arXiv subjects

Farzana Nasrin

Publications and source records attributed to Farzana Nasrin.

10 recordsLinked to original sources

arXiv2026

Structured Learning on Mapper Representations

Modern machine learning (ML) methods are highly effective for prediction tasks, but many commonly used representations reduce complex data to fixed dimensional embeddings that may suppress multiscale structural organization. The Mapper algorithm from topological data analysis (TDA) provides a different perspective by decomposing data into overlapping local regions connected through a nerve construction, producing a structured representation that captures geometric organization, local statistical behavior, and relational connectivity simultaneously. In this work, we develop a framework for learning over Mapper induced structured representations. Rather than treating Mapper as a preprocessing step that produces a graph for downstream learning, we treat the full Mapper construction as part of the representation itself. We study mathematical properties of these representations, including invariance under relabeling, a distance functional on the space of Mapper representations, structural complexity of multiscale decompositions, and learning oriented stability under representation perturbations. Experiments on time series and graph classification datasets validate the proposed framework through controlled studies of representation ablation, Mapper parameter sensitivity, and the geometry of the induced representation space. Together, these results demonstrate how the proposed mathematical framework enables systematic comparison, interpretation, and analysis of Mapper representations, providing practical tools for studying representation geometry, structural complexity, and learning stability in learning tasks.

stat.ML↗

arXiv2026

Stochastic Dynamics on Persistence Diagram Space via Reinforcement Learning

Persistence diagrams (PDs) provide stable and interpretable summaries of multiscale topological structure. While substantial progress has been made in the statistical analysis of PDs, existing literature often treats diagrams as static objects and provide limited frameworks for probabilistic modeling and stochastic evolution on PD space. We introduce a reinforcement learning framework for stochastic dynamics on PD space, where diagrams evolve through topology aware local edit operations. The dynamics define controlled Markov processes on spaces of finite PDs with variable cardinality. We establish conditions under which the induced Markov chains are irreducible, aperiodic, and geometrically ergodic, implying the existence of unique stationary probability laws on PD space. To guide the dynamics toward scientifically relevant topological targets, we formulate objectives that encompass distribution matching, task specific topological statistics, and structure-preserving compression. The resulting rewards balance task specific distributional targets, diagram fidelity, and complexity reduction, and yield a framework for adaptive topological simplification and probabilistic modeling. Experiments on synthetic and neuroimaging PDs demonstrate that the proposed framework can preserve dominant topological structure while reducing diagram complexity.

stat.ML↗

arXiv2025

Bayesian Inference for Left-Truncated Log-Logistic Distributions for Time-to-event Data Analysis

Parameter estimation is a foundational step in statistical modeling, enabling us to extract knowledge from data and apply it effectively. Bayesian estimation of parameters incorporates prior beliefs with observed data to infer distribution parameters probabilistically and robustly. Moreover, it provides full posterior distributions, allowing uncertainty quantification and regularization, especially useful in small or truncated samples. Utilizing the left-truncated log-logistic (LTLL) distribution is particularly well-suited for modeling time-to-event data where observations are subject to a known lower bound such as precipitation data and cancer survival times. In this paper, we propose a Bayesian approach for estimating the parameters of the LTLL distribution with a fixed truncation point \( x_L > 0 \). Given a random variable \( X \sim LL(α, β; x_L) \), where \( α> 0 \) is the scale parameter and \( β> 0 \) is the shape parameter, the likelihood function is derived based on a truncated sample \( X_1, X_2, \dots, X_N \) with \( X_i > x_L \). We assume independent prior distributions for the parameters, and the posterior inference is conducted via Markov Chain Monte Carlo sampling, specifically using the Metropolis-Hastings algorithm to obtain posterior estimates \( \hatα \) and \( \hatβ \). Through simulation studies and real-world applications, we demonstrate that Bayesian estimation provides more stable and reliable parameter estimates, particularly when the likelihood surface is irregular due to left truncation. The results highlight the advantages of Bayesian inference outperform the estimation of parameter uncertainty in truncated distributions for time to event data analysis.

stat.ME↗

arXiv2024

Position: Topological Deep Learning is the New Frontier for Relational Learning

Topological deep learning (TDL) is a rapidly evolving field that uses topological features to understand and design deep learning models. This paper posits that TDL is the new frontier for relational learning. TDL may complement graph representation learning and geometric deep learning by incorporating topological concepts, and can thus provide a natural choice for various machine learning settings. To this end, this paper discusses open problems in TDL, ranging from practical benefits to theoretical foundations. For each problem, it outlines potential solutions and future research opportunities. At the same time, this paper serves as an invitation to the scientific community to actively participate in TDL research to unlock the potential of this emerging field.

cs.LG↗

arXiv2022

Genomics Data Analysis via Spectral Shape and Topology

Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and to retain information that may be lost using standard dimension-reduction algorithms. We propose a novel workflow to process and analyze RNA-seq data from tumor and healthy subjects integrating Mapper and differential gene expression. Precisely, we show that a Gaussian mixture approximation method can be used to produce graphical structures that successfully separate tumor and healthy subjects, and produce two subgroups of tumor subjects. A further analysis using DESeq2, a popular tool for the detection of differentially expressed genes, shows that these two subgroups of tumor cells bear two distinct gene regulations, suggesting two discrete paths for forming lung cancer, which could not be highlighted by other popular clustering methods, including t-SNE. Although Mapper shows promise in analyzing high-dimensional data, building tools to statistically analyze Mapper graphical structures is limited in the existing literature. In this paper, we develop a scoring method using heat kernel signatures that provides an empirical setting for statistical inferences such as hypothesis testing, sensitivity analysis, and correlation analysis.

q-bio.GN↗

arXiv2022

A Random Persistence Diagram Generator

Topological data analysis (TDA) studies the shape patterns of data. Persistent homology is a widely used method in TDA that summarizes homological features of data at multiple scales and stores them in persistence diagrams (PDs). In this paper, we propose a random persistence diagram generator (RPDG) method that generates a sequence of random PDs from the ones produced by the data. RPDG is underpinned by a model based on pairwise interacting point processes, and a reversible jump Markov chain Monte Carlo (RJ-MCMC) algorithm. A first example, which is based on a synthetic dataset, demonstrates the efficacy of RPDG and provides a comparison with another method for sampling PDs. A second example demonstrates the utility of RPDG to solve a materials science problem given a real dataset of small sample size.

stat.ML↗

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 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↗