A phenotype-based AI pipeline outperforms human experts in differentially diagnosing rare diseases using EHRs.

Rare diseases, affecting ~350 million people worldwide, pose significant challenges in clinical diagnosis due to the lack of experienced physicians and the complexity of differentiating between numerous rare diseases. To address these challenges, we introduce PhenoBrain, a fully automated artificial intelligence pipeline. PhenoBrain utilizes a BERT-based natural language processing model to extract phenotypes from clinical texts in EHRs and employs five new diagnostic models for differential diagnoses of rare diseases. The AI system was developed and evaluated on diverse, multi-country rare disease datasets, comprising 2271 cases with 431 rare diseases. In 1936 test cases, PhenoBrain achieved an average predicted top-3 recall of 0.513 and a top-10 recall of 0.654, surpassing 13 leading prediction methods. In a human-computer study with 75 cases, PhenoBrain exhibited exceptional performance with a top-3 recall of 0.613 and a top-10 recall of 0.813, surpassing the performance of 50 specialist physicians and large language models like ChatGPT and GPT-4. Combining PhenoBrain's predictions with specialists increased the top-3 recall to 0.768, demonstrating its potential to enhance diagnostic accuracy in clinical workflows.