Using MPI: portable parallel programming with the message-passing interface
Using MPI: portable parallel programming with the message-passing interface
Estimation of Distribution Algorithms: A New Tool for Evolutionary Computation
Estimation of Distribution Algorithms: A New Tool for Evolutionary Computation
String barcoding: uncovering optimal virus signatures
Proceedings of the sixth annual international conference on Computational biology
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
The Design of Innovation: Lessons from and for Competent Genetic Algorithms
The Design of Innovation: Lessons from and for Competent Genetic Algorithms
Multiple Objective Optimization with Vector Evaluated Genetic Algorithms
Proceedings of the 1st International Conference on Genetic Algorithms
From Recombination of Genes to the Estimation of Distributions I. Binary Parameters
PPSN IV Proceedings of the 4th International Conference on Parallel Problem Solving from Nature
Bayesian optimization algorithm: from single level to hierarchy
Bayesian optimization algorithm: from single level to hierarchy
Group Testing With DNA Chips: Generating Designs and Decoding Experiments
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Integer linear programming approaches for non-unique probe selection
Discrete Applied Mathematics
Techniques for highly multiobjective optimisation: some nondominated points are better than others
Proceedings of the 9th annual conference on Genetic and evolutionary computation
Non-unique probe selection and group testing
Theoretical Computer Science
Note: On the complexity of non-unique probe selection
Theoretical Computer Science
An Evolutionary Approach to the Non-unique Oligonucleotide Probe Selection Problem
Transactions on Computational Systems Biology X
Bayesian Optimization Algorithm for the Non-unique Oligonucleotide Probe Selection Problem
PRIB '09 Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics
Space pruning monotonic search for the non-unique probe selection problem
International Journal of Bioinformatics Research and Applications
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One of the applications of DNA microarrays is recognizing the presence or absence of different biological components (targets) in a sample. Hence, the quality of the microarrays design which includes selecting short Oligonucleotide sequences (probes) to be affixed on the surface of the microarray becomes a major issue. A good design is the one that contains the minimum possible number of probes while having an acceptable ability in identifying the targets existing in the sample. This paper focuses on the problem of computing the minimal set of probes which is able to identify each target of a sample, referred to as non-unique oligonucleotide probe selection. We present the application of an estimation of distribution algorithm (EDA) named Bayesian optimization algorithm (BOA) to this problem, for the first time. The proposed approach considers integration of BOA and one simple heuristic introduced for the non-unique probe selection problem. The results provided by this approach compare favorably with the state-of-the-art methods in the single target case. While most of the recent research works on this problem has been focusing on the single target case only, we present the application of our method in integration with decoding approach in a multiobjective optimization framework for solving the problem in the case of multiple targets.