arXiv subjects

Anne Cori

Publications and source records attributed to Anne Cori.

5 recordsLinked to original sources

arXiv2026

Evaluating AI-based Scientific Knowledge Synthesis with Epidemiological Systematic Reviews

Systematic literature reviews (SLRs) are a demanding and high-stakes form of scientific knowledge synthesis that remains underspecified as an evaluation setting for large language models (LLMs). We introduce AgentSLR, a large-scale evaluation harness comprising an SLR automation workflow and an expert annotated dataset covering 16,248 articles, designed to test LLM capabilities across the stages of SLRs in epidemiology. Reference annotations were derived from peer-reviewed studies on WHO priority pathogens and produced by domain experts. The harness evaluates each review stage as a separate unit with dedicated metrics enabling targeted failure analysis. We evaluated five frontier reasoning models and found that no single model dominated across all tasks, showing sub-task specialisation often hidden by aggregate benchmarks. Structured data extraction is a major bottleneck, with no model exceeding an average field-level F1 of 0.67. Estimated costs vary substantially, by up to 96 times across evaluated models. Documented failure modes suggest that the evaluated models are not yet reliable enough for unsupervised deployment in epidemiology, where findings can inform public policy.

cs.IR↗

arXiv2025

A statistical framework for comparing epidemic forests

Inferring who infected whom in an outbreak is essential for characterising transmission dynamics and guiding public health interventions. However, this task is challenging due to limited surveillance data and the complexity of immunological and social interactions. Instead of a single definitive transmission tree, epidemiologists often consider multiple plausible trees forming \textit{epidemic forests}. Various inference methods and assumptions can yield different epidemic forests, yet no formal test exists to assess whether these differences are statistically significant. We propose such a framework using a chi-square test and permutational multivariate analysis of variance (PERMANOVA). We assessed each method's ability to distinguish simulated epidemic forests generated under different offspring distributions. While both methods achieved perfect specificity for forests with 100+ trees, PERMANOVA consistently outperformed the chi-square test in sensitivity across all epidemic and forest sizes. Implemented in the R package \textit{mixtree}, we provide the first statistical framework to robustly compare epidemic forests.

q-bio.QM↗

arXiv2024

Mathematical modelling to inform outbreak response vaccination

Mathematical models are established tools to assist in outbreak response. They help characterise complex patterns in disease spread, simulate control options to assist public health authorities in decision-making, and longer-term operational and financial planning. In the context of vaccine-preventable diseases (VPDs), vaccines are one of the most-cost effective outbreak response interventions, with the potential to avert significant morbidity and mortality through timely delivery. Models can contribute to the design of vaccine response by investigating the importance of timeliness, identifying high-risk areas, prioritising the use of limited vaccine supply, highlighting surveillance gaps and reporting, and determining the short- and long-term benefits. In this review, we examine how models have been used to inform vaccine response for 10 VPDs, and provide additional insights into the challenges of outbreak response modelling, such as data gaps, key vaccine-specific considerations, and communication between modellers and stakeholders. We illustrate that while models are key to policy-oriented outbreak vaccine response, they can only be as good as the surveillance data that inform them.

q-bio.PE↗

arXiv2024

Best practices for estimating and reporting epidemiological delay distributions of infectious diseases using public health surveillance and healthcare data

Epidemiological delays, such as incubation periods, serial intervals, and hospital lengths of stay, are among key quantities in infectious disease epidemiology that inform public health policy and clinical practice. This information is used to inform mathematical and statistical models, which in turn can inform control strategies. There are three main challenges that make delay distributions difficult to estimate. First, the data are commonly censored (e.g., symptom onset may only be reported by date instead of the exact time of day). Second, delays are often right truncated when being estimated in real time (not all events that have occurred have been observed yet). Third, during a rapidly growing or declining outbreak, overrepresentation or underrepresentation, respectively, of recently infected cases in the data can lead to bias in estimates. Studies that estimate delays rarely address all these factors and sometimes report several estimates using different combinations of adjustments, which can lead to conflicting answers and confusion about which estimates are most accurate. In this work, we formulate a checklist of best practices for estimating and reporting epidemiological delays with a focus on the incubation period and serial interval. We also propose strategies for handling common biases and identify areas where more work is needed. Our recommendations can help improve the robustness and utility of reported estimates and provide guidance for the evaluation of estimates for downstream use in transmission models or other analyses.

stat.ME↗

arXiv2022

Evaluating Forecasts with scoringutils in R

Evaluating forecasts is essential to understand and improve forecasting and make forecasts useful to decision makers. A variety of R packages provide a broad variety of scoring rules, visualisations and diagnostic tools. One particular challenge, which scoringutils aims to address, is handling the complexity of evaluating and comparing forecasts from several forecasters across multiple dimensions such as time, space, and different types of targets. scoringutils extends the existing landscape by offering a convenient and flexible data.table-based framework for evaluating and comparing probabilistic forecasts (forecasts represented by a full predictive distribution). Notably, scoringutils is the first package to offer extensive support for probabilistic forecasts in the form of predictive quantiles, a format that is currently used by several infectious disease Forecast Hubs. The package is easily extendable, meaning that users can supply their own scoring rules or extend existing classes to handle new types of forecasts. scoringutils provides broad functionality to check the data and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and to visualise the results of the evaluation. The paper presents the package and its core functionality and illustrates common workflows using example data of forecasts for COVID-19 cases and deaths submitted to the European COVID-19 Forecast Hub.

stat.ME↗