25,003 research outputs found
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.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS755 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Bayesian Inverse Quantum Theory
A Bayesian approach is developed to determine quantum mechanical potentials
from empirical data. Bayesian methods, combining empirical measurements and "a
priori" information, provide flexible tools for such empirical learning
problems. The paper presents the basic theory, concentrating in particular on
measurements of particle coordinates in quantum mechanical systems at finite
temperature. The computational feasibility of the approach is demonstrated by
numerical case studies. Finally, it is shown how the approach can be
generalized to such many-body and few-body systems for which a mean field
description is appropriate. This is done by means of a Bayesian inverse
Hartree-Fock approximation.Comment: LaTex, 32 pages, 19 figure
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Gaussian process regression for virtual metrology of microchip quality and the resulting strategic sampling scheme
Manufacturing of integrated circuits involves many sequential processes, often ex- ecuted to nanoscale tolerances, and the yield depends on the often unmeasured quality of intermediate steps. In the high-throughput industry of fabricating microelectronics on semi-conducting wafers, scheduling measurements of product quality before the electrical test of the complete IC can be expensive. We therefore seek to predict metrics of product quality based on sensor readings describing the environment within the relevant tool during the processing of each wafer, or to apply the concept of virtual metrology (VM) to monitor these intermediate steps. We model the data using Gaussian process regression (GPR), adapted to simultaneously learn the nonlinear dynamics that govern the quality characteristic, as well as their operating space, expressed by a linear embedding of the sensor traces’ features. Such Bayesian models predict a distribution for the target metric, such as a critical dimension, so one may assess the model’s credibility through its predictive uncertainty. Assuming measurements of the quality characteristic of interest are budgeted, we seek to hasten convergence of the GPR model to a credible form through an active sampling scheme, whereby the predictive uncertainty informs which wafer’s quality to measure next. We evaluate this convergence when predicting and updating online, as if in a factory, using a large dataset for plasma-enhanced chemical vapor deposition (PECVD), with measured thicknesses for ~32,000 wafers. By approximately optimizing the information extracted from this seemingly repetitive data describing a tightly controlled process, GPR achieves ~10% greater accuracy on average than a baseline linear model based on partial least squares (PLS). In a derivative study, we seek to discern the degree of drift in the process over the several months the data spans. We express this drift by how unusual the relevant features, as embedded by the GPR model, appear as the in- puts compensate for degrading conditions. This method detects the onset of consistently unusual behavior that extends to a bimodal thickness fault, anticipating its flagging by as much as two days.Mechanical Engineerin
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