Parallel branch-and-bound approach with MPI technology in inferring chemical compounds with path frequency

作者: Kun-Ming Yu , Chun-Yuan Lin , Hui-Yuan Wang , Chuan Yi Tang , Jiayi Zhou

DOI: 10.1109/GRC.2009.5255025

关键词: Statistical classificationFeature vectorBranch and boundComputationAlgorithmAlgorithm designKernel (statistics)Feature (computer vision)Kernel methodComputer science

摘要: Drug design is the approach of finding drugs by using computational tools. When designing a new drug, structure drug molecule can be modeled classification potential chemical compounds. Kernel Methods have been successfully used in classifying Frequency labeled paths has proposed to map compounds into feature order classify characteristics target In this study, we an algorithm based on method via parallel computing technology reduce computation time. This less constrain timing allows us aim at back tracking full scheme all possible pre-images, regardless their difference molecular structure, only if they shared with same vector. Our modified BB-CIPF and MPI The experimental results show that our algorithms time effectively for compound inference problem.

参考文章(18)
Raffaele Scapellato, Josef Lauri, Topics in Graph Automorphisms and Reconstruction ,(2003)
Gökhan H. Bakır, Alexander Zien, Koji Tsuda, Learning to Find Graph Pre-images joint pattern recognition symposium. pp. 253- 261 ,(2004) , 10.1007/978-3-540-28649-3_31
Koji Tsuda, Akihiro Inokuchi, Hisashi Kashima, Marginalized kernels between labeled graphs international conference on machine learning. pp. 321- 328 ,(2003)
TATSUYA AKUTSU, DAIJI FUKAGAWA, INFERRING A CHEMICAL STRUCTURE FROM A FEATURE VECTOR BASED ON FREQUENCY OF LABELED PATHS AND SMALL FRAGMENTS asia-pacific bioinformatics conference. pp. 165- 174 ,(2007) , 10.1142/9781860947995_0019
Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert, Graph Kernels for Molecular Structure−Activity Relationship Analysis with Support Vector Machines Journal of Chemical Information and Modeling. ,vol. 45, pp. 939- 951 ,(2005) , 10.1021/CI050039T
Osamu Maruyama, Satoru Miyano, Inferring a tree from walks Theoretical Computer Science. ,vol. 161, pp. 289- 300 ,(1996) , 10.1016/0304-3975(95)00156-5
Tatsuya Akutsu, Daiji Fukagawa, Jesper Jansson, Kunihiko Sadakane, Inferring a graph from path frequency Discrete Applied Mathematics. ,vol. 160, pp. 1416- 1428 ,(2012) , 10.1016/J.DAM.2012.02.002
C. John Harris, Adrian P. Stevens, Chemogenomics: structuring the drug discovery process to gene families. Drug Discovery Today. ,vol. 11, pp. 880- 888 ,(2006) , 10.1016/J.DRUDIS.2006.08.013
William Gropp, Ewing Lusk, Nathan Doss, Anthony Skjellum, A high-performance, portable implementation of the MPI message passing interface standard parallel computing. ,vol. 22, pp. 789- 828 ,(1996) , 10.1016/0167-8191(96)00024-5