Creating a computer assisted ICD coding system: performance metric choice and use of the ICD hierarchy

Abstract

Objective: Machine learning methods hold the promise of leveraging available data and generating higher quality data while alleviating the data collection burden on healthcare professionals. International Classification of Diseases (ICD) diagnoses data, collected globally for billing and epidemiological purposes, represents a valuable source of structured information. However, ICD coding is a challenging task. While numerous previous studies reported promising results in automatic ICD classification, they often describe input data specific model architectures, that are heterogeneously evaluated with different performance metrics and ICD code subsets. This study aims to explore the evaluation and construction of more effective Computer Assisted Coding (CAC) systems using generic approaches, focusing on the use of ICD hierarchy, medication data and a feed forward neural network architecture. Methods: We conduct comprehensive experiments using the MIMIC-III clinical database, mapped to the OMOP data model. Our evaluations encompass various performance metrics, alongside investigations into multitask, hierarchical, and imbalanced learning for neural networks. Results: We introduce a novel metric, RE@R, tailored to the ICD coding task, which offers interpretable insights for healthcare informatics practitioners, aiding them in assessing the quality of assisted coding systems. Our findings highlight that selectively cherry-picking ICD codes diminish retrieval performance without performance improvement over the selected subset. We show that optimizing for metrics such as NDCG and AUPRC outperforms traditional F1-based metrics in ranking performance. We observe that Neural Network training on different ICD levels simultaneously offers minor benefits for ranking and significant runtime gains. However, our models do not derive benefits from hierarchical or class imbalance correction techniques for ICD code retrieval. Conclusion: This study offers valuable insights for researchers and healthcare practitioners interested in developing and evaluating CAC systems. Using a straightforward sequential neural network model, we confirm that medical prescriptions are a rich data source for CAC systems, providing competitive retrieval capabilities for a fraction of the computational load compared to text-based models. Our study underscores the importance of metric selection and challenges existing practices related to ICD code sub-setting for model training and evaluation.