Using real-valued metaclassifiers to integrate binding site predictions

Abstract

Currently the best algorithms for transcription factor binding site prediction are severely limited in accuracy. There is good reason to believe that predictions from these different classes of algorithms could be used in conjunction to improve the quality of predictions. In this paper, we apply single layer networks, rules sets and support vector machines on predictions from 12 key real valued algorithms. Furthermore, we use a ‘window’ of consecutive results in the input vector in order to contextualise the neighbouring results. We improve the classification result with the aid of under- and over- sampling techniques. We find that support vector machines outperform each of the original individual algorithms and the other classifiers employed in this work. In particular they have a better tradeoff between recall and precision.