arXiv subjects

Vasileios Maroulas

Publications and source records attributed to Vasileios Maroulas.

At least 37 records · Page 2Linked to original sources

arXiv2022

Quantum Persistent Homology

Persistent homology is a powerful mathematical tool that summarizes useful information about the shape of data allowing one to detect persistent topological features while one adjusts the resolution. However, the computation of such topological features is often a rather formidable task necessitating the subsampling the underlying data. To remedy this, we develop an efficient quantum computation of persistent Betti numbers, which track topological features of data across different scales. Our approach employs a persistent Dirac operator whose square yields the persistent combinatorial Laplacian, and in turn the underlying persistent Betti numbers which capture the persistent features of data. We also test our algorithm on point cloud data.

quant-ph↗

arXiv2022

Simplicial Complex Representation Learning

Simplicial complexes form an important class of topological spaces that are frequently used in many application areas such as computer-aided design, computer graphics, and simulation. Representation learning on graphs, which are just 1-d simplicial complexes, has witnessed a great attention in recent years. However, there has not been enough effort to extend representation learning to higher dimensional simplicial objects due to the additional complexity these objects hold, especially when it comes to entire-simplicial complex representation learning. In this work, we propose a method for simplicial complex-level representation learning that embeds a simplicial complex to a universal embedding space in a way that complex-to-complex proximity is preserved. Our method uses our novel geometric message passing schemes to learn an entire simplicial complex representation in an end-to-end fashion. We demonstrate the proposed model on publicly available mesh dataset. To the best of our knowledge, this work presents the first method for learning simplicial complex-level representation.

cs.LG↗

arXiv2021

Topological Deep Learning

This work introduces the Topological CNN (TCNN), which encompasses several topologically defined convolutional methods. Manifolds with important relationships to the natural image space are used to parameterize image filters which are used as convolutional weights in a TCNN. These manifolds also parameterize slices in layers of a TCNN across which the weights are localized. We show evidence that TCNNs learn faster, on less data, with fewer learned parameters, and with greater generalizability and interpretability than conventional CNNs. We introduce and explore TCNN layers for both image and video data. We propose extensions to 3D images and 3D video.

cs.LG↗

arXiv2021

Materials Fingerprinting Classification

Significant progress in many classes of materials could be made with the availability of experimentally-derived large datasets composed of atomic identities and three-dimensional coordinates. Methods for visualizing the local atomic structure, such as atom probe tomography (APT), which routinely generate datasets comprised of millions of atoms, are an important step in realizing this goal. However, state-of-the-art APT instruments generate noisy and sparse datasets that provide information about elemental type, but obscure atomic structures, thus limiting their subsequent value for materials discovery. The application of a materials fingerprinting process, a machine learning algorithm coupled with topological data analysis, provides an avenue by which here-to-fore unprecedented structural information can be extracted from an APT dataset. As a proof of concept, the material fingerprint is applied to high-entropy alloy APT datasets containing body-centered cubic (BCC) and face-centered cubic (FCC) crystal structures. A local atomic configuration centered on an arbitrary atom is assigned a topological descriptor, with which it can be characterized as a BCC or FCC lattice with near perfect accuracy, despite the inherent noise in the dataset. This successful identification of a fingerprint is a crucial first step in the development of algorithms which can extract more nuanced information, such as chemical ordering, from existing datasets of complex materials.

cond-mat.mtrl-sci↗

arXiv2020

Bayesian Topological Learning for Classifying the Structure of Biological Networks

Actin cytoskeleton networks generate local topological signatures due to the natural variations in the number, size, and shape of holes of the networks. Persistent homology is a method that explores these topological properties of data and summarizes them as persistence diagrams. In this work, we analyze and classify these filament networks by transforming them into persistence diagrams whose variability is quantified via a Bayesian framework on the space of persistence diagrams. The proposed generalized Bayesian framework adopts an independent and identically distributed cluster point process characterization of persistence diagrams and relies on a substitution likelihood argument. This framework provides the flexibility to estimate the posterior cardinality distribution of points in a persistence diagram and the posterior spatial distribution simultaneously. We present a closed form of the posteriors under the assumption of Gaussian mixtures and binomials for prior intensity and cardinality respectively. Using this posterior calculation, we implement a Bayes factor algorithm to classify the actin filament networks and benchmark it against several state-of-the-art classification methods.

