arXiv subjects

Kevin M. Woods

Publications and source records attributed to Kevin M. Woods.

5 recordsLinked to original sources

arXiv2010

A finite calculus approach to Ehrhart polynomials

A rational polytope is the convex hull of a finite set of points in $\R^d$ with rational coordinates. Given a rational polytope $P \subseteq \R^d$, Ehrhart proved that, for $t\in\Z_{\ge 0}$, the function $#(tP \cap \Z^d)$ agrees with a quasi-polynomial $L_P(t)$, called the Ehrhart quasi-polynomial. The Ehrhart quasi-polynomial can be regarded as a discrete version of the volume of a polytope. We use that analogy to derive a new proof of Ehrhart's theorem. This proof also allows us to quickly prove two other facts about Ehrhart quasi-polynomials: McMullen's theorem about the periodicity of the individual coefficients of the quasi-polynomial and the Ehrhart-Macdonald theorem on reciprocity.

math.CO↗

arXiv2005

Parametric inference of recombination in HIV genomes

Recombination is an important event in the evolution of HIV. It affects the global spread of the pandemic as well as evolutionary escape from host immune response and from drug therapy within single patients. Comprehensive computational methods are needed for detecting recombinant sequences in large databases, and for inferring the parental sequences. We present a hidden Markov model to annotate a query sequence as a recombinant of a given set of aligned sequences. Parametric inference is used to determine all optimal annotations for all parameters of the model. We show that the inferred annotations recover most features of established hand-curated annotations. Thus, parametric analysis of the hidden Markov model is feasible for HIV full-length genomes, and it improves the detection and annotation of recombinant forms. All computational results, reference alignments, and C++ source code are available at http://bio.math.berkeley.edu/recombination/.

q-bio.GN↗

arXiv2004

Computing the period of an Ehrhart quasi-polynomial

If P is a rational polytope in R^d, then $i_P(t):=#(tP\cap Z^d)$ is a quasi-polynomial in t, called the Ehrhart quasi-polynomial of P. A period of i_P(t) is D(P), the smallest positive integer D such that D*P has integral vertices. Often, D(P) is the minimum period of i_P(t), but, in several interesting examples, the minimum period is smaller. We prove that, for fixed d, there is a polynomial time algorithm which, given a rational polytope P in R^d and an integer n, decides whether n is a period of i_P(t). In particular, there is a polynomial time algorithm to decide whether i_P(t) is a polynomial. We conjecture that, for fixed d, there is a polynomial time algorithm to compute the minimum period of i_P(t). The tools we use are rational generating functions.

math.CO↗

arXiv2004

Neighborhood complexes and generating functions for affine semigroups

Given a_1,a_2,...,a_n in Z^d, we examine the set, G, of all non-negative integer combinations of these a_i. In particular, we examine the generating function f(z)=\sum_{b\in G} z^b. We prove that one can write this generating function as a rational function using the neighborhood complex (sometimes called the complex of maximal lattice-free bodies or the Scarf complex) on a particular lattice in Z^n. In the generic case, this follows from algebraic results of D. Bayer and B. Sturmfels. Here we prove it geometrically in all cases, and we examine a generalization involving the neighborhood complex on an arbitrary lattice.

math.CO↗

arXiv2003

The Minimum Period of the Ehrhart Quasi-polynomial of a Rational Polytope

If $P\subset \R^d$ is a rational polytope, then $i_P(n):=#(nP\cap \Z^d)$ is a quasi-polynomial in $n$, called the Ehrhart quasi-polynomial of $P$. The period of $i_P(n)$ must divide $\LL(P)= \min \{n \in \Z_{> 0} \colon nP \text{is an integral polytope}\}$. Few examples are known where the period is not exactly $\LL(P)$. We show that for any $\LL$, there is a 2-dimensional triangle $P$ such that $\LL(P)=\LL$ but such that the period of $i_P(n)$ is 1, that is, $i_P(n)$ is a polynomial in $n$. We also characterize all polygons $P$ such that $i_P(n)$ is a polynomial. In addition, we provide a counterexample to a conjecture by T. Zaslavsky about the periods of the coefficients of the Ehrhart quasi-polynomial.

math.CO↗