4,213 research outputs found
Localization of adaptive variants in human genomes using averaged one-dependence estimation.
Statistical methods for identifying adaptive mutations from population genetic data face several obstacles: assessing the significance of genomic outliers, integrating correlated measures of selection into one analytic framework, and distinguishing adaptive variants from hitchhiking neutral variants. Here, we introduce SWIF(r), a probabilistic method that detects selective sweeps by learning the distributions of multiple selection statistics under different evolutionary scenarios and calculating the posterior probability of a sweep at each genomic site. SWIF(r) is trained using simulations from a user-specified demographic model and explicitly models the joint distributions of selection statistics, thereby increasing its power to both identify regions undergoing sweeps and localize adaptive mutations. Using array and exome data from 45 ‡Khomani San hunter-gatherers of southern Africa, we identify an enrichment of adaptive signals in genes associated with metabolism and obesity. SWIF(r) provides a transparent probabilistic framework for localizing beneficial mutations that is extensible to a variety of evolutionary scenarios
Non-Parametric Calibration of Probabilistic Regression
The task of calibration is to retrospectively adjust the outputs from a
machine learning model to provide better probability estimates on the target
variable. While calibration has been investigated thoroughly in classification,
it has not yet been well-established for regression tasks. This paper considers
the problem of calibrating a probabilistic regression model to improve the
estimated probability densities over the real-valued targets. We propose to
calibrate a regression model through the cumulative probability density, which
can be derived from calibrating a multi-class classifier. We provide three
non-parametric approaches to solve the problem, two of which provide empirical
estimates and the third providing smooth density estimates. The proposed
approaches are experimentally evaluated to show their ability to improve the
performance of regression models on the predictive likelihood
- …