相关论文: Polyhedral Combinatorics of UPGMA Cones

We study the Bergman complex B(M) of a matroid M: a polyhedral complex which arises in algebraic geometry, but which we describe purely combinatorially. We prove that a natural subdivision of the Bergman complex of M is a geometric…

This paper deals with lattice congruences of the weak order on the symmetric group, and initiates the investigation of the cover graphs of the corresponding lattice quotients. These graphs also arise as the skeleta of the so-called…

A shape of a combinatorial polytope is a convex embedding into Euclidean space. We provide necessary and sufficient conditions for a piecewise linear map between two shapes of the same polytope to be a compression (respectively a weak…

Some combinatorial properties of fixed boundary rhombus random tilings with octagonal symmetry are studied. A geometrical analysis of their configuration space is given as well as a description in terms of discrete dynamical systems, thus…

Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…

We consider the problem of learning the structure of undirected graphical models with bounded treewidth, within the maximum likelihood framework. This is an NP-hard problem and most approaches consider local search techniques. In this…

We propose an approach to analyze the asymptotic behavior of P\'olya urns based on the contraction method. For this, a new combinatorial discrete time embedding of the evolution of the urn into random rooted trees is developed. A…

The phylogenetic tree space, introduced by Billera, Holmes, and Vogtmann, is a cone over a simplicial complex. In this short article, we construct this complex from local gluings of classical polytopes, the associahedron and the…

Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…

The plucking polynomial is an invariant of rooted trees with connections to knot theory. The polynomial was constructed in 2014 as a tool to analyze lattice crossings after taking the quotient by the Kauffman bracket skein relations. In…

Matrix Factorization plays an important role in machine learning such as Non-negative Matrix Factorization, Principal Component Analysis, Dictionary Learning, etc. However, most of the studies aim to minimize the loss by measuring the…

This paper presents a computational framework for the Principal Geodesic Analysis of merge trees (MT-PGA), a novel adaptation of the celebrated Principal Component Analysis (PCA) framework [87] to the Wasserstein metric space of merge trees…

Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…

Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees.…

Preorder polytopes, defined from preorders on finite sets, are introduced and studied from a lattice point enumeration point of view. They naturally generalize arbor polytopes, recently introduced and studied by the second named author.…

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…

In this work we present a general and versatile algorithmic framework for exhaustively generating a large variety of different combinatorial objects, based on encoding them as permutations. This approach provides a unified view on many…

For large ranks, there is no good algorithm that decides whether a given lattice has an orthonormal basis. But when the lattice is given with enough symmetry, we can construct a provably deterministic polynomial-time algorithm to accomplish…

Exploratory data analysis is crucial for developing and understanding classification models from high-dimensional datasets. We explore the utility of a new unsupervised tree ensemble called uncharted forest for visualizing class…

We study rational homology groups of one-point compactifications of spaces of complex monic polynomials with multiple roots. These spaces are indexed by number partitions. A standard reformulation in terms of quotients of orbit arrangements…