Abstract
Motivated by applications in cancer genomics and following the work of Hajirasouliha and Raphael (WABI 2014), Hujdurović 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. Hujdurović 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.
We give new formulations of the two problems, showing that the problems are equivalent to two optimization problems on branchings in a derived directed acyclic graph. Building on these formulations, we obtain new results on the two problems, including: (i) a strengthening of the heuristic by Hujdurović et al. via a new min-max result in digraphs generalizing Dilworth’s theorem, (ii) APX-hardness results for both problems, (iii) two approximation algorithms for the MCRS problem, and (iv) a 2-approximation algorithm for the MDCRS problem.
This work is supported in part by the Slovenian Research Agency (I0-0035, research program P1-0285 and research projects N1-0032, J1-5433, J1-6720, J1-6743, and J1-7051) and by the Academy of Finland (grant 274977).
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Hujdurović, A., Husić, E., Milanič, M., Rizzi, R., Tomescu, A.I. (2017). The Minimum Conflict-Free Row Split Problem Revisited. In: Bodlaender, H., Woeginger, G. (eds) Graph-Theoretic Concepts in Computer Science. WG 2017. Lecture Notes in Computer Science(), vol 10520. Springer, Cham. https://doi.org/10.1007/978-3-319-68705-6_23
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