11,100 research outputs found
Ensemble feature learning of genomic data using support vector machine
© 2016 Anaissi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The identification of a subset of genes having the ability to capture the necessary information to distinguish classes of patients is crucial in bioinformatics applications. Ensemble and bagging methods have been shown to work effectively in the process of gene selection and classification. Testament to that is random forest which combines random decision trees with bagging to improve overall feature selection and classification accuracy. Surprisingly, the adoption of these methods in support vector machines has only recently received attention but mostly on classification not gene selection. This paper introduces an ensemble SVM-Recursive Feature Elimination (ESVM-RFE) for gene selection that follows the concepts of ensemble and bagging used in random forest but adopts the backward elimination strategy which is the rationale of RFE algorithm. The rationale behind this is, building ensemble SVM models using randomly drawn bootstrap samples from the training set, will produce different feature rankings which will be subsequently aggregated as one feature ranking. As a result, the decision for elimination of features is based upon the ranking of multiple SVM models instead of choosing one particular model. Moreover, this approach will address the problem of imbalanced datasets by constructing a nearly balanced bootstrap sample. Our experiments show that ESVM-RFE for gene selection substantially increased the classification performance on five microarray datasets compared to state-of-the-art methods. Experiments on the childhood leukaemia dataset show that an average 9% better accuracy is achieved by ESVM-RFE over SVM-RFE, and 5% over random forest based approach. The selected genes by the ESVM-RFE algorithm were further explored with Singular Value Decomposition (SVD) which reveals significant clusters with the selected data
Exploring signature multiplicity in microarray data using ensembles of randomized trees
A challenging and novel direction for feature selection research
in computational biology is the analysis of signature multiplicity. In this work, we propose to investigate the eect of signature multiplicity on feature importance scores derived from tree-based ensemble methods. We show that looking at individual tree rankings in an ensemble could highlight the existence of multiple signatures and we propose a simple
post-processing method based on clustering that can return smaller signatures with better predictive performance than signatures derived from the global tree ranking at almost no additional cost
Stable Feature Selection for Biomarker Discovery
Feature selection techniques have been used as the workhorse in biomarker
discovery applications for a long time. Surprisingly, the stability of feature
selection with respect to sampling variations has long been under-considered.
It is only until recently that this issue has received more and more attention.
In this article, we review existing stable feature selection methods for
biomarker discovery using a generic hierarchal framework. We have two
objectives: (1) providing an overview on this new yet fast growing topic for a
convenient reference; (2) categorizing existing methods under an expandable
framework for future research and development
Weighted Heuristic Ensemble of Filters
Feature selection has become increasingly important in data mining in recent years due to the rapid increase in the dimensionality of big data. However, the reliability and consistency of feature selection methods (filters) vary considerably on different data and no single filter performs consistently well under various conditions. Therefore, feature selection ensemble has been investigated recently to provide more reliable and effective results than any individual one but all the existing feature selection ensemble treat the feature selection methods equally regardless of their performance. In this paper, we present a novel framework which applies weighted feature selection ensemble through proposing a systemic way of adding different weights to the feature selection methods-filters. Also, we investigate how to determine the appropriate weight for each filter in an ensemble. Experiments based on ten benchmark datasets show that theoretically and intuitively adding more weight to ‘good filters’ should lead to better results but in reality it is very uncertain. This assumption was found to be correct for some examples in our experiment. However, for other situations, filters which had been assumed to perform well showed bad performance leading to even worse results. Therefore adding weight to filters might not achieve much in accuracy terms, in addition to increasing complexity, time consumption and clearly decreasing the stability
EFSIS: Ensemble Feature Selection Integrating Stability
Ensemble learning that can be used to combine the predictions from multiple
learners has been widely applied in pattern recognition, and has been reported
to be more robust and accurate than the individual learners. This ensemble
logic has recently also been more applied in feature selection. There are
basically two strategies for ensemble feature selection, namely data
perturbation and function perturbation. Data perturbation performs feature
selection on data subsets sampled from the original dataset and then selects
the features consistently ranked highly across those data subsets. This has
been found to improve both the stability of the selector and the prediction
accuracy for a classifier. Function perturbation frees the user from having to
decide on the most appropriate selector for any given situation and works by
aggregating multiple selectors. This has been found to maintain or improve
classification performance. Here we propose a framework, EFSIS, combining these
two strategies. Empirical results indicate that EFSIS gives both high
prediction accuracy and stability.Comment: 20 pages, 3 figure
Radar-based Road User Classification and Novelty Detection with Recurrent Neural Network Ensembles
Radar-based road user classification is an important yet still challenging
task towards autonomous driving applications. The resolution of conventional
automotive radar sensors results in a sparse data representation which is tough
to recover by subsequent signal processing. In this article, classifier
ensembles originating from a one-vs-one binarization paradigm are enriched by
one-vs-all correction classifiers. They are utilized to efficiently classify
individual traffic participants and also identify hidden object classes which
have not been presented to the classifiers during training. For each classifier
of the ensemble an individual feature set is determined from a total set of 98
features. Thereby, the overall classification performance can be improved when
compared to previous methods and, additionally, novel classes can be identified
much more accurately. Furthermore, the proposed structure allows to give new
insights in the importance of features for the recognition of individual
classes which is crucial for the development of new algorithms and sensor
requirements.Comment: 8 pages, 9 figures, accepted paper for 2019 IEEE Intelligent Vehicles
Symposium (IV), Paris, France, June 201
Pairwise meta-rules for better meta-learning-based algorithm ranking
In this paper, we present a novel meta-feature generation method in the context of meta-learning, which is based on rules that compare the performance of individual base learners in a one-against-one manner. In addition to these new meta-features, we also introduce a new meta-learner called Approximate Ranking Tree Forests (ART Forests) that performs very competitively when compared with several state-of-the-art meta-learners. Our experimental results are based on a large collection of datasets and show that the proposed new techniques can improve the overall performance of meta-learning for algorithm ranking significantly. A key point in our approach is that each performance figure of any base learner for any specific dataset is generated by optimising the parameters of the base learner separately for each dataset
- …