Ejection chains, reference structures and alternating path methods for traveling salesman problems
Discrete Applied Mathematics - Special volume: first international colloquium on graphs and optimization (GOI), 1992
DNA sequence design using templates
New Generation Computing
Stochastic Local Search Algorithms for DNA Word Design
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
On Template Method for DNA Sequence Design
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
An Ejection Chain Approach for the Generalized Assignment Problem
INFORMS Journal on Computing
Hairpin-based state machine and conformational addressing: Design and experiment
Natural Computing: an international journal
Linear constructions for DNA codes
Theoretical Computer Science
Hybrid randomised neighbourhoods improve stochastic local search for DNA code design
AI'03 Proceedings of the 16th Canadian society for computational studies of intelligence conference on Advances in artificial intelligence
Dynamic neighborhood searches for thermodynamically designing DNA sequence
DNA13'07 Proceedings of the 13th international conference on DNA computing
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We propose a local-search based algorithm to design DNA sequence sets that satisfy several combinatorial constraints about hamming-distance criteria. To deal with the constraints in the local search, we adopt elaborate (and dynamic) neighborhood search frameworks called the Variable Neighborhood Search (VNS) and the Variable Depth Search (VDS). Although our algorithm can deal with many types of hamming distance-based constraints and is easy to extend (e.g., also applicable for other constraints), in computational experiments, we succeeded in generating better sequence sets than the ones generated by exiting methods of more specified constraints.