Understanding the effect of knowledge graph extraction error on downstream graph analyses: a case study on affiliation graphs

Abstract Knowledge graphs (KGs) are useful for analyzing social structures, community dynamics, institutional memberships, and other complex relationships across domains from sociology to public health. While recent advances in large language models (LLMs) have improved the scalability and accessibility of automated KG extraction from large text corpora, the impacts of extraction errors on downstream analyses are poorly understood, especially for applied scientists who depend on accurate KGs for real-world insights. To address this gap, we conducted the first evaluation of KG extraction performance at two levels: (1) micro-level edge accuracy, which is consistent with standard NLP evaluations, and manual identification of common error sources; (2) macro-level graph metrics that assess structural properties such as community detection and connectivity, which are relevant to real-world applications. Focusing on affiliation graphs of person membership in organizations extracted from social register books, our study identifies a range of extraction performance where biases across most downstream graph analysis metrics are near zero. However, as extraction performance declines, we find that many metrics exhibit increasingly pronounced biases, with each metric tending toward a consistent direction of either over- or under-estimation. Through simulations, we further show that error models commonly used in the literature do not capture these bias patterns, indicating the need for more realistic error models for KG extraction. Our findings provide actionable insights for practitioners and underscore the importance of advancing extraction methods and error modeling to ensure reliable and meaningful downstream analyses.