BackgroundAnalysis of gene expression data in terms of a priori-defined gene sets has recently received significant attention as this approach typically yields more compact and interpretable results than those produced by traditional methods that rely on individual genes. The set-level strategy can also be adopted with similar benefits in predictive classification tasks accomplished with machine learning algorithms. Initial studies into the predictive performance of set-level classifiers have yielded rather controversial results. The goal of this study is to provide a more conclusive evaluation by testing various components of the set-level framework within a large collection of machine learning experiments.ResultsGenuine curated gene sets constitute better features for classification than sets assembled without biological relevance. For identifying the best gene sets for classification, the Global test outperforms the gene-set methods GSEA and SAM-GS as well as two generic feature selection methods. To aggregate expressions of genes into a feature value, the singular value decomposition (SVD) method as well as the SetSig technique improve on simple arithmetic averaging. Set-level classifiers learned with 10 features constituted by the Global test slightly outperform baseline gene-level classifiers learned with all original data features although they are slightly less accurate than gene-level classifiers learned with a prior feature-selection step.ConclusionSet-level classifiers do not boost predictive accuracy, however, they do achieve competitive accuracy if learned with the right combination of ingredients.AvailabilityOpen-source, publicly available software was used for classifier learning and testing. The gene expression datasets and the gene set database used are also publicly available. The full tabulation of experimental results is available at http://ida.felk.cvut.cz/CESLT.

The adequate management of scientific workflow applications strongly depends on the availability of accurate performance models of sub-tasks. Numerous approaches use machine learning to generate such models autonomously, thus alleviating the human effort associated to this process. However, these standalone models may lack robustness, leading to a decay on the quality of information provided to workflow systems on top. This paper presents a novel approach for learning ensemble prediction models of tasks runtime. The ensemble-learning method entitled bootstrap aggregating (bagging) is used to produce robust ensembles of M5P regression trees of better predictive performance than could be achieved by standalone models. Our approach has been tested on gene expression analysis workflows. The results show that the ensemble method leads to significant prediction-error reductions when compared with learned standalone models. This is the first initiative using ensemble learning for generating performance prediction models. These promising results encourage further research in this direction.

No abstract

Abstract. We describe a statistical relational learning framework called Gaussian Logic capable to work efficiently with combinations of relational and numerical data. The framework assumes that, for a fixed relational structure, the numerical data can be modelled by a multivariate normal distribution. We demonstrate how the Gaussian Logic framework can be applied to predictive classification problems. In experiments, we first show an application of the framework for the prediction of DNAbinding propensity of proteins. Next, we show how the Gaussian Logic framework can be used to find motifs describing highly correlated gene groups in gene-expression data which are then used in a set-level-based classification method.

No abstract