BeamGA Median: A Hybrid Heuristic Search Framework
Badr, Ghada . 2016
BeamGA is a general hybrid heuristic framework that can be used to solve the median problem in comparative genomics, where any distance function can be used. It starts with a heuristic search approach (local beam search) in order to generate a number of solutions. Then a Genetic Algorithm (GA) is applied to refine the solutions. It considers true biological evolution scenarios by applying the concept of common intervals during the GA optimization process.
Motivation: The negative binomial distribution has been shown to be a good model for counts data from both bulk and single-cell RNA-sequencing (RNA-seq). Gaussian process (GP) regression provides…
The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation…
BeamGA is a general hybrid heuristic framework that can be used to solve the median problem in comparative genomics, where any distance function can be used. It starts with a heuristic search…