Patrick R. Alba

Hannah Eyre, Alec B Chapman, Kelly S Peterson et al.

Despite impressive success of machine learning algorithms in clinical natural language processing (cNLP), rule-based approaches still have a prominent role. In this paper, we introduce medspaCy, an extensible, open-source cNLP library based on spaCy framework that allows flexible integration of rule-based and machine learning-based algorithms adapted to clinical text. MedspaCy includes a variety of components that meet common cNLP needs such as context analysis and mapping to standard terminologies. By utilizing spaCy's clear and easy-to-use conventions, medspaCy enables development of custom pipelines that integrate easily with other spaCy-based modules. Our toolkit includes several core components and facilitates rapid development of pipelines for clinical text.

Jianlin Shi, Qiwei Gan, Elizabeth Hanchrow et al.

Clinical natural language processing (NLP) is increasingly in demand in both clinical research and operational practice. However, most of the state-of-the-art solutions are transformers-based and require high computational resources, limiting their accessibility. We propose a hybrid NLP framework that integrates rule-based filtering, a Support Vector Machine (SVM) classifier, and a BERT-based model to improve efficiency while maintaining accuracy. We applied this framework in a dementia identification case study involving 4.9 million veterans with incident hypertension, analyzing 2.1 billion clinical notes. At the patient level, our method achieved a precision of 0.90, a recall of 0.84, and an F1-score of 0.87. Additionally, this NLP approach identified over three times as many dementia cases as structured data methods. All processing was completed in approximately two weeks using a single machine with dual A40 GPUs. This study demonstrates the feasibility of hybrid NLP solutions for large-scale clinical text analysis, making state-of-the-art methods more accessible to healthcare organizations with limited computational resources.