Related papers: Reticulation-visible networks
An important issue in neural network research is how to choose the number of nodes and layers such as to solve a classification problem. We provide new intuitions based on earlier results by An et al. (2015) by deriving an upper bound on…
Detecting and visualizing what are the most relevant changes in an evolving network is an open challenge in several domains. We present a fast algorithm that filters subsets of the strongest nodes and edges representing an evolving weighted…
A directed acyclic network is considered where all the terminals need to recover the sum of the symbols generated at all the sources. We call such a network a sum-network. It is shown that there exists a solvably (and linear solvably)…
We show that determining if an $n$-vertex graph has twin-width at most 4 is NP-complete, and requires time $2^{\Omega(n/\log n)}$ unless the Exponential-Time Hypothesis fails. Along the way, we give an elementary proof that $n$-vertex…
We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rNNI (rooted Nearest Neighbour Interchange) and rSPR (rooted Subtree Prune and Regraft). Recently, these moves were generalized to rooted…
We consider the natural problem of learning a ReLU network from queries, which was recently remotivated by model extraction attacks. In this work, we present a polynomial-time algorithm that can learn a depth-two ReLU network from queries…
We study the broadcast problem on dynamic networks with $n$ processes. The processes communicate in synchronous rounds along an arbitrary rooted tree. The sequence of trees is given by an adversary whose goal is to maximize the number of…
We extend the observability model to multiplex networks. We present mathematical frameworks, valid under the treelike ansatz, able to describe the emergence of the macroscopic cluster of mutually observable nodes in both synthetic and…
Reticulate evolution can be modelled using phylogenetic networks. Tree-based networks, which are one of the more general classes of phylogenetic networks, have recently gained eminence for its ability to represent evolutionary histories…
Tree-child networks are one of the most prominent network classes for modeling evolutionary processes which contain reticulation events. Several recent studies have addressed counting questions for bicombining tree-child networks in which…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
Here we show that, given a set of clusters C on a set of taxa X, where |X|=n, it is possible to determine in time f(k).poly(n) whether there exists a level-<= k network (i.e. a network where each biconnected component has reticulation…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
We investigate the computational complexity of various problems for simple recurrent neural networks (RNNs) as formal models for recognizing weighted languages. We focus on the single-layer, ReLU-activation, rational-weight RNNs with…
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…
In this paper, we present a complete characterization of mutual-visibility sets in trees. It is shown that a subset $S$ is a mutual-visibility set of a tree $T$ if and only if it coincides with the set of leaves of the Steiner subtree…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…