Graph-Constrained Policy Learning for Extreme Clinical Code Prediction
Authors: Amritpal Singh, Sebastian Torres, Khawar Shakeel, Syed Ahmad Chan Bukhari
Organizations: Division of Computer Science, Mathematics and Science St. John’s University, New York, NY, USA
Abstract
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.
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.
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.
Electronic Health Records (EHRs) are widely used for clinical risk prediction using machine learning. International Classification of Diseases (ICD) codes provide structured information about patient diagnoses, but representing them effectively remains challenging. Existing approaches often face a trade-off between predictive performance and interpretability: grouping-based representations are interpretable but may lose information, while embedding-based representations achieve strong predictive performance but are difficult to interpret. We propose Explainable Representation of Multiple ICD Codes (xMICD), a method for constructing low-dimensional patient representations from sets of ICD codes. xMICD combines clinically meaningful diagnostic groupings with similarity in a pre-trained ICD embedding space. Instead of using binary group membership, the method assigns codes to groups via similarity-based relative assignments, yielding features that reflect how closely a patient's diagnoses align with each clinical group. Experiments on large-scale EHR datasets demonstrate that xMICD achieves predictive performance comparable to embedding-based representations such as ICD2Vec across multiple clinical prediction tasks. At the same time, the resulting features remain clinically interpretable because each dimension corresponds to a recognizable diagnostic group. xMICD therefore provides a practical way to integrate embedding-based semantic relationships into interpretable clinical feature spaces for machine learning models.
Pat Vatiwutipong, Kumkup Keeratisiwakul, Albert Phuoc Kien Van Truong +4