Electronic phenotyping entails using electronic health records (EHRs) to identify patients with specific health outcomes and determine when those outcomes occurred. Unstructured clinical notes, which contain a vast amount of information, are a valuable resource for electronic phenotyping. However, traditional methods, such as rule-based labeling functions or neural networks, require significant manual effort to tune and may not generalize well to multiple indications. To address these challenges, we propose HyDE (hybrid diagnosis extractor). HyDE is a simple framework for electronic phenotyping that integrates labeling functions and a disease-agnostic neural network to assign diagnoses to patients. By training HyDE’s model to correct predictions made by labeling functions, we are able to disambiguate hypertension true positives and false positives with a supervised area under the precision-recall curve (AUPRC) of 0.85. We extend this hypertension-trained model to zero-shot evaluation of four other diseases, generating AUPRC values ranging from 0.82 - 0.95 and outperforming a labeling function baseline by 44 points in F1 score and a Word2Vec baseline by 24 points in F1 score on average. Furthermore, we demonstrate a speedup of >4x by pruning the length of inputs into our language model to ~2.3% of the full clinical notes, with negligible impact to the AUPRC. HyDE has the potential to improve the efficiency and efficacy of interpreting large-scale unstructured clinical notes for accurate EHR phenotyping.

Motivated by the scarcity of high-quality labeled biomedical text, as well as the success of data programming, we introduce KRISS-Search. By leveraging the Unified Medical Language Systems (UMLS) ontology, KRISS-Search addresses an interactive few-shot span recommendation task that we propose. We first introduce unsupervised KRISS-Search and show that our method outperforms existing methods in identifying spans that are semantically similar to a given span of interest, with >50% AUPRC improvement relative to PubMedBERT. We then introduce supervised KRISS-Search, which leverages human interaction to improve the notion of similarity used by unsupervised KRISS-Search. Through simulated human feedback, we demonstrate an enhanced F1 score of 0.68 in classifying spans as semantically similar or different in the low-label setting, outperforming PubMedBERT by 2 F1 points. Finally, supervised KRISS-Search demonstrates competitive or superior performance compared to PubMedBERT in few-shot biomedical named entity recognition (NER) across five benchmark datasets, with an average improvement of 5.6 F1 points. We envision KRISS-Search increasing the efficiency of programmatic data labeling and also providing broader utility as an interactive biomedical search engine.