xMICD provides a practical way to integrate embedding-based semantic relationships into interpretable clinical feature spaces for machine learning models, and achieves predictive performance comparable to embedding-based representations such as ICD2Vec across multiple clinical prediction tasks.
Abstract
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.
This work proposes Knowledge-Guided Reasoning over Clinical Evidence with LLMs (KREL), a framework that leverages LLMs for clinical text understanding and reasoning while integrating external ICD coding guidelines as structured knowledge, and enables tight coupling between domain knowledge and LLM reasoning.
Xubin Chen, Yipeng Zhou, Wenxin Sun et al.· 0 citations
BERT-LER is presented, a BERT-style model for coded EHR timelines pretrained and fine-tuned from a de-identified EHR dataset of 75 million patients, that encodes laboratory test results as discrete tokens while retaining graded information through percentile-based binning, paired with Integrated Gradients for token-level attributions grounded in the input EHR sequence.
Jun Ni Du, Lukas Adamek, Maxim A Kryukov et al.· 0 citations
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.
Yihan Cheng, Veronica Liesaputra, A. Trotman· 0 citations
International Classification of Diseases (ICD) codes enable correct billing, insurance reimbursement, and healthcare analytics. However, manual coding is time-consuming, expensive, and error-prone, creating bottlenecks in clinical workflow and limiting scalability. Artificial intelligence (AI) has emerged as a promising solution for automated ICD code assignment from unstructured clinical text. This systematic review explores the current state of automated ICD coding research, examining models applied to diverse clinical documents including discharge summaries, electronic health records, nursing notes, and pathology reports. Following PRISMA guidelines, we searched six databases for studies published between 2019 and 2024, selecting 54 relevant studies from 4,280 initial citations. Our analysis reveals the use of diverse datasets, preprocessing techniques, and feature extraction methods, alongside a clear evolution from traditional machine learning to deep learning approaches, with substantial architectural diversity across convolutional, recurrent, transformer, and hybrid models. Performance varies considerably across dataset configurations, with models achieving higher accuracy on frequent code subsets compared to full label spaces. However, critical gaps persist: overreliance on single-language, single-institution datasets limits generalizability; difficulties in predicting rare codes remain unresolved; lack of model interpretability undermines clinical trust; and inconsistent evaluation protocols hinder meaningful comparison. To address these challenges, we propose a 5P evidence-grounded research agenda: Population Diversity, Performance Robustness, Prediction of Rare Codes, Provenance Transparency, and Practical Integration. These findings underscore AI’s potential to transform ICD coding while highlighting the need for standardized benchmarks, rigorous external validation, multilingual datasets, and explainable architectures to enable equitable and effective deployment in real-world healthcare systems.
Abdul Rehman Khalid, Haider Ali, Kounen Fathima et al.· Journal of medical systems· 0 citations
OBJECTIVE
The analysis of care trajectories derived from electronic health records and claims data has become increasingly common in biomedical informatics. This has enabled large-scale studies of care processes, yet widely used binary code representations result in high-dimensional, sparse data that fail to capture semantic relationships between medical concepts. Learning dense vector representations (embeddings) has emerged as a promising approach to address these limitations. We aimed to construct and share joint embeddings for the International Classification of Diseases (ICD-10) and the Anatomical Therapeutic Chemical (ATC) classification system, providing reusable semantic representations of diagnoses and treatments from real-world claims data.
MATERIALS AND METHODS
Using claims records from 1.5 million patients, we defined code co-occurrences within temporal windows and constructed a Positive Pointwise Mutual Information (PPMI) matrix spanning ICD-10 and ATC codes. Singular Value Decomposition (SVD) was applied to derive a low-dimensional embedding space. Evaluation combined UMAP visualization, nearest-neighbor retrieval, and a code-level classification task based on ICD chapters and ATC classes.
RESULTS
The embeddings reflected the hierarchical organization of ICD-10 and ATC and revealed associations across coding systems, including clinically relevant diagnosis-treatment relationships. The classification task achieved mean AUCs of 0.93 for ICD-10 and 0.90 for ATC, indicating strong grouping of semantically related codes.
DISCUSSION
The embeddings provide a reusable, code-level semantic representation that can support code retrieval, reduce manual code grouping, and be aggregated into patient-level features without training a task-specific model.
CONCLUSION
We release the first openly available joint ICD-10-ATC embedding space derived from real-world claims data, providing a reusable resource for biomedical informatics research.
C. Faujour, S. Bouée, C. Emery et al.· JAMIA Journal of the America...· 0 citations
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.
