arXiv subjects

Seyoon Ko

Publications and source records attributed to Seyoon Ko.

8 recordsLinked to original sources

arXiv2026

Scaling Hawkes Processes

Hawkes processes (HP) are a large class of stochastic point process models scientists have used to analyze contagion phenomena ranging from earthquakes, infectious diseases and biological neurons to financial trading activity, memes on social media and gun violence. We introduce applications of HP to the latter before reviewing general strategies for fitting HP to data, paying attention to the influence of model structure on computational scalability considerations. We then apply a recently developed high-performance computing powered Bayesian inference strategy for the spatiotemporal HP analysis of 412,376 acts of gun violence in the U.S. between 2014 and 2024. We finish with a discussion of model fit and directions for future research.

stat.CO↗

arXiv2024

Scaling Hawkes processes to one million COVID-19 cases

Hawkes stochastic point process models have emerged as valuable statistical tools for analyzing viral contagion. The spatiotemporal Hawkes process characterizes the speeds at which viruses spread within human populations. Unfortunately, likelihood-based inference using these models requires $O(N^2)$ floating-point operations, for $N$ the number of observed cases. Recent work responds to the Hawkes likelihood's computational burden by developing efficient graphics processing unit (GPU)-based routines that enable Bayesian analysis of tens-of-thousands of observations. We build on this work and develop a high-performance computing (HPC) strategy that divides 30 Markov chains between 4 GPU nodes, each of which uses multiple GPUs to accelerate its chain's likelihood computations. We use this framework to apply two spatiotemporal Hawkes models to the analysis of one million COVID-19 cases in the United States between March 2020 and June 2023. In addition to brute-force HPC, we advocate for two simple strategies as scalable alternatives to successful approaches proposed for small data settings. First, we use known county-specific population densities to build a spatially varying triggering kernel in a manner that avoids computationally costly nearest neighbors search. Second, we use a cut-posterior inference routine that accounts for infections' spatial location uncertainty by iteratively sampling latent locations uniformly within their respective counties of occurrence, thereby avoiding full-blown latent variable inference for 1,000,000 infection locations.

stat.CO↗

arXiv2020

DistStat.jl: Towards Unified Programming for High-Performance Statistical Computing Environments in Julia

The demand for high-performance computing (HPC) is ever-increasing for everyday statistical computing purposes. The downside is that we need to write specialized code for each HPC environment. CPU-level parallelization needs to be explicitly coded for effective use of multiple nodes in cluster supercomputing environments. Acceleration via graphics processing units (GPUs) requires to write kernel code. The Julia software package DistStat.jl implements a data structure for distributed arrays that work on both multi-node CPU clusters and multi-GPU environments transparently. This package paves a way to developing high-performance statistical software in various HPC environments simultaneously. As a demonstration of the transparency and scalability of the package, we provide applications to large-scale nonnegative matrix factorization, multidimensional scaling, and $\ell_1$-regularized Cox proportional hazards model on an 8-GPU workstation and a 720-CPU-core virtual cluster in Amazon Web Services (AWS) cloud. As a case in point, we analyze the on-set of type-2 diabetes from the UK Biobank with 400,000 subjects and 500,000 single nucleotide polymorphisms using the $\ell_1$-regularized Cox proportional hazards model. Fitting a half-million-variate regression model took less than 50 minutes on AWS.

stat.CO↗

arXiv2020

High-Performance Statistical Computing in the Computing Environments of the 2020s

Technological advances in the past decade, hardware and software alike, have made access to high-performance computing (HPC) easier than ever. We review these advances from a statistical computing perspective. Cloud computing makes access to supercomputers affordable. Deep learning software libraries make programming statistical algorithms easy and enable users to write code once and run it anywhere -- from a laptop to a workstation with multiple graphics processing units (GPUs) or a supercomputer in a cloud. Highlighting how these developments benefit statisticians, we review recent optimization algorithms that are useful for high-dimensional models and can harness the power of HPC. Code snippets are provided to demonstrate the ease of programming. We also provide an easy-to-use distributed matrix data structure suitable for HPC. Employing this data structure, we illustrate various statistical applications including large-scale positron emission tomography and $\ell_1$-regularized Cox regression. Our examples easily scale up to an 8-GPU workstation and a 720-CPU-core cluster in a cloud. As a case in point, we analyze the onset of type-2 diabetes from the UK Biobank with 200,000 subjects and about 500,000 single nucleotide polymorphisms using the HPC $\ell_1$-regularized Cox regression. Fitting this half-million-variate model takes less than 45 minutes and reconfirms known associations. To our knowledge, this is the first demonstration of the feasibility of penalized regression of survival outcomes at this scale.

