Related papers: Hypergraph covering problems motivated by genome a…
The problem of computing all maximal induced subgraphs of a graph G that have a graph property P, also called the maximal P-subgraphs problem, is considered. This problem is studied for hereditary, connected-hereditary and rooted-hereditary…
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…
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",…
Hypergeometric sequences obey first-order linear recurrence relations with polynomial coefficients and are commonplace throughout the mathematical and computational sciences. For certain classes of hypergeometric sequences, we prove linear…
We investigate the parameterized complexity of finding subgraphs with hereditary properties on graphs belonging to a hereditary graph class. Given a graph $G$, a non-trivial hereditary property $\Pi$ and an integer parameter $k$, the…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
Convolutional neural networks (CNNs) leverage the great power in representation learning on regular grid data such as image and video. Recently, increasing attention has been paid on generalizing CNNs to graph or network data which is…
Graphs are used to represent and analyze data in domains as diverse as physics, biology, chemistry, planetary science, and the social sciences. Across domains, random graph models relate generative processes to expected graph properties,…
We investigate the relationship between several enumeration complexity classes and focus in particular on problems having enumeration algorithms with incremental and polynomial delay (IncP and DelayP respectively). We show that, for some…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
The role of polymorphisms in determining the complexity of constraint satisfaction problems is well established. In this context we study the stability of CSP complexity and polymorphism properties under some basic graph theoretic…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
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…
A convex geometric hypergraph (abbreviated cgh) consists of a collection of subsets of a strictly convex set of points in the plane. Extremal problems for cgh's have been extensively studied in the literature, and in this paper we consider…
Our starting point is the observation that if graphs in a class C have low descriptive complexity in first order logic, then the isomorphism problem for C is solvable by a fast parallel algorithm (essentially, by a simple combinatorial…
Fox, Gromov, Lafforgue, Naor, and Pach proved a regularity lemma for semi-algebraic $k$-uniform hypergraphs of bounded complexity, showing that for each $\epsilon>0$ the vertex set can be equitably partitioned into a bounded number of parts…
Critical node problems involve identifying a subset of critical nodes from an undirected graph whose removal results in optimizing a pre-defined measure over the residual graph. As useful models for a variety of practical applications,…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…