Abstract
Motivated by applications in cancer genomics and following the work of Hajirasouliha and Raphael (WABI 2014), Hujdurovic et al. (IEEE TCBB, to appear) introduced the minimum conflict-free row split (MCRS) problem: split each row of a given binary matrix into a bitwise OR of a set of rows so that the resulting matrix corresponds to a perfect phylogeny and has the minimum number of rows among all matrices with this property. Hajirasouliha and Raphael also proposed the study of a similar problem, referred to as the minimum distinct conflict-free row split (MDCRS) problem, in which the task is to minimize the number of distinct rows of the resulting matrix. Hujdurovic et al. proved that both problems are NP-hard, gave a related characterization of transitively orientable graphs, and proposed a polynomial-time heuristic algorithm for the MCRS problem based on coloring cocomparability graphs.
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