stat.CO↗

arXiv2019

Splitting with Near-Circulant Linear Systems: Applications to Total Variation CT and PET

Many imaging problems, such as total variation reconstruction of X-ray computed tomography (CT) and positron-emission tomography (PET), are solved via a convex optimization problem with near-circulant, but not actually circulant, linear systems. The popular methods to solve these problems, alternating direction method of multipliers (ADMM) and primal-dual hybrid gradient (PDHG), do not directly utilize this structure. Consequently, ADMM requires a costly matrix inversion as a subroutine, and PDHG takes too many iterations to converge. In this paper, we present near-circulant splitting (NCS), a novel splitting method that leverages the near-circulant structure. We show that NCS can converge with an iteration count close to that of ADMM, while paying a computational cost per iteration close to that of PDHG. Through experiments on a CUDA GPU, we empirically validate the theory and demonstrate that NCS can effectively utilize the parallel computing capabilities of CUDA.

math.OC↗

arXiv2019

OPENMENDEL: A Cooperative Programming Project for Statistical Genetics

Statistical methods for genomewide association studies (GWAS) continue to improve. However, the increasing volume and variety of genetic and genomic data make computational speed and ease of data manipulation mandatory in future software. In our view, a collaborative effort of statistical geneticists is required to develop open source software targeted to genetic epidemiology. Our attempt to meet this need is called the OPENMENDELproject (https://openmendel.github.io). It aims to (1) enable interactive and reproducible analyses with informative intermediate results, (2) scale to big data analytics, (3) embrace parallel and distributed computing, (4) adapt to rapid hardware evolution, (5) allow cloud computing, (6) allow integration of varied genetic data types, and (7) foster easy communication between clinicians, geneticists, statisticians, and computer scientists. This article reviews and makes recommendations to the genetic epidemiology community in the context of the OPENMENDEL project.

stat.AP↗

arXiv2017

Easily parallelizable and distributable class of algorithms for structured sparsity, with optimal acceleration

Many statistical learning problems can be posed as minimization of a sum of two convex functions, one typically a composition of non-smooth and linear functions. Examples include regression under structured sparsity assumptions. Popular algorithms for solving such problems, e.g., ADMM, often involve non-trivial optimization subproblems or smoothing approximation. We consider two classes of primal-dual algorithms that do not incur these difficulties, and unify them from a perspective of monotone operator theory. From this unification we propose a continuum of preconditioned forward-backward operator splitting algorithms amenable to parallel and distributed computing. For the entire region of convergence of the whole continuum of algorithms, we establish its rates of convergence. For some known instances of this continuum, our analysis closes the gap in theory. We further exploit the unification to propose a continuum of accelerated algorithms. We show that the whole continuum attains the theoretically optimal rate of convergence. The scalability of the proposed algorithms, as well as their convergence behavior, is demonstrated up to 1.2 million variables with a distributed implementation.

stat.ML↗

arXiv2016

Revealing Fundamental Physics from the Daya Bay Neutrino Experiment using Deep Neural Networks

Experiments in particle physics produce enormous quantities of data that must be analyzed and interpreted by teams of physicists. This analysis is often exploratory, where scientists are unable to enumerate the possible types of signal prior to performing the experiment. Thus, tools for summarizing, clustering, visualizing and classifying high-dimensional data are essential. In this work, we show that meaningful physical content can be revealed by transforming the raw data into a learned high-level representation using deep neural networks, with measurements taken at the Daya Bay Neutrino Experiment as a case study. We further show how convolutional deep neural networks can provide an effective classification filter with greater than 97% accuracy across different classes of physics events, significantly better than other machine learning approaches.

stat.ML↗