title: Supervised feature ranking using a genetic algorithm optimized artificial neural network.
abstract: A genetic algorithm optimized artificial neural network GNW has been designed to rank features for two diversified multivariate data sets. The dimensions of these data sets are 85x24 and 62x25 for 24 or 25 molecular descriptors being computed for 85 matrix metalloproteinase-1 inhibitors or 62 hepatitis C virus NS3 protease inhibitors, respectively. Each molecular descriptor computed is treated as a feature and input into an input layer node of the artificial neural network. To optimize the artificial neural network by the genetic algorithm, each interconnected weight between input and hidden or between hidden and output layer nodes is binary encoded as a 16 bits string in a chromosome, and the chromosome is evolved by crossover and mutation operations. Each input layer node and its associated weights of the trained GNW are systematically omitted once (the self-depleted weights), and the corresponding weight adjustments due to the omission are computed to keep the overall network behavior unchanged. The primary feature ranking index defined as the sum of self-depleted weights and the corresponding weight adjustments computed is found capable of separating good from bad features for some artificial data sets of known feature rankings tested. The final feature indexes used to rank the data sets are computed as a sum of the weighted frequency of each feature being ranked in a particular rank for each data set being partitioned into numerous clusters. The two data sets are also clustered by a standard K-means method and trained by a support vector machine (SVM) for feature ranking using the computed F-scores as feature ranking index. It is found that GNW outperforms the SVM method on three artificial as well as the matrix metalloproteinase-1 inhibitor data sets studied. A clear-cut separation of good from bad features is offered by the GNW but not by the SVM method for a feature pool of known feature ranking.
authors.affiliation: Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC. thlin@life.nthu.edu.tw
authors.forename: Thy-Hou
authors.initials: TH
authors.lastname: Lin
authors.forename: Shih-Hau
authors.initials: SH
authors.lastname: Chiu
authors.forename: Keng-Chang
authors.initials: KC
authors.lastname: Tsai
mesh_terms: D000465:Algorithms; D061965:Matrix Metalloproteinase Inhibitors; D016571:Neural Networks, Computer; D011480:Protease Inhibitors / Q000737:chemistry / Q000494:pharmacology; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D061965:Matrix Metalloproteinase Inhibitors; D011480:Protease Inhibitors; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases