Related papers: Linear-Time Tree Containment in Phylogenetic Netwo…
Tree kernels have been proposed to be used in many areas as the automatic learning of natural language applications. In this paper, we propose a new linear time algorithm based on the concept of weighted tree automata for SubTree kernel…
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…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Deciding whether a graph can be embedded in a grid using only unit-length edges is NP-complete, even when restricted to binary trees. However, it is not difficult to devise a number of graph classes for which the problem is polynomial, even…
Finding a maximum clique in a given graph is one of the fundamental NP-hard problems. We compare two multi-core thread-parallel adaptations of a state-of-the-art branch and bound algorithm for the maximum clique problem, and provide a novel…
Given a network represented by a weighted directed graph G, we consider the problem of finding a bounded cost set of nodes S such that the influence spreading from S in G, within a given time bound, is as large as possible. The dynamic that…
In this paper, we consider different constrained partition problems for weighted trees and cactus graphs. We focus on the (l,u)-partition problem, which is the problem of partitioning a weighted graph into connected clusters such that each…
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 history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
Hybridization networks are representations of evolutionary histories that allow for the inclusion of reticulate events like recombinations, hybridizations, or lateral gene transfers. The recent growth in the number of hybridization network…
In this paper we propose a dynamic data structure that supports efficient algorithms for updating and querying singly connected Bayesian networks (causal trees and polytrees). In the conventional algorithms, new evidence in absorbed in time…
A seed in a word is a relaxed version of a period in which the occurrences of the repeating subword may overlap. We show a linear-time algorithm computing a linear-size representation of all the seeds of a word (the number of seeds might be…
The complexity of the maximum common connected subgraph problem in partial $k$-trees is still not fully understood. Polynomial-time solutions are known for degree-bounded outerplanar graphs, a subclass of the partial $2$-trees. On the other…
Inspired by a growing interest in analyzing network data, we study the problem of node classification on graphs, focusing on approaches based on kernel machines. Conventionally, kernel machines are linear classifiers in the implicit feature…
The problem of determining whether a graph $G$ contains another graph $H$ as a minor, referred to as the minor containment problem, is a fundamental problem in the field of graph algorithms. While it is NP-complete when $G$ and $H$ are…
Motivated by the cabling of solar farms, we study the problem Constrained Layer Tree. At its core, it asks whether there exists a tree that connects a set of sources (the leaves) to one sink (the root) such that certain capacity constraints…
In the context of classification problems, Deep Learning (DL) approaches represent state of art. Many DL approaches are based on variations of standard multi-layer feed-forward neural networks. These are also referred to as deep networks.…
The minimum-cost arborescence problem is a well-studied problem in the area of graph theory, with known polynomial-time algorithms for solving it. Previous literature introduced new variations on the original problem with different…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
We consider a natural variant of the well-known Feedback Vertex Set problem, namely the problem of deleting a small subset of vertices or edges to a full binary tree. This version of the problem is motivated by real-world scenarios that are…