Abstract
Virtual screening (VS) is widely used during computational drug discovery to reduce costs. Chemogenomics-based virtual screening (CGBVS) can be used to predict new compound-protein interactions (CPIs) from known CPI network data using several methods, including machine learning and data mining. Although CGBVS facilitates highly efficient and accurate CPI prediction, it has poor performance for prediction of new compounds for which CPIs are unknown. The pairwise kernel method (PKM) is a state-of-the-art CGBVS method and shows high accuracy for prediction of new compounds. In this study, on the basis of link mining, we improved the PKM by combining link indicator kernel (LIK) and chemical similarity and evaluated the accuracy of these methods. The proposed method obtained an average area under the precision-recall curve (AUPR) value of 0.562, which was higher than that achieved by the conventional Gaussian interaction profile (GIP) method (0.425), and the calculation time was only increased by a few percent.
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Notes
- 1.
Let \( k:X \times X \to {\mathbb{R}} \) be a positive definite kernel and \( f:X \to {\mathbb{R}} \) be an arbitrary function. Then, the kernel \( k^{{\prime }} ({\mathbf{x}},{\mathbf{y}}) = f({\mathbf{x}})k({\mathbf{x}},{\mathbf{y}})f({\mathbf{y}})\;\;({\mathbf{x}},{\mathbf{y}} \in X) \) is also positive definite.
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Acknowledgments
This work was partially supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (grant numbers 24240044 and 15K16081), and Core Research for Evolutional Science and Technology (CREST) “Extreme Big Data” (grant number JPMJCR1303) from the Japan Science and Technology Agency (JST).
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Ohue, M., Yamazaki, T., Ban, T., Akiyama, Y. (2017). Link Mining for Kernel-Based Compound-Protein Interaction Predictions Using a Chemogenomics Approach. In: Huang, DS., Jo, KH., Figueroa-García, J. (eds) Intelligent Computing Theories and Application. ICIC 2017. Lecture Notes in Computer Science(), vol 10362. Springer, Cham. https://doi.org/10.1007/978-3-319-63312-1_48
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