Publications:Why neural networks should not be used for HIV-1 protease cleavage site prediction

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Title Why neural networks should not be used for HIV-1 protease cleavage site prediction
Author Thorsteinn Rögnvaldsson and Liwen You
Year 2004
PublicationType Journal Paper
Journal Bioinformatics
HostPublication
Conference
DOI http://dx.doi.org/10.1093/bioinformatics/bth144
Diva url http://hh.diva-portal.org/smash/record.jsf?searchId=1&pid=diva2:237404
Abstract Several papers have been published where non-linear machine learning algorithms, e.g. artificial neural networks, support vector machines and decision trees, have been used to model the specificity of the HIV-1 protease and extract specificity rules. We show that the dataset used in these studies is linearly separable and that it is a misuse of nonlinear classifiers to apply them to this problem. The best solution on this dataset is achieved using a linear classifier like the simple perceptron or the linear support vector machine, and it is straightforward to extract rules from these linear models. We identify key residues in peptides that are efficiently cleaved by the HIV-1 protease and list the most prominent rules, relating them to experimental results for the HIV-1 protease. Motivation: Understanding HIV-1 protease specificity is important when designing HIV inhibitors and several different machine learning algorithms have been applied to the problem. However, little progress has been made in understanding the specificity because nonlinear and overly complex models have been used. Results: We show that the problem is much easier than what has previously been reported and that linear classifiers like the simple perceptron or linear support vector machines are at least as good predictors as nonlinear algorithms. We also show how sets of specificity rules can be generated from the resulting linear classifiers.