相关论文: Polyhedral Combinatorics of UPGMA Cones

The tree complex is a simplicial complex defined in recent work of Belk, Lanier, Margalit, and Winarski with natural applications to mapping class groups and complex dynamics. In this article, we connect this setting with the study of…

Dimensionality reduction on Riemannian manifolds is challenging due to the complex nonlinear data structures. While probabilistic principal geodesic analysis~(PPGA) has been proposed to generalize conventional principal component analysis…

Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…

We study the problem of decomposing (clustering) a tree with respect to costs attributed to pairs of nodes, so as to minimize the sum of costs for those pairs of nodes that are in the same component (cluster). For the general case and for…

Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The…

We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…

We describe an implementation of a genetic algorithm on partially commutative groups and apply it to the double coset search problem on a subclass of groups. This transforms a combinatorial group theory problem to a problem of combinatorial…

We present an alternative method for calculating likelihoods in molecular phylogenetics. Our method is based on partial likelihood tensors, which are generalizations of partial likelihood vectors, as used in Felsenstein's approach.…

We provide a robust and general algorithm for computing distribution functions associated to induced orthogonal polynomial measures. We leverage several tools for orthogonal polynomials to provide a spectrally-accurate method for a broad…

We present two algorithms for computing the geodesic distance between phylogenetic trees in tree space, as introduced by Billera, Holmes, and Vogtmann (2001). We show that the possible combinatorial types of shortest paths between two trees…

With this work we aim to show how Mathematica can be a useful tool to investigate properties of combinatorial structures. Specifically, we will face enumeration problems on independent subsets of powers of paths and cycles, trying to…

We develop continuous-stage Runge-Kutta methods based on weighted orthogonal polynomials in this paper. There are two main highlighted merits for developing such methods: Firstly, we do not need to study the tedious solution of…

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…

Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…

Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is…

The polygonal distributions are a class of distributions that can be defined via the mixture of triangular distributions over the unit interval. The class includes the uniform and trapezoidal distributions, and is an alternative to the beta…

Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…

Various algebraic structures of degenerate four-wave mixing equations of optical phase conjugation are analyzed. Two approaches (the spinorial and the Lax-pair based), complementary to each other, are utilized for a systematic derivation of…

We study the first step of the weight filtration on the cohomology of a proper complex algebraic variety, which we call the combinatorial part. We obtain a natural upper bound on its size, which gives rather strong information about the…

There is a long tradition of the axiomatic study of consensus methods in phylogenetics that satisfy certain desirable properties. One recently-introduced property is associative stability, which is desirable because it confers a…