arXiv subjects

James Peng

Publications and source records attributed to James Peng.

5 recordsLinked to original sources

arXiv2026

Estimating the Wasserstein barycenter of one-dimensional distributions under sparse sampling

We study distributional data under sparse sampling where each unit is represented by a probability distribution on the real line observed only through a small i.i.d.~sample. A natural notion of central tendency for one-dimensional distributional data is the Wasserstein barycenter, whose quantile function is the pointwise average of the unit-level quantile functions. We focus on pointwise estimation of the Wasserstein barycenter quantile function: at a given quantile level, the target is the population mean of the corresponding unit-level quantiles. A naive plug-in estimator is the empirical Wasserstein barycenter, which treats observed unit-level empirical distributions as the true latent unit-level distributions. Under sparse sampling, however, this estimator can be severely biased. We propose an approach that avoids directly estimating either the unit-level distributions or the full population law of distributions. We start with the more ambitious goal of characterizing the distribution of latent unit-level quantiles at a given quantile level. We show that this distribution can be written in terms of the marginal distributions of the unit-level CDF values, which can be estimated using binomial mixture methods. This motivates our estimator, the marginal-constructed barycenter (MCB) estimator, obtained by taking the mean of the estimated distribution of latent unit-level quantiles. We establish conditions under which the MCB estimator is pointwise consistent and asymptotically normal, and show through simulations that it can substantially outperform the empirical Wasserstein barycenter under sparse sampling. We illustrate the method in an analysis of HIV-1 sequence data from the HVTN 502/503 vaccine efficacy trials, using the barycenter to summarize and compare within-participant distributions of viral sequence features when only a small number of sequences are available per participant.

stat.ME↗

arXiv2025

Vaccine sieve analysis on deep sequencing data using competing risks Cox regression with failure type subject to misclassification

Understanding how vaccines perform against different pathogen genotypes is crucial for developing effective prevention strategies, particularly for highly genetically diverse pathogens like HIV. Sieve analysis is a statistical framework used to determine whether a vaccine selectively prevents acquisition of certain genotypes while allowing breakthrough of other genotypes that evade immune responses. Traditionally, these analyses are conducted with a single sequence available per individual acquiring the pathogen. However, modern sequencing technology can provide detailed characterization of intra-individual viral diversity by capturing up to hundreds of pathogen sequences per person. In this work, we introduce methodology that extends sieve analysis to account for intra-individual viral diversity. Our approach estimates vaccine efficacy against viral populations with varying true (unobservable) frequencies of vaccine-mismatched mutations. To account for differential resolution of information from differing sequence counts per person, we use competing risks Cox regression with modeled causes of failure and propose an empirical Bayes approach for the classification model. Simulation studies demonstrate that our approach reduces bias, provides nominal confidence interval coverage, and improves statistical power compared to conventional methods. We apply our method to the HVTN 705 Imbokodo trial, which assessed the efficacy of a heterologous vaccine regimen in preventing HIV-1 acquisition.

stat.ME↗

arXiv2024

A Surrogate Endpoint Based Provisional Approval Causal Roadmap

For many rare diseases with no approved preventive interventions, promising interventions exist, yet it has been difficult to conduct a pivotal phase 3 trial that could provide direct evidence demonstrating a beneficial effect on the target disease outcome. When a promising putative surrogate endpoint(s) for the target outcome is available, surrogate-based provisional approval of an intervention may be pursued. We apply the Causal Roadmap rubric to define a surrogate endpoint based provisional approval causal roadmap, which combines observational study data that estimates the relationship between the putative surrogate and the target outcome, with a phase 3 surrogate endpoint study that collects the same data but is very under-powered to assess the treatment effect (TE) on the target outcome. The objective is conservative estimation/inference for the TE with an estimated lower uncertainty bound that allows (through two bias functions) for an imperfect surrogate and imperfect transport of the conditional target outcome risk in the untreated between the observational and phase 3 studies. Two estimators of TE (plug-in, nonparametric efficient one-step) with corresponding inference procedures are developed. Finite-sample performance of the plug-in estimator is evaluated in two simulation studies, with R code provided. The roadmap is illustrated with contemporary Group B Streptococcus vaccine development.

stat.ME↗

arXiv2024

TALICS$^3$: Tape Library Cloud Storage System Simulator

High performance computing data is surging fast into the exabyte-scale world, where tape libraries are the main platform for long-term durable data storage besides high-cost DNA. Tape libraries are extremely hard to model, but accurate modeling is critical for system administrators to obtain valid performance estimates for their designs. This research introduces a discrete--event tape simulation platform that realistically models tape library behavior in a networked cloud environment, by incorporating real-world phenomena and effects. The platform addresses several challenges, including precise estimation of data access latency, rates of robot exchange, data collocation, deduplication/compression ratio, and attainment of durability goals through replication or erasure coding. Using the {proposed} simulator, {one can} compare the single enterprise configuration with multiple commodity library configurations, making it a useful tool for system administrators and reliability engineers. This makes the simulator a valuable tool for system administrators and reliability engineers, enabling them to acquire practical and dependable performance estimates for their enduring, cost-efficient cold data storage architecture designs.

cs.DC↗

arXiv2019

A Data-Assisted Reliability Model for Carrier-Assisted Cold Data Storage Systems

Cold data storage systems are used to allow long term digital preservation for institutions' archives. The common functionality among cold and warm/hot data storage is that the data is stored on some physical medium for read-back at a later time. However in cold storage, write and read operations are not necessarily done in the same exact geographical location. Hence, a third party assistance is typically utilized to bring together the medium and the drive. On the other hand, the reliability modeling of such a decomposed system poses few challenges that do not necessarily exist in other warm/hot storage alternatives such as fault detection and absence of the carrier, all totaling up to the data unavailability issues. In this paper, we propose a generalized non-homogenous Markov model that encompasses the aging of the carriers in order to address the requirements of today's cold data storage systems in which the data is encoded and spread across multiple nodes for the long-term data retention. We have derived useful lower/upper bounds on the overall system availability. Furthermore, the collected field data is used to estimate parameters of a Weibull distribution to accurately predict the lifetime of the carriers in an example scale-out setting. In this study, we numerically demonstrate the significance of carriers' presence and the key role that their timely maintenance plays on the long-term reliability and availability of the stored content.

cs.PF↗