EpiLens: Lightweight RAG for Epidemiological Knowledge Acquisition

Important: e-prints posted on arXiv are not peer-reviewed by arXiv; they should not be relied upon without context to guide clinical practice or health-related behavior and should not be reported in news media as established information without consulting multiple experts in the field.

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.

Computation and Language (cs.CL); Digital Libraries (cs.DL); Physics and Society (physics.soc-ph)

arXiv:2610.26730 [cs.CL]

(or arXiv:2610.26730v1 [cs.CL] for this version)

https://doi.org/10.48550/arXiv.2610.26730 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.

Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.

Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.