Sean D. Mooney

Chao Yan, Yao Yan, Zhiyu Wan et al.

Synthetic health data have the potential to mitigate privacy concerns when sharing data to support biomedical research and the development of innovative healthcare applications. Modern approaches for data generation based on machine learning, generative adversarial networks (GAN) methods in particular, continue to evolve and demonstrate remarkable potential. Yet there is a lack of a systematic assessment framework to benchmark methods as they emerge and determine which methods are most appropriate for which use cases. In this work, we introduce a generalizable benchmarking framework to appraise key characteristics of synthetic health data with respect to utility and privacy metrics. We apply the framework to evaluate synthetic data generation methods for electronic health records (EHRs) data from two large academic medical centers with respect to several use cases. The results illustrate that there is a utility-privacy tradeoff for sharing synthetic EHR data. The results further indicate that no method is unequivocally the best on all criteria in each use case, which makes it evident why synthetic data generation methods need to be assessed in context.

Yao Yan, Thomas Yu, Kathleen Muenzen et al.

Objective The evaluation of natural language processing (NLP) models for clinical text de-identification relies on the availability of clinical notes, which is often restricted due to privacy concerns. The NLP Sandbox is an approach for alleviating the lack of data and evaluation frameworks for NLP models by adopting a federated, model-to-data approach. This enables unbiased federated model evaluation without the need for sharing sensitive data from multiple institutions. Materials and Methods We leveraged the Synapse collaborative framework, containerization software, and OpenAPI generator to build the NLP Sandbox (nlpsandbox.io). We evaluated two state-of-the-art NLP de-identification focused annotation models, Philter and NeuroNER, using data from three institutions. We further validated model performance using data from an external validation site. Results We demonstrated the usefulness of the NLP Sandbox through de-identification clinical model evaluation. The external developer was able to incorporate their model into the NLP Sandbox template and provide user experience feedback. Discussion We demonstrated the feasibility of using the NLP Sandbox to conduct a multi-site evaluation of clinical text de-identification models without the sharing of data. Standardized model and data schemas enable smooth model transfer and implementation. To generalize the NLP Sandbox, work is required on the part of data owners and model developers to develop suitable and standardized schemas and to adapt their data or model to fit the schemas. Conclusions The NLP Sandbox lowers the barrier to utilizing clinical data for NLP model evaluation and facilitates federated, multi-site, unbiased evaluation of NLP models.

Kurmanbek Kaiyrbekov, Nicholas J Dobbins, Sean D Mooney

Objective: Traditional phone-based surveys are among the most accessible and widely used methods to collect biomedical and healthcare data, however, they are often costly, labor intensive, and difficult to scale effectively. To overcome these limitations, we propose an end-to-end survey collection framework driven by conversational Large Language Models (LLMs). Materials and Methods: Our framework consists of a researcher responsible for designing the survey and recruiting participants, a conversational phone agent powered by an LLM that calls participants and administers the survey, a second LLM (GPT-4o) that analyzes the conversation transcripts generated during the surveys, and a database for storing and organizing the results. To test our framework, we recruited 8 participants consisting of 5 native and 3 non-native english speakers and administered 40 surveys. We evaluated the correctness of LLM-generated conversation transcripts, accuracy of survey responses inferred by GPT-4o and overall participant experience. Results: Survey responses were successfully extracted by GPT-4o from conversation transcripts with an average accuracy of 98% despite transcripts exhibiting an average per-line word error rate of 7.7%. While participants noted occasional errors made by the conversational LLM agent, they reported that the agent effectively conveyed the purpose of the survey, demonstrated good comprehension, and maintained an engaging interaction. Conclusions: Our study highlights the potential of LLM agents in conducting and analyzing phone surveys for healthcare applications. By reducing the workload on human interviewers and offering a scalable solution, this approach paves the way for real-world, end-to-end AI-powered phone survey collection systems.