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Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Symmetries occur naturally in CSP or SAT problems and are not very difficult to discover, but using them to prune the search space tends to be very challenging. Indeed, this usually requires finding specific elements in a group of…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
To enumerate 3-manifold triangulations with a given property, one typically begins with a set of potential face pairing graphs (also known as dual 1-skeletons), and then attempts to flesh each graph out into full triangulations using an…
In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…
DenseNet architectures have demonstrated impressive performance in image classification tasks, but limited research has been conducted on using character-level DenseNet (char-DenseNet) architectures for text classification tasks. It is not…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
In this paper we develop a very special substitution method for solving a general linear programming problem (LPP). Of course the substitution is a kind of elimination of variable but this method must not be confused with the so-called…
The Densest Subgraph Problem (DSP) is widely used to identify community structures and patterns in networks such as bioinformatics and social networks. While solvable in polynomial time, traditional exact algorithms face computational and…
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,…
Partial-label learning (PLL) is a multi-class classification problem, where each training example is associated with a set of candidate labels. Even though many practical PLL methods have been proposed in the last two decades, there lacks a…
The partial Latin square extension problem is to fill as many as possible empty cells of a partially filled Latin square. This problem is a useful model for a wide range of applications in diverse domains. This paper presents the first…
In the problem of $\texttt{Generalised Pattern Matching}\ (\texttt{GPM})$ [STOC'94, Muthukrishnan and Palem], we are given a text $T$ of length $n$ over an alphabet $\Sigma_T$, a pattern $P$ of length $m$ over an alphabet $\Sigma_P$, and a…
Customized image generation, which seeks to synthesize images with consistent characters, holds significant relevance for applications such as storytelling, portrait generation, and character design. However, previous approaches have…
We consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover ($cc$) to such problems.…
Temporal graphs are a special class of graphs for which a temporal component is added to edges, that is, each edge possesses a set of times at which it is available and can be traversed. Many classical problems on graphs can be translated…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
In this paper, we are interested in algorithms that take in input an arbitrary graph $G$, and that enumerate in output all the (inclusion-wise) maximal "subgraphs" of $G$ which fulfil a given property $\Pi$. All over this paper, we study…
In this paper, we propose two new methods for solving Set Constraint Problems, as well as a potential polynomial solution for NP-Complete problems using quantum computation. While current methods of solving Set Constraint Problems focus on…
An improved characteristic set algorithm for solving Boolean polynomial systems is proposed. This algorithm is based on the idea of converting all the polynomials into monic ones by zero decomposition, and using additions to obtain…