arXiv subjects

Jacqueline M. Hughes-Oliver

Publications and source records attributed to Jacqueline M. Hughes-Oliver.

3 recordsLinked to original sources

arXiv2021

Inference for Hit Enrichment Curves, with Applications to Drug Discovery

In virtual screening for drug discovery, hit enrichment curves are widely used to assess the performance of ranking algorithms with regard to their ability to identify early enrichment. Unfortunately, researchers almost never consider the uncertainty associated with estimating such curves before declaring differences between performance of competing algorithms. Appropriate inference is complicated by two sources of correlation that are often overlooked: correlation across different testing fractions within a single algorithm, and correlation between competing algorithms. Additionally, researchers are often interested in making comparisons along the entire curve, not only at a few testing fractions. We develop inferential procedures to address both the needs of those interested in a few testing fractions, as well as those interested in the entire curve. For the former, four hypothesis testing and (pointwise) confidence intervals are investigated, and a newly developed EmProc approach is found to be most effective. For inference along entire curves, EmProc-based confidence bands are recommended for simultaneous coverage and minimal width. Our inferential procedures trivially extend to enrichment factors, as well.

stat.AP↗

arXiv2018

Population and Empirical PR Curves for Assessment of Ranking Algorithms

The ROC curve is widely used to assess the quality of prediction/classification/ranking algorithms, and its properties have been extensively studied. The precision-recall (PR) curve has become the de facto replacement for the ROC curve in the presence of imbalance, namely where one class is far more likely than the other class. While the PR and ROC curves tend to be used interchangeably, they have some very different properties. Properties of the PR curve are the focus of this paper. We consider: (1) population PR curves, where complete distributional assumptions are specified for scores from both classes; and (2) empirical estimators of the PR curve, where we observe scores and no distributional assumptions are made. The properties have direct consequence on how the PR curve should, and should not, be used. For example, the empirical PR curve is not consistent when scores in the class of primary interest come from discrete distributions. On the other hand, a normal approximation can fit quite well for points on the empirical PR curve from continuously-defined scores, but convergence can be heavily influenced by the distributional setting, the amount of imbalance, and the point of interest on the PR curve.

stat.ML↗

arXiv2012

Efficient, adaptive cross-validation for tuning and comparing models, with application to drug discovery

Cross-validation (CV) is widely used for tuning a model with respect to user-selected parameters and for selecting a "best" model. For example, the method of $k$-nearest neighbors requires the user to choose $k$, the number of neighbors, and a neural network has several tuning parameters controlling the network complexity. Once such parameters are optimized for a particular data set, the next step is often to compare the various optimized models and choose the method with the best predictive performance. Both tuning and model selection boil down to comparing models, either across different values of the tuning parameters or across different classes of statistical models and/or sets of explanatory variables. For multiple large sets of data, like the PubChem drug discovery cheminformatics data which motivated this work, reliable CV comparisons are computationally demanding, or even infeasible. In this paper we develop an efficient sequential methodology for model comparison based on CV. It also takes into account the randomness in CV. The number of models is reduced via an adaptive, multiplicity-adjusted sequential algorithm, where poor performers are quickly eliminated. By exploiting matching of individual observations, it is sometimes even possible to establish the statistically significant inferiority of some models with just one execution of CV.

stat.AP↗