相关论文: Hypergraph covering problems motivated by genome a…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…
We connect the mixing behaviour of random walks over a graph to the power of the local-consistency algorithm for the solution of the corresponding constraint satisfaction problem (CSP). We extend this connection to arbitrary CSPs and their…
We consider a variant of the path cover problem, namely, the $k$-fixed-endpoint path cover problem, or kPC for short, on interval graphs. Given a graph $G$ and a subset $\mathcal{T}$ of $k$ vertices of $V(G)$, a $k$-fixed-endpoint path…
Constraint satisfaction problems are computational problems that naturally appear in many areas of theoretical computer science. One of the central themes is their computational complexity, and in particular the border between…
The Promise Constraint Satisfaction Problem (PCSP for short) is a generalization of the well-studied Constraint Satisfaction Problem (CSP). The PCSP has its roots in such classic problems as the Approximate Graph Coloring and the…
We study consistent query answering via different graph representations. First, we introduce solution-conflict hypergraphs in which nodes represent facts and edges represent either conflicts or query solutions. Considering a monotonic query…
The Maximum Common Subgraph is a computationally challenging problem with countless practical applications. Even if it has been long proven NP-hard, its importance still motivates searching for exact solutions. This work starts by…
Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from…
We describe two BQP-complete problems concerning properties of sparse graphs having a certain symmetry. The graphs are specified by efficiently computable functions which output the adjacent vertices for each vertex. Let i and j be two…
The {\em overlap number} of a finite $(d+1)$-uniform hypergraph $H$ is defined as the largest constant $c(H)\in (0,1]$ such that no matter how we map the vertices of $H$ into $\R^d$, there is a point covered by at least a $c(H)$-fraction of…
The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
We study homomorphism polynomials, which are polynomials that enumerate all homomorphisms from a pattern graph $H$ to $n$-vertex graphs. These polynomials have received a lot of attention recently for their crucial role in several new…
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…
Contemporary genetic programming (GP) systems for general program synthesis have been primarily concerned with evolving programs that can manipulate values from a standard set of primitive data types and simple indexed data structures. In…
Persistent homology is a popular tool in Topological Data Analysis. It provides numerical characteristics of data sets which reflect global geometric properties. In order to be useful in practice, for example for feature generation in…
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…
We consider the problem of finding a 1-planar drawing for a general graph, where a 1-planar drawing is a drawing in which each edge participates in at most one crossing. Since this problem is known to be NP-hard we investigate the…
The maximum clique problem (MCP) is a fundamental problem in graph theory and in computational complexity. Given a graph G, the problem is that of finding the largest clique (complete subgraph) in G. The MCP has many important applications…
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…