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Modeling of Compound Profiling Experiments Using Support Vector Machines
Author(s) -
Balfer Jenny,
Heikamp Kathrin,
Laufer Stefan,
Bajorath Jürgen
Publication year - 2014
Publication title -
chemical biology and drug design
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.59
H-Index - 77
eISSN - 1747-0285
pISSN - 1747-0277
DOI - 10.1111/cbdd.12294
Subject(s) - support vector machine , profiling (computer programming) , bayesian probability , artificial intelligence , pattern recognition (psychology) , false positive rate , naive bayes classifier , computer science , data mining , machine learning , computational biology , biology , operating system
Profiling of compounds against target families has become an important approach in pharmaceutical research for the identification of hits and analysis of selectivity and promiscuity patterns. We report on modeling of profiling experiments involving 429 potential inhibitors and a panel of 24 different kinases using support vector machine ( SVM ) techniques and naïve Bayesian classification. The experimental matrix contained many different activity profiles. SVM predictions achieved overall high accuracy due to consistently low false‐positive and consistently high true‐negative rates. However, predictions for promiscuous inhibitors were affected by false‐negative rates. Combined target‐based SVM classifiers reached or exceeded the performance of SVM profile prediction methods and were superior to Bayesian classification. The classifiers displayed different prediction characteristics including diverse combinations of false‐positive and true‐negative rates. Predicted and experimentally observed compound activity profiles were compared in detail, revealing activity patterns modeled with different accuracy.