Finding and Counting Permutations via CSPs

Permutation patterns and pattern avoidance have been intensively studied in combinatorics and computer science, going back at least to the seminal work of Knuth on stack-sorting (1968). Perhaps the most natural algorithmic question in this area is deciding whether a given permutation of length n contains a given pattern of length k. In this work we give two new algorithms for this well-studied problem, one whose running time is n^{k/4 + o(k)}, and a polynomial-space algorithm whose running time is the better of O(1.6181^n) and O(n^{k/2 + 1}). These results improve the earlier best bounds of n^{0.47k + o(k)} and O(1.79^n) due to Ahal and Rabinovich (2000) resp. Bruner and Lackner (2012) and are the fastest algorithms for the problem when k in Omega(log{n}). We show that both our new algorithms and the previous exponential-time algorithms in the literature can be viewed through the unifying lens of constraint-satisfaction. Our algorithms can also count, within the same running time, the number of occurrences of a pattern. We show that this result is close to optimal: solving the counting problem in time f(k) * n^{o(k/log{k})} would contradict the exponential-time hypothesis (ETH). For some special classes of patterns we obtain improved running times. We further prove that 3-increasing and 3-decreasing permutations can, in some sense, embed arbitrary permutations of almost linear length, which indicates that an algorithm with sub-exponential running time is unlikely, even for patterns from these restricted classes

Average-case analysis of perfect sorting by reversals (Journal Version)

Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any common interval. B\'erard et al. (2007) make use of strong interval trees to describe an algorithm for sorting signed permutations by reversals. Combinatorial properties of this family of trees are essential to the algorithm analysis. Here, we use the expected value of certain tree parameters to prove that the average run-time of the algorithm is at worst, polynomial, and additionally, for sufficiently long permutations, the sorting algorithm runs in polynomial time with probability one. Furthermore, our analysis of the subclass of commuting scenarios yields precise results on the average length of a reversal, and the average number of reversals.Comment: A preliminary version of this work appeared in the proceedings of Combinatorial Pattern Matching (CPM) 2009. See arXiv:0901.2847; Discrete Mathematics, Algorithms and Applications, vol. 3(3), 201