Person:

Hong, Chuan

We propose a nonparametric shrinkage estimator for the median survival times from several independent samples of right-censored data, which combines the samples and hypothesis information to improve the efficiency. We compare efficiency of the proposed shrinkage estimation procedure to unrestricted estimator and combined estimator through extensive simulation studies. Our results indicate that performance of these estimators depends on the strength of homogeneity of the medians. When homogeneity holds, the combined estimator is the most efficient estimator. However, it becomes inconsistent when homogeneity fails. On the other hand, the proposed shrinkage estimator remains efficient. Its efficiency decreases as the equality of the survival medians is deviated, but is expected to be as good as or equal to the unrestricted estimator. Our simulation studies also indicate that the proposed shrinkage estimator is robust to moderate levels of censoring. We demonstrate application of these methods to estimating median time for trauma patients to receive red blood cells in the Prospective Observational Multi-center Major Trauma Transfusion (PROMMTT) study.

Phenotypes are the foundation for clinical and genetic studies of disease risk and outcomes. The growth of biobanks linked to electronic medical record (EMR) data has both facilitated and increased the demand for efficient, accurate, and robust approaches for phenotyping millions of patients. Challenges to phenotyping using EMR data include variation in the accuracy of codes, as well as the high level of manual input required to identify features for the algorithm and to obtain gold standard labels. To address these challenges, we developed PheCAP, a high-throughput semi-supervised phenotyping pipeline. PheCAP begins with data from the EMR, including structured data and information extracted from the narrative notes using natural language processing (NLP). The standardized steps integrate automated procedures reducing the level of manual input, and machine learning approaches for algorithm training. PheCAP itself can be executed in 1-2 days if all data are available; however, the timing is largely dependent on the chart review step which typically requires at least 2 weeks. The final products of PheCAP include a phenotype algorithm, the probability of the phenotype for all patients, and a phenotype classification (yes/no).