arXiv subjects

Trisha Dawn

Publications and source records attributed to Trisha Dawn.

4 recordsLinked to original sources

arXiv2025

Spatially Varying Gene Regulatory Networks via Bayesian Nonparametric Covariate-Dependent Directed Cyclic Graphical Models

Spatial transcriptomics technologies enable the measurement of gene expression with spatial context, providing opportunities to understand how gene regulatory networks vary across tissue regions. However, existing graphical models focus primarily on undirected graphs or directed acyclic graphs, limiting their ability to capture feedback loops that are prevalent in gene regulation. Moreover, ensuring the so-called stability condition of cyclic graphs, while allowing graph structures to vary continuously with spatial covariates, presents significant statistical and computational challenges. We propose BNP-DCGx, a Bayesian nonparametric approach for learning spatially varying gene regulatory networks via covariate-dependent directed cyclic graphical models. Our method introduces a covariate-dependent random partition as an intermediary layer in a hierarchical model, which discretizes the covariate space into clusters with cluster-specific stable directed cyclic graphs. Through partition averaging, we obtain smoothly varying graph structures over space while maintaining theoretical guarantees of stability. We develop an efficient parallel tempered Markov chain Monte Carlo algorithm for posterior inference and demonstrate through simulations that our method accurately recovers both piecewise constant and continuously varying graph structures. Application to spatial transcriptomics data from human dorsolateral prefrontal cortex reveals spatially varying regulatory networks with feedback loops, identifies potential cell subtypes within established cell types based on distinct regulatory mechanisms, and provides new insights into spatial organization of gene regulation in brain tissue.

stat.ME↗

arXiv2025

Covariate-assisted graph matching

Data integration is essential across diverse domains, from historical records to biomedical research, facilitating joint statistical inference. A crucial initial step in this process involves merging multiple data sources based on matching individual records, often in the absence of unique identifiers. When the datasets are networks, this problem is typically addressed through graph matching methodologies. For such cases, auxiliary features or covariates associated with nodes or edges can be instrumental in achieving improved accuracy. However, most existing graph matching techniques do not incorporate this information, limiting their performance against non-identifiable and erroneous matches. To overcome these limitations, we propose two novel covariate-assisted seeded graph matching methods, where a partial alignment for a set of nodes, called seeds, is known. The first one solves a quadratic assignment problem (QAP) over the whole graph, while the second one only leverages the local neighborhood structure of seed nodes for computational scalability. Both methods are grounded in a conditional modeling framework, where elements of one graph's adjacency matrix are modeled using a generalized linear model (GLM), given the other graph and the available covariates. We establish theoretical guarantees for model estimation error and exact recovery of the solution of the QAP. The effectiveness of our methods is demonstrated through numerical experiments and in an application to matching the statistics academic genealogy and the collaboration networks. By leveraging additional covariates, we achieve improved alignment accuracy. Our work highlights the power of integrating covariate information in the classical graph matching setup, offering a practical and improved framework for combining network data with wide-ranging applications.

stat.ME↗

arXiv2022

Sequential Gradient Descent and Quasi-Newton's Method for Change-Point Analysis

One common approach to detecting change-points is minimizing a cost function over possible numbers and locations of change-points. The framework includes several well-established procedures, such as the penalized likelihood and minimum description length. Such an approach requires finding the cost value repeatedly over different segments of the data set, which can be time-consuming when (i) the data sequence is long and (ii) obtaining the cost value involves solving a non-trivial optimization problem. This paper introduces a new sequential method (SE) that can be coupled with gradient descent (SeGD) and quasi-Newton's method (SeN) to find the cost value effectively. The core idea is to update the cost value using the information from previous steps without re-optimizing the objective function. The new method is applied to change-point detection in generalized linear models and penalized regression. Numerical studies show that the new approach can be orders of magnitude faster than the Pruned Exact Linear Time (PELT) method without sacrificing estimation accuracy.

stat.ML↗

arXiv2021

Some Clustering-based Change-point Detection Methods Applicable to High Dimension, Low Sample Size Data

Detection of change-points in a sequence of high-dimensional observations is a very challenging problem, and this becomes even more challenging when the sample size (i.e., the sequence length) is small. In this article, we propose some change-point detection methods based on clustering, which can be conveniently used in such high dimension, low sample size situations. First, we consider the single change-point problem. Using k-means clustering based on some suitable dissimilarity measures, we propose some methods for testing the existence of a change-point and estimating its location. High-dimensional behavior of these proposed methods are investigated under appropriate regularity conditions. Next, we extend our methods for detection of multiple change-points. We carry out extensive numerical studies to compare the performance of our proposed methods with some state-of-the-art methods.

stat.ME↗