Graph Motif Problems Parameterized by Dual
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Let G=(V,E) be a vertex-colored graph, where C is the set of colors used to color V. The Graph Motif (or GM) problem takes as input G, a multiset M of colors built from C, and asks whether there is a subset S⊆ V such that (i) G[S] is connected and (ii) the multiset of colors obtained from S equals M. The Colorful Graph Motif (or CGM) problem is the special case of GM in which M is a set, and the List-Colored Graph Motif (or LGM) problem is the extension of GM in which each vertex v of V may choose its color from a list L(v)⊆ C of colors. We study the three problems GM, CGM, and LGM, parameterized by the dual parameter ℓ:=|V|-|M|. For general graphs, we show that, assuming the strong exponential time hypothesis, CGM has no (2-ϵ)^ℓ· |V|^O(1)-time algorithm, which implies that a previous algorithm, running in O(2^ℓ· |E|) time is optimal [Betzler et al., IEEE/ACM TCBB 2011]. We also prove that LGM is W[1]-hard with respect to ℓ even if we restrict ourselves to lists of at most two colors. If we constrain the input graph to be a tree, then we show that GM can be solved in O(3^ℓ· |V|) time but admits no polynomial-size problem kernel, while CGM can be solved in O(√(2)^ℓ + |V|) time and admits a polynomial-size problem kernel.
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