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Branch-and-bound (BnB) algorithms are widely used to solve combinatorial problems, and the performance crucially depends on its branching heuristic.In this work, we consider a typical problem of maximum common subgraph (MCS), and propose a…
The study of genetic map linearization leads to a combinatorial hard problem, called the {\em minimum breakpoint linearization} (MBL) problem. It is aimed at finding a linearization of a partial order which attains the minimum breakpoint…
The graph isomorphism problem is considered. We assign modified $n$-variable characteristic polynomials for graphs and reduce the graph isomorphism problem to the problem of the polynomials isomorphism. It is required to find out, is there…
In this paper, we introduce the Maximum Matrix Contraction problem, where we aim to contract as much as possible a binary matrix in order to maximize its density. We study the complexity and the polynomial approximability of the problem.…
Molecular machine learning has gained popularity with the advancements of geometric deep learning. In parallel, retrieval-augmented generation has become a principled approach commonly used with language models. However, the optimal…
We consider integer and linear programming problems for which the linear constraints exhibit a (recursive) block-structure: The problem decomposes into independent and efficiently solvable sub-problems if a small number of constraints is…
The induced matching width of a tree decomposition of a graph $G$ is the cardinality of a largest induced matching $M$ of $G$, such that there exists a bag that intersects every edge in $M$. The induced matching treewidth of a graph $G$,…
RNA secondary structures prediction is one of the main issues in bioinformatics. It seeks to elucidate structural conserved regions within a set of RNA sequences. Unfortunately, finding an accurate conserved structure is a very hard task to…
A subset of Q^n is called semilinear (or piecewise linear) if it is Boolean combination of linear half-spaces. We study the computational complexity of the constraint satisfaction problem (CSP) over the rationals when all the constraints…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
We study planted problems---finding hidden structures in random noisy inputs---through the lens of the sum-of-squares semidefinite programming hierarchy (SoS). This family of powerful semidefinite programs has recently yielded many new…
We study the Parallel Task Scheduling problem $Pm|size_j|C_{\max}$ with a constant number of machines. This problem is known to be strongly NP-complete for each $m \geq 5$, while it is solvable in pseudo-polynomial time for each $m \leq 3$.…
This paper focuses on finding a spanning tree of a graph to maximize the number of its internal vertices. We present an approximation algorithm for this problem which can achieve a performance ratio $\frac{4}{3}$ on undirected simple…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
The automaton constrained tree knapsack problem is a variant of the knapsack problem in which the items are associated with the vertices of the tree, and we can select a subset of items that is accepted by a top-down tree automaton. If the…
In Polyamorous Scheduling, we are given an edge-weighted graph and must find a periodic schedule of matchings in this graph which minimizes the maximal weighted waiting time between consecutive occurrences of the same edge. This NP-hard…
This paper presents new results for the (partial) maximum a posteriori (MAP) problem in Bayesian networks, which is the problem of querying the most probable state configuration of some of the network variables given evidence. First, it is…
We consider the following problem: Given an undirected (mixed) network and a set of ordered source-target, or cause-effect pairs, direct all edges so as to maximize the number of pairs that admit a directed source-target path. This is…
In length-constrained minimum spanning tree (MST) we are given an $n$-node graph $G = (V,E)$ with edge weights $w : E \to \mathbb{Z}_{\geq 0}$ and edge lengths $l: E \to \mathbb{Z}_{\geq 0}$ along with a root node $r \in V$ and a…
Connected Submodular Maximization (CSM) is a graph problem with important applications to wireless network deployment, path planning, epidemic outbreaks, and cancer genome studies. In CSM, we are given a graph $G$, a non-negative monotone…