Evolutionary Algorithms with Self-adjusting Asymmetric Mutation

Evolutionary Algorithms (EAs) and other randomized search heuristics are often considered as unbiased algorithms that are invariant with respect to different transformations of the underlying search space. However, if a certain amount of domain knowledge is available the use of biased search operators in EAs becomes viable. We consider a simple (1+1) EA for binary search spaces and analyze an asymmetric mutation operator that can treat zero- and one-bits differently. This operator extends previous work by Jansen and Sudholt (ECJ 18(1), 2010) by allowing the operator asymmetry to vary according to the success rate of the algorithm. Using a self-adjusting scheme that learns an appropriate degree of asymmetry, we show improved runtime results on the class of functions OneMax$_a$ describing the number of matching bits with a fixed target $a\in\{0,1\}^n$.Comment: 16 pages. An extended abstract of this paper will be published in the proceedings of PPSN 202

Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

<p>Abstract</p> <p>Background</p> <p>Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights.</p> <p>Methods</p> <p>We generated a series of predicted models (decoys) of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys.</p> <p>Results and conclusion</p> <p>We found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD) to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å) as <it>fpair </it>and propose to use it for evaluation of the accuracy of multiple protein docking.</p