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

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

An efficient ant colony system based on receding horizon control for the aircraft arrival sequencing and scheduling problem

The aircraft arrival sequencing and scheduling (ASS) problem is a salient problem in air traffic control (ATC), which proves to be nondeterministic polynomial (NP) hard. This paper formulates the ASS problem in the form of a permutation problem and proposes a new solution framework that makes the first attempt at using an ant colony system (ACS) algorithm based on the receding horizon control (RHC) to solve it. The resultant RHC-improved ACS algorithm for the ASS problem (termed the RHC-ACS-ASS algorithm) is robust, effective, and efficient, not only due to that the ACS algorithm has a strong global search ability and has been proven to be suitable for these kinds of NP-hard problems but also due to that the RHC technique can divide the problem with receding time windows to reduce the computational burden and enhance the solution's quality. The RHC-ACS-ASS algorithm is extensively tested on the cases from the literatures and the cases randomly generated. Comprehensive investigations are also made for the evaluation of the influences of ACS and RHC parameters on the performance of the algorithm. Moreover, the proposed algorithm is further enhanced by using a two-opt exchange heuristic local search. Experimental results verify that the proposed RHC-ACS-ASS algorithm generally outperforms ordinary ACS without using the RHC technique and genetic algorithms (GAs) in solving the ASS problems and offers high robustness, effectiveness, and efficienc

A new sequential covering strategy for inducing classification rules with ant colony algorithms

Ant colony optimization (ACO) algorithms have been successfully applied to discover a list of classification rules. In general, these algorithms follow a sequential covering strategy, where a single rule is discovered at each iteration of the algorithm in order to build a list of rules. The sequential covering strategy has the drawback of not coping with the problem of rule interaction, i.e., the outcome of a rule affects the rules that can be discovered subsequently since the search space is modified due to the removal of examples covered by previous rules. This paper proposes a new sequential covering strategy for ACO classification algorithms to mitigate the problem of rule interaction, where the order of the rules is implicitly encoded as pheromone values and the search is guided by the quality of a candidate list of rules. Our experiments using 18 publicly available data sets show that the predictive accuracy obtained by a new ACO classification algorithm implementing the proposed sequential covering strategy is statistically significantly higher than the predictive accuracy of state-of-the-art rule induction classification algorithms

Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.This work is jointly supported by the FundaciónSéneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants 15290/PI/2010 and 18946/JLI/13, by the Spanish MEC and European Commission FEDER under grant with reference TEC2012-37945-C02-02 and TIN2012-31345, by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). We also thank NVIDIA for hardware donation within UCAM GPU educational and research centers.Ingeniería, Industria y Construcció