Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2610.26730

EpiLens: Lightweight RAG for Epidemiological Knowledge Acquisition

Vincenzo Perri·Ciro Cattuto·Daniela Paolotti
View original source ↗Read source document ↗Export metadata ↓

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.

Explore related subjects

cs.CLcs.DLphysics.soc-ph

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Vincenzo Perri, Ciro Cattuto, Daniela Paolotti. 2026-10-19. EpiLens: Lightweight RAG for Epidemiological Knowledge Acquisition. https://arxiv.org/abs/2610.26730

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Post-hoc Disentanglement of Textual and Acoustic Features in Pre-trained Speech Encoders

Pre-trained speech models build entangled internal representations, which capture a variety of features (e.g., pitch, loudness, syntax, or semantics of an utterance) in a distributed encoding. This entanglement makes it difficult to track how such representations rely on textual versus acoustic information when used in downstream applications, limiting their interpretability and transparency. In this paper, we explore an approach to post-hoc disentanglement that builds on the Information Bottleneck principle. We take representations from pre-trained speech encoders as input, and separate them into two distinct components in a cascaded fashion: first we learn a vector encoding content (i.e., what can be transcribed as text), and nothing else; second, we learn a vector encoding all complementary acoustic features relevant to a target task. We apply and evaluate our proposed setup to emotion recognition and speaker identification target tasks, quantifying the relative contribution of textual and acoustic features at each model layer. Finally, we use the approach for disentangled feature attribution as it allows us to identify the most salient speech frames from both the textual and acoustic perspectives.

cs.CL↗
arXiv2026

The Super Emotion Dataset

Despite the wide-scale usage and development of emotion classification datasets in NLP, the field lacks a standardized, large-scale resource that follows a psychologically grounded taxonomy. Existing datasets either use inconsistent emotion categories, suffer from limited sample size, or focus on specific domains. The SuperEmotion dataset addresses this gap by harmonizing diverse text sources into a unified framework based on Shaver's empirically validated emotion taxonomy, enabling more consistent cross-domain emotion recognition research. This report describes version 2 of the dataset. We also report baseline results for a fine-tuned ModernBERT encoder.

cs.CL↗
arXiv2026

AutoMind: Adaptive Knowledgeable Agent for Automated Data Science

Large Language Model (LLM) agents have shown great potential in addressing real-world data science problems. LLM-driven data science agents promise to automate the entire machine learning pipeline, yet their real-world effectiveness remains limited. Existing frameworks depend on rigid, pre-defined workflows and inflexible coding strategies; consequently, they excel only on relatively simple, classical problems and fail to capture the empirical expertise that human practitioners bring to complex, innovative tasks. In this work, we introduce AutoMind, an adaptive, knowledgeable LLM-agent framework that overcomes these deficiencies through three key advances: (1) a curated expert knowledge base that grounds the agent in domain expert knowledge, (2) an agentic knowledgeable tree search algorithm that strategically explores possible solutions, and (3) a self-adaptive coding strategy that dynamically tailors code generation to task complexity. Evaluations on two automated data science benchmarks demonstrate that AutoMind delivers superior performance versus state-of-the-art baselines. Additional analyses confirm favorable effectiveness, efficiency, and qualitative solution quality, highlighting AutoMind as an efficient and robust step toward fully automated data science. Code is at https://github.com/zjunlp/AutoMind.

cs.CL↗