Automated Medical Coding

Provider queries are clarifying requests sent by clinical documentation specialists to physicians to close gaps in the clinical note and ensure accurate billing. Prior work automates note drafting, ICD-10 coding, and order extraction assuming a complete transcript, leaving these gaps unaddressed. We study whether an LLM can automate the query loop, termed DAU (Draft, Ask, Update), across those three tasks. An audit of 3,000 real visits identifies the sources of missing documentation, from which we build five transcript-degradation benchmarks on public data. Analyzing 21k clarification turns on real conversations, we find useful-question predictors are task-specific: oracle confidence dominates, but note completeness needs only simple recall questions while ICD-10 coding needs harder, multi-option ones. About 9% of turns hurt performance, driven by redundant questions and non-answers that still trigger a rewrite. Deployment depends on learning "when not" as much as "what to" ask.

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.

Clinical coding agents repeatedly encounter the same failure modes, including unsupported codes, missed documented conditions, specificity errors, and procedure-coding convention mismatches. We introduce Learn-Then-Act, an inference-time adaptation framework that converts errors from a small labeled LEARN batch into a structured Mistake Knowledge Database (MistakeKDB). False-negative lessons are routed to a recall-oriented Coder, while false-positive lessons are routed to a precision-oriented Judge. We instantiate the framework in LearnActCoder, a Coder-Judge clinical coding pipeline with lookup-table grounding where available. On 150 matched MIMIC-III notes, structured MistakeKDB improves CPT F1 by 5.9 percentage points, while raw-example and reflection-style memories remain near the no-memory baseline; the ICD-9 improvement is not significant. On a matched MIMIC-IV cohort, memory shifts ICD-10 coding toward higher precision at a recall cost, leaving F1 statistically unchanged. Applying the same memory to 1,000 held-out MIMIC-III notes maintains a stable ICD operating point, providing scale/stability evidence. Overall, the results are consistent with structured, feedback-derived error memory being useful for adapting clinical coding behavior across cases without weight updates or changes to the underlying workflow. Absolute CPT/HCPCS performance remains low, and the system is evaluated retrospectively rather than in clinical deployment.

Standardizing clinical language to SNOMED CT supports interoperability, analytics, and reusable phenotyping, but concept recommendation remains difficult when relevant concepts are rare or absent from training data. We present a masked-concept recommendation benchmark using the SNOMED CT Entity Linking Challenge v1.2.1 data derived from MIMIC-IV-Note. The dataset contains 75,491 annotations across 272 discharge summaries, with 204 notes used for training and 68 for historical testing. For each unique note-concept pair, the target mention is masked from a local clinical context and the system ranks SNOMED CT concepts observed during training. We compare a popularity baseline, sparse TF-IDF concept prototypes, dense latent semantic analysis embeddings, sparse-dense fusion, retrieved-note evidence, and a retrieval-augmented hybrid. Sparse TF-IDF performs best, achieving Recall@1 of 14.81%, Recall@10 of 33.43%, MRR of 0.2114, and nDCG@10 of 0.2297. Retrieval augmentation does not improve this baseline, with Recall@10 of 31.99% and MRR of 0.1937. Performance is strongly affected by concept frequency: Recall@10 is 7.74% for concepts appearing in only one or two training notes versus 43.90% for concepts appearing in more than ten. In addition, 9.66% of test note-concept pairs contain concepts unseen during training. These findings show that local lexical context and terminology coverage are major determinants of recommendation quality in low-resource settings and provide a reproducible baseline for future ontology-grounded and biomedical-encoder retrieval systems.

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.

Medical coding is the task of assigning a set of diagnosis and procedure codes for a hospitalization using recorded notes. It requires aggregating information from different parts of the text and focus to different sections for each individual code, making it a very difficult problem even for professional human coders. We model the task as a multi-label text classification problem. To overcome the mentioned difficulties, we propose a deep neural model consisting of a multi-layer temporal convolution network (TCN) followed by label-wise attention. While multi-layer TCN helps extract a global document representation with the ability to learn relations over very long sequences, label-specific attention mechanism allows the model to focus on different aspects of the same document for each individual label. Our method achieves significantly better F-1 scores (9% increase) compared to the previous state-of-the-art model, with a remarkable increase in recall score (28% increase), which we believe is the more important metric for a clinical decision support setting.

We present OntoBook, a method that converts medical ontology structure into pretraining signal for encoder language models. Our approach has three stages: random walks through ontology graphs capture hierarchical and causal relations between medical codes, a large language model reformulates these walks into fluent textbook-style prose, and the resulting text is used to train ModernCamemBERT, a 149M-parameter French encoder, with two objectives on the same data: masked language modeling and relation prediction between code pairs. On three French medical coding benchmarks (FRACCO, Cantemist-FR, Distemist-FR), OntoBook achieves significant improvements over MLM-only pretraining, with +2.5 micro-F1 on FRACCO and +8.0 micro-F1 on Distemist. We find that alignment between objectives is necessary: misaligned training, where each task uses different data, causes a 30-point degradation. We release 1.3 million LLM-reformulated medical textbooks across three French ontologies (CIM-10, CCAM, ATC) and pretrained model checkpoints.

