Beyond ICD Codes: Semantic IDs for Generative Medical Coding

Automated International Classification of Diseases (ICD) coding is a core medical-coding task for billing, epidemiology, and clinical decision support. Generative large language models (LLMs) are often reported as weak medical coders, but this finding mainly comes from inference-time settings such as prompting, retrieval, reranking, or tool use, leaving the role of task-specific post-training underexplored. We present a controlled empirical study of post-training for generative ICD coding, comparing discriminative baselines with LLM coders across prompting, supervised fine-tuning, and reinforcement learning under a common protocol and metric set. To our knowledge, this is the first study to evaluate RL-based post-training for generative LLM coders in ICD coding. We further introduce PHI, a diagnostic curriculum that extends GRPO to refine missed-code cases. Our results show that prompting-only evaluation substantially underestimates the potential of LLMs for ICD coding. SFT provides the main capability jump, GRPO further improves code-set prediction beyond SFT, and PHI provides targeted gains on macro-level performance. These findings suggest that the main bottleneck is not the generative formulation alone, but how the model is adapted and optimized for full-taxonomy recall. We release our code, data splits, and checkpoints at https://github.com/AlexandreWANG915/LLM4ICD.

Automatic medical coding assigns ICD codes to clinical notes, but it remains challenging due to long documents, imbalanced label distributions, and diverse terms. These challenges are especially severe for rare codes, which have limited training instances and are easily confused with semantically similar labels. We introduce CoLa-ICD, a knowledge-enhanced framework for long-tail prediction. CoLa-ICD enriches ICD labels with external terms, models dependencies among related codes, and learns stronger alignment between label semantics and clinical evidence for long-tail prediction. Experiments show that CoLa-ICD improves long-tail prediction with larger gains in larger and sparser label spaces and achieves state-of-the-art performance in AUC, F1, and P@k. Our code is available at https://github.com/youwillbethebest/Cola-ICD.

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.