Classification of eight dimensional perfect forms

In this paper, we classify the perfect lattices in dimension 8. There are 10916 of them. Our classification heavily relies on exploiting symmetry in polyhedral computations. Here we describe algorithms making the classification possible.Comment: 14 page

Polyhedral Combinatorics of UPGMA Cones

Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive orthant induced by classifying the input vectors according to tree topologies returned by the algorithm. The partition lattice informs the study of UPGMA trees. We give a closed form for the extreme rays of UPGMA cones on n taxa, and compute the normalized volumes of the UPGMA cones for small n. Keywords: phylogenetic trees, polyhedral combinatorics, partition lattic

The tropical double description method

We develop a tropical analogue of the classical double description method allowing one to compute an internal representation (in terms of vertices) of a polyhedron defined externally (by inequalities). The heart of the tropical algorithm is a characterization of the extreme points of a polyhedron in terms of a system of constraints which define it. We show that checking the extremality of a point reduces to checking whether there is only one minimal strongly connected component in an hypergraph. The latter problem can be solved in almost linear time, which allows us to eliminate quickly redundant generators. We report extensive tests (including benchmarks from an application to static analysis) showing that the method outperforms experimentally the previous ones by orders of magnitude. The present tools also lead to worst case bounds which improve the ones provided by previous methods.Comment: 12 pages, prepared for the Proceedings of the Symposium on Theoretical Aspects of Computer Science, 2010, Nancy, Franc

Tropical polar cones, hypergraph transversals, and mean payoff games

We discuss the tropical analogues of several basic questions of convex duality. In particular, the polar of a tropical polyhedral cone represents the set of linear inequalities that its elements satisfy. We characterize the extreme rays of the polar in terms of certain minimal set covers which may be thought of as weighted generalizations of minimal transversals in hypergraphs. We also give a tropical analogue of Farkas lemma, which allows one to check whether a linear inequality is implied by a finite family of linear inequalities. Here, the certificate is a strategy of a mean payoff game. We discuss examples, showing that the number of extreme rays of the polar of the tropical cyclic polyhedral cone is polynomially bounded, and that there is no unique minimal system of inequalities defining a given tropical polyhedral cone.Comment: 27 pages, 6 figures, revised versio