Andrew Bate

Jeffery L. Painter, François Haguinet, Andrew Bate

ClinicalTrials .gov (CT .gov) is the largest publicly accessible registry of clinical studies, yet its registry-oriented architecture and heterogeneous adverse event (AE) terminology limit systematic pharmacovigilance (PV) analytics. AEs are typically recorded as investigator-reported text rather than standardized identifiers, requiring manual reconciliation to identify coherent safety concepts. We present the ClinicalTrials .gov Transformation Database (CTG-DB), an open-source pipeline that ingests the complete CT .gov XML archive and produces a relational database aligned to standardized AE terminology using the Medical Dictionary for Regulatory Activities (MedDRA). CTG-DB preserves arm-level denominators, represents placebo and comparator arms, and normalizes AE terminology using deterministic exact and fuzzy matching to ensure transparent and reproducible mappings. This framework enables concept-level retrieval and cross-trial aggregation for scalable placebo-referenced safety analyses and integration of clinical trial evidence into downstream PV signal detection.

Joe B Hakim, Jeffery L Painter, Darmendra Ramcharran et al.

Large language models (LLMs) are useful tools with the capacity for performing specific types of knowledge work at an effective scale. However, LLM deployments in high-risk and safety-critical domains pose unique challenges, notably the issue of ``hallucination,'' where LLMs can generate fabricated information. This is particularly concerning in settings such as drug safety, where inaccuracies could lead to patient harm. To mitigate these risks, we have developed and demonstrated a proof of concept suite of guardrails specifically designed to mitigate certain types of hallucinations and errors for drug safety, and potentially applicable to other medical safety-critical contexts. These guardrails include mechanisms to detect anomalous documents to prevent the ingestion of inappropriate data, identify incorrect drug names or adverse event terms, and convey uncertainty in generated content. We integrated these guardrails with an LLM fine-tuned for a text-to-text task, which involves converting both structured and unstructured data within adverse event reports into natural language. This method was applied to translate individual case safety reports, demonstrating effective application in a pharmacovigilance processing task. Our guardrail framework offers a set of tools with broad applicability across various domains, ensuring LLMs can be safely used in high-risk situations by eliminating the occurrence of key errors, including the generation of incorrect pharmacovigilance-related terms, thus adhering to stringent regulatory and quality standards in medical safety-critical environments.

Jeffery L Painter, François Haguinet, Gregory E Powell et al.

Semantic similarity measures (SSMs) are widely used in biomedical research but remain underutilized in pharmacovigilance. This study evaluates six ontology-based SSMs for clustering MedDRA Preferred Terms (PTs) in drug safety data. Using the Unified Medical Language System (UMLS), we assess each method's ability to group PTs around medically meaningful centroids. A high-throughput framework was developed with a Java API and Python and R interfaces support large-scale similarity computations. Results show that while path-based methods perform moderately with F1 scores of 0.36 for WUPALMER and 0.28 for LCH, intrinsic information content (IC)-based measures, especially INTRINSIC-LIN and SOKAL, consistently yield better clustering accuracy (F1 score of 0.403). Validated against expert review and standard MedDRA queries (SMQs), our findings highlight the promise of IC-based SSMs in enhancing pharmacovigilance workflows by improving early signal detection and reducing manual review.

Jeffery L Painter, Gregory E Powell, Andrew Bate

Reliable drug safety reference databases are essential for pharmacovigilance, yet existing resources like SIDER are outdated and static. We introduce PVLens, an automated system that extracts labeled safety information from FDA Structured Product Labels (SPLs) and maps terms to MedDRA. PVLens integrates automation with expert oversight through a web-based review tool. In validation against 97 drug labels, PVLens achieved an F1 score of 0.882, with high recall (0.983) and moderate precision (0.799). By offering a scalable, more accurate and continuously updated alternative to SIDER, PVLens enhances real-time pharamcovigilance with improved accuracy and contemporaneous insights.

François Haguinet, Jeffery L Painter, Gregory E Powell et al.

We present a Bayesian dynamic borrowing (BDB) approach to enhance the quantitative identification of adverse events (AEs) in spontaneous reporting systems (SRSs). The method embeds a robust meta-analytic predictive (MAP) prior with a Bayesian hierarchical model and incorporates semantic similarity measures (SSMs) to enable weighted information sharing from clinically similar MedDRA Preferred Terms (PTs) to the target PT. This continuous similarity-based borrowing overcomes limitations of rigid hierarchical grouping in current disproportionality analysis (DPA). Using data from the FDA Adverse Event Reporting System (FAERS) between 2015 and 2019, we evaluate our approach -- termed IC SSM -- against traditional Information Component (IC) analysis and IC with borrowing at the MedDRA high-level group term level (IC HLGT). A reference set (PVLens), derived from FDA product label update, enabled prospective evaluation of method performance in identifying AEs prior to official labeling. The IC SSM approach demonstrated higher sensitivity (1332/2337=0.570, Youden's J=0.246) than traditional IC (Se=0.501, J=0.250) and IC HLGT (Se=0.556, J=0.225), consistently identifying more true positives and doing so on average 5 months sooner than traditional IC. Despite a marginally lower aggregate F1-score and Youden's index, IC SSM showed higher performance in early post-marketing periods or when the detection threshold was raised, providing more stable and relevant alerts than IC HLGT and traditional IC. These findings support the use of SSM-informed Bayesian borrowing as a scalable and context-aware enhancement to traditional DPA methods, with potential for validation across other datasets and exploration of additional similarity metrics and Bayesian strategies using case-level data.

Jeffery L. Painter, Venkateswara Rao Chalamalasetti, Raymond Kassekert et al.

Objective: To enhance the efficiency and accuracy of information retrieval from pharmacovigilance (PV) databases by employing Large Language Models (LLMs) to convert natural language queries (NLQs) into Structured Query Language (SQL) queries, leveraging a business context document. Materials and Methods: We utilized OpenAI's GPT-4 model within a retrieval-augmented generation (RAG) framework, enriched with a business context document, to transform NLQs into syntactically precise SQL queries. Each NLQ was presented to the LLM randomly and independently to prevent memorization. The study was conducted in three phases, varying query complexity, and assessing the LLM's performance both with and without the business context document. Results: Our approach significantly improved NLQ-to-SQL accuracy, increasing from 8.3\% with the database schema alone to 78.3\% with the business context document. This enhancement was consistent across low, medium, and high complexity queries, indicating the critical role of contextual knowledge in query generation. Discussion: The integration of a business context document markedly improved the LLM's ability to generate accurate and contextually relevant SQL queries. Performance achieved a maximum of 85\% when high complexity queries are excluded, suggesting promise for routine deployment. Conclusion: This study presents a novel approach to employing LLMs for safety data retrieval and analysis, demonstrating significant advancements in query generation accuracy. The methodology offers a framework applicable to various data-intensive domains, enhancing the accessibility and efficiency of information retrieval for non-technical users.

Andrew Bate, Boris Motik, Bernardo Cuenca Grau et al.

Consequence-based calculi are a family of reasoning algorithms for description logics (DLs), and they combine hypertableau and resolution in a way that often achieves excellent performance in practice. Up to now, however, they were proposed for either Horn DLs (which do not support disjunction), or for DLs without counting quantifiers. In this paper we present a novel consequence-based calculus for SRIQ---a rich DL that supports both features. This extension is non-trivial since the intermediate consequences that need to be derived during reasoning cannot be captured using DLs themselves. The results of our preliminary performance evaluation suggest the feasibility of our approach in practice.