相关论文: Hardness Results for the Gapped Consecutive-Ones P…

The Consecutive-Ones Property (C1P) is a classical concept in discrete mathematics that has been used in several genomics applications, from physical mapping of contemporary genomes to the assembly of ancient genomes. A common issue in…

A binary matrix $M$ has the consecutive ones property ($C1P$) for rows (resp. columns) if there is a permutation of its columns (resp. rows) that arranges the ones consecutively in all the rows (resp. columns). If $M$ has the $C1P$ for rows…

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…

A $(0,1)$-matrix has the consecutive-ones property (C1P) if its columns can be permuted to make the $1$'s in each row appear consecutively. This property was characterised in terms of forbidden submatrices by Tucker in 1972. Several graph…

A $(0,1)$-matrix has the Consecutive Ones Property (C1P) for the rows if there is a permutation of its columns such that the ones in each row appear consecutively. We say a $(0, 1)$-matrix is nested if it has the consecutive ones property…

Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…

Permutation Pattern Matching (PPM) is the problem of deciding for a given pair of permutations P and T whether the pattern P is contained in the text T. Bose, Buss and Lubiw showed that PPM is NP-complete. In view of this result, it is…

A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1s on each row are consecutive. These matrices are used for DNA physical mapping and ancestral genome reconstruction in…

The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…

We introduce a new -as far as we know- problem, according to which we are asked to match sequences of two digits in matrices having entries among those two digits (but others too) and prove that this problem is NP-complete

The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…

We study the complexity of constraint satisfaction problems for templates $\Gamma$ that are first-order definable in $(\Bbb Z; succ)$, the integers with the successor relation. Assuming a widely believed conjecture from finite domain…

We prove that deciding whether a given input word contains as subsequence every possible permutation of integers $\{1,2,\ldots,n\}$ is coNP-complete. The coNP-completeness holds even when given the guarantee that the input word contains as…

The $k$-tuple domination problem, for a fixed positive integer $k$, is to find a minimum sized vertex subset such that every vertex in the graph is dominated by at least $k$ vertices in this set. The $k$-tuple domination is NP-hard even for…

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…

Permutation Pattern Matching (or PPM) is a decision problem whose input is a pair of permutations $\pi$ and $\tau$, represented as sequences of integers, and the task is to determine whether $\tau$ contains a subsequence order-isomorphic to…

Inspired by computational complexity results for the quantified constraint satisfaction problem, we study the clones of idempotent polymorphisms of certain digraph classes. Our first results are two algebraic dichotomy, even "gap",…

A symmetric matrix $C$ is completely positive (CP) if there exists an entrywise nonnegative matrix $B$ such that $C=BB^T$. The CP-completion problem is to study whether we can assign values to the missing entries of a partial matrix (i.e.,…

Given a directed graph D = (N, A) and a sequence of positive integers 1 <= c_1 < c_2 < ... < c_m <= |N|, we consider those path and cycle polytopes that are defined as the convex hulls of simple paths and cycles of D of cardinality c_p for…

This paper presents the following results on sets that are complete for NP. 1. If there is a problem in NP that requires exponential time at almost all lengths, then every many-one NP-complete set is complete under length-increasing…