3,456 research outputs found
Phylogenetic toric varieties on graphs
We define phylogenetic projective toric model of a trivalent graph as a
generalization of a binary symmetric model of a trivalent phylogenetic tree.
Generators of the pro- jective coordinate ring of the models of graphs with one
cycle are explicitly described. The phylogenetic models of graphs with the same
topological invariants are deforma- tion equivalent and share the same Hilbert
function. We also provide an algorithm to compute the Hilbert function.Comment: 36 pages, improved expositio
Trees, Tight-Spans and Point Configuration
Tight-spans of metrics were first introduced by Isbell in 1964 and
rediscovered and studied by others, most notably by Dress, who gave them this
name. Subsequently, it was found that tight-spans could be defined for more
general maps, such as directed metrics and distances, and more recently for
diversities. In this paper, we show that all of these tight-spans as well as
some related constructions can be defined in terms of point configurations.
This provides a useful way in which to study these objects in a unified and
systematic way. We also show that by using point configurations we can recover
results concerning one-dimensional tight-spans for all of the maps we consider,
as well as extend these and other results to more general maps such as
symmetric and unsymmetric maps.Comment: 21 pages, 2 figure
Latent tree models
Latent tree models are graphical models defined on trees, in which only a
subset of variables is observed. They were first discussed by Judea Pearl as
tree-decomposable distributions to generalise star-decomposable distributions
such as the latent class model. Latent tree models, or their submodels, are
widely used in: phylogenetic analysis, network tomography, computer vision,
causal modeling, and data clustering. They also contain other well-known
classes of models like hidden Markov models, Brownian motion tree model, the
Ising model on a tree, and many popular models used in phylogenetics. This
article offers a concise introduction to the theory of latent tree models. We
emphasise the role of tree metrics in the structural description of this model
class, in designing learning algorithms, and in understanding fundamental
limits of what and when can be learned
Tropical Convexity
The notions of convexity and convex polytopes are introduced in the setting
of tropical geometry. Combinatorial types of tropical polytopes are shown to be
in bijection with regular triangulations of products of two simplices.
Applications to phylogenetic trees are discussed.
Theorem 29 and Corollary 30 in the paper, relating tropical polytopes to
injective hulls, are incorrect. See the erratum at
http://www.math.uiuc.edu/documenta/vol-09/vol-09-eng.html .Comment: 20 pages, 6 figure
Principal components analysis in the space of phylogenetic trees
Phylogenetic analysis of DNA or other data commonly gives rise to a
collection or sample of inferred evolutionary trees. Principal Components
Analysis (PCA) cannot be applied directly to collections of trees since the
space of evolutionary trees on a fixed set of taxa is not a vector space. This
paper describes a novel geometrical approach to PCA in tree-space that
constructs the first principal path in an analogous way to standard linear
Euclidean PCA. Given a data set of phylogenetic trees, a geodesic principal
path is sought that maximizes the variance of the data under a form of
projection onto the path. Due to the high dimensionality of tree-space and the
nonlinear nature of this problem, the computational complexity is potentially
very high, so approximate optimization algorithms are used to search for the
optimal path. Principal paths identified in this way reveal and quantify the
main sources of variation in the original collection of trees in terms of both
topology and branch lengths. The approach is illustrated by application to
simulated sets of trees and to a set of gene trees from metazoan (animal)
species.Comment: Published in at http://dx.doi.org/10.1214/11-AOS915 the Annals of
Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical
Statistics (http://www.imstat.org
Toric Cubes
A toric cube is a subset of the standard cube defined by binomial
inequalities. These basic semialgebraic sets are precisely the images of
standard cubes under monomial maps. We study toric cubes from the perspective
of topological combinatorics. Explicit decompositions as CW-complexes are
constructed. Their open cells are interiors of toric cubes and their boundaries
are subcomplexes. The motivating example of a toric cube is the edge-product
space in phylogenetics, and our work generalizes results known for that space.Comment: to appear in Rendiconti del Circolo Matematico di Palermo (special
issue on Algebraic Geometry
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