public health data teams

Abstract: To prepare for future outbreaks, researchers need to know what studies have been done and what data they use. Mapping a large literature by hand is slow, while large language models alone can misstate or conflate sources. We present EpiLens, a lightweight, open-source retrieval-augmented generation package that applies a fixed retrieval template and output schema to every paper in a corpus and links outputs to source passages. We build a corpus of 2,297 papers from the sources of a multi-pathogen parameter study and evaluate EpiLens's paper-classification workflow against 214 manually labelled papers. Without task-specific training data, the classifier matches or exceeds the tested supervised and zero-shot baselines across four tasks. The study's early extraction sheets cite published sources for 327 estimates. We link each estimate to a cited document or to corpus studies included by a review. Then, we use the classifier's labels to compare the papers associated with different parameters and pathogens. EpiLens labels more papers linked to reproduction numbers than fatality risks as model-based (54% versus 22%, compared with 62% versus 24% in the manual labels). The gap is consistent with the frequent use of transmission models to estimate reproduction numbers and persists within each of five pathogens compared. Beyond the contrast between parameters, the model-based share of papers linked to incubation-period estimates differs by pathogen: 55% for SARS-CoV-2 versus 6% for mpox.

Abstract: Standard Bayesian experimental design (BED) methods assume the experimenter alone will act on the data, choosing the best action given their own beliefs and goals. In practice, data are often acted on by external parties whose procedures the experimenter cannot change and may not know, particularly when the data are released publicly. To extend BED to such settings, we introduce usage-aware experimental design, a framework in which an adaptive design policy is trained to minimise the usage risk: the experimenter's expected loss when one or more external rules act on the collected data. These rules may be non-Bayesian or black-box, and when several may apply, we either average over them or take the worst case. We show that, unlike in standard BED, more informative data can be harmful under such rules, so the usage risk cannot in general be expressed as an expected uncertainty reduction; our framework thus strictly generalises standard BED. We then use it to tackle a range of problems that are difficult to address with existing approaches.

Abstract: Representing individual-level behavioral heterogeneity is challenging in epidemiological modeling, particularly when empirical behavioral data are sparse. We assess the potential of large language model (LLM)-generated behavioral outputs in addressing this challenge, using hepatitis C virus-related behaviors among people who inject drugs as a case study. Correspondence with epidemiological patterns was evaluated using external benchmarks: literature-informed association directions, correlations from an agent-based model (ABM), and survey associations. Across three LLMs, unconditional directional recovery across 28 retained literature-informed associations was 46-68%, compared with 82-93% agreement when LLMs were directly asked to classify the same associations. Mean absolute differences from ABM and survey correlation patterns were 0.11-0.13 and 0.15-0.18, respectively. Together, these findings show partial alignment between LLM-generated behavioral relationships and epidemiological evidence, despite higher knowledge-probe agreement. More systematic evaluation is needed before incorporating LLM-generated behavioral outputs into epidemiological models that simulate transmission dynamics.

Abstract: Weekly influenza surveillance counts guide vaccine distribution and public-health alerts, yet they are hard to forecast. Each region offers only a few seasons, waves shift in timing and height every year, and information that helps while a wave grows misleads after its peak, whereas last season's shape stays informative for a year. Existing epidemic graph models and general forecasters read a short fixed window and treat all past information alike, so they neither exploit earlier seasons nor discard stale associations when the epidemic phase changes. To address these limitations, we propose TERN, a forecaster built around a delta-rule fast-weight memory that decays channel-wise and erases along a learned address under gates driven by local epidemic-phase features, combined with an explicit seasonal reference and online adaptation. On three Cola-GNN influenza benchmarks, TERN outperformed epidemic graph models and general forecasters, matched or exceeded seasonal references, and a controlled comparison confirmed the contribution of the memory itself.