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Vikneswaran Gopal

Publications and source records attributed to Vikneswaran Gopal.

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Confidence Intervals for the F1 Score: A Comparison of Four Methods

In Natural Language Processing (NLP), binary classification algorithms are often evaluated using the F1 score. Because the sample F1 score is an estimate of the population F1 score, it is not sufficient to report the sample F1 score without an indication of how accurate it is. Confidence intervals are an indication of how accurate the sample F1 score is. However, most studies either do not report them or report them using methods that demonstrate poor statistical properties. In the present study, I review current analytical methods (i.e., Clopper-Pearson method and Wald method) to construct confidence intervals for the population F1 score, propose two new analytical methods (i.e., Wilson direct method and Wilson indirect method) to do so, and compare these methods based on their coverage probabilities and interval lengths, as well as whether these methods suffer from overshoot and degeneracy. Theoretical results demonstrate that both proposed methods do not suffer from overshoot and degeneracy. Experimental results suggest that both proposed methods perform better, as compared to current methods, in terms of coverage probabilities and interval lengths. I illustrate both current and proposed methods on two suggestion mining tasks. I discuss the practical implications of these results, and suggest areas for future research.

stat.ME

Simultaneous SNP identification in association studies with missing data

Association testing aims to discover the underlying relationship between genotypes (usually Single Nucleotide Polymorphisms, or SNPs) and phenotypes (attributes, or traits). The typically large data sets used in association testing often contain missing values. Standard statistical methods either impute the missing values using relatively simple assumptions, or delete them, or both, which can generate biased results. Here we describe the Bayesian hierarchical model BAMD (Bayesian Association with Missing Data). BAMD is a Gibbs sampler, in which missing values are multiply imputed based upon all of the available information in the data set. We estimate the parameters and prove that updating one SNP at each iteration preserves the ergodic property of the Markov chain, and at the same time improves computational speed. We also implement a model selection option in BAMD, which enables potential detection of SNP interactions. Simulations show that unbiased estimates of SNP effects are recovered with missing genotype data. Also, we validate associations between SNPs and a carbon isotope discrimination phenotype that were previously reported using a family based method, and discover an additional SNP associated with the trait. BAMD is available as an R-package from http://cran.r-project.org/package=BAMD

stat.AP