Clinical code prediction maps unstructured discharge summaries to ICD-10-CM leaf codes in a large, sparse, and deeply hierarchical label space. Most systems treat the task as flat multi-label classification, scoring codes independently and providing limited training signal for rare labels. We propose a graph-constrained traversal policy that formulates ICD prediction as a finite-horizon decision process over a pruned code hierarchy. A single language model descends the graph level by level, selecting valid child nodes until billable leaf codes are reached. This converts extreme multi-label prediction into sparse, hierarchy-aware subset decisions while guaranteeing structurally valid outputs. On MIMIC-IV discharge summaries, our best supervised policy, SFT-1+, achieves 0.709 micro-F1 on a curated 50-code subset and 0.527 micro-F1 on the full 15,761-code space, outperforming flat baselines including CAML, LAAT, and PLM-ICD. In the full setting, SFT-1+ improves over the strongest flat baseline by 0.044 micro-F1 and 0.157 macro-F1, suggesting that graph-constrained decomposition mitigates the rare-code bottleneck. A controlled factorial study evaluates architecture, training algorithm, and data budget. Across both scales, one shared policy matches a three-specialist cascade while avoiding its context-window overflow on 28-32% of full-space test notes. Increasing supervised trajectory data is the only intervention that consistently improves performance, while GRPO reinforcement learning provides no benefit over supervised continuation with matched data. These results show that simple graph-constrained policy learning can outperform more complex flat, cascaded, and reinforcement-learning alternatives for extreme clinical code prediction.

Automatic mapping between disease classification systems, such as the International Classification of Diseases (ICD), is a challenging yet essential task for integrating health data and conducting longitudinal data analysis. Existing embedding-based methods primarily focus on \emph{one-to-one} mappings, overlooking more complex \emph{one-to-many} scenarios. The threshold-based and top-K methods offer natural extensions; however, they involve inherent trade-offs between \emph{precision}, \emph{recall} and \emph{mapping coverage} -- the proportion of source codes with at least one mapping to a target code. To address this challenge, we introduce a novel method, which is inspired by the \emph{blocking-and-matching} pipeline commonly used in \emph{entity resolution}. In particular, we first generate a block of candidate matches (\emph{blocking}) and then employ a large language model (LLM) to identify all valid mappings within each block (\emph{matching}). Empirically, we show that the proposed method achieves higher precision with comparable recall and broader coverage across multiple ICD version pairs (ICD-9-CM$\leftrightarrow$ICD-10-CM and ICD-10-AM$\leftrightarrow$ICD-11). Our source code and dataset is available at: https://tinyurl.com/46kyn7wp.

Objective: ICD codes are central to reimbursement, research, and population health surveillance, yet automated coding systems often struggle to integrate diagnostic signals from both clinical narratives and structured electronic health record (EHR) variables. We evaluated whether frozen medical large language model (LLM) representations can serve as a shared embedding space for multimodal primary diagnosis category prediction. Materials and Methods: We constructed a MIMIC-IV cohort of 13,645 admissions from the 10 most frequent primary ICD-10 codes, consolidated into seven categories. Structured variables were serialized into clinical narratives and combined with leakage-pruned discharge notes. Using a frozen MedFound-Llama3-8B-finetuned backbone, we extracted hidden states from five transformer layers and trained linear probes for structured-only, unstructured-only, and combined inputs, comparing against XGBoost and information-matched PLM-ICD baselines and evaluating MIMIC-III adaptation with a compact bottleneck adapter. Results: The combined probe performed best on MIMIC-IV (87.69% strict; 91.45% medical accuracy), exceeding both single-modality probes and baselines. The structured-only probe outperformed its standard baseline by 6.19 points in medical accuracy. Diagnostic information became increasingly linearly separable in deeper layers, and a 2M-parameter adapter restored cross-dataset transfer to MIMIC-III using only 5% of target labels. Discussion: LLM embeddings can unify structured and narrative EHR information for multimodal diagnosis prediction, supporting efficient reuse of clinical representations across modalities and datasets through a small representation-level module. Conclusion: Multimodal probing of frozen medical LLM representations provides a practical approach for studying EHR modalities and adapting clinical representations across datasets.

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.

Large language models (LLMs) can generate or synthesize clinical text for a wide range of applications, from improving clinical documentation to augmenting clinical text analytics. Yet evaluations typically focus on a narrow aspect -- such as similarity or utility comparisons -- even though these aspects are complementary and best viewed in parallel. In this study, we aim to conduct a systematic evaluation of LLM-generated clinical text, which includes intrinsic, extrinsic, and factuality evaluations of synthetic clinical notes rephrased from MIMIC databases at million-note scale. Our analysis demonstrates that synthetic notes preserve core clinical information and predictive utility for coarse-grained tasks despite substantial linguistic changes, but lose fine-grained details for task like ICD coding. We show this loss of detail can be substantially mitigated by rephrasing notes by chunks rather than by the whole note, but at the cost of reduced factual precision under incomplete context. Through fact-checking and error analysis, we further find that synthesis errors are dominated by misinterpretation of clinical context, alongside temporal confusion, measurement errors, and fabricated claims. Finally, we show that the synthetic notes -- despite their task-agnostic nature -- can effectively augment task-specific training for rare ICD codes.

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.

Automated ICD-10 coding from clinical discharge summaries requires models that are both accurate on long-tailed multi-label classification tasks and interpretable to clinicians. Concept Bottleneck Models (CBMs) offer a principled framework for interpretability by routing predictions through human-interpretable concepts, but this transparency often comes at a cost: compressing rich clinical text representations into a narrow concept layer can restrict gradient flow and limit predictive capacity. We present ShifaMind, a concept-grounded architecture built around a Multiplicative Concept Bottleneck (MCB), which changes the form, rather than the width, of the bottleneck. Instead of projecting through a narrow concept layer, ShifaMind uses a learned multiplicative gate over a concept-grounded representation while retaining a scalar concept interface for inspection. On MIMIC-IV top-50 ICD-10 coding, ShifaMind achieves performance competitive with LAAT, the strongest baseline, across F1, AUC, and ranking metrics, while outperforming five additional ICD-coding baselines and providing concept-mediated explanations. Its substantial gains over a capacity-matched Vanilla CBM in both predictive performance and interpretability-oriented metrics highlight the importance of the bottleneck design.