Related papers: Hardness of Permutation Pattern Matching
In this note we show that pattern matching in permutations is polynomial time reducible to pattern matching in set partitions. In particular, pattern matching in set partitions is NP-Complete.
A binary matrix satisfies the consecutive ones property (COP) if its columns can be permuted such that the ones in each row of the resulting matrix are consecutive. Equivalently, a family of sets F = {Q_1,..,Q_m}, where Q_i is subset of R…
Recently, B\'ona and Smith defined strong pattern avoidance, saying that a permutation $\pi$ strongly avoids a pattern $\tau$ if $\pi$ and $\pi^2$ both avoid $\tau$. They conjectured that for every positive integer $k$, there is a…
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
Constraint-solving-based program invariant synthesis takes a parametric invariant template and encodes the (inductive) invariant conditions into constraints. The problem of characterizing the set of all valid parameter assignments is…
In a simple pattern matching problem one has a pattern $w$ and a text $t$, which are words over a finite alphabet $\Sigma$. One may ask whether $w$ occurs in $t$, and if so, where? More generally, we may have a set $P$ of patterns and a set…
A permutation $\pi$ is said to avoid a chain $(\sigma:\tau)$ of patterns if $\pi$ avoids $\sigma$ and $\pi^2$ avoids $\tau.$ In this paper, we define a notion of pattern avoidance for compositions of positive integers and use that idea to…
A decision problem is called parameterized if its input is a pair of strings. One of these strings is referred to as a parameter. The problem: given a propositional logic program P and a non-negative integer k, decide whether P has a stable…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
We study a combinatorial problem arising from microarrays synthesis. The synthesis is done by a light-directed chemical process. The objective is to minimize unintended illumination that may contaminate the quality of experiments.…
In this work, we study the discrete logarithm problem in the context of TFNP - the complexity class of search problems with a syntactically guaranteed existence of a solution for all instances. Our main results establish that suitable…
A polynomial Turing compression (PTC) for a parameterized problem $L$ is a polynomial time Turing machine that has access to an oracle for a problem $L'$ such that a polynomial in the input parameter bounds each query. Meanwhile, a…
An instance $I$ of the Stable Matching Problem (SMP) is given by a bipartite graph with a preference list of neighbors for every vertex. A swap in $I$ is the exchange of two consecutive vertices in a preference list. A swap can be viewed as…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…
We study the problem of finding solutions to the stable matching problem that are robust to errors in the input and we obtain a polynomial time algorithm for a special class of errors. In the process, we also initiate work on a new…
While known algorithms for sensitivity analysis and parameter tuning in probabilistic networks have a running time that is exponential in the size of the network, the exact computational complexity of these problems has not been established…
The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem…
The Set Packing problem is, given a collection of sets $\mathcal{S}$ over a ground set $\mathcal{U}$, to find a maximum collection of sets that are pairwise disjoint. The problem is among the most fundamental NP-hard optimization problems…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…