1 research outputs found
A QUBO formulation for the Tree Containment problem
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that
are widely used to represent the evolutionary relationships between entities
such as species, languages, cancer cells, and viruses. To reconstruct and
analyze phylogenetic networks, the problem of deciding whether or not a given
rooted phylogenetic network embeds a given rooted phylogenetic tree is of
recurring interest. This problem, formally know as Tree Containment, is
NP-complete in general and polynomial-time solvable for certain classes of
phylogenetic networks. In this paper, we connect ideas from quantum computing
and phylogenetics to present an efficient Quadratic Unconstrained Binary
Optimization formulation for Tree Containment in the general setting. For an
instance (N,T) of Tree Containment, where N is a phylogenetic network with n_N
vertices and T is a phylogenetic tree with n_T vertices, the number of logical
qubits that are required for our formulation is O(n_N n_T).Comment: final version accepted for publication in Theoretical Computer
Scienc