We present new and improved approximation and FPT algorithms for computing rooted and unrooted maximum agreement forests (MAFs) of pairs of phylogenetic trees. Their sizes correspond to the subtree-prune-and-regraft distances and the tree-bisection-and-reconnection distances of the trees, respectively. We also provide the first bounded search tree FPT algorithm for computing rooted maximum acyclic agreement forests (MAAFs) of pairs of phylogenetic trees, whose sizes are the hybridization numbers of these pairs of trees. These distance metrics are essential tools for understanding reticulate evolution.
Two algorithms for computing rooted SPR distances, SPRdist @cite_30 and TreeSAT @cite_28 , express the problem of computing maximum agreement forests as an integer linear program (ILP) and a satisfiability problem (SAT), respectively, and employ efficient ILP and SAT solvers to obtain a solution. SPRdist has been shown to outperform EEEP and Lattrans @cite_30 . Although such algorithms draw on the close scrutiny that has been applied to these problems, experiments show that these algorithms cannot compete with the rooted SPR algorithm presented in this paper @cite_4 .
@cite_30 @cite_28 @cite_4
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We improve on earlier FPT algorithms for computing a rooted maximum agreement forest (MAF) or a maximum acyclic agreement forest (MAAF) of a pair of phylogenetic trees. Their sizes give the subtree-prune-and-regraft (SPR) distance and the hybridization number of the trees, respectively. We introduce new branching rules that reduce the running time of the algorithms from O(3kn) and O(3kn logn) to O(2.42kn) and O(2.42kn logn), respectively. In practice, the speed up may be much more than predicted by the worst-case analysis. We confirm this intuition experimentally by computing MAFs for simulated trees and trees inferred from protein sequence data. We show that our algorithm is orders of magnitude faster and can handle much larger trees and SPR distances than the best previous methods, treeSAT and sprdist. Given an arc-weighted directed graph G = (V, A, spl lscr ) and a pair of nodes s, t, we seek to find an s-t walk of length at most B that maximizes some given function f of the set of nodes visited by the walk. The simplest case is when we seek to maximize the number of nodes visited: this is called the orienteering problem. Our main result is a quasi-polynomial time algorithm that yields an O(log OPT) approximation for this problem when f is a given submodular set function. We then extend it to the case when a node v is counted as visited only if the walk reaches v in its time window [R(v), D(v)]. We apply the algorithm to obtain several new results. First, we obtain an O(log OPT) approximation for a generalization of the orienteering problem in which the profit for visiting each node may vary arbitrarily with time. This captures the time window problem considered earlier for which, even in undirected graphs, the best approximation ratio known [Bansal, (2004)] is O(log sup 2 OPT). The second application is an O(log sup 2 k) approximation for the k-TSP problem in directed graphs (satisfying asymmetric triangle inequality). This is the first non-trivial approximation algorithm for this problem. The third application is an O(log sup 2 k) approximation (in quasi-poly time) for the group Steiner problem in undirected graphs where k is the number of groups. This improves earlier ratios (Garg, ) by a logarithmic factor and almost matches the inapproximability threshold on trees (Halperin and Krauthgamer, 2003). This connection to group Steiner trees also enables us to prove that the problem we consider is hard to approximate to a ratio better than spl Omega (log sup 1- spl epsi OPT), even in undirected graphs. Even though our algorithm runs in quasi-poly time, we believe that the implications for the approximability of several basic optimization problems are interesting. We study approaches for the exact solution of the NP-hard minimum spanning tree problem under conflict constraints. Given a graph (G(V,E) ) and a set (C E E ) of conflicting edge pairs, the problem consists of finding a conflict-free minimum spanning tree, i.e. feasible solutions are allowed to include at most one of the edges from each pair in (C ). The problem was introduced recently in the literature, with several results on its complexity and approximability. Some formulations and both exact and heuristic algorithms were also discussed, but computational results indicate considerably large duality gaps and a lack of optimality certificates for benchmark instances. In this paper, we build on the representation of conflict constraints using an auxiliary conflict graph ( G (E,C) ), where stable sets correspond to conflict-free subsets of (E ). We introduce a general preprocessing method and a branch and cut algorithm using an IP formulation with exponentially sized classes of valid inequalities for both the spanning tree and the stable set polytopes. Encouraging computational results indicate that the dual bounds of our approach are significantly stronger than those previously available, already in the initial LP relaxation, and we are able to provide new feasibility and optimality certificates. We present a general approximation technique for a large class of graph problems. Our technique mostly applies to problems of covering, at minimum cost, the vertices of a graph with trees, cycles or paths satisfying certain requirements. In particular, many basic combinatorial optimization problems fit in this framework, including the shortest path, minimum-cost spanning tree, minimum-weight perfect matching, traveling salesman and Steiner tree problems. Our technique produces approximation algorithms that run in @math time and come within a factor of 2 of optimal for most of these problems. For instance, we obtain a 2-approximation algorithm for the minimum-weight perfect matching problem under the triangle inequality. Our running time of @math time compares favorably with the best strongly polynomial exact algorithms running in @math time for dense graphs. A similar result is obtained for the 2-matching problem and its variants. We also derive the first approximation algorithms for many NP-complete problems, including the non-fixed point-to-point connection problem, the exact path partitioning problem and complex location-design problems. Moreover, for the prize-collecting traveling salesman or Steiner tree problems, we obtain 2-approximation algorithms, therefore improving the previously best-known performance guarantees of 2.5 and 3, respectively [Math. Programming, 59 (1993), pp. 413--420].