9,817 research outputs found
A fast algorithm for detecting gene-gene interactions in genome-wide association studies
With the recent advent of high-throughput genotyping techniques, genetic data
for genome-wide association studies (GWAS) have become increasingly available,
which entails the development of efficient and effective statistical
approaches. Although many such approaches have been developed and used to
identify single-nucleotide polymorphisms (SNPs) that are associated with
complex traits or diseases, few are able to detect gene-gene interactions among
different SNPs. Genetic interactions, also known as epistasis, have been
recognized to play a pivotal role in contributing to the genetic variation of
phenotypic traits. However, because of an extremely large number of SNP-SNP
combinations in GWAS, the model dimensionality can quickly become so
overwhelming that no prevailing variable selection methods are capable of
handling this problem. In this paper, we present a statistical framework for
characterizing main genetic effects and epistatic interactions in a GWAS study.
Specifically, we first propose a two-stage sure independence screening (TS-SIS)
procedure and generate a pool of candidate SNPs and interactions, which serve
as predictors to explain and predict the phenotypes of a complex trait. We also
propose a rates adjusted thresholding estimation (RATE) approach to determine
the size of the reduced model selected by an independence screening.
Regularization regression methods, such as LASSO or SCAD, are then applied to
further identify important genetic effects. Simulation studies show that the
TS-SIS procedure is computationally efficient and has an outstanding finite
sample performance in selecting potential SNPs as well as gene-gene
interactions. We apply the proposed framework to analyze an
ultrahigh-dimensional GWAS data set from the Framingham Heart Study, and select
23 active SNPs and 24 active epistatic interactions for the body mass index
variation. It shows the capability of our procedure to resolve the complexity
of genetic control.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS771 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Practical Block-wise Neural Network Architecture Generation
Convolutional neural networks have gained a remarkable success in computer
vision. However, most usable network architectures are hand-crafted and usually
require expertise and elaborate design. In this paper, we provide a block-wise
network generation pipeline called BlockQNN which automatically builds
high-performance networks using the Q-Learning paradigm with epsilon-greedy
exploration strategy. The optimal network block is constructed by the learning
agent which is trained sequentially to choose component layers. We stack the
block to construct the whole auto-generated network. To accelerate the
generation process, we also propose a distributed asynchronous framework and an
early stop strategy. The block-wise generation brings unique advantages: (1) it
performs competitive results in comparison to the hand-crafted state-of-the-art
networks on image classification, additionally, the best network generated by
BlockQNN achieves 3.54% top-1 error rate on CIFAR-10 which beats all existing
auto-generate networks. (2) in the meanwhile, it offers tremendous reduction of
the search space in designing networks which only spends 3 days with 32 GPUs,
and (3) moreover, it has strong generalizability that the network built on
CIFAR also performs well on a larger-scale ImageNet dataset.Comment: Accepted to CVPR 201
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