arXiv subjects
Publications and source records attributed to Thomas Hackl.
A drawing of a graph is {\em $x$-monotone} if every vertical line intersects each edge of the graph at most once. We present an $O(n^5)$ time algorithm for deciding whether a simple drawing of the complete graph $K_n$ is weakly isomorphic to an $x$-monotone drawing. We note that this algorithm can also decide whether a drawing of $K_n$ is strongly isomorphic to an $x$-monotone drawing.
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools often fail to efficiently integrate the diverse datasets produced in comparative genomics, lack intuitive interfaces to construct complex plots and are missing functionalities to inspect the underlying data iteratively and at scale. Here, we introduce gggenomes, a versatile R package designed to overcome these challenges by extending the widely used ggplot2 framework for comparative genomics. gggenomes is available from CRAN and GitHub, accompanied by detailed and user-friendly documentation (https://thackl.github.io/gggenomes).
Given two distinct point sets $P$ and $Q$ in the plane, we say that $Q$ \emph{blocks} $P$ if no two points of $P$ are adjacent in any Delaunay triangulation of $P\cup Q$. Aichholzer et al. (2013) showed that any set $P$ of $n$ points in general position can be blocked by $\frac{3}{2}n$ points and that every set $P$ of $n$ points in convex position can be blocked by $\frac{5}{4}n$ points. Moreover, they conjectured that, if $P$ is in convex position, $n$ blocking points are sufficient and necessary. The necessity was recently shown by Biniaz (2021) who proved that every point set in general position requires $n$ blocking points. Here we investigate the variant, where blocking points can only lie outside of the convex hull of the given point set. We show that $\frac{5}{4}n-O(1)$ such \emph{exterior-blocking} points are sometimes necessary, even if the given point set is in convex position. As a consequence we obtain that, if the conjecture of Aichholzer et al. for the original setting was true, then minimal blocking sets of some point configurations $P$ would have to contain points inside of the convex hull of $P$.
The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies - a crucial step towards unlocking the biology of the organism of interest - has remained a complex challenge that often requires advanced bioinformatics expertise. Here we present MOSGA, a genome annotation framework for eukaryotic genomes with a user-friendly web-interface that generates and integrates annotations from various tools. The aggregated results can be analyzed with a fully integrated genome browser and are provided in a format ready for submission to NCBI. MOSGA is built on a portable, customizable, and easily extendible Snakemake backend, and thus, can be tailored to a wide range of users and projects. We provide MOSGA as a publicly free available web service at https://mosga.mathematik.uni-marburg.de and as a docker container at registry.gitlab.com/mosga/mosga:latest. Source code can be found at https://gitlab.com/mosga/mosga
We consider the following question: How many edge-disjoint plane spanning trees are contained in a complete geometric graph $GK_n$ on any set $S$ of $n$ points in general position in the plane? We show that this number is in $\Omega(\sqrt{n})$. Further, we consider variants of this problem by bounding the diameter and the degree of the trees (in particular considering spanning paths).
Given a set of points in the plane, we want to establish a connection network between these points that consists of several disjoint layers. Motivated by sensor networks, we want that each layer is spanning and plane, and that no edge is very long (when compared to the minimum length needed to obtain a spanning graph). We consider two different approaches: first we show an almost optimal centralized approach to extract two graphs. Then we show a constant factor approximation for a distributed model in which each point can compute its adjacencies using only local information. In both cases the obtained layers are plane
Let $P$ be a finite set of points in