Related papers: constNJ: an algorithm to reconstruct sets of phylo…
We propose a novel tree-like curvilinear structure reconstruction algorithm based on supervised learning and graph theory. In this work we analyze image patches to obtain the local major orientations and the rankings that correspond to the…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
Motion planning problems have been studied by both the robotics and the controls research communities for a long time, and many algorithms have been developed for their solution. Among them, incremental sampling-based motion planning…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Recently there has been a lot of work on pruning filters from deep convolutional neural networks (CNNs) with the intention of reducing computations. The key idea is to rank the filters based on a certain criterion (say, $l_1$-norm, average…
An algorithm is proposed for constructing directed spanning forests of the minimum weight, in which the maximum possible degree of affinity between the minimum forests is preserved when the number of trees changes. The correctness of the…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
In this paper we design and prove correct a fully dynamic distributed algorithm for maintaining an approximate Steiner tree that connects via a minimum-weight spanning tree a subset of nodes of a network (referred as Steiner members or…
In this paper we present a novel probabilistic sampling-based motion planning algorithm called the Fast Marching Tree algorithm (FMT*). The algorithm is specifically aimed at solving complex motion planning problems in high-dimensional…
Tree projections provide a unifying framework to deal with most structural decomposition methods of constraint satisfaction problems (CSPs). Within this framework, a CSP instance is decomposed into a number of sub-problems, called views,…
The Neighbor Joining Algorithm is among the most fundamental algorithmic results in computational biology. However, its definition and correctness proof are not straightforward. In particular, ''the question ''what does the NJ method seek…
Inference problems in graphical models are often approximated by casting them as constrained optimization problems. Message passing algorithms, such as belief propagation, have previously been suggested as methods for solving these…
Recurrent neural networks (RNNs) have been widely adopted in temporal sequence analysis, where realtime performance is often in demand. However, RNNs suffer from heavy computational workload as the model often comes with large weight…
Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…
Convolutional neural networks (CNNs) are reported to be overparametrized. The search for optimal (minimal) and sufficient architecture is an NP-hard problem as the hyperparameter space for possible network configurations is vast. Here, we…
Network pruning reduces the size of neural networks by removing (pruning) neurons such that the performance drop is minimal. Traditional pruning approaches focus on designing metrics to quantify the usefulness of a neuron which is often…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Man-made environments typically comprise planar structures that exhibit numerous geometric relationships, such as parallelism, coplanarity, and orthogonality. Making full use of these relationships can considerably improve the robustness of…