Related papers: Ranking top-k trees in tree-based phylogenetic net…
Retrieving relevant targets from an extremely large target set under computational limits is a common challenge for information retrieval and recommendation systems. Tree models, which formulate targets as leaves of a tree with trainable…
Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
The problem of constructing an optimal rooted phylogenetic network from a set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet which tries to construct an optimal rooted phylogenetic…
We consider the minimum spanning tree problem with predictions, using the weight-arrival model, i.e., the graph is given, together with predictions for the weights of all edges. Then the actual weights arrive one at a time and an…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
In this paper, we investigate adaptive nonlinear regression and introduce tree based piecewise linear regression algorithms that are highly efficient and provide significantly improved performance with guaranteed upper bounds in an…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
The entities in directed networks arising from real-world interactions are often naturally organized under some hierarchical structure. Given a directed, weighted, graph with edges and node labels, we introduce ranking problem where the…
The dynamic trees problem is to maintain a forest subject to edge insertions and deletions while facilitating queries such as connectivity, path weights, and subtree weights. Dynamic trees are a fundamental building block of a large number…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
We give the first data structure for the problem of maintaining a dynamic set of n elements drawn from a partially ordered universe described by a tree. We define the Line-Leaf Tree, a linear-sized data structure that supports the…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…
There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
In 1996, Bodlaender showed the celebrated result that an optimal tree decomposition of a graph of bounded treewidth can be found in linear time. The algorithm is based on an algorithm of Bodlaender and Kloks that computes an optimal tree…
Despite the latest prevailing success of deep neural networks (DNNs), several concerns have been raised against their usage, including the lack of intepretability the gap between DNNs and other well-established machine learning models, and…