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
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
Space pruning monotonic search for the non-unique probe selection problem
International Journal of Bioinformatics Research and Applications
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DNA microarrays are used in order to recognize the presence or absence of different biological components (targets ) in a sample. Therefore, the design of the microarrays which includes selecting short Oligonucleotide sequences (probes ) to be affixed on the surface of the microarray becomes a major issue. 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 presented approach considers integration of BOA and state-of-the-art heuristics introduced for the non-unique probe selection problem. This approach provides results that compare favorably with the state-of-the-art methods. It is also able to provide biologists with more information about the dependencies between the probe sequences of each dataset.