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.