stat.ML↗

arXiv2019

Bayesian Topological Learning for Brain State Classification

Investigation of human brain states through electroencephalograph (EEG) signals is a crucial step in human-machine communications. However, classifying and analyzing EEG signals are challenging due to their noisy, nonlinear and nonstationary nature. Current methodologies for analyzing these signals often fall short because they have several regularity assumptions baked in. This work provides an effective, flexible and noise-resilient scheme to analyze EEG by extracting pertinent information while abiding by the 3N (noisy, nonlinear and nonstationary) nature of data. We implement a topological tool, namely persistent homology, that tracks the evolution of topological features over time intervals and incorporates individual's expectations as prior knowledge by means of a Bayesian framework to compute posterior distributions. Relying on these posterior distributions, we apply Bayes factor classification to noisy EEG measurements. The performance of this Bayesian classification scheme is then compared with other existing methods for EEG signals.

stat.ML↗

arXiv2019

A Stable Cardinality Distance for Topological Classification

This work incorporates topological features via persistence diagrams to classify point cloud data arising from materials science. Persistence diagrams are multisets summarizing the connectedness and holes of given data. A new distance on the space of persistence diagrams generates relevant input features for a classification algorithm for materials science data. This distance measures the similarity of persistence diagrams using the cost of matching points and a regularization term corresponding to cardinality differences between diagrams. Establishing stability properties of this distance provides theoretical justification for the use of the distance in comparisons of such diagrams. The classification scheme succeeds in determining the crystal structure of materials on noisy and sparse data retrieved from synthetic atom probe tomography experiments.

stat.ML↗

arXiv2019

A Bayesian Framework for Persistent Homology

Persistence diagrams offer a way to summarize topological and geometric properties latent in datasets. While several methods have been developed that utilize persistence diagrams in statistical inference, a full Bayesian treatment remains absent. This paper, relying on the theory of point processes, presents a Bayesian framework for inference with persistence diagrams relying on a substitution likelihood argument. In essence, we model persistence diagrams as Poisson point processes with prior intensities and compute posterior intensities by adopting techniques from the theory of marked point processes. We then propose a family of conjugate prior intensities via Gaussian mixtures to obtain a closed form of the posterior intensity. Finally we demonstrate the utility of this Bayesian framework with a classification problem in materials science using Bayes factors.

stat.ME↗

arXiv2018

Bayesian Point Set Registration

Point set registration involves identifying a smooth invertible transformation between corresponding points in two point sets, one of which may be smaller than the other and possibly corrupted by observation noise. This problem is traditionally decomposed into two separate optimization problems: (i) assignment or correspondence, and (ii) identification of the optimal transformation between the ordered point sets. In this work, we propose an approach solving both problems simultaneously. In particular, a coherent Bayesian formulation of the problem results in a marginal posterior distribution on the transformation, which is explored within a Markov chain Monte Carlo scheme. Motivated by Atomic Probe Tomography (APT), in the context of structure inference for high entropy alloys (HEA), we focus on the registration of noisy sparse observations of rigid transformations of a known reference configuration.Lastly, we test our method on synthetic data sets.

stat.AP↗

arXiv2018

Nonparametric Estimation of Probability Density Functions of Random Persistence Diagrams

We introduce a nonparametric way to estimate the global probability density function for a random persistence diagram. Precisely, a kernel density function centered at a given persistence diagram and a given bandwidth is constructed. Our approach encapsulates the number of topological features and considers the appearance or disappearance of features near the diagonal in a stable fashion. In particular, the structure of our kernel individually tracks long persistence features, while considering features near the diagonal as a collective unit. The choice to describe short persistence features as a group reduces computation time while simultaneously retaining accuracy. Indeed, we prove that the associated kernel density estimate converges to the true distribution as the number of persistence diagrams increases and the bandwidth shrinks accordingly. We also establish the convergence of the mean absolute deviation estimate, defined according to the bottleneck metric. Lastly, examples of kernel density estimation are presented for typical underlying datasets.

math.ST↗

arXiv2017

Sequential Empirical Bayes method for filtering dynamic spatiotemporal processes

We consider online prediction of a latent dynamic spatiotemporal process and estimation of the associated model parameters based on noisy data. The problem is motivated by the analysis of spatial data arriving in real-time and the current parameter estimates and predictions are updated using the new data at a fixed computational cost. Estimation and prediction is performed within an empirical Bayes framework with the aid of Markov chain Monte Carlo samples. Samples for the latent spatial field are generated using a sampling importance resampling algorithm with a skewed-normal proposal and for the temporal parameters using Gibbs sampling with their full conditionals written in terms of sufficient quantities which are updated online. The spatial range parameter is estimated by a novel online implementation of an empirical Bayes method, called herein sequential empirical Bayes method. A simulation study shows that our method gives similar results as an offline Bayesian method. We also find that the skewed-normal proposal improves over the traditional Gaussian proposal. The application of our method is demonstrated for online monitoring of radiation after the Fukushima nuclear accident.

