arXiv research

Improved phylogenetic tree reconstruction using flexible branch length distributions.

Improved phylogenetic inference with normalizing flows.

Improved phylogenetic inference using VBPI-Mixtures for tree topology and branch length.

Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special features, including "sampled ancestors" in which we sequence a genotype along wit…

We define sink marks for branched complexes and find conditions for them to determine a branched surface structure. These will be used to construct branched surfaces in knot and tangle complements. We will extend Delman's theorem and prove that a Montesinos knot $K$ of length at least 3 has a persistently laminar branc…

New partial solution to Hurwitz problem for surface branched covers.

Branching Flows generates sequences of varying lengths using binary trees.

We prove existence and a.e. regularity of an area minimizing soap film with a bound on energy spanning a given Jordan curve in R^3. The energy of a film is defined to be the sum of its surface area and the length of its singular branched set. The class of surfaces over which area is minimized includes images of disks, …

For a branched cover between two closed orientable surfaces, the Riemann-Hurwitz formula relates the Euler characteristics of the surfaces, the total degree of the cover, and the total length of the partitions of the degree given by the local degrees at the preimages of the branching points. A very old problem asks whe…

Cube edges curves minimize systole length.

We show that a closed, connected, oriented, Riemannian $n$-manifold, admitting a branched cover of bounded length distortion from $\mathbb R^n$, has a virtually Abelian fundamental group.

\noindent Given a Riemann surface $M$, the \emph{complexity} of a branched cover of $M$ to the Riemann sphere $S^2$, of degree $d$ and with branching set of cardinality $n \geq 3$, is defined as $d$ times the hyperbolic area of the complement of its branching set in $S^2$. A branched cover $p \colon M \to S^2$ of degre…

The study introduces hyperbolic angles in Lorentzian spaces and characterizes curvature bounds.

Stability of branched immersions with energy constraints.

Study on minimal surfaces with constraints on index and branching order.

Closed geodesic nets on surfaces have limited branch points

We find a constructive bound for the word length of a generating set for the centralizer of an element of the Mapping Class Group. As a consequence, we show that it is algorithmically decidable whether two postcritically finite branched coverings of the sphere are Thurston equivalent.

This paper extends the work in [Suzuki, 1996] and presents an efficient depth-first branch-and-bound algorithm for learning Bayesian network structures, based on the minimum description length (MDL) principle, for a given (consistent) variable ordering. The algorithm exhaustively searches through all network structures…

A new variational method speeds up Bayesian phylogenetic inference.

We consider surface branch data with base surface the sphere, odd degree d, three branching points, and two partitions of d of the form (2,...,2,1) and (2,...,2,2h+1). If the third partition has length L, this datum satisfies the Riemann-Hurwitz necessary condition for realizability if h-L is odd and at least -1. For s…

Researchers create coordinates for hyperbolic surfaces, proving a magic formula.

Given a hyperbolic 3-manifold with torus boundary, we bound the change in volume under a Dehn filling where all slopes have length at least 2π. This result is applied to give explicit diagrammatic bounds on the volumes of many knots and links, as well as their Dehn fillings and branched covers. Finally, we use this res…

Study length functions on various groups and prove homomorphisms to finite groups.

We view closed orientable 3-manifolds as covers of S^3 branched over hyperbolic links. For a p-fold cover M \to S^3, branched over a hyperbolic link L, we assign the complexity p Vol(S^3 minus L) (where Vol is the hyperbolic volume). We define an invariant of 3-manifolds, called the link volume and denoted LV, that ass…

Analytic convex bodies' Poincaré series extended holomorphically.

Rational maps structure theorem with geometric decomposition and realizability proof.

The paper extends completeness notions to low-regularity spacetimes.

Study on moduli spaces of branched projective structures on surfaces.

We define a laminar branched surface to be a branched surface satisfying the following conditions: (1) Its horizontal boundary is incompressible; (2) there is no monogon; (3) there is no Reeb component; (4) there is no sink disk (after eliminating trivial bubbles in the branched surface). The first three conditions are…

We consider finite-sheeted, regular, possibly branched covering spaces of compact surfaces with boundary and the associated liftable and symmetric mapping class groups. In particular, we classify when either of these subgroups coincides with the entire mapping class group of the surface. As a consequence, we construct …

New criterion for branched covers between 2-spheres.

Given a branched covering of degree d between closed surfaces, it determines a collection of partitions of d, the branch data. In this work we show that any branch data are realized by an indecomposable primitive branched covering on a connected close surface N with Euler's characteristic less than or equal to 0. This …

Uniformly branching trees are equivalent to certain metric spaces.

The paper studies which branched covers can be lifted to braided embeddings.

We consider 3-dimensional pseudo-manifolds M with a given set of marked point V such that M-V is the interior of a compact 3-manifold with boundary. An ideal triangulation T of (M, V ) has V as its set of vertices. A branching (T, b) enhances T to a Delta-complex. Branched triangulations of (M, V ) are considered up to…

We propose to describe the variety of galaxies from SDSS by using only one affine parameter. To this aim, we build the Principal Curve (P-curve) passing through the spine of the data point cloud, considering the eigenspace derived from Principal Component Analysis of morphological, physical and photometric galaxy prope…

We present a method for the reconstruction of networks, based on the order of nodes visited by a stochastic branching process. Our algorithm reconstructs a network of minimal size that ensures consistency with the data. Crucially, we show that global consistency with the data can be achieved through purely local consid…

This article introduces the degenerate special Lagrangian equation (DSL) and develops the basic analytic tools to construct and study its solutions. The DSL governs geodesics in the space of positive graph Lagrangians in $\mathbb{C}^n.$ Existence of geodesics in the space of positive Lagrangians is an important step in…

The paper details folding of branched covers of the 3-sphere over knots.

In this work we characterize branch data of branched coverings of even degree over the projective plane which are realizable by indecomposable branched coverings.

Course on knots using branched coverings.

A branched covering surface-knot is a surface-knot in the form of a branched covering over an oriented surface-knot $F$, where we include the case when the covering has no branch points. A branched covering surface-knot is presented by a graph called a chart on a surface diagram of $F$. We can simplify a branched cover…

Techniques for constructing codimension 2 embeddings and immersions of the 2 and 3-fold branched covers of the 3 and 4-dimensional spheres are presented. These covers are in braided form, and it is in this sense that they are folded. More precisely the composition of the embedding (or immersion) and the canonical proje…

Formula compares metrics on branched coverings of line bundles.

A branched covering surface-knot is a surface-knot in the form of a branched covering over a surface-knot. For a branched covering surface-knot, we have a numerical invariant called the simplifying number. We show that branched covering surface-knots with degree three have the simplifying numbers less than three.

New examples show transverse knots are determined by their branched covers.

We establish a calculus for branched spines of 3-manifolds by means of branched Matveev-Piergallini moves and branched bubble-moves. We briefly indicate some of its possible applications in the study and definition of State-Sum Quantum Invariants.

Quantized Coulomb branches linked to skein algebras.