ViCTree: an automated framework for taxonomic classification from protein sequences

Motivation: The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. Results: To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. Availability: ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/

Cooperative co-evolution of GA-based classifiers based on input increments

Genetic algorithms (GAs) have been widely used as soft computing techniques in various applications, while cooperative co-evolution algorithms were proposed in the literature to improve the performance of basic GAs. In this paper, a new cooperative co-evolution algorithm, namely ECCGA, is proposed in the application domain of pattern classification. Concurrent local and global evolution and conclusive global evolution are proposed to improve further the classification performance. Different approaches of ECCGA are evaluated on benchmark classification data sets, and the results show that ECCGA can achieve better performance than the cooperative co-evolution genetic algorithm and normal GA. Some analysis and discussions on ECCGA and possible improvement are also presented

Discovering predictive variables when evolving cognitive models

A non-dominated sorting genetic algorithm is used to evolve models of learning from different theories for multiple tasks. Correlation analysis is performed to identify parameters which affect performance on specific tasks; these are the predictive variables. Mutation is biased so that changes to parameter values tend to preserve values within the population's current range. Experimental results show that optimal models are evolved, and also that uncovering predictive variables is beneficial in improving the rate of convergence

An intelligent system for risk classification of stock investment projects

The proposed paper demonstrates that a hybrid fuzzy neural network can serve as a risk classifier of stock investment projects. The training algorithm for the regular part of the network is based on bidirectional incremental evolution proving more efficient than direct evolution. The approach is compared with other crisp and soft investment appraisal and trading techniques, while building a multimodel domain representation for an intelligent decision support system. Thus the advantages of each model are utilised while looking at the investment problem from different perspectives. The empirical results are based on UK companies traded on the London Stock Exchange