Enhancing random forests performance in microarray data classification

Random forests are receiving increasing attention for classification of microarray datasets. We evaluate the effects of a feature selection process on the performance of a random forest classifier as well as on the choice of two critical parameters, i.e. the forest size and the number of features chosen at each split in growing trees. Results of our experiments suggest that parameters lower than popular default values can lead to effective and more parsimonious classification models. Growing few trees on small subsets of selected features, while randomly choosing a single variable at each split, results in classification performance that compares well with state-of-art studies

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

BioCloud Search EnGene: Surfing Biological Data on the Cloud

The massive production and spread of biomedical data around the web introduces new challenges related to identify computational approaches for providing quality search and browsing of web resources. This papers presents BioCloud Search EnGene (BSE), a cloud application that facilitates searching and integration of the many layers of biological information offered by public large-scale genomic repositories. Grounding on the concept of dataspace, BSE is built on top of a cloud platform that severely curtails issues associated with scalability and performance. Like popular online gene portals, BSE adopts a gene-centric approach: researchers can find their information of interest by means of a simple “Google-like” query interface that accepts standard gene identification as keywords. We present BSE architecture and functionality and discuss how our strategies contribute to successfully tackle big data problems in querying gene-based web resources. BSE is publically available at: http://biocloud-unica.appspot.com/

Exploiting biomedical web resources: a case study

An increasing number of web resources continue to be extensively used by healthcare operators to obtain more accurate diagnostic results. In particular, health care is reaping the benefits of technological advances in genomic for facing the demand of genetic tests that allow a better comprehension of diagnostic results. Within this context, Gene Ontology (GO) is a popular and effective mean for extracting knowledge from a list of genes and evaluating their semantic similarity. This paper investigates about the potential and any limits of GO ontology as support for capturing information about a set of genes which are supposed to play a significant role in a pathological condition. In particular, we present a case study that exploits some biomedical web resources for devising several groups of functionally coherent genes and experiments about the evaluation of their semantic similarity over GO. Due to the GO structure and content, results reveal limitations that not affect the evaluation of the semantic similarity when genes exhibit simple correlations but influence the estimation of the relatedness of genes belonging to complex organizations

A comparative analysis of biomarker selection techniques

Feature selection has become the essential step in biomarker discovery from high-dimensional genomics data. It is recognized that different feature selection techniques may result in different set of biomarkers, i.e. different groups of genes highly correlated to a given pathological condition, but few direct comparisons exist that quantify these differences in a systematic way. In this paper, we propose a general methodology for comparing the outcomes of different selection techniques in the context of biomarker discovery. The comparison is carried out along two dimensions: (i) measuring the similarity/dissimilarity of selected gene sets, (ii) evaluating the implications of these differences in terms of both predictive performance and stability of selected gene sets. As a case study, we considered three benchmarks deriving from DNA micro-array experiments and conducted a comparative analysis among eight selection methods, representative of different classes of feature selection techniques. Our results show that the proposed approach can provide useful insight about the pattern of agreement of biomarker discovery techniques

Exploiting the ensemble paradigm for stable feature selection: A case study on high-dimensional genomic data

Ensemble classification is a well-established approach that involves fusing the decisions of multiple predictive models. A similar “ensemble logic” has been recently applied to challenging feature selection tasks aimed at identifying the most informative variables (or features) for a given domain of interest. In this work, we discuss the rationale of ensemble feature selection and evaluate the effects and the implications of a specific ensemble approach, namely the data perturbation strategy. Basically, it consists in combining multiple selectors that exploit the same core algorithm but are trained on different perturbed versions of the original data. The real potential of this approach, still object of debate in the feature selection literature, is here investigated in conjunction with different kinds of core selection algorithms (both univariate and multivariate). In particular, we evaluate the extent to which the ensemble implementation improves the overall performance of the selection process, in terms of predictive accuracy and stability (i.e., robustness with respect to changes in the training data). Furthermore, we measure the impact of the ensemble approach on the final selection outcome, i.e. on the composition of the selected feature subsets. The results obtained on ten public genomic benchmarks provide useful insight on both the benefits and the limitations of such ensemble approach, paving the way to the exploration of new and wider ensemble schemes

An evolutionary approach for balancing effectiveness and representation level in gene selection

As data mining develops and expands to new application areas, feature selection also reveals various aspects to be considered. This paper underlines two aspects that seem to categorize the large body of available feature selection algorithms: the effectiveness and the representation level. The effectiveness deals with selecting the minimum set of variables that maximize the accuracy of a classifier and the representation level concerns discovering how relevant the variables are for the domain of interest. For balancing the above aspects, the paper proposes an evolutionary framework for feature selection that expresses a hybrid method, organized in layers, each of them exploits a specific model of search strategy. Extensive experiments on gene selection from DNA-microarray datasets are presented and discussed. Results indicate that the framework compares well with different hybrid methods proposed in literature as it has the capability of finding well suited subsets of informative features while improving classification accurac

A model for term selection in text categorization problems

In the last ten years, automatic Text Categorization (TC) has been gaining an increasing interest from the research community, due to the need to organize a massive number of digital documents. Following a machine learning paradigm, this paper presents a model which regards TC as a classification task supported by a wrapper approach and combines the utilization of a Genetic Algorithm (GA) with a filter. First, a filter is used to weigh the relevance of terms in documents. Then, the top-ranked terms are grouped in several nested sets of relatively small size. These sets are explored by a GA which extracts the subset of terms that best categorize documents. Experimental results on the Reuters-21578 dataset state the effectiveness of the proposed model and its competitiveness with the learning approaches proposed in the TC literature

A Fully Semantic Approach to Large Scale Text Categorization.

Text categorization is usually performed by supervised algorithms on the large amount of hand-labelled documents which are labor-intensive and often not available. To avoid this drawback, this paper proposes a text categorization approach that is designed to fully exploiting semantic resources. It employs the ontological knowledge not only as lexical support for disambiguating terms and deriving their sense inventory, but also to classify documents in topic categories. Specifically, our work relates to apply two corpus-based thesauri (i.e. WordNet and WordNet Domains) for selecting the correct sense of words in a document while utilizing domain names for classification purposes. Experiments presented show how our approach performs well in classifying a large corpus of documents. A key part of the paper is the discussion of important aspects related to the use of surrounding words and different methods for word sense disambiguatio