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In the past decade a surge in the amount of electronic health record (EHR) data in the United States, attributed to a favorable policy environment created by the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009 and the 21st Century Cures Act of 2016. Clinical notes for patients' assessments, diagnoses, and treatments are captured in these EHRs in free-form text by physicians, who spend a considerable amount of time entering and editing them. Manually writing clinical notes takes a considerable amount of a doctor's valuable time, increasing the patient's waiting time and possibly delaying diagnoses. Large language models (LLMs) possess the ability to generate news articles that closely resemble human-written ones. We investigate the usage of Chain-of-Thought (CoT) prompt engineering to improve the LLM's response in clinical note generation. In our prompts, we use as input International Classification of Diseases (ICD) codes and basic patient information. We investigate a strategy that combines the traditional CoT with semantic search results to improve the quality of generated clinical notes. Additionally, we infuse a knowledge graph (KG) built from clinical ontology to further enrich the domain-specific knowledge of generated clinical notes. We test our prompting technique on six clinical cases from the CodiEsp test dataset using GPT-4 and our results show that it outperformed the clinical notes generated by standard one-shot prompts.

Accordingly, the word embeddings are learned to inherit those relationships.

Automated International Classification of Diseases (ICD) coding assigns standardized diagnosis and procedure codes to clinical records, playing a critical role in healthcare systems. However, existing methods face challenges such as semantic gaps between clinical text and ICD codes, poor performance on rare and long-tail codes, and limited interpretability. To address these issues, we propose TraceCoder, a novel framework integrating multi-source external knowledge to enhance traceability and explainability in ICD coding. TraceCoder dynamically incorporates diverse knowledge sources, including UMLS, Wikipedia, and large language models (LLMs), to enrich code representations, bridge semantic gaps, and handle rare and ambiguous codes. It also introduces a hybrid attention mechanism to model interactions among labels, clinical context, and knowledge, improving long-tail code recognition and making predictions interpretable by grounding them in external evidence. Experiments on MIMIC-III-ICD9, MIMIC-IV-ICD9, and MIMIC-IV-ICD10 datasets demonstrate that TraceCoder achieves state-of-the-art performance, with ablation studies validating the effectiveness of its components. TraceCoder offers a scalable and robust solution for automated ICD coding, aligning with clinical needs for accuracy, interpretability, and reliability.

Automatic ICD coding, the task of assigning disease and procedure codes to electronic medical records, is crucial for clinical documentation and billing. While existing methods primarily enhance model understanding of code hierarchies and synonyms, they often overlook the pervasive use of medical acronyms in clinical notes, a key factor in ICD code inference. To address this gap, we propose a novel effective data augmentation technique that leverages large language models to expand medical acronyms, allowing models to be trained on their full form representations. Moreover, we incorporate consistency training to regularize predictions by enforcing agreement between the original and augmented documents. Extensive experiments on the MIMIC-III dataset demonstrate that our approach, ACE-ICD establishes new state-of-the-art performance across multiple settings, including common codes, rare codes, and full-code assignments. Our code is publicly available.

Clinical notes contain unstructured text provided by clinicians during patient encounters. These notes are usually accompanied by a sequence of diagnostic codes following the International Classification of Diseases (ICD). Correctly assigning and ordering ICD codes are essential for medical diagnosis and reimbursement. However, automating this task remains challenging. State-of-the-art methods treated this problem as a classification task, leading to ignoring the order of ICD codes that is essential for different purposes. In this work, as a first attempt, we approach this task from a retrieval system perspective to consider the order of codes, thus formulating this problem as a classification and ranking task. Our results and analysis show that the proposed framework has a superior ability to identify high-priority codes compared to other methods. For instance, our model accuracy in correctly ranking primary diagnosis codes is 47%, compared to 20% for the state-of-the-art classifier. Additionally, in terms of classification metrics, the proposed model achieves a micro- and macro-F1 scores of 0.6065 and 0.2904, respectively, surpassing the previous best model with scores of 0.597 and 0.2660.

Electronic health records contain inconsistently structured or free-text data, requiring efficient preprocessing to enable predictive health care models. Although artificial intelligence-driven natural language processing tools show promise for automating diagnosis classification, their comparative performance and clinical reliability require systematic evaluation. The aim of this study is to evaluate the performance of 4 large language models (GPT-3.5, GPT-4o, Llama 3.2, and Gemini 1.5) and BioBERT in classifying cancer diagnoses from structured and unstructured electronic health records data. We analyzed 762 unique diagnoses (326 International Classification of Diseases (ICD) code descriptions, 436free-text entries) from 3456 records of patients with cancer. Models were tested on their ability to categorize diagnoses into 14predefined categories. Two oncology experts validated classifications. BioBERT achieved the highest weighted macro F1-score for ICD codes (84.2) and matched GPT-4o in ICD code accuracy (90.8). For free-text diagnoses, GPT-4o outperformed BioBERT in weighted macro F1-score (71.8 vs 61.5) and achieved slightly higher accuracy (81.9 vs 81.6). GPT-3.5, Gemini, and Llama showed lower overall performance on both formats. Common misclassification patterns included confusion between metastasis and central nervous system tumors, as well as errors involving ambiguous or overlapping clinical terminology. Although current performance levels appear sufficient for administrative and research use, reliable clinical applications will require standardized documentation practices alongside robust human oversight for high-stakes decision-making.

Identifying disease interconnections through manual analysis of large-scale clinical data is labor-intensive, subjective, and prone to expert disagreement. While machine learning (ML) shows promise, three critical challenges remain: (1) selecting optimal methods from the vast ML landscape, (2) determining whether real-world clinical data (e.g., electronic health records, EHRs) or structured disease descriptions yield more reliable insights, (3) the lack of "ground truth," as some disease interconnections remain unexplored in medicine. Large language models (LLMs) demonstrate broad utility, yet they often lack specialized medical knowledge. Our framework integrates the following: (i) a statistical co-occurrence analysis and a masked language modeling (MLM) approach using real clinical data; (ii) domain-specific BERT variants (Med-BERT and BioClinicalBERT); (iii) a general-purpose BERT and document retrieval; and (iv) four LLMs (Mistral, DeepSeek, Qwen, and Y andexGPT). Our graph-based comparison of the obtained interconnection matrices shows that the LLM-based approach produces interconnections with the lowest diversity of ICD code connections to different diseases compared to other methods, including text-based and domain-based approaches. This suggests an important implication: LLMs have limited potential for discovering new interconnections. In the absence of ground truth databases for medical interconnections between ICD codes, our results constitute a valuable medical disease ontology that can serve as a founda-tional resource for future clinical research and artificial intelligence applications in healthcare. Electronic health records (EHRs) provide a valuable resource for studying disease progression and relationships between diagnoses. Machine learning (ML) can help discover hidden patterns in medical data, but many existing models are hard to interpret. In particular, it is not always clear whether large language models (LLMs) make predictions based on meaningful medical knowledge or simply rely on textual similarities between diagnosis descriptions (Cui et al., 2025). This is especially critical in healthcare, where model decisions must align with established medical knowledge and pathophysiological mechanisms. We also analyze and compare the obtained results and summarize it into medical disease ontology.