Towards predicting Protein-Protein Interactions in novel organisms
by Patrick Shaughnessy, Gary Livingston, Michael V. Graves
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 1, No. 3, 2008

Abstract: Machine learning methods are often used to predict Protein-Protein Interactions (PPI). It is common to develop methods using known PPI from well-characterised reference organisms, drawing from that organism data for inferring a predictive model and evaluating the model. We present evidence that this practice does not give a meaningful indication of the model's performance on genetically distinct organisms. We conclude that this practice cannot be applied to proteins inferred from the genetic sequence of a novel organism for which no PPI data is available, and that there is need for evaluating such methods on organisms distinct from their training organisms.

Online publication date: Wed, 26-Nov-2008

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