The Maximum Colorful Arborescence problem parameterized by the structure of its color hierarchy graph

Let G=(V,A) be a vertex-colored arc-weighted directed acyclic graph (DAG) rooted in some vertex r, and let H be its color hierarchy graph, defined as follows: V(H) is the color set C of G, and an arc from color c to color c' exists in H if there is an arc in G from a vertex of color c to a vertex of color c'. In this paper, we study the MAXIMUM COLORFUL ARBORESCENCE problem (or MCA), which takes as input a DAG G with the additional constraint that H is also a DAG, and aims at finding in G an arborescence rooted in r, of maximum weight, and in which no color appears more than once. The MCA problem is motivated by the inference of unknown metabolites from mass spectrometry experiments. However, whereas the problem has been studied for roughly ten years, the crucial property that H is necessarily a DAG has only been pointed out and exploited very recently. In this paper, we further investigate MCA under this new light, by providing algorithmic results for the problem, with a specific focus on fixed-parameterized tractability (FPT) issues, and relatively to different structural parameters of H. In particular, we provide an O*(3^{nhs}) time algorithm for solving MCA, where nhs is the number of vertices of indegree at least two in H, thereby improving the O*(3^{|C|}) algorithm from [Böcker et al. 2008]. We also prove that MCA is W[2]-hard relatively to the treewidth Ht of H, and further show that it is FPT relatively to Ht+lc, where lc = |V| - |C|.