An evaluation of GPT models for phenotype concept recognition

Objective: Clinical deep phenotyping plays a critical role in both the diagnosis of patients with rare disorders as well as in building care coordination plans. The process relies on modelling and curating patient profiles using ontology concepts, usually from the Human Phenotype Ontology. Machine learning methods have been widely adopted to support this phenotype concept recognition task. With the significant shift in the use of large language models (LLMs) for most NLP tasks, herewithin, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT in clinical deep phenotyping. Materials and Methods: The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5 and gpt-4.0) and an established gold standard for phenotype recognition. Results: Our results show that, currently, these models have not yet achieved state of the art performance. The best run, using few-shots learning, achieved 0.41 F1 score, compared to a 0.62 F1 score achieved by the current best in class tool. Conclusion: The non-deterministic nature of the outcomes and the lack of concordance between different runs using the same prompt and input makes the use of these LLMs in clinical settings problematic.