Multimodal Dual-Encoder Retrieval for Automated ICD Coding

Abstract

Accurate International Classification of Diseases (ICD) coding is crucial for large-scale clinical research, documentation, and billing. There are three primary problems with current ICD prediction methods: (1) They are unable to comprehend multimodal patient data because they rely on either structured EHR data or unstructured clinical notes. (2) They also struggle with scalability to a larger amount of ICD codes (9K+ codes in ICD-9), as traditional classifiers need dense output layers and often do not generalize well to long tail rare diseases. (3) They lack transparency for clinical use. To address these challenges, this research proposes a two-stage framework that first retrieves ICD codes using a multimodal dual-encoder retrieval model, where structured and unstructured patient data are integrated through gated fusion. The second stage refines the top-k retrieved candidates with an LLM-based re-ranker that provides ranked codes with clinically relevant explanations. Our experiments show that the proposed approach improves Micro-F1 and Precision over a multimodal dual-fusion classifier baseline. These improvements demonstrate that combining a gated multimodal retrieval system with LLM-based re-ranking is a practical alternative to dense multi-label classification for automated ICD coding.