Searching for discrimination rules in protease proteolytic cleavage activity using genetic programming with a min-max scoring function

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@Article{ZhengRongYang:2003:BS,

• author = "Zheng Rong Yang and Rebecca Thomson and T. Charles Hodgman and Jonathan Dry and Austin K. Doyle and Ajit Narayanan and XiKun Wu",
• title = "Searching for discrimination rules in protease proteolytic cleavage activity using genetic programming with a min-max scoring function",
• journal = "Biosystems",
• year = "2003",
• volume = "72",
• number = "1-2",
• pages = "159--176",
• month = nov,
• keywords = "genetic algorithms, genetic programming, Amino acid similarity matrix, The reverse Polish notation, Proteolytic cleavage analysis",
• URL = "http://www.sciencedirect.com/science/article/B6T2K-49N9DN6-2/2/0d63ebb7904ac33ae0d20ce4f6477a57",
• DOI = "doi:10.1016/S0303-2647(03)00141-2",
• abstract = "We present an algorithm which is able to extract discriminant rules from oligopeptides for protease proteolytic cleavage activity prediction. The algorithm is developed using previous genetic programming. Three important components in the algorithm are a min-max scoring function, the reverse Polish notation (RPN) and the use of minimum description length. The min-max scoring function is developed using amino acid similarity matrices for measuring the similarity between an oligopeptide and a rule, which is a complex algebraic equation of amino acids rather than a simple pattern sequence. The Fisher ratio is then calculated on the scoring values using the class label associated with the oligopeptides. The discriminant ability of each rule can therefore be evaluated. The use of RPN makes the evolutionary operations simpler and therefore reduces the computational cost. To prevent overfitting, the concept of minimum description length is used to penalize over-complicated rules. A fitness function is therefore composed of the Fisher ratio and the use of minimum description length for an efficient evolutionary process. In the application to four protease datasets (Trypsin, Factor Xa, Hepatitis C Virus and HIV protease cleavage site prediction), our algorithm is superior to C5, a conventional method for deriving decision trees.",

}

Genetic Programming entries for Zheng Rong Yang Rebecca Thomson T Charles Hodgman Jonathan Dry Austin K Doyle Ajit Narayanan XiKun Wu

Citations