Related papers: Constructing Semi-Directed Level-1 Phylogenetic Ne…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
In distributed systems, knowledge of the network structure of the connections among the unitary components is often a requirement for an accurate prediction of the emerging collective dynamics. However, in many real-world situations, one…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…
Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…
Improving information flow in deep networks helps to ease the training difficulties and utilize parameters more efficiently. Here we propose a new convolutional neural network architecture with alternately updated clique (CliqueNet). In…
Labelled networks are an important class of data, naturally appearing in numerous applications in science and engineering. A typical inference goal is to determine how the vertex labels (or features) affect the network's structure. In this…
Motivation: Inferring the structure of gene regulatory networks from high--throughput datasets remains an important and unsolved problem. Current methods are hampered by problems such as noise, low sample size, and incomplete…
We consider a model for the formation of a river network in which erosion process plays a role only at the initial stage. Once a global connectivity is achieved, no further evolution takes place. In spite of this, the network reproduces…
We use a generalised version of the individual-based Tangled Nature model of evolutionary ecology to study the relationship between ecosystem structure and evolutionary history. Our evolved model ecosystems typically exhibit interaction…
Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if $\mathcal T$ and $\mathcal T'$ are rooted binary phylogenetic $X$-trees that infers the same set of…
Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploidy level (number of complete chromosome sets found in a cell)…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
In this paper we present a new approach to construct the set of numerical semigroups with a fixed genus. Our methodology is based on the construction of the set of numerical semigroups with fixed Frobenius number and genus. An equivalence…
Deep neural networks (DNNs) are nowadays witnessing a major success in solving many pattern recognition tasks including skeleton-based classification. The deployment of DNNs on edge-devices, endowed with limited time and memory resources,…
A semi-supervised learning framework using the feedforward-designed convolutional neural networks (FF-CNNs) is proposed for image classification in this work. One unique property of FF-CNNs is that no backpropagation is used in model…
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,…
In this paper, we consider the problem of reconstructing a directed graph using path queries. In this query model of learning, a graph is hidden from the learner, and the learner can access information about it with path queries. For a…
Algebraic techniques in phylogenetics have historically been successful at proving identifiability results and have also led to novel reconstruction algorithms. In this paper, we study the ideal of phylogenetic invariants of the…
We introduce a simple one-parameter network growth algorithm which is able to reproduce a wide variety of realistic network structures but without having to invoke any global information about node degrees such as preferential-attachment…