stat.CO↗

arXiv2015

Tracking rapid intracellular movements: A Bayesian random set approach

We focus on the biological problem of tracking organelles as they move through cells. In the past, most intracellular movements were recorded manually, however, the results are too incomplete to capture the full complexity of organelle motions. An automated tracking algorithm promises to provide a complete analysis of noisy microscopy data. In this paper, we adopt statistical techniques from a Bayesian random set point of view. Instead of considering each individual organelle, we examine a random set whose members are the organelle states and we establish a Bayesian filtering algorithm involving such set states. The propagated multi-object densities are approximated using a Gaussian mixture scheme. Our algorithm is applied to synthetic and experimental data.

stat.AP↗

arXiv2015

Adaptive Trait Evolution in Random Environment

Current phylogenetic comparative methods generally employ the Ornstein-Uhlenbeck(OU) process for modeling trait evolution. Being able of tracking the optimum of a trait within a group of related species, the OU process provides information about the stabilizing selection where the population mean adopts a particular trait value. The optima of a trait may follow certain stochastic dynamics along the evolutionary history. In this paper, we extend the current framework by adopting a rate of evolution which behave according to pertinent stochastic dynamics. The novel model is applied to analyze about 225 datasets collected from the existing literature. Results validate that the new framework provides a better fit for the majority of these datasets.

stat.AP↗

arXiv2014

Phylogenetic Ornstein-Uhlenbeck regression curves

Regression curves for studying trait relationships are developed herein. The adaptive evolution model is considered an Ornstein-Uhlenbeck system whose parameters are estimated by a novel engagement of generalized least-squares and optimization. Our algorithm is implemented to ecological data.

stat.ME↗

arXiv2011

A drift homotopy Monte Carlo approach to particle filtering for multi-target tracking

We present a novel approach for improving particle filters for multi-target tracking. The suggested approach is based on drift homotopy for stochastic differential equations. Drift homotopy is used to design a Markov Chain Monte Carlo step which is appended to the particle filter and aims to bring the particle filter samples closer to the observations. Also, we present a simple Metropolis Monte Carlo algorithm for tackling the target-observation association problem. We have used the proposed approach on the problem of multi-target tracking for both linear and nonlinear observation models. The numerical results show that the suggested approach can improve significantly the performance of a particle filter.

math.NA↗

arXiv2011

Path sampling for particle filters with application to multi-target tracking

In recent work (arXiv:1006.3100v1), we have presented a novel approach for improving particle filters for multi-target tracking. The suggested approach was based on drift homotopy for stochastic differential equations. Drift homotopy was used to design a Markov Chain Monte Carlo step which is appended to the particle filter and aims to bring the particle filter samples closer to the observations. In the current work, we present an alternative way to append a Markov Chain Monte Carlo step to a particle filter to bring the particle filter samples closer to the observations. Both current and previous approaches stem from the general formulation of the filtering problem. We have used the currently proposed approach on the problem of multi-target tracking for both linear and nonlinear observation models. The numerical results show that the suggested approach can improve significantly the performance of a particle filter.

math.NA↗

arXiv2010

Sensitivity of health-related scales is a non-decreasing function of their classes

In biomedical research the use of discrete scales which describe characteristics of individuals are widely applied for the evaluation of clinical conditions. However, the number of classes (partitions) used in a discrete scale has never been mathematically evaluated against the accuracy of a scale to predict the true cases. This work, using as accuracy markers the sensitivity and specificity, revealed that the number of classes of a discrete scale affects its estimating ability of correctly classifying the true diseased. In particular, it was proved that the sensitivity of scales is a non-decreasing function of the number of their classes. This result has particular interest in clinical research providing a methodology for developing more accurate tools for disease diagnosis.

stat.ME↗

arXiv2010

Large deviations for stochastic flows of diffeomorphisms

A large deviation principle is established for a general class of stochastic flows in the small noise limit. This result is then applied to a Bayesian formulation of an image matching problem, and an approximate maximum likelihood property is shown for the solution of an optimization problem involving the large deviations rate function.

math.ST↗