Yihan Deng

Patients presenting to neurology clinics commonly have a complex history of comorbidities and partially documented health trajectories, making it essential to reliably extract comorbidity information from historical records. However, existing extraction methods, ranging from rule-based systems to classical machine learning (ML), often have limited accuracy, scalability, or adaptability across diverse documents. We present a large language model (LLM)–based framework for comorbidity extraction from diagnostic texts, capable of handling various prompt formats and textual sources such as patient history, comorbidities, and sleep assessments. The instruction fine-tuned Mistral-24B (Instruct-2501) model achieves 95% macro classification accuracy and 92% F1 score across six common classes of comorbidities, achieving strong performance that is competitive with metrics reported in prior clinical phenotyping and information extraction studies, while complementing recent transformer-based clinical NLP frameworks. The proposed method extracts comorbidities through a transparent hierarchical approach, thereby supporting clinical analysis and providing interpretable insights for disease modeling and personalized treatment planning in sleep medicine.

Patients presenting to neurology clinics commonly have a complex history of comorbidities and partially documented health trajectories, making it essential to reliably extract comorbidity information from historical records. However, existing extraction methods, ranging from rule-based systems to classical machine learning (ML), often fall short in accuracy, scalability, or adaptability across diverse document types.In this study, we present a large language model (LLM)-based framework for comorbidity extraction from diagnostic texts, capable of handling various prompt formats and textual sources such as patient history, prior diagnoses, and structured sleep assessments. The fine-tuned Mistral-24B (Instruct-2501) model achieves 95% macro classification accuracy and 92% F1 measure across six common classes of comorbidities, substantially outperforming prior state-of-the-art approaches. The proposed method extracts comorbidities through a transparent hierarchical approach, thereby supporting clinical analysis and providing interpretable insights for disease modeling and personalized treatment planning in sleep medicine.

The Swiss classification of surgical interventions (CHOP) has to be used in daily practice by physicians to classify clinical procedures. Its purpose is to encode the delivered healthcare services for the sake of quality assurance and billing. For encoding a procedure, a code of a maximal of 6-digits has to be selected from the classification system, which is currently realized by a rule-based system composed of encoding experts and a manual search in the CHOP catalog. In this paper, we will investigate the possibility of automatic CHOP code generation based on a short query to enable automatic support of manual classification. The wide and deep hierarchy of CHOP and the differences between text used in queries and catalog descriptions are two apparent obstacles for training and deploying a learning-based algorithm. Because of these challenges, there is a need for an appropriate classification approach. We evaluate different strategies (multi-class non-terminal and per-node classifications) with different configurations so that a flexible modular solution with high accuracy and efficiency can be provided. The results clearly show that the per-node binary classification outperforms the non-terminal multi-class classification with an F1-micro measure between 92.6 and 94%. The hierarchical prediction based on per-node binary classifiers achieved a high exact match by the single code assignment on the 5-fold cross-validation. In conclusion, the hierarchical context from the CHOP encoding can be employed by both classifier training and representation learning. The hierarchical features have all shown improvement in the classification performances under different configurations, respectively: the stacked autoencoder and training examples aggregation using true path rules as well as the unified vocabulary space have largely increased the utility of hierarchical features. Additionally, the threshold adaption through Bayesian aggregation has largely increased the vertical reachability of the per node classification. All the trainable nodes can be triggered after the threshold adaption, while the F1 measures at code levels 3–6 have been increased from 6 to 89% after the threshold adaption.