A practical approach to feature selection
ML92 Proceedings of the ninth international workshop on Machine learning
Machine Learning
Analysis of the Functional Block Involved in the Design of Radial Basis Function Networks
Neural Processing Letters
Margin based feature selection - theory and algorithms
ICML '04 Proceedings of the twenty-first international conference on Machine learning
Probability Estimates for Multi-class Classification by Pairwise Coupling
The Journal of Machine Learning Research
GI '05 Proceedings of Graphics Interface 2005
Kernel methods for predicting protein--protein interactions
Bioinformatics
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Predictive Integration of Gene Ontology-Driven Similarity and Functional Interactions
ICDMW '06 Proceedings of the Sixth IEEE International Conference on Data Mining - Workshops
An assessment of the uses of homologous interactions
Bioinformatics
Computers in Biology and Medicine
Computers in Biology and Medicine
IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics
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In modern proteomics, prediction of protein-protein interactions (PPIs) is a key research line, as these interactions take part in most essential biological processes. In this paper, a new approach is proposed to PPI data classification based on the extraction of genomic and proteomic information from well-known databases and the incorporation of semantic measures. This approach is carried out through the application of data mining techniques and provides very accurate models with high levels of sensitivity and specificity in the classification of PPIs. The well-known support vector machine paradigm is used to learn the models, which will also return a new confidence score which may help expert researchers to filter out and validate new external PPIs. One of the most-widely analyzed organisms, yeast, will be studied. We processed a very high-confidence dataset by extracting up to 26 specific features obtained from the chosen databases, half of them calculated using two new similarity measures proposed in this paper. Then, by applying a filter-wrapper algorithm for feature selection, we obtained a final set composed of the eight most relevant features for predicting PPIs, which was validated by a ROC analysis. The prediction capability of the support vector machine model using these eight features was tested through the evaluation of the predictions obtained in a set of external experimental, computational, and literature-collected datasets.