Related papers: Minimal Conflicting Sets for the Consecutive Ones …
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…
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…
Let C be a finite set of N elements and R = r_1,r_2,..., r_m a family of M subsets of C. A subset X of R verifies the Consecutive Ones Property (C1P) if there exists a permutation P of C such that each r_i in X is an interval of P. A…
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…
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…
Motivated by problems of comparative genomics and paleogenomics, in [Chauve et al., 2009], the authors introduced the Gapped Consecutive-Ones Property Problem (k,delta)-C1P: given a binary matrix M and two integers k and delta, can the…
The Consecutive Ones Property is an important notion for binary matrices, both from a theoretical and applied point of view. Tucker gave in 1972 a characterization of matrices that do not satisfy the Consecutive Ones Property in terms of…
In various areas of computer science, we deal with a set of constraints to be satisfied. If the constraints cannot be satisfied simultaneously, it is desirable to identify the core problems among them. Such cores are called minimal…
Let C be a finite set of $N elements and R = {R_1,R_2, ..,R_m} a family of M subsets of C. The family R verifies the consecutive ones property if there exists a permutation P of C such that each R_i in R is an interval of P. There already…
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…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
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…
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa,…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Trust in counterfactual explanations depends critically on whether their recommended changes are truly minimal: suboptimal explanations may vastly overshoot the actual changes needed to alter a decision, and heuristic errors can affect…
A combinatorial rectangle may be viewed as a matrix whose entries are all +-1. The discrepancy of an m by n matrix is the maximum among the absolute values of its m row sums and n column sums. In this paper, we investigate combinatorial…
A forcing set $S$ in a combinatorial problem is a set of elements such that there is a unique solution that contains all the elements in $S$. An anti-forcing set is the symmetric concept: a set $S$ of elements is called an anti-forcing set…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
A variant of the well-known Set Covering Problem is studied in this paper, where subsets of a collection have to be selected, and pairwise conflicts among subsets of items exist. The selection of each subset has a cost, and the inclusion of…