HubScan: Detecting Hubness Poisoning in Retrieval-Augmented Generation Systems

Abstract: Retrieval-Augmented Generation (RAG) systems are essential to contemporary AI applications, allowing LLMs to obtain external knowledge via vector similarity search. Nevertheless, these systems encounter a significant security flaw: hubness - items that frequently appear in the top-k retrieval results for a disproportionately high number of varied queries. These hubs can be exploited to introduce harmful content, alter search rankings, bypass content filtering, and decrease system performance. We introduce hubscan, an open-source security scanner that evaluates vector indices and embeddings to identify hubs in RAG systems. Hubscan presents a multi-detector architecture that integrates: (1) robust statistical hubness detection utilizing median/MAD-based z-scores, (2) cluster spread analysis to assess cross-cluster retrieval patterns, (3) stability testing under query perturbations, and (4) domain-aware and modality-aware detection for category-specific and cross-modal attacks. Our solution accommodates several vector databases (FAISS, Pinecone, Qdrant, Weaviate) and offers versatile retrieval techniques, including vector similarity, hybrid search, and lexical matching with reranking capabilities. We evaluate hubscan on Food-101, MS-COCO, and FiQA adversarial hubness benchmarks constructed using state-of-the-art gradient-optimized and centroid-based hub generation methods. hubscan achieves 90% recall at a 0.2% alert budget and 100% recall at 0.4%, with adversarial hubs ranking above the 99.8th percentile. Domain-scoped scanning recovers 100% of targeted attacks that evade global detection. Production validation on 1M real web documents from MS MARCO demonstrates significant score separation between clean documents and adversarial content. Our work provides a practical, extensible framework for detecting hubness threats in production RAG systems.