate is intended to be computationally fast, albeit suboptimal, but its warping creates a larger, flexible class of density functions, resulting in substantially improved estimation. The search for optimal warping is accomplished by mapping diffeomorphic functions to the tangent space of a Hilbert sphere, a vector space whose elements can be expressed using an orthogonal basis. Using a truncated basis expansion, we estimate the optimal warping under a (penalized) likelihood criterion and, thus, the optimal density estimate. This framework is introduced for univariate, unconditional pdf estimation and then extended to conditional pdf estimation. The approach avoids many of the computational pitfalls associated with classical conditional-density estimation methods, without losing on estimation performance. We derive asymptotic convergence rates of the density estimator and demonstrate this approach using both synthetic datasets and real data, the latter relating to the association of a toxic metabolite on preterm birth.

stat.ME↗

arXiv2017

Trend and Variable-Phase Seasonality Estimation from Functional Data

The problem of estimating trend and seasonal variation in time-series data has been studied over several decades, although mostly using single time series. This paper studies the problem of estimating these components from functional data, i.e. multiple time series, in situations where seasonal effects exhibit arbitrary time warpings or phase variability across different observations. Rather than ignoring the phase variability, or using an off-the-shelf alignment method to remove phase, we take a model-based approach and seek MLEs of the trend and the seasonal effects, while performing alignments over the seasonal effects at the same time. The MLEs of trend, seasonality, and phase are computed using a coordinate-descent based optimization method. We use bootstrap replication for computing confidence bands and for testing hypothesis about the estimated components. We also utilize log-likelihood for selecting the trend subspace, and for comparisons with other candidate models. This framework is demonstrated using experiments involving synthetic data and three real data (Berkeley Growth Velocity, U.S. electricity price, and USD exchange fluctuation).

stat.AP↗

arXiv2017

Nonparametric Spherical Regression Using Diffeomorphic Mappings

Spherical regression explores relationships between variables on spherical domains. We develop a nonparametric model that uses a diffeomorphic map from a sphere to itself. The restriction of this mapping to diffeomorphisms is natural in several settings. The model is estimated in a penalized maximum-likelihood framework using gradient-based optimization. Towards that goal, we specify a first-order roughness penalty using the Jacobian of diffeomorphisms. We compare the prediction performance of the proposed model with state-of-the-art methods using simulated and real data involving cloud deformations, wind directions, and vector-cardiograms. This model is found to outperform others in capturing relationships between spherical variables.

stat.OT↗

arXiv2016

Numerical Inversion of SRNF Maps for Elastic Shape Analysis of Genus-Zero Surfaces

Recent developments in elastic shape analysis (ESA) are motivated by the fact that it provides comprehensive frameworks for simultaneous registration, deformation, and comparison of shapes. These methods achieve computational efficiency using certain square-root representations that transform invariant elastic metrics into Euclidean metrics, allowing for applications of standard algorithms and statistical tools. For analyzing shapes of embeddings of $\mathbb{S}^2$ in $\mathbb{R}^3$, Jermyn et al. introduced square-root normal fields (SRNFs) that transformed an elastic metric, with desirable invariant properties, into the $\mathbb{L}^2$ metric. These SRNFs are essentially surface normals scaled by square-roots of infinitesimal area elements. A critical need in shape analysis is to invert solutions (deformations, averages, modes of variations, etc) computed in the SRNF space, back to the original surface space for visualizations and inferences. Due to the lack of theory for understanding SRNFs maps and their inverses, we take a numerical approach and derive an efficient multiresolution algorithm, based on solving an optimization problem in the surface space, that estimates surfaces corresponding to given SRNFs. This solution is found effective, even for complex shapes, e.g. human bodies and animals, that undergo significant deformations including bending and stretching. Specifically, we use this inversion for computing elastic shape deformations, transferring deformations, summarizing shapes, and for finding modes of variability in a given collection, while simultaneously registering the surfaces. We demonstrate the proposed algorithms using a statistical analysis of human body shapes, classification of generic surfaces and analysis of brain structures.

cs.GR↗

arXiv2016

Phase-Amplitude Separation and Modeling of Spherical Trajectories

This paper studies the problem of separating phase-amplitude components in sample paths of a spherical process (longitudinal data on a unit two-sphere). Such separation is essential for efficient modeling and statistical analysis of spherical longitudinal data in a manner that is invariant to any phase variability. The key idea is to represent each path or trajectory with a pair of variables, a starting point and a Transported Square-Root Velocity Curve (TSRVC). A TSRVC is a curve in the tangent (vector) space at the starting point and has some important invariance properties under the L2 norm. The space of all such curves forms a vector bundle and the L2 norm, along with the standard Riemannian metric on S2, provides a natural metric on this vector bundle. This invariant representation allows for separating phase and amplitude components in given data, using a template-based idea. Furthermore, the metric property is useful in deriving computational procedures for clustering, mean computation, principal component analysis (PCA), and modeling. This comprehensive framework is demonstrated using two datasets: a set of bird-migration trajectories and a set of hurricane paths in the Atlantic ocean.

