Mapping echocardiogram reports to a structured ontology: a task for statistical machine learning or large language models?

Background Big data has the potential to revolutionize echocardiography by enabling novel research and rigorous, scalable quality improvement. Text reports are a critical part of such analyses, and ontology is a key strategy for promoting interoperability of heterogeneous data through consistent tagging. Currently, echocardiogram reports include both structured and free text and vary across institutions, hampering attempts to mine text for useful insights. Natural language processing (NLP) can help and includes both non-deep learning and deep-learning (e.g., large language model, or LLM) based techniques. Challenges to date in using echo text with LLMs include small corpus size, domain-specific language, and high need for accuracy and clinical meaning in model results. Methods We tested whether we could map echocardiography text to a structured, three-level hierarchical ontology using NLP. We used two methods: statistical machine learning (EchoMap) and one-shot inference using the Generative Pre-trained Transformer (GPT) large language model. We tested against eight datasets from 24 different institutions and compared both methods against clinician-scored ground truth. Results Despite all adhering to clinical guidelines, there were notable differences by institution in what information was included in data dictionaries for structured reporting. EchoMap performed best in mapping test set sentences to the ontology, with validation accuracy of 98% for the first level of the ontology, 93% for the first and second level, and 79% for the first, second, and third levels. EchoMap retained good performance across external test datasets and displayed the ability to extrapolate to examples not initially included in training. EchoMap’s accuracy was comparable to one-shot GPT at the first level of the ontology and outperformed GPT at second and third levels. Conclusions We show that statistical machine learning can achieve good performance on text mapping tasks and may be especially useful for small, specialized text datasets. Furthermore, this work highlights the utility of a high-resolution, standardized cardiac ontology to harmonize reports across institutions.