arXiv subjects

Adam Kapelner

Publications and source records attributed to Adam Kapelner.

26 records · Page 2Linked to original sources

arXiv2014

Variable selection for BART: An application to gene regulation

We consider the task of discovering gene regulatory networks, which are defined as sets of genes and the corresponding transcription factors which regulate their expression levels. This can be viewed as a variable selection problem, potentially with high dimensionality. Variable selection is especially challenging in high-dimensional settings, where it is difficult to detect subtle individual effects and interactions between predictors. Bayesian Additive Regression Trees [BART, Ann. Appl. Stat. 4 (2010) 266-298] provides a novel nonparametric alternative to parametric regression approaches, such as the lasso or stepwise regression, especially when the number of relevant predictors is sparse relative to the total number of available predictors and the fundamental relationships are nonlinear. We develop a principled permutation-based inferential approach for determining when the effect of a selected predictor is likely to be real. Going further, we adapt the BART procedure to incorporate informed prior information about variable importance. We present simulations demonstrating that our method compares favorably to existing parametric and nonparametric procedures in a variety of data settings. To demonstrate the potential of our approach in a biological context, we apply it to the task of inferring the gene regulatory network in yeast (Saccharomyces cerevisiae). We find that our BART-based procedure is best able to recover the subset of covariates with the largest signal compared to other variable selection methods. The methods developed in this work are readily available in the R package bartMachine.

stat.ME↗

arXiv2014

bartMachine: Machine Learning with Bayesian Additive Regression Trees

We present a new package in R implementing Bayesian additive regression trees (BART). The package introduces many new features for data analysis using BART such as variable selection, interaction detection, model diagnostic plots, incorporation of missing data and the ability to save trees for future prediction. It is significantly faster than the current R implementation, parallelized, and capable of handling both large sample sizes and high-dimensional data.

stat.ML↗

arXiv2014

Using Regression Kernels to Forecast A Failure to Appear in Court

Forecasts of prospective criminal behavior have long been an important feature of many criminal justice decisions. There is now substantial evidence that machine learning procedures will classify and forecast at least as well, and typically better, than logistic regression, which has to date dominated conventional practice. However, machine learning procedures are adaptive. They "learn" inductively from training data. As a result, they typically perform best with very large datasets. There is a need, therefore, for forecasting procedures with the promise of machine learning that will perform well with small to moderately-sized datasets. Kernel methods provide precisely that promise. In this paper, we offer an overview of kernel methods in regression settings and compare such a method, regularized with principle components, to stepwise logistic regression. We apply both to a timely and important criminal justice concern: a failure to appear (FTA) at court proceedings following an arraignment. A forecast of an FTA can be an important factor is a judge's decision to release a defendant while awaiting trial and can influence the conditions imposed on that release. Forecasting accuracy matters, and our kernel approach forecasts far more accurately than stepwise logistic regression. The methods developed here are implemented in the R package kernReg currently available on CRAN.

stat.AP↗

arXiv2014

Peeking Inside the Black Box: Visualizing Statistical Learning with Plots of Individual Conditional Expectation

This article presents Individual Conditional Expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. Classical partial dependence plots (PDPs) help visualize the average partial relationship between the predicted response and one or more features. In the presence of substantial interaction effects, the partial response relationship can be heterogeneous. Thus, an average curve, such as the PDP, can obfuscate the complexity of the modeled relationship. Accordingly, ICE plots refine the partial dependence plot by graphing the functional relationship between the predicted response and the feature for individual observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate, suggesting where and to what extent heterogeneities might exist. In addition to providing a plotting suite for exploratory analysis, we include a visual test for additive structure in the data generating model. Through simulated examples and real data sets, we demonstrate how ICE plots can shed light on estimated models in ways PDPs cannot. Procedures outlined are available in the R package ICEbox.

stat.AP↗

arXiv2014

Bayesian Additive Regression Trees With Parametric Models of Heteroskedasticity

We incorporate heteroskedasticity into Bayesian Additive Regression Trees (BART) by modeling the log of the error variance parameter as a linear function of prespecified covariates. Under this scheme, the Gibbs sampling procedure for the original sum-of- trees model is easily modified, and the parameters for the variance model are updated via a Metropolis-Hastings step. We demonstrate the promise of our approach by providing more appropriate posterior predictive intervals than homoskedastic BART in heteroskedastic settings and demonstrating the model's resistance to overfitting. Our implementation will be offered in an upcoming release of the R package bartMachine.

stat.ME↗

arXiv2014

Prediction with Missing Data via Bayesian Additive Regression Trees

We present a method for incorporating missing data in non-parametric statistical learning without the need for imputation. We focus on a tree-based method, Bayesian Additive Regression Trees (BART), enhanced with "Missingness Incorporated in Attributes," an approach recently proposed incorporating missingness into decision trees (Twala, 2008). This procedure takes advantage of the partitioning mechanisms found in tree-based models. Simulations on generated models and real data indicate that our proposed method can forecast well on complicated missing-at-random and not-missing-at-random models as well as models where missingness itself influences the response. Our procedure has higher predictive performance and is more stable than competitors in many cases. We also illustrate BART's abilities to incorporate missingness into uncertainty intervals and to detect the influence of missingness on the model fit.

stat.ML↗

arXiv2013

Matching on-the-fly in Sequential Experiments for Higher Power and Efficiency

We propose a dynamic allocation procedure that increases power and efficiency when measuring an average treatment effect in sequential randomized trials. Subjects arrive iteratively and are either randomized or paired via a matching criterion to a previously randomized subject and administered the alternate treatment. We develop estimators for the average treatment effect that combine information from both the matched pairs and unmatched subjects as well as an exact test. Simulations illustrate the method's higher efficiency and power over competing allocation procedures in both controlled scenarios and historical experimental data.

stat.ME↗

arXiv2012

Breaking Monotony with Meaning: Motivation in Crowdsourcing Markets

We conduct the first natural field experiment to explore the relationship between the "meaningfulness" of a task and worker effort. We employed about 2,500 workers from Amazon's Mechanical Turk (MTurk), an online labor market, to label medical images. Although given an identical task, we experimentally manipulated how the task was framed. Subjects in the meaningful treatment were told that they were labeling tumor cells in order to assist medical researchers, subjects in the zero-context condition (the control group) were not told the purpose of the task, and, in stark contrast, subjects in the shredded treatment were not given context and were additionally told that their work would be discarded. We found that when a task was framed more meaningfully, workers were more likely to participate. We also found that the meaningful treatment increased the quantity of output (with an insignificant change in quality) while the shredded treatment decreased the quality of output (with no change in quantity). We believe these results will generalize to other short-term labor markets. Our study also discusses MTurk as an exciting platform for running natural field experiments in economics.

stat.OT↗