[HTML][HTML] A comparison of methods for interpreting random forest models of genetic association in the presence of non-additive interactions
Background Non-additive interactions among genes are frequently associated with a
number of phenotypes, including known complex diseases such as Alzheimer's, diabetes …
number of phenotypes, including known complex diseases such as Alzheimer's, diabetes …
Random forests for genetic association studies
The Random Forests (RF) algorithm has become a commonly used machine learning
algorithm for genetic association studies. It is well suited for genetic applications since it is …
algorithm for genetic association studies. It is well suited for genetic applications since it is …
EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis
Motivation: We developed an EM-random forest (EMRF) for Haseman–Elston quantitative
trait linkage analysis that accounts for marker ambiguity and weighs each sib-pair according …
trait linkage analysis that accounts for marker ambiguity and weighs each sib-pair according …
[HTML][HTML] Neural networks for modeling gene-gene interactions in association studies
F Günther, N Wawro, K Bammann - BMC genetics, 2009 - Springer
Background Our aim is to investigate the ability of neural networks to model different two-
locus disease models. We conduct a simulation study to compare neural networks with two …
locus disease models. We conduct a simulation study to compare neural networks with two …
[HTML][HTML] SNPInterForest: a new method for detecting epistatic interactions
M Yoshida, A Koike - BMC bioinformatics, 2011 - Springer
Background Multiple genetic factors and their interactive effects are speculated to contribute
to complex diseases. Detecting such genetic interactive effects, ie, epistatic interactions …
to complex diseases. Detecting such genetic interactive effects, ie, epistatic interactions …
Maximal conditional chi-square importance in random forests
Motivation: High-dimensional data are frequently generated in genome-wide association
studies (GWAS) and other studies. It is important to identify features such as single …
studies (GWAS) and other studies. It is important to identify features such as single …
[HTML][HTML] The behaviour of random forest permutation-based variable importance measures under predictor correlation
KK Nicodemus, JD Malley, C Strobl, A Ziegler - BMC bioinformatics, 2010 - Springer
Background Random forests (RF) have been increasingly used in applications such as
genome-wide association and microarray studies where predictor correlation is frequently …
genome-wide association and microarray studies where predictor correlation is frequently …
A comparison of analytical methods for genetic association studies
AA Motsinger‐Reif, DM Reif, TJ Fanelli… - … Official Publication of …, 2008 - Wiley Online Library
The explosion of genetic information over the last decade presents an analytical challenge
for genetic association studies. As the number of genetic variables examined per individual …
for genetic association studies. As the number of genetic variables examined per individual …
Power of data mining methods to detect genetic associations and interactions
AM Molinaro, N Carriero, R Bjornson, P Hartge… - Human Heredity, 2011 - karger.com
Background: Genetic association studies, thus far, have focused on the analysis of individual
main effects of SNP markers. Nonetheless, there is a clear need for modeling epistasis or …
main effects of SNP markers. Nonetheless, there is a clear need for modeling epistasis or …
Supervising random forest using attribute interaction networks
Genome-wide association studies (GWAS) have become a powerful and affordable tool to
study the genetic variations associated with common human diseases. However, only few of …
study the genetic variations associated with common human diseases. However, only few of …