Phylogenetic Analysis Via DC Programming

The evolutionary history of species may be described by a phylogenetic tree whose topology captures ancestral relationships among the species, and whose branch lengths denote evolution times. For a fixed topology and an assumed probabilistic model of nucleotide substitution, we show that the likelihood of a given tree is a d.c. (difference of convex) function … Read more

Solving Large-Scale Semidefinite Programs in Parallel

We describe an approach to the parallel and distributed solution of large-scale, block structured semidefinite programs using the spectral bundle method. Various elements of this approach (such as data distribution, an implicitly restarted Lanczos method tailored to handle block diagonal structure, a mixed polyhedral-semidefinite subdifferential model, and other aspects related to parallelism) are combined in … Read more