Variants of Constrained Longest Common Subsequence

In this work, we consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s1 and s2 over an alphabet A, a set C_s of strings, and a function Co from A to N, the DC-LCS problem consists in finding the longest subsequence s of s1 and s2 such that s is a supersequence of all the strings in Cs and such that the number of occurrences in s of each symbol a in A is upper bounded by Co(a). The DC-LCS problem provides a clear mathematical formulation of a sequence comparison problem in Computational Biology and generalizes two other constrained variants of the LCS problem: the Constrained LCS and the Repetition-Free LCS. We present two results for the DC-LCS problem. First, we illustrate a fixed-parameter algorithm where the parameter is the length of the solution. Secondly, we prove a parameterized hardness result for the Constrained LCS problem when the parameter is the number of the constraint strings and the size of the alphabet A. This hardness result also implies the parameterized hardness of the DC-LCS problem (with the same parameters) and its NP-hardness when the size of the alphabet is constant

Algebraic aspects of increasing subsequences

We present a number of results relating partial Cauchy-Littlewood sums, integrals over the compact classical groups, and increasing subsequences of permutations. These include: integral formulae for the distribution of the longest increasing subsequence of a random involution with constrained number of fixed points; new formulae for partial Cauchy-Littlewood sums, as well as new proofs of old formulae; relations of these expressions to orthogonal polynomials on the unit circle; and explicit bases for invariant spaces of the classical groups, together with appropriate generalizations of the straightening algorithm.Comment: LaTeX+amsmath+eepic; 52 pages. Expanded introduction, new references, other minor change

Orthogonal polynomial ensembles in probability theory

We survey a number of models from physics, statistical mechanics, probability theory and combinatorics, which are each described in terms of an orthogonal polynomial ensemble. The most prominent example is apparently the Hermite ensemble, the eigenvalue distribution of the Gaussian Unitary Ensemble (GUE), and other well-known ensembles known in random matrix theory like the Laguerre ensemble for the spectrum of Wishart matrices. In recent years, a number of further interesting models were found to lead to orthogonal polynomial ensembles, among which the corner growth model, directed last passage percolation, the PNG droplet, non-colliding random processes, the length of the longest increasing subsequence of a random permutation, and others. Much attention has been paid to universal classes of asymptotic behaviors of these models in the limit of large particle numbers, in particular the spacings between the particles and the fluctuation behavior of the largest particle. Computer simulations suggest that the connections go even farther and also comprise the zeros of the Riemann zeta function. The existing proofs require a substantial technical machinery and heavy tools from various parts of mathematics, in particular complex analysis, combinatorics and variational analysis. Particularly in the last decade, a number of fine results have been achieved, but it is obvious that a comprehensive and thorough understanding of the matter is still lacking. Hence, it seems an appropriate time to provide a surveying text on this research area.Comment: Published at http://dx.doi.org/10.1214/154957805100000177 in the Probability Surveys (http://www.i-journals.org/ps/) by the Institute of Mathematical Statistics (http://www.imstat.org