Related papers: constNJ: an algorithm to reconstruct sets of phylo…
The search for the optimal pair of active and protection paths in a network with Shared Risk Link Groups (SRLG) is a challenging but high-value problem in the industry that is inevitable in ensuring reliable connections on the modern…
The sorting problem is one of the most relevant problems in computer science. Within the scope of modern computer science it has been studied for more than 70 years. In spite of these facts, new sorting algorithms have been developed in…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
We propose to prune a random forest (RF) for resource-constrained prediction. We first construct a RF and then prune it to optimize expected feature cost & accuracy. We pose pruning RFs as a novel 0-1 integer program with linear constraints…
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…
Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large…
For the task of subdecimeter aerial imagery segmentation, fine-grained semantic segmentation results are usually difficult to obtain because of complex remote sensing content and optical conditions. Recently, convolutional neural networks…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
In this work we introduce a new linear time compression algorithm, called "Re-pair for Trees", which compresses ranked ordered trees using linear straight-line context-free tree grammars. Such grammars generalize straight-line context-free…
Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical…
36 single genes of six plants inferred 18 unique trees using maximum parsimony. Such incongruence is an important issue and how to reconstruct the congruent tree still is one of the most challenges in molecular phylogenetics. For resolving…
A variety of modeling techniques have been developed in the past decade to reduce the computational expense and improve the accuracy of modeling. In this study, a new framework of modeling is suggested. Compared with other popular methods,…
Given an ensemble of randomized regression trees, it is possible to restructure them as a collection of multilayered neural networks with particular connection weights. Following this principle, we reformulate the random forest method of…
As a popular channel pruning method for convolutional neural networks (CNNs), network slimming (NS) has a three-stage process: (1) it trains a CNN with $\ell_1$ regularization applied to the scaling factors of the batch normalization…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
In this paper, we consider deep neural networks for solving inverse problems that are robust to forward model mis-specifications. Specifically, we treat sensing problems with model mismatch where one wishes to recover a sparse…