PLeDO: Pain Level Detection for Osteoarthritis from EMR Data

Osteoarthritis (OA) is a progressive chronic joint disease resulting in a breakdown of articular cartilage and bone when damaged joint tissues are not able to normally repair themselves. The aim of this pilot research study is to understand the pain severity for OA from patients' primary care Electronic Medical Records (EMR), both from the structured medical data and the unstructured chart note data using information extraction, natural language processing and machine learning techniques. We propose SPaDe, a Synonym-based Pain level Detection tool to categorize patients into having mild or moderate-to-severe pain to understand diagnosis and treatment methods based on only the pain related expressions in the unstructured chart note. Expressions are subjective, objective, and influenced by cultural background and demography which poses a difficult challenge. Therefore, we improve the model by incorporating the medication information from the structured EMR data and pain scale related information from the chart note to propose an integrated pain level detection tool for OA called PLeDO. With the help of human labeled gold standard data, we demonstrate that both SPaDe and PLeDO can detect mild and moderate-to-severe pain from the EMR data to analyze and potentially improve the quality of care in primary care setting.

Do It Right! A Methodology for Successful NLP System Development

Natural language processing (NLP) is a common method for supplying data to clinical research and decision making by extracting information from electronic medical records. Numerous textbooks and tutorials describe specific algorithms and applications for text processing, yet algorithmic knowledge is only one ingredient of a successful NLP project. Drawing on the available literature, this paper presents a stepwise approach that applies the Systems Development Life Cycle (SDLC) to projects that rely on data extraction through language processing.

Medi-Gemma: A Hybrid Clinical Decision Support System Integrating Deterministic EMR Analytics and Retrieval-Augmented Generation

Deploying Large Language Models (LLMs) in high-stakes clinical settings remains limited by structural hallucinations, weak deterministic reasoning over tabular patient data, and omissions in vector retrieval. This paper presents the architecture and validation of Medi-Gemma, a Clinical Decision Support System (CDSS) for wound pathology triage and workflow automation. The platform introduces a decoupled framework that separates clinical perception from data orchestration while preserving traceable reasoning. Medi-Gemma uses a multi-stage pipeline coordinated by a centralized ClinicalOrchestrator. Data requests are handled without generative inference by a DataManager that cleans unstructured Electronic Medical Record (EMR) files through type coercion. Natural language queries are processed by a hierarchical IntentRouter, which routes requests to deterministic analytics paths executed by a PandasQueryEngine or to patient-specific reasoning managed by a ClinicalRAGEngine using a CPU-optimized vector store. A key contribution is the Ground Truth Injection Module, which intercepts patient-specific queries, extracts numeric identification tokens, queries the structured dataframe via Pandas, retrieves the latest validated clinical state, and embeds this snapshot as an overriding context block in the LLM prompt before generation. Safety compliance is enforced by a deterministic ProtocolManager that maps clinical terminology to fixed evidence-based risk pathways, while a SafetyVerifier phrase filter prevents output rule violations. Validation shows that this architecture eliminates semantic context drift, prevents database compilation crashes, and improves factual adherence to backend clinical repositories. These results support Medi-Gemma as a safer pattern for LLM-based clinical decision support where structured data fidelity, retrieval grounding, and deterministic safeguards are essential.

An ambiguity taxonomy for evaluating large language model performance on clinical registry abstraction: a multi-site prospective study

Objective: To evaluate large language model (LLM) performance on unprocessed electronic medical record (EMR) data for clinical registry abstraction. Methods: We evaluated LLM performance answering registry questions for the American College of Cardiology National Cardiovascular Data Registry (ACC NCDR). In a pilot study at an academic medical center, the model identified candidate data sources for each registry question and experienced abstractors used these results to define question-specific document sets. In a validation study at a second center with a second ACC NCDR registry, the LLM answered questions using the question-specific document sets. Before reviewing any output, two abstractors independently established the ground truth and assigned each question to one of six categories, ordered by the ambiguity and clinical reasoning required to resolve it: Medication/Event Flag, Binary Clinical Presence, Administrative, Quantitative Laboratory/Physiologic, Clinical Interpretation, and Event Timing. Results: The analytical sample comprised 9,430 abstractor answers reconciled to 4,715 consensus answers (501 pilot; 4,214 validation). In the pilot, candidate data sources per question averaged between 14.6 (SD 13.9) for demographics and 89.2 (SD 56.1) for history and risk factors. In validation, human inter-rater agreement was approximately 98\% while 87\% of LLM answers exactly matched consensus, 2\% partially, and 9\% did not. Mean question-level accuracy was 91.5\% (SD 13.4\%) across 157 questions with at least 20 answers, and declined as ambiguity increased, from 96\% for Medication/Event Flag to 62\% for Event Timing questions. Conclusions: LLMs answering clinical registry questions on unprocessed EMR data achieved far lower accuracy than human abstractors. LLM accuracy fell steadily as ambiguity and the level of required clinical reasoning increased.

Lung-R1: A Knowledge Graph-Guided LLM for Pulmonary Diagnostic Reasoning

Diagnosing pulmonary diseases requires integrating heterogeneous evidence amid phenotypic variability and cross-disease overlap. Although large language models (LLMs) have shown progress on pulmonary knowledge question answering (QA) and information-processing tasks, reliable pulmonary diagnosis requires patient-specific, relation-aware reasoning over electronic medical record (EMR) evidence rather than isolated knowledge recall. We define this gap between pulmonary knowledge and case-level diagnostic reasoning as the Pulmonary Knowledge-to-Diagnosis Gap. To address it, we introduce LungKG, the first structured pulmonary knowledge graph for diagnostic knowledge organization and record-grounded reasoning. LungKG contains 59,038 nodes and 164,308 edges across 15 entity types and 112 relation types, serving as both a reusable pulmonary knowledge resource and the foundation for LungKG-guided model adaptation. Built on LungKG, we propose Lung-R1, a LungKG-guided pulmonary LLM trained through KG-constrained reasoning-chain construction and KG-guided reinforcement learning. In a 20-system evaluation, Lung-R1-14B achieves state-of-the-art performance across Choice, Pulmonary-QA, and EMR Diagnosis, reaching an EMR Diagnosis score of 4.3583 and surpassing the strongest non-Lung-R1 baseline by 0.1476 points. These results demonstrate the value of LungKG-guided training for EMR-based pulmonary diagnosis.

Synthetic but Not Realistic: The Evaluation Challenge in Generative Modelling for Structured Electronic Medical Records

Synthetic healthcare data are widely proposed as privacy-preserving substitutes for real patient data, yet their evaluation remains dominated by statistical similarity and predictive performance that do not reflect clinical validity. We introduce a multi-dimensional evaluation framework grounded in epidemiology, assessing descriptive fidelity, clinical utility, and structural validity, corresponding to descriptive, predictive, and causal questions. We evaluate four representative generative paradigms - GAN-based, VAE-boosted, diffusion-based, and masked modelling - using PRIME-CVD, a 50,000-person cohort with known ground-truth structure. While all models reproduce marginal distributions, none simultaneously preserve subgroup structure, effect estimates, and dependency structure. Notably, models with strong distributional fidelity can exhibit poor calibration and distorted relationships, leading to unreliable inference. These results show that current evaluation practices can overestimate synthetic data quality and motivate domain-informed assessment based on the ability to support valid clinical and scientific conclusions.