Abstract: Predicting protein-protein interactions represent a key step in understanding proteins functions. This is due to the fact that proteins usually work in context of other proteins and rarely function alone. Machine learning techniques have been applied to predict protein-protein interactions. However, most of these techniques address this problem as a binary classification problem. Although it is easy to get a dataset of interacting proteins as positive examples, there are no experimentally confirmed non-interacting proteins to be considered as negative examples. Therefore, in this paper we solve this problem as a one-class classification problem using one-class support vector machines (SVM). Using only positive examples (interacting protein pairs) in training phase, the one-class SVM achieves accuracy of about 80%. These results imply that protein-protein interaction can be predicted using one-class classifier with comparable accuracy to the binary classifiers that use artificially constructed negative examples.
Abstract: Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.
Abstract: The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein interactions. However, in a recent study, a research group has reported a very high accuracy of 94% using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80%. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.
Abstract: Understanding proteins functions is a major goal in
the post-genomic era. Proteins usually work in context of other
proteins and rarely function alone. Therefore, it is highly relevant to
study the interaction partners of a protein in order to understand its
function. Machine learning techniques have been widely applied to
predict protein-protein interactions. Kernel functions play an
important role for a successful machine learning technique. Choosing
the appropriate kernel function can lead to a better accuracy in a
binary classifier such as the support vector machines. In this paper,
we describe a Bayesian kernel for the support vector machine to
predict protein-protein interactions. The use of Bayesian kernel can
improve the classifier performance by incorporating the probability
characteristic of the available experimental protein-protein
interactions data that were compiled from different sources. In
addition, the probabilistic output from the Bayesian kernel can assist
biologists to conduct more research on the highly predicted
interactions. The results show that the accuracy of the classifier has
been improved using the Bayesian kernel compared to the standard
SVM kernels. These results imply that protein-protein interaction can
be predicted using Bayesian kernel with better accuracy compared to
the standard SVM kernels.