Understanding the Limits of Agentic ICD Coding

Clinical coding maps clinical documentation to standardized medical codes, an essential yet time-consuming administrative task that could benefit from automation. Current models on ICD coding are typically optimized for codes from a specific ICD version. However, in reality, ICD systems evolve continuously, and different versions are adopted across time periods and regions. Moreover, ICD coding suffers from the long-tail problem, and rare code performance can be a bottleneck for developing implementable models. We examine whether it is viable to train version-independent models by combining data annotated in different ICD versions, which may help address these challenges. We add ICD-9 data to the training of a modified label-wise attention model for ICD-10 prediction, and find that despite the version mismatch, adding ICD-9 yields a 27% increase in micro F1 for 18K rare ICD codes compared to training on ICD-10 alone. On 8K frequent ICD-10 codes, the multi-version training also substantially improves macro metrics, with far fewer model parameters.

Next-encounter ICD forecasting predicts which standardized diagnosis codes will be documented at a future visit from the longitudinal record available beforehand. The task is prospective and multi-label: the target note does not yet exist, and several codes may be correct. Structured EHR foundation models capture recurrence and temporal progression, whereas language foundation models generate flexible diagnostic hypotheses. We introduce ICD-Deepresearch, a DeepResearch workflow that composes these predictive foundation models with medical search and ICD dictionaries. Because no source reveals the future code set, research evaluates candidate transitions by linking patient evidence, external clinical relations, and exact code semantics under a fixed top-K budget. Candidate Generation uses SparseEHR to produce an EHR Prior that initializes two bounded Research Expansion rounds; an independent GPT-5 Direct Forecast supplies complementary candidates. Final Selection validates, deduplicates, and jointly ranks both paths, after which a separate module writes rationales without changing predictions. Finally ICD-Deepresearch achieves patient-averaged precision/recall of 24.60/35.09% on MIMIC-III and 25.14/48.32% on MIMIC-IV. Physicians rate 51% and 68% of its retrieved documents useful, compared with 22% and 39% for standalone GPT-5 web search and 32% and 41% for Medical Deep Research. ICD-Deepresearch therefore improves over the registered local comparators while retrieving evidence with higher physician-rated usefulness than the standalone research systems

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.