Assessing similarity of feature selection techniques in high-dimensional domains

Recent research efforts attempt to combine multiple feature selection techniques instead of using a single one. However, this combination is often made on an “ad hoc” basis, depending on the specific problem at hand, without considering the degree of diversity/similarity of the involved methods. Moreover, though it is recognized that different techniques may return quite dissimilar outputs, especially in high dimensional/small sample size domains, few direct comparisons exist that quantify these differences and their implications on classification performance. This paper aims to provide a contribution in this direction by proposing a general methodology for assessing the similarity between the outputs of different feature selection methods in high dimensional classification problems. Using as benchmark the genomics domain, an empirical study has been conducted to compare some of the most popular feature selection methods, and useful insight has been obtained about their pattern of agreement

Determining appropriate approaches for using data in feature selection

Feature selection is increasingly important in data analysis and machine learning in big data era. However, how to use the data in feature selection, i.e. using either ALL or PART of a dataset, has become a serious and tricky issue. Whilst the conventional practice of using all the data in feature selection may lead to selection bias, using part of the data may, on the other hand, lead to underestimating the relevant features under some conditions. This paper investigates these two strategies systematically in terms of reliability and effectiveness, and then determines their suitability for datasets with different characteristics. The reliability is measured by the Average Tanimoto Index and the Inter-method Average Tanimoto Index, and the effectiveness is measured by the mean generalisation accuracy of classification. The computational experiments are carried out on ten real-world benchmark datasets and fourteen synthetic datasets. The synthetic datasets are generated with a pre-set number of relevant features and varied numbers of irrelevant features and instances, and added with different levels of noise. The results indicate that the PART approach is more effective in reducing the bias when the size of a dataset is small but starts to lose its advantage as the dataset size increases

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

Infinite Latent Feature Selection: A Probabilistic Latent Graph-Based Ranking Approach

Feature selection is playing an increasingly significant role with respect to many computer vision applications spanning from object recognition to visual object tracking. However, most of the recent solutions in feature selection are not robust across different and heterogeneous set of data. In this paper, we address this issue proposing a robust probabilistic latent graph-based feature selection algorithm that performs the ranking step while considering all the possible subsets of features, as paths on a graph, bypassing the combinatorial problem analytically. An appealing characteristic of the approach is that it aims to discover an abstraction behind low-level sensory data, that is, relevancy. Relevancy is modelled as a latent variable in a PLSA-inspired generative process that allows the investigation of the importance of a feature when injected into an arbitrary set of cues. The proposed method has been tested on ten diverse benchmarks, and compared against eleven state of the art feature selection methods. Results show that the proposed approach attains the highest performance levels across many different scenarios and difficulties, thereby confirming its strong robustness while setting a new state of the art in feature selection domain.Comment: Accepted at the IEEE International Conference on Computer Vision (ICCV), 2017, Venice. Preprint cop

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

Improving Feature Selection Techniques for Machine Learning

As a commonly used technique in data preprocessing for machine learning, feature selection identifies important features and removes irrelevant, redundant or noise features to reduce the dimensionality of feature space. It improves efficiency, accuracy and comprehensibility of the models built by learning algorithms. Feature selection techniques have been widely employed in a variety of applications, such as genomic analysis, information retrieval, and text categorization. Researchers have introduced many feature selection algorithms with different selection criteria. However, it has been discovered that no single criterion is best for all applications. We proposed a hybrid feature selection framework called based on genetic algorithms (GAs) that employs a target learning algorithm to evaluate features, a wrapper method. We call it hybrid genetic feature selection (HGFS) framework. The advantages of this approach include the ability to accommodate multiple feature selection criteria and find small subsets of features that perform well for the target algorithm. The experiments on genomic data demonstrate that ours is a robust and effective approach that can find subsets of features with higher classification accuracy and/or smaller size compared to each individual feature selection algorithm. A common characteristic of text categorization tasks is multi-label classification with a great number of features, which makes wrapper methods time-consuming and impractical. We proposed a simple filter (non-wrapper) approach called Relation Strength and Frequency Variance (RSFV) measure. The basic idea is that informative features are those that are highly correlated with the class and distribute most differently among all classes. The approach is compared with two well-known feature selection methods in the experiments on two standard text corpora. The experiments show that RSFV generate equal or better performance than the others in many cases

Dissimilarity-based representation for radiomics applications

Radiomics is a term which refers to the analysis of the large amount of quantitative tumor features extracted from medical images to find useful predictive, diagnostic or prognostic information. Many recent studies have proved that radiomics can offer a lot of useful information that physicians cannot extract from the medical images and can be associated with other information like gene or protein data. However, most of the classification studies in radiomics report the use of feature selection methods without identifying the machine learning challenges behind radiomics. In this paper, we first show that the radiomics problem should be viewed as an high dimensional, low sample size, multi view learning problem, then we compare different solutions proposed in multi view learning for classifying radiomics data. Our experiments, conducted on several real world multi view datasets, show that the intermediate integration methods work significantly better than filter and embedded feature selection methods commonly used in radiomics.Comment: conference, 6 pages, 2 figure

Embedding Feature Selection for Large-scale Hierarchical Classification

Large-scale Hierarchical Classification (HC) involves datasets consisting of thousands of classes and millions of training instances with high-dimensional features posing several big data challenges. Feature selection that aims to select the subset of discriminant features is an effective strategy to deal with large-scale HC problem. It speeds up the training process, reduces the prediction time and minimizes the memory requirements by compressing the total size of learned model weight vectors. Majority of the studies have also shown feature selection to be competent and successful in improving the classification accuracy by removing irrelevant features. In this work, we investigate various filter-based feature selection methods for dimensionality reduction to solve the large-scale HC problem. Our experimental evaluation on text and image datasets with varying distribution of features, classes and instances shows upto 3x order of speed-up on massive datasets and upto 45% less memory requirements for storing the weight vectors of learned model without any significant loss (improvement for some datasets) in the classification accuracy. Source Code: https://cs.gmu.edu/~mlbio/featureselection.Comment: IEEE International Conference on Big Data (IEEE BigData 2016