Flexible protein folding by ant colony optimization

Protein structure prediction is one of the most challenging topics in bioinformatics. As the protein structure is found to be closely related to its functions, predicting the folding structure of a protein to judge its functions is meaningful to the humanity. This chapter proposes a flexible ant colony (FAC) algorithm for solving protein folding problems (PFPs) based on the hydrophobic-polar (HP) square lattice model. Different from the previous ant algorithms for PFPs, the pheromones in the proposed algorithm are placed on the arcs connecting adjacent squares in the lattice. Such pheromone placement model is similar to the one used in the traveling salesmen problems (TSPs), where pheromones are released on the arcs connecting the cities. Moreover, the collaboration of effective heuristic and pheromone strategies greatly enhances the performance of the algorithm so that the algorithm can achieve good results without local search methods. By testing some benchmark two-dimensional hydrophobic-polar (2D-HP) protein sequences, the performance shows that the proposed algorithm is quite competitive compared with some other well-known methods for solving the same protein folding problems

Memory-based immigrants for genetic algorithms in dynamic environments

Copyright @ 2005 ACMInvestigating and enhancing the performance of genetic algorithms in dynamic environments have attracted a growing interest from the community of genetic algorithms in recent years. This trend reflects the fact that many real world problems are actually dynamic, which poses serious challenge to traditional genetic algorithms. Several approaches have been developed into genetic algorithms for dynamic optimization problems. Among these approches, random immigrants and memory schemes have shown to be beneficial in many dynamic problems. This paper proposes a hybrid memory and random immigrants scheme for genetic algorithms in dynamic environments. In the hybrid scheme, the best solution in memory is retrieved and acts as the base to create random immigrants to replace the worst individuals in the population. In this way, not only can diversity be maintained but it is done more efficiently to adapt the genetic algorithm to the changing environment. The experimental results based on a series of systematically constructed dynamic problems show that the proposed memory based immigrants scheme efficiently improves the performance of genetic algorithms in dynamic environments

Population-based incremental learning with memory scheme for changing environments

Copyright @ 2005 ACMIn recent years there has been a growing interest in studying evolutionary algorithms for dynamic optimization problems due to its importance in real world applications. Several approaches have been developed, such as the memory scheme. This paper investigates the application of the memory scheme for population-based incremental learning (PBIL) algorithms, a class of evolutionary algorithms, for dynamic optimization problems. A PBIL-specific memory scheme is proposed to improve its adaptability in dynamic environments. In this memory scheme the working probability vector is stored together with the best sample it creates in the memory and is used to reactivate old environments when change occurs. Experimental study based on a series of dynamic environments shows the efficiency of the memory scheme for PBILs in dynamic environments. In this paper, the relationship between the memory scheme and the multipopulation scheme for PBILs in dynamic environments is also investigated. The experimental results indicate a negative interaction of the multi-population scheme on the memory scheme for PBILs in the dynamic test environments

Edge Potential Functions (EPF) and Genetic Algorithms (GA) for Edge-Based Matching of Visual Objects

Edges are known to be a semantically rich representation of the contents of a digital image. Nevertheless, their use in practical applications is sometimes limited by computation and complexity constraints. In this paper, a new approach is presented that addresses the problem of matching visual objects in digital images by combining the concept of Edge Potential Functions (EPF) with a powerful matching tool based on Genetic Algorithms (GA). EPFs can be easily calculated starting from an edge map and provide a kind of attractive pattern for a matching contour, which is conveniently exploited by GAs. Several tests were performed in the framework of different image matching applications. The results achieved clearly outline the potential of the proposed method as compared to state of the art methodologies. (c) 2007 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works

Local search: A guide for the information retrieval practitioner

There are a number of combinatorial optimisation problems in information retrieval in which the use of local search methods are worthwhile. The purpose of this paper is to show how local search can be used to solve some well known tasks in information retrieval (IR), how previous research in the field is piecemeal, bereft of a structure and methodologically flawed, and to suggest more rigorous ways of applying local search methods to solve IR problems. We provide a query based taxonomy for analysing the use of local search in IR tasks and an overview of issues such as fitness functions, statistical significance and test collections when conducting experiments on combinatorial optimisation problems. The paper gives a guide on the pitfalls and problems for IR practitioners who wish to use local search to solve their research issues, and gives practical advice on the use of such methods. The query based taxonomy is a novel structure which can be used by the IR practitioner in order to examine the use of local search in IR

Protein folding in hydrophobic-polar lattice model: a flexible ant colony optimization approach

This paper proposes a flexible ant colony (FAC) algorithm for solving protein folding problems based on the hydrophobic-polar square lattice model. Collaborations of novel pheromone and heuristic strategies in the proposed algorithm make it more effective in predicting structures of proteins compared with other state-of-the-art algorithms

Easy over Hard: A Case Study on Deep Learning

While deep learning is an exciting new technique, the benefits of this method need to be assessed with respect to its computational cost. This is particularly important for deep learning since these learners need hours (to weeks) to train the model. Such long training time limits the ability of (a)~a researcher to test the stability of their conclusion via repeated runs with different random seeds; and (b)~other researchers to repeat, improve, or even refute that original work. For example, recently, deep learning was used to find which questions in the Stack Overflow programmer discussion forum can be linked together. That deep learning system took 14 hours to execute. We show here that applying a very simple optimizer called DE to fine tune SVM, it can achieve similar (and sometimes better) results. The DE approach terminated in 10 minutes; i.e. 84 times faster hours than deep learning method. We offer these results as a cautionary tale to the software analytics community and suggest that not every new innovation should be applied without critical analysis. If researchers deploy some new and expensive process, that work should be baselined against some simpler and faster alternatives.Comment: 12 pages, 6 figures, accepted at FSE201