Related papers: Invariant Based Quartet Puzzling
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
We introduce the zip tree, a form of randomized binary search tree that integrates previous ideas into one practical, performant, and pleasant-to-implement package. A zip tree is a binary search tree in which each node has a numeric rank…
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}…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
Tree search algorithms, such as branch-and-bound, are the most widely used tools for solving combinatorial and nonconvex problems. For example, they are the foremost method for solving (mixed) integer programs and constraint satisfaction…
We present a simple 4-approximation algorithm for computing a maximum agreement forest of multiple unrooted binary trees. This algorithm applies LP rounding to an extension of a recent ILP formulation of the maximum agreement forest problem…
We use machine learning to classify examples of braids (or flat braids) as trivial or non-trivial. Our ML takes form of supervised learning using neural networks (multilayer perceptrons). When they achieve good results in classification, we…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
The problem of pattern selection arises when the evolution equations have many solutions, whereas observed patterns constitute a much more restricted set. An approach is advanced for treating the problem of pattern selection by defining the…
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 are concerned with catalyst-assisted probabilistic entanglement transformations. A necessary and sufficient condition is presented under which there exist partial catalysts that can increase the maximal transforming probability of a…
Clustering is a widely used unsupervised learning method for finding structure in the data. However, the resulting clusters are typically presented without any guarantees on their robustness; slightly changing the used data sample or…
A common approach to aggregate classification estimates in an ensemble of decision trees is to either use voting or to average the probabilities for each class. The latter takes uncertainty into account, but not the reliability of the…
There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present LvD, (Likelihood via Decomposition), an alternative to…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Probabilistic inference algorithms for finding the most probable explanation, the maximum aposteriori hypothesis, and the maximum expected utility and for updating belief are reformulated as an elimination--type algorithm called bucket…
This paper develops likelihood-based methods for estimation, inference, model selection, and forecasting of continuous-time integer-valued trawl processes. The full likelihood of integer-valued trawl processes is, in general, highly…
The hierarchical and recursive expressive capability of rooted trees is applicable to represent statistical models in various areas, such as data compression, image processing, and machine learning. On the other hand, such hierarchical…
Achieving invariance to nuisance transformations is a fundamental challenge in the construction of robust and reliable vision systems. Existing approaches to invariance scale exponentially with the dimension of the family of…
We study Thurston equivalence classes of quadratic post-critically finite branched coverings. For these maps, we introduce and study invariant spanning trees. We give a computational procedure for searching for invariant spanning trees.…