Symphony for Medical Coding: A Next-Generation Agentic System for Scalable and Explainable Medical Coding

Accurate medical coding requires consulting authoritative resources such as the ICD tabular list and coding guidelines. Existing LLM-based automated methods largely rely on LLMs' internal knowledge, which is prone to hallucination and cannot keep pace with guideline updates. We introduce RAG-Coding, an agentic, training-free method that augments LLMs with structured external knowledge: the tabular list is encoded as a knowledge graph capturing hierarchical and instructional code relationships, and the guidelines are distilled into concise, code-specific summaries rather than retrieved as raw text. To enable our study, we also introduce MDACE-2025, expert re-annotations of the MDACE dataset under the 2025 ICD-10-CM/PCS guidelines, adding code sequencing and justification comments. On MDACE, RAG-Coding outperforms the best LLM-based baseline by 3--13% in micro-F1 across five LLM backbones, and achieves comparable micro- and macro-F1 to the supervised state-of-the-art, with higher recall ($+$11%) at the cost of precision ($-$6%). On MDACE-2025, RAG-Coding outperforms all baselines, demonstrating effective generalisation to updated guidelines. Ablations confirm stepwise gains, highlighting the importance of integrating structured external knowledge for LLM-based medical coding.

Improving the accuracy and reliability of medical coding reduces clinician burnout and supports revenue cycle processes, freeing providers to focus more on patient care. However, automating the assignment of ICD-10-CM and CPT codes from clinical documentation remains a challenge due to heterogeneous records, nuanced coding guidelines, and long-tail distributions. Large language models have been proposed to help or automate specific medical coding tasks. However, foundation models are not explicitly trained for medical coding and zero-shot coding has yielded poor results. We investigate whether a modern open-weight foundation model can be adapted for an expert-level medical coding task using privacy-preserving synthetic training data derived from electronic health records. We fine-tune Llama 3-70B on pairs of clinical notes and gold codes generated from EHR-grounded templates and coding policies, then evaluate exact-code prediction for ICD-10-CM and CPT. A zero-shot baseline with the unadapted model achieved an F1 score of 0.18 for exact code match. After fine-tuning on the synthetic corpus, exact-match F1 exceeded 0.70, representing a large absolute gain across both code systems. Notably, performance remained high on complex categories that often require multi-step clinical reasoning and code composition, including Advanced Illness and Frailty classes, and the model retained its performance on medical comprehension tasks. These results indicate that synthetic, policy-aware data can efficiently teach a general-purpose large language model to support precise medical coding without exposing protected health information. The approach offers a practical path for training coding agents safely and iteratively on specific tasks that represent real-world populations.

In automated clinical coding, where the label space spans tens of thousands of diagnosis and procedure codes, models are currently evaluated against a single gold annotation, treating any deviation as error. But we find when two teams code the same 110 ACI-Bench encounters, they agree on only 73% of codes (Jaccard similarity) for the same note; even after an independent clinical audit removes erroneous codes, agreement rises only to 77%. Is that gap error or something systematic? We model the systematic component as coding style $ψ$, a coder- or site-specific policy over what to code and how much to document, and recast coding as $p(\mathrm{code}\mid\mathrm{note},ψ)$, estimating $ψ$ with a 10-dimension rubric. If style were noise, conditioning on it would do nothing. Instead, across five datasets a model conditioned with a data-matching style raises ICD F1 by up to 26 points and an extreme mismatched one lowers it by up to 21. Four prompt based coding methods spanning 39-49 F1 converge to 52-56 once style is supplied (All p<0.05). Much of what single-gold evaluation charges to model error is recoverable, unmodeled style.