stat.ME↗

arXiv2016

Elastic Functional Coding of Riemannian Trajectories

Visual observations of dynamic phenomena, such as human actions, are often represented as sequences of smoothly-varying features . In cases where the feature spaces can be structured as Riemannian manifolds, the corresponding representations become trajectories on manifolds. Analysis of these trajectories is challenging due to non-linearity of underlying spaces and high-dimensionality of trajectories. In vision problems, given the nature of physical systems involved, these phenomena are better characterized on a low-dimensional manifold compared to the space of Riemannian trajectories. For instance, if one does not impose physical constraints of the human body, in data involving human action analysis, the resulting representation space will have highly redundant features. Learning an effective, low-dimensional embedding for action representations will have a huge impact in the areas of search and retrieval, visualization, learning, and recognition. The difficulty lies in inherent non-linearity of the domain and temporal variability of actions that can distort any traditional metric between trajectories. To overcome these issues, we use the framework based on transported square-root velocity fields (TSRVF); this framework has several desirable properties, including a rate-invariant metric and vector space representations. We propose to learn an embedding such that each action trajectory is mapped to a single point in a low-dimensional Euclidean space, and the trajectories that differ only in temporal rates map to the same point. We utilize the TSRVF representation, and accompanying statistical summaries of Riemannian trajectories, to extend existing coding methods such as PCA, KSVD and Label Consistent KSVD to Riemannian trajectories or more generally to Riemannian functions.

cs.CV↗

arXiv2015

Functional Data Analysis of Amplitude and Phase Variation

The abundance of functional observations in scientific endeavors has led to a significant development in tools for functional data analysis (FDA). This kind of data comes with several challenges: infinite-dimensionality of function spaces, observation noise, and so on. However, there is another interesting phenomena that creates problems in FDA. The functional data often comes with lateral displacements/deformations in curves, a phenomenon which is different from the height or amplitude variability and is termed phase variation. The presence of phase variability artificially often inflates data variance, blurs underlying data structures, and distorts principal components. While the separation and/or removal of phase from amplitude data is desirable, this is a difficult problem. In particular, a commonly used alignment procedure, based on minimizing the $\mathbb{L}^2$ norm between functions, does not provide satisfactory results. In this paper we motivate the importance of dealing with the phase variability and summarize several current ideas for separating phase and amplitude components. These approaches differ in the following: (1) the definition and mathematical representation of phase variability, (2) the objective functions that are used in functional data alignment, and (3) the algorithmic tools for solving estimation/optimization problems. We use simple examples to illustrate various approaches and to provide useful contrast between them.

stat.ME↗

arXiv2015

Gauge Invariant Framework for Shape Analysis of Surfaces

This paper describes a novel framework for computing geodesic paths in shape spaces of spherical surfaces under an elastic Riemannian metric. The novelty lies in defining this Riemannian metric directly on the quotient (shape) space, rather than inheriting it from pre-shape space, and using it to formulate a path energy that measures only the normal components of velocities along the path. In other words, this paper defines and solves for geodesics directly on the shape space and avoids complications resulting from the quotient operation. This comprehensive framework is invariant to arbitrary parameterizations of surfaces along paths, a phenomenon termed as gauge invariance. Additionally, this paper makes a link between different elastic metrics used in the computer science literature on one hand, and the mathematical literature on the other hand, and provides a geometrical interpretation of the terms involved. Examples using real and simulated 3D objects are provided to help illustrate the main ideas.

math.DG↗

arXiv2015

Video-Based Action Recognition Using Rate-Invariant Analysis of Covariance Trajectories

Statistical classification of actions in videos is mostly performed by extracting relevant features, particularly covariance features, from image frames and studying time series associated with temporal evolutions of these features. A natural mathematical representation of activity videos is in form of parameterized trajectories on the covariance manifold, i.e. the set of symmetric, positive-definite matrices (SPDMs). The variable execution-rates of actions implies variable parameterizations of the resulting trajectories, and complicates their classification. Since action classes are invariant to execution rates, one requires rate-invariant metrics for comparing trajectories. A recent paper represented trajectories using their transported square-root vector fields (TSRVFs), defined by parallel translating scaled-velocity vectors of trajectories to a reference tangent space on the manifold. To avoid arbitrariness of selecting the reference and to reduce distortion introduced during this mapping, we develop a purely intrinsic approach where SPDM trajectories are represented by redefining their TSRVFs at the starting points of the trajectories, and analyzed as elements of a vector bundle on the manifold. Using a natural Riemannain metric on vector bundles of SPDMs, we compute geodesic paths and geodesic distances between trajectories in the quotient space of this vector bundle, with respect to the re-parameterization group. This makes the resulting comparison of trajectories invariant to their re-parameterization. We demonstrate this framework on two applications involving video classification: visual speech recognition or lip-reading and hand-gesture recognition. In both cases we achieve results either comparable to or better than the current literature.

cs.CV↗

arXiv2015

Bayesian Clustering of Shapes of Curves

Unsupervised clustering of curves according to their shapes is an important problem with broad scientific applications. The existing model-based clustering techniques either rely on simple probability models (e.g., Gaussian) that are not generally valid for shape analysis or assume the number of clusters. We develop an efficient Bayesian method to cluster curve data using an elastic shape metric that is based on joint registration and comparison of shapes of curves. The elastic-inner product matrix obtained from the data is modeled using a Wishart distribution whose parameters are assigned carefully chosen prior distributions to allow for automatic inference on the number of clusters. Posterior is sampled through an efficient Markov chain Monte Carlo procedure based on the Chinese restaurant process to infer (1) the posterior distribution on the number of clusters, and (2) clustering configuration of shapes. This method is demonstrated on a variety of synthetic data and real data examples on protein structure analysis, cell shape analysis in microscopy images, and clustering of shaped from MPEG7 database.

stat.ML↗