Statistical learning with phylogenetic network invariants

Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a Markov process on a phylogenetic network. Previous work has shown that a site-pattern probability distributions from a Jukes-Cantor phylogenetic network model must satisfy certain algebraic invariants. As a corollary, aspects of the phylogenetic network are theoretically identifiable from site-pattern frequencies. In practice, because of the probabilistic nature of sequence evolution, the phylogenetic network invariants will rarely be satisfied, even for data generated under the model. Thus, using network invariants for inferring phylogenetic networks requires some means of interpreting the residuals, or deviations from zero, when observed site-pattern frequencies are substituted into the invariants. In this work, we propose a method of utilizing invariant residuals and support vector machines to infer 4-leaf level-one phylogenetic networks, from which larger networks can be reconstructed. Given data for a set of species, the support vector machine is first trained on model data to learn the patterns of residuals corresponding to different network structures to classify the network that produced the data. We demonstrate the performance of our method on simulated data from the specified model and primate data.Comment: 27 pages, 8 figure

Principal Landau Determinants

We reformulate the Landau analysis of Feynman integrals with the aim of advancing the state of the art in modern particle-physics computations. We contribute new algorithms for computing Landau singularities, using tools from polyhedral geometry and symbolic/numerical elimination. Inspired by the work of Gelfand, Kapranov, and Zelevinsky (GKZ) on generalized Euler integrals, we define the principal Landau determinant of a Feynman diagram. We illustrate with a number of examples that this algebraic formalism allows to compute many components of the Landau singular locus. We adapt the GKZ framework by carefully specializing Euler integrals to Feynman integrals. For instance, ultraviolet and infrared singularities are detected as irreducible components of an incidence variety, which project dominantly to the kinematic space. We compute principal Landau determinants for the infinite families of one-loop and banana diagrams with different mass configurations, and for a range of cutting-edge Standard Model processes. Our algorithms build on the Julia package Landau.jl and are implemented in the new open-source package PLD.jl available at https://mathrepo.mis.mpg.de/PLD/.Comment: 72 page

Geometric and Topological Combinatorics

The 2007 Oberwolfach meeting “Geometric and Topological Combinatorics” presented a great variety of investigations where topological and algebraic methods are brought into play to solve combinatorial and geometric problems, but also where geometric and combinatorial ideas are applied to topological questions

Learning Algebraic Varieties from Samples

We seek to determine a real algebraic variety from a fixed finite subset of points. Existing methods are studied and new methods are developed. Our focus lies on aspects of topology and algebraic geometry, such as dimension and defining polynomials. All algorithms are tested on a range of datasets and made available in a Julia package

On the Heegaard Floer homology of Dehn surgery and unknotting number

n this thesis we generalise three theorems from the literature on Heegaard Floer homology and Dehn surgery: one by Ozsv ́ath and Szab ́o on deficiency symmetries in half-integral L -space surgeries, and two by Greene which use Donaldson’s diagonali- sation theorem as an obstruction to integral and half-integral L -space surgeries. Our generalisation is two-fold: first, we eliminate the L -space conditions, opening these techniques up for use with much more general 3-manifolds, and second, we unify the integral and half-integral surgery results into a broader theorem applicable to non- zero rational surgeries in S 3 which bound sharp, simply connected, negative-definite smooth 4-manifolds. Such 3-manifolds are quite common and include, for example, a huge number of Seifert fibred spaces. Over the course of the first three chapters, we begin by introducing background material on knots in 3-manifolds, the intersection form of a simply connected 4- manifold, Spin- and Spin c -structures on 3- and 4-manifolds, and Heegaard Floer ho- mology (including knot Floer homology). While none of the results in these chapters are original, all of them are necessary to make sense of what follows. In Chapter 4, we introduce and prove our main theorems, using arguments that are predominantly algebraic or combinatorial in nature. We then apply these new theorems to the study of unknotting number in Chapter 5, making considerable headway into the extremely difficult problem of classifying the 3-strand pretzel knots with unknotting number one. Finally, in Chapter 6, we present further applications of the main theorems, ranging from a plan of attack on the famous Seifert fibred space realisation problem to more biologically motivated problems concerning rational tangle replacement. An appendix on the implications of our theorems for DNA topology is provided at the end.Open Acces