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OBJECTIVE Predictive models that generate individualized estimates for medically relevant outcomes are playing increasing roles in clinical care and translational research. However, current methods for calibrating these estimates lose valuable information. Our goal is to develop a new calibration method to conserve as much information as possible, and would(More)
Many healthcare facilities enforce security on their electronic health records (EHRs) through a corrective mechanism: some staff nominally have almost unrestricted access to the records, but there is a strict ex post facto audit process for inappropriate accesses, i.e., accesses that violate the facility’s security and privacy policies. This process is(More)
Genome data are becoming increasingly important for modern medicine. As the rate of increase in DNA sequencing outstrips the rate of increase in disk storage capacity, the storage and data transferring of large genome data are becoming important concerns for biomedical researchers. We propose a two-pass lossless genome compression algorithm, which(More)
Determination of the minimum gene set for cellular life is one of the central goals in biology. Genome-wide essential gene identification has progressed rapidly in certain bacterial species; however, it remains difficult to achieve in most eukaryotic species. Several computational models have recently been developed to integrate gene features and used as(More)
Traditional Data Mining and Knowledge Discovery algorithms assume free access to data, either at a centralized location or in federated form. Increasingly, privacy and security concerns restrict this access, thus derailing data mining projects. What we need is distributed knowledge discovery that is sensitive to this problem. The key is to obtain valid(More)
Classical data mining algorithms implicitly assume complete access to all data, either in centralized or federated form. However, privacy and security concerns often prevent sharing of data, thus derailing data mining projects. Recently , there has been growing focus on finding solutions to this problem. Several algorithms have been proposed that do(More)
iDASH (integrating data for analysis, anonymization, and sharing) is the newest National Center for Biomedical Computing funded by the NIH. It focuses on algorithms and tools for sharing data in a privacy-preserving manner. Foundational privacy technology research performed within iDASH is coupled with innovative engineering for collaborative tool(More)
In many real-world applications of machine learning classifiers, it is essential to predict the probability of an example belonging to a particular class. This paper proposes a simple technique for predicting probabilities based on optimizing a ranking loss, followed by isotonic regression. This semi-parametric technique offers both good ranking and(More)
OBJECTIVE The classification of complex or rare patterns in clinical and genomic data requires the availability of a large, labeled patient set. While methods that operate on large, centralized data sources have been extensively used, little attention has been paid to understanding whether models such as binary logistic regression (LR) can be developed in a(More)