Chapter

Pattern Recognition in Bioinformatics

Volume 4774 of the series Lecture Notes in Computer Science pp 84-97

Generalized Schemata Theorem Incorporating Twin Removal for Protein Structure Prediction

  • Md Tamjidul HoqueAffiliated withGippsland School of Information Technology (GSIT), Monash University, Churchill VIC 3842
  • , Madhu ChettyAffiliated withGippsland School of Information Technology (GSIT), Monash University, Churchill VIC 3842
  • , Laurence S. DooleyAffiliated withGippsland School of Information Technology (GSIT), Monash University, Churchill VIC 3842

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Abstract

The schemata theorem, on which the working of Genetic Algorithm (GA) is based in its current form, has a fallacious selection procedure and incomplete crossover operation. In this paper, generalization of the schemata theorem has been provided by correcting and removing these limitations. The analysis shows that similarity growth within GA population is inherent due to its stochastic nature. While the stochastic property helps in GA’s convergence. The similarity growth is responsible for stalling and becomes more prevalent for hard optimization problem like protein structure prediction (PSP). While it is very essential that GA should explore the vast and complicated search landscape, in reality, it is often stuck in local minima. This paper shows that, removal of members of population having certain percentage of similarity would keep GA perform better, balancing and maintaining convergence property intact as well as avoids stalling.

Keywords

Schemata theorem twin removal protein structure prediction similarity in population hard optimization problem