FHIR-Former: enhancing clinical predictions through Fast Healthcare Interoperability Resources and large language models
Merlin Engelke, Giulia Baldini, Jens Kleesiek, Felix Nensa, Amin Dada
Abstract
OBJECTIVE: To address the challenges of data heterogeneity and manual feature engineering in clinical predictive modeling, we introduce FHIR-Former, an open-source framework integrating Fast Healthcare Interoperability Resources (FHIR) with large language models (LLMs) to automate and standardize clinical prediction tasks. MATERIALS AND METHODS: FHIR-Former dynamically processes structured (eg, lab results, medications) and unstructured (eg, clinical notes) data from FHIR resources. The pipeline supports multiple classification tasks, including 30-day readmission, imaging study prediction, and ICD code classification. Leveraging open-source LLMs (GeBERTa), we trained models on 1.1 million data points across ten FHIR resources using retrospective inpatient data (2018-2024). Hyperparameters were optimized via Bayesian methods, and outputs were mapped to FHIR RiskAssessment resources for interoperability. RESULTS: FHIR-Former achieved an F1-score of 70.7% and accuracy of 72.9% for 30-day readmission, 51.8% F1-score (88.1% accuracy) for mortality prediction, and 61% macro F1-score for imaging study classification. The ICD code prediction model attained 94% accuracy. Performance demonstrated promising performance for readmission and showed scalability across tasks without manual feature engineering. DISCUSSION: FHIR-Former eliminates institution-specific preprocessing by adapting to diverse FHIR implementations, enabling seamless integration of multimodal data. Its configurable architecture outperformed prior frameworks reliant on static inputs or limited to unstructured text. Real-time risk scores embedded in FHIR servers enhance clinical workflows without disrupting existing practices. CONCLUSION: By harmonizing FHIR standardization with LLM flexibility, FHIR-Former advances scalable, interoperable predictive modeling in healthcare. The open-source framework facilitates automation, improves resource allocation, and supports personalized decision-making, bridging gaps between AI innovation and clinical practice.