Integrating binding site predictions using meta classification methods
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 and support vector machines on predictions from 12 key algorithms. Furthermore, we use a ‘window’ of consecutive results for the input vectors in order to contextualise the neighbouring results. Moreover, we improve the classification result with the aid of under- and over- sampling techniques. We find that by integrating 12 base algorithms, support vector machines and single layer networks can give better binding site predictions.
KeywordsSupport Vector Machine Minority Class Site Prediction Imbalanced Dataset Window Input
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