Related papers: Solving the Tree Containment Problem Using Graph N…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
In the point set embeddability problem, we are given a plane graph $G$ with $n$ vertices and a point set $S$ with $n$ points. Now the goal is to answer the question whether there exists a straight-line drawing of $G$ such that each vertex…
The Steiner Tree Problem (STP) in graphs is an important problem with various applications in many areas such as design of integrated circuits, evolution theory, networking, etc. In this paper, we propose an algorithm to solve the STP. The…
Graph neural network (GNN)'s success in graph classification is closely related to the Weisfeiler-Lehman (1-WL) algorithm. By iteratively aggregating neighboring node features to a center node, both 1-WL and GNN obtain a node representation…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
In this paper, we present an exact algorithm for the Steiner tree problem. The algorithm is based on certain pre-computed index structures. Our algorithm offers a practical solution for the Steiner tree problems on graphs of large size and…
In deep neural networks, better results can often be obtained by increasing the complexity of previously developed basic models. However, it is unclear whether there is a way to boost performance by decreasing the complexity of such models.…
The last in-tree recognition problem asks whether a given spanning tree can be derived by connecting each vertex with its rightmost left neighbor of some search ordering. In this study, we demonstrate that the last-in-tree recognition…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
In recent years, machine learning and deep learning approaches such as artificial neural networks have gained in popularity for the resolution of automatic puzzle resolution problems. Indeed, these methods are able to extract high-level…
Orchard and tree-child networks share an important property with phylogenetic trees: they can be completely reduced to a single node by iteratively deleting cherries and reticulated cherries. As it is the case with phylogenetic trees, the…
In this paper, we introduce the Fixed Topology Minimum-Length Tree with Neighborhood Problem, which aims to embed a rooted tree-shaped graph into a $d$-dimensional metric space while minimizing its total length provided that the nodes must…
Solving arithmetic word problems is a cornerstone task in assessing language understanding and reasoning capabilities in NLP systems. Recent works use automatic extraction and ranking of candidate solution equations providing the answer to…