4,576 research outputs found
The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures
Motivation: Biomarker discovery from high-dimensional data is a crucial
problem with enormous applications in biology and medicine. It is also
extremely challenging from a statistical viewpoint, but surprisingly few
studies have investigated the relative strengths and weaknesses of the plethora
of existing feature selection methods. Methods: We compare 32 feature selection
methods on 4 public gene expression datasets for breast cancer prognosis, in
terms of predictive performance, stability and functional interpretability of
the signatures they produce. Results: We observe that the feature selection
method has a significant influence on the accuracy, stability and
interpretability of signatures. Simple filter methods generally outperform more
complex embedded or wrapper methods, and ensemble feature selection has
generally no positive effect. Overall a simple Student's t-test seems to
provide the best results. Availability: Code and data are publicly available at
http://cbio.ensmp.fr/~ahaury/
Feature Selection via Binary Simultaneous Perturbation Stochastic Approximation
Feature selection (FS) has become an indispensable task in dealing with
today's highly complex pattern recognition problems with massive number of
features. In this study, we propose a new wrapper approach for FS based on
binary simultaneous perturbation stochastic approximation (BSPSA). This
pseudo-gradient descent stochastic algorithm starts with an initial feature
vector and moves toward the optimal feature vector via successive iterations.
In each iteration, the current feature vector's individual components are
perturbed simultaneously by random offsets from a qualified probability
distribution. We present computational experiments on datasets with numbers of
features ranging from a few dozens to thousands using three widely-used
classifiers as wrappers: nearest neighbor, decision tree, and linear support
vector machine. We compare our methodology against the full set of features as
well as a binary genetic algorithm and sequential FS methods using
cross-validated classification error rate and AUC as the performance criteria.
Our results indicate that features selected by BSPSA compare favorably to
alternative methods in general and BSPSA can yield superior feature sets for
datasets with tens of thousands of features by examining an extremely small
fraction of the solution space. We are not aware of any other wrapper FS
methods that are computationally feasible with good convergence properties for
such large datasets.Comment: This is the Istanbul Sehir University Technical Report
#SHR-ISE-2016.01. A short version of this report has been accepted for
publication at Pattern Recognition Letter
Exploiting the accumulated evidence for gene selection in microarray gene expression data
Machine Learning methods have of late made signicant efforts to solving multidisciplinary problems in the field of cancer classification using microarray gene expression data. Feature subset selection methods can play an important role in the modeling process, since these tasks are characterized by a large number of features and a few observations, making the modeling a non-trivial undertaking. In this particular scenario, it is extremely important to select genes by taking into account the possible interactions with other gene subsets. This paper shows that, by accumulating the evidence in favour (or against) each gene along the search process, the obtained gene subsets may constitute better solutions, either in terms of predictive accuracy or gene size, or in both. The proposed technique is extremely simple and applicable at a negligible overhead in cost.Postprint (published version
Ranking to Learn: Feature Ranking and Selection via Eigenvector Centrality
In an era where accumulating data is easy and storing it inexpensive, feature
selection plays a central role in helping to reduce the high-dimensionality of
huge amounts of otherwise meaningless data. In this paper, we propose a
graph-based method for feature selection that ranks features by identifying the
most important ones into arbitrary set of cues. Mapping the problem on an
affinity graph-where features are the nodes-the solution is given by assessing
the importance of nodes through some indicators of centrality, in particular,
the Eigen-vector Centrality (EC). The gist of EC is to estimate the importance
of a feature as a function of the importance of its neighbors. Ranking central
nodes individuates candidate features, which turn out to be effective from a
classification point of view, as proved by a thoroughly experimental section.
Our approach has been tested on 7 diverse datasets from recent literature
(e.g., biological data and object recognition, among others), and compared
against filter, embedded and wrappers methods. The results are remarkable in
terms of accuracy, stability and low execution time.Comment: Preprint version - Lecture Notes in Computer Science - Springer 201
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