NehlTech/ClinicalShield: ClinicalShield: A Multi-Layer Defence Framework for Detecting and Neutralizing Indirect Prompt Injection Attacks in RAG-Based Clinical Decision Support Systems

Abstract

ClinicalShield — Major Revision Release This release accompanies the major revision of the manuscript submitted to Scientific Reports. All code, data, notebooks and results files have been rebuilt from scratch for this version. What is included Five pipeline modules: encoding-aware ingestion with canonicalisation (Module 1), PubMedBERT-based detection (Module 2), semantic intent verification (Module 3), utility-preserving sanitisation (Module 4), and clinical fact verification against openFDA (Module 5). Assembled pipeline with a three-option policy layer (sanitise and pass, verify or block, detect and block). Thirteen notebooks (NB01–NB13) covering corpus construction, attack generation, leakage-safe splitting, all five modules, baselines, end-to-end evaluation, ablation, aggregation and figure generation. A suite of eleven automated tests confirming all modules run correctly. The full openFDA corpus: 5,353 passages across 336 drugs and 1,604 label sections, with leakage-safe 70/15/15 splits. Every results file read by the manuscript, generated by the notebooks and cross-checked before any table is written. A pinned requirements file listing all software versions needed to reproduce the results. Key results Accuracy 0.9726 ± 0.0123, recall 0.9427 ± 0.0281, FPR 0.0011 ± 0.0024, across five seeds on 701 held-out passages. All five encoding formats recovered at 100%. CEPS 0.6066 (preservation 0.8677, removal 0.7043). End-to-end attack success reduced from 23.0% to 6.0% after sanitisation (73.9% reduction, McNemar p = 5.4 × 10⁻⁹). Note on the Medical Prompt Injection Benchmark The MPIB payload registry is subject to non-redistribution terms and does not appear in this repository. The benchmark is cited by reference only. Readers wishing to reproduce the MPIB evaluation should request the benchmark from its original authors and use the official restoration tool provided with it. Corresponding author: Adu-Boahene Bright, baduboahene@st.knust.edu.gh