2,726 research outputs found
Feature selection for microarray gene expression data using simulated annealing guided by the multivariate joint entropy
In this work a new way to calculate the multivariate joint entropy is presented. This measure is the basis for a fast information-theoretic based evaluation of gene relevance in a Microarray Gene Expression data context. Its low complexity is based on the reuse of previous computations to calculate current feature relevance. The mu-TAFS algorithm --named as such to differentiate it from previous TAFS algorithms-- implements a simulated annealing technique specially designed for feature subset selection. The algorithm is applied to the maximization of gene subset relevance in several public-domain microarray data sets. The experimental results show a notoriously high classification performance and low size subsets formed by biologically meaningful genes.Postprint (published version
Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks
We present a procedure for effective estimation of entropy and mutual
information from small-sample data, and apply it to the problem of inferring
high-dimensional gene association networks. Specifically, we develop a
James-Stein-type shrinkage estimator, resulting in a procedure that is highly
efficient statistically as well as computationally. Despite its simplicity, we
show that it outperforms eight other entropy estimation procedures across a
diverse range of sampling scenarios and data-generating models, even in cases
of severe undersampling. We illustrate the approach by analyzing E. coli gene
expression data and computing an entropy-based gene-association network from
gene expression data. A computer program is available that implements the
proposed shrinkage estimator.Comment: 18 pages, 3 figures, 1 tabl
A Triclustering Approach for Time Evolving Graphs
This paper introduces a novel technique to track structures in time evolving
graphs. The method is based on a parameter free approach for three-dimensional
co-clustering of the source vertices, the target vertices and the time. All
these features are simultaneously segmented in order to build time segments and
clusters of vertices whose edge distributions are similar and evolve in the
same way over the time segments. The main novelty of this approach lies in that
the time segments are directly inferred from the evolution of the edge
distribution between the vertices, thus not requiring the user to make an a
priori discretization. Experiments conducted on a synthetic dataset illustrate
the good behaviour of the technique, and a study of a real-life dataset shows
the potential of the proposed approach for exploratory data analysis
Effect of Feature Selection on Gene Expression Datasets Classification Accurac
Feature selection attracts researchers who deal with machine learning and data mining. It consists of selecting the variables that have the greatest impact on the dataset classification, and discarding the rest. This dimentionality reduction allows classifiers to be fast and more accurate. This paper traits the effect of feature selection on the accuracy of widely used classifiers in literature. These classifiers are compared with three real datasets which are pre-processed with feature selection methods. More than 9% amelioration in classification accuracy is observed, and k-means appears to be the most sensitive classifier to feature selection
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