# EpidemIQs: Prompt-to-Paper LLM Agents for Epidemic Modeling and Analysis

arXiv: https://arxiv.org/abs/2510.00024 · HTML: https://mlsanity.com/paper/2510.00024/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Placed in Social simulation and multi-agent debate, one of 16 directions in LLM agents and tool use.
- Builds on 32 of its 60 references that are in the map.
- First posted on arXiv 24 Sep 2025.

## Placed in

- LLM agents and tool use / [Social simulation and multi-agent debate](https://mlsanity.com/agents/social-simulation-and-multi-agent-debate/)

## Builds on (most cited first, 30 of 32)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Reflexion: Language Agents with Verbal Reinforcement Learning](https://mlsanity.com/paper/2303.11366/) (2023)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [Generative Agents: Interactive Simulacra of Human Behavior](https://mlsanity.com/paper/2304.03442/) (2023)
- [SWE-bench: Can Language Models Resolve Real-World GitHub Issues?](https://mlsanity.com/paper/2310.06770/) (2023)
- [AutoGen: Enabling Next-Gen LLM Applications via Multi-Agent Conversation](https://mlsanity.com/paper/2308.08155/) (2023)
- [MetaGPT: Meta Programming for A Multi-Agent Collaborative Framework](https://mlsanity.com/paper/2308.00352/) (2023)
- [The Rise and Potential of Large Language Model Based Agents: A Survey](https://mlsanity.com/paper/2309.07864/) (2023)
- [CAMEL: Communicative Agents for "Mind" Exploration of Large Language Model Society](https://mlsanity.com/paper/2303.17760/) (2023)
- [Code as Policies: Language Model Programs for Embodied Control](https://mlsanity.com/paper/2209.07753/) (2022)
- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [OpenHands: An Open Platform for AI Software Developers as Generalist Agents](https://mlsanity.com/paper/2407.16741/) (2024)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Agent Laboratory: Using LLM Agents as Research Assistants](https://mlsanity.com/paper/2501.04227/) (2025)
- [Can AI-Generated Text be Reliably Detected?](https://mlsanity.com/paper/2303.11156/) (2023)
- [MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning](https://mlsanity.com/paper/2311.10537/) (2023)
- [ToolkenGPT: Augmenting Frozen Language Models with Massive Tools via Tool Embeddings](https://mlsanity.com/paper/2305.11554/) (2023)
- [ResearchAgent: Iterative Research Idea Generation over Scientific Literature with Large Language Models](https://mlsanity.com/paper/2404.07738/) (2024)
- [DSBench: How Far Are Data Science Agents from Becoming Data Science Experts?](https://mlsanity.com/paper/2409.07703/) (2024)
- [Towards Accurate Differential Diagnosis with Large Language Models](https://mlsanity.com/paper/2312.00164/) (2023)
- [Let Me Speak Freely? A Study on the Impact of Format Restrictions on Performance of Large Language Models](https://mlsanity.com/paper/2408.02442/) (2024)
- [Proof or Bluff? Evaluating LLMs on 2025 USA Math Olympiad](https://mlsanity.com/paper/2503.21934/) (2025)
- [Multi-hop Question Answering](https://mlsanity.com/paper/2204.09140/) (2022)
- ["We Need Structured Output": Towards User-centered Constraints on Large Language Model Output](https://mlsanity.com/paper/2404.07362/) (2024)
- [LLM-Based Human-Agent Collaboration and Interaction Systems: A Survey](https://mlsanity.com/paper/2505.00753/) (2025)
- [Advancing Agentic Systems: Dynamic Task Decomposition, Tool Integration and Evaluation using Novel Metrics and Dataset](https://mlsanity.com/paper/2410.22457/) (2024)
- [LLM Can be a Dangerous Persuader: Empirical Study of Persuasion Safety in Large Language Models](https://mlsanity.com/paper/2504.10430/) (2025)
- [Automating Exploratory Proteomics Research via Language Models](https://mlsanity.com/paper/2411.03743/) (2024)

## Built on by (most cited first, 4 of 4)

- [EpiEvolve: Self-Evolving Agents for Streaming Pandemic Forecasting under Regime Shifts](https://mlsanity.com/paper/2606.05513/) (2026)
- [Prompt-to-Paper: Agentic AI System for Bioinformatics](https://mlsanity.com/paper/2607.05456/) (2026)
- [ARIES: A Scalable Multi-Agent Orchestration Framework for Real-Time Epidemiological Surveillance and Outbreak Monitoring](https://mlsanity.com/paper/2601.01831/) (2026)
- [The Epi-LLM Framework: probing LLM behavioral priors through epidemiological agent-based models](https://mlsanity.com/paper/2606.02867/) (2026)

## Abstract (arXiv)

Large Language Models (LLMs) offer new opportunities to accelerate complex interdisciplinary research domains. Epidemic modeling, characterized by its complexity and reliance on network science, dynamical systems, epidemiology, and stochastic simulations, represents a prime candidate for leveraging LLM-driven automation. We introduce EpidemIQs, a novel multi-agent LLM framework that integrates user inputs and autonomously conducts literature review, analytical derivation, network modeling, mechanistic modeling, stochastic simulations, data visualization and analysis, and finally documentation of findings in a structured manuscript, through five predefined research phases. We introduce two types of agents: a scientist agent for planning, coordination, reflection, and generation of final results, and a task-expert agent to focus exclusively on one specific duty serving as a tool to the scientist agent. The framework consistently generated complete reports in scientific article format. Specifically, using GPT 4.1 and GPT 4.1 Mini as backbone LLMs for scientist and task-expert agents, respectively, the autonomous process completes with average total token usage 870K at a cost of about 1.57 per study, successfully executing all phases and final report. We evaluate EpidemIQs across several different epidemic scenarios, measuring computational cost, workflow reliability, task success rate, and LLM-as-Judge and human expert reviews to estimate the overall quality and technical correctness of the generated results. Through our experiments, the framework consistently addresses evaluation scenarios with an average task success rate of 79%. We compare EpidemIQs to an iterative single-agent LLM, benefiting from the same system prompts and tools, iteratively planning, invoking tools, and revising outputs until task completion. The comparisons suggest a consistently higher performance of EpidemIQs.