arXiv subjects

Alyssa Bilinski

Publications and source records attributed to Alyssa Bilinski.

7 recordsLinked to original sources

arXiv2026

Fast, Frequentist Estimation of Epidemic Reproduction Numbers

The effective reproduction number $R_t$ is one of the most important indicators of epidemic dynamics. Estimating $R_t$, typically from case reports or hospitalization counts, poses a challenging inverse problem. One key issue is lag: $R_t$ acts at the moment of transmission, while the data it generates surface days later. To handle this delay and infer recent infections in real time, popular methods take a Bayesian approach, which can be slow and sensitive to prior specification. As an alternative, we propose ConvRt, a frequentist method for retrospective and real-time estimation. ConvRt deconvolves latent infections and then estimates $R_t$ with successive penalized-likelihood steps, using a spline basis to model smooth curves. Across both stylized and data-driven simulations, we demonstrate favorable performance in point estimation, uncertainty quantification, and runtime. Moreover, by untangling smoothness from future projections, ConvRt enables researchers to assess which qualitative narratives about $R_t$ the data support.

stat.AP↗

arXiv2026

On the Equivalence of Instantaneous and Mechanistic Reproduction Numbers

The effective reproduction number ($R_t$) is widely used to track epidemic dynamics in real time. The standard estimation framework uses "instantaneous $R_t$," defined via the renewal equation, which relates new infections to past infections through a generation interval distribution. Compartmental models like SEIR yield a seemingly distinct quantity, "mechanistic $R_t$," based on the effective contact rate and duration of infectiousness. We prove these two definitions are equivalent under homogeneous mixing, the standard assumption in compartmental modeling. We also derive the generation interval distribution implied by SEIR dynamics. A practical consequence is that generation intervals, often treated as assumption-light inputs to renewal equation estimators, in fact encode specific compartmental structure.

q-bio.PE↗

arXiv2025

Estimating Time-Varying Epidemic Severity Rates with Adaptive Deconvolution

Several key metrics in public health convey the probability that a primary event will lead to a more serious secondary event in the future.Several key metrics in public health convey the probability that a primary event will lead to a more serious secondary event in the future. These "severity rates" can change over the course of an epidemic in response to shifting conditions like new therapeutics, variants, or public health interventions. In practice, time-varying parameters such as the case-fatality rate are typically estimated from aggregate count data. Prior work has demonstrated that commonly-used ratio-based estimators can be highly biased, motivating the development of new methods. In this paper, we develop an adaptive deconvolution approach based on approximating a Poisson-binomial model for secondary events, and we regularize the maximum likelihood solution in this model with a trend filtering penalty to produce smooth but locally adaptive estimates of severity rates over time. This enables us to compute severity rates both retrospectively and in real time. Experiments based on COVID-19 death and hospitalization data show that our deconvolution estimator is generally more accurate than the standard ratio-based methods, and displays reasonable robustness to model misspecification.

stat.AP↗

arXiv2025

Defining and Estimating Outcomes Directly Averted by a Vaccination Program when Rollout Occurs Over Time

During the COVID-19 pandemic, estimating the total deaths averted by vaccination has been of great public health interest. Instead of estimating total deaths averted by vaccination among both vaccinated and unvaccinated individuals, some studies empirically estimated only "directly averted" deaths among vaccinated individuals, typically suggesting that vaccines prevented more deaths overall than directly due to the indirect effect. Here, we define the causal estimand to quantify outcomes "directly averted" by vaccination$\unicode{x2014}$i.e., the impact of vaccination for vaccinated individuals, holding vaccination coverage fixed$\unicode{x2014}$for vaccination at multiple time points, and show that this estimand is a lower bound on the total outcomes averted when the indirect effect is non-negative. We develop an unbiased estimator for the causal estimand in a one-stage randomized controlled trial (RCT) and explore the bias of a popular "hazard difference" estimator frequently used in empirical studies. We show that even in an RCT, the hazard difference estimator is biased if vaccination has a non-null effect, as it fails to incorporate the greater depletion of susceptibles among the unvaccinated individuals. In simulations, the overestimation is small for averted deaths when infection-fatality rate is low, as for many important pathogens. However, the overestimation can be large for averted infections given a high basic reproduction number. Additionally, we define and compare estimand and estimators for avertible outcomes (i.e., outcomes that could have been averted by vaccination, but were not due to failure to vaccinate). Future studies can explore the identifiability of the causal estimand in observational settings.

q-bio.PE↗

arXiv2024

Difference-in-Differences for Health Policy and Practice: A Review of Modern Methods

Difference-in-differences (DiD) is the most popular observational causal inference method in health policy, employed to evaluate the real-world impact of policies and programs. To estimate treatment effects, DiD relies on the "parallel trends assumption", that on average treatment and comparison groups would have had parallel trajectories in the absence of an intervention. Historically, DiD has been considered broadly applicable and straightforward to implement, but recent years have seen rapid advancements in DiD methods. This paper reviews and synthesizes these innovations for medical and health policy researchers. We focus on four topics: (1) assessing the parallel trends assumption in health policy contexts; (2) relaxing the parallel trends assumption when appropriate; (3) employing estimators to account for staggered treatment timing; and (4) conducting robust inference for analyses in which normal-based clustered standard errors are inappropriate. For each, we explain challenges and common pitfalls in traditional DiD and modern methods available to address these issues.

stat.AP↗

arXiv2023

What's Trending in Difference-in-Differences? A Synthesis of the Recent Econometrics Literature

This paper synthesizes recent advances in the econometrics of difference-in-differences (DiD) and provides concrete recommendations for practitioners. We begin by articulating a simple set of ``canonical'' assumptions under which the econometrics of DiD are well-understood. We then argue that recent advances in DiD methods can be broadly classified as relaxing some components of the canonical DiD setup, with a focus on $(i)$ multiple periods and variation in treatment timing, $(ii)$ potential violations of parallel trends, or $(iii)$ alternative frameworks for inference. Our discussion highlights the different ways that the DiD literature has advanced beyond the canonical model, and helps to clarify when each of the papers will be relevant for empirical work. We conclude by discussing some promising areas for future research.

econ.EM↗

arXiv2018

Nothing to See Here? A non-inferiority approach to parallel trends

Difference-in-differences is a popular method for observational health policy evaluation. It relies on a causal assumption that in the absence of intervention, treatment groups' outcomes would have evolved in parallel to those of comparison groups. Researchers frequently look for parallel trends in the pre-intervention period to bolster confidence in this assumption. The popular "parallel trends test" evaluates a null hypothesis of parallel trends and, failing to find evidence against the null, concludes that the assumption holds. This tightly controls the probability of falsely concluding that trends are not parallel but may have low power to detect non-parallel trends. When used as a screening step, it can also introduce bias in treatment effect estimates. We propose a non-inferiority/equivalence approach that tightly controls the probability of missing large violations of parallel trends measured on the scale of the treatment effect. Our framework nests several common use cases, including linear trend tests and event studies. We show that our approach may induce no or minimal bias when used as a screening step under commonly-assumed error structures, and absent violations, can offer a higher-power alternative to testing treatment effects in more flexible models. We illustrate our ideas by re-considering a study of the impact of the Affordable Care Act's dependent coverage provision.

stat.ME↗