Related papers: Hypergraph covering problems motivated by genome a…
Motivated by the question of how macromolecules assemble, the notion of an {\it assembly tree} of a graph is introduced. Given a graph $G$, the paper is concerned with enumerating the number of assembly trees of $G$, a problem that applies…
In the constraint programming framework, state-of-the-art static and dynamic decomposition techniques are hard to apply to problems with complete initial constraint graphs. For such problems, we propose a hybrid approach of these techniques…
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
The Minimum Path Cover problem on directed acyclic graphs (DAGs) is a classical problem that provides a clear and simple mathematical formulation for several applications in different areas and that has an efficient algorithmic solution. In…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
It is a well-known fact that genetic sequences may contain sections with repeated units, called repeats, that differ in length over a population, with a length distribution of geometric type. A simple class of recombination models with…
Counting small cohesive subgraphs in a graph is a fundamental operation with numerous applications in graph analysis. Previous studies on cohesive subgraph counting are mainly based on the clique model, which aim to count the number of…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
The purpose of this article is to study the uniqueness problem for meromorphic mappings from $\mathbb{C}^{n}$ into the complex projective space $\mathbb{P}^{N}(\mathbb{C}).$ By making using of the method of dealing with multiple values due…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
A $3$-uniform hypergraph is a generalization of simple graphs where each hyperedge is a subset of vertices of size $3$. The degree of a vertex in a hypergraph is the number of hyperedges incident with it. The degree sequence of a hypergraph…
Biclustering techniques have been widely used to identify homogeneous subgroups within large data matrices, such as subsets of genes similarly expressed across subsets of patients. Mining a max-sum sub-matrix is a related but distinct…
Most existing neural networks for learning graphs address permutation invariance by conceiving of the network as a message passing scheme, where each node sums the feature vectors coming from its neighbors. We argue that this imposes a…
The need to count and localize repeating objects in an image arises in different scenarios, such as biological microscopy studies, production lines inspection, and surveillance recordings analysis. The use of supervised Convoutional Neural…
Complex real-world optimization problems often involve both discrete decisions and nonlinear relationships between variables. Many such problems can be modeled as polynomial-objective integer programs, encompassing cases with quadratic and…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
The decision problem of perfect matchings in uniform hypergraphs is famously an NP-complete problem. It has been shown by Keevash--Knox--Mycroft [STOC, 2013] that for every $\varepsilon>0$, such decision problem restricted to $k$-uniform…
Hypergraphs naturally represent group interactions, which are omnipresent in many domains: collaborations of researchers, co-purchases of items, and joint interactions of proteins, to name a few. In this work, we propose tools for answering…
In the last few years, graph convolutional networks (GCN) have become a popular research direction in the machine learning community to tackle NP-hard combinatorial optimization problems (COPs) defined on graphs. While the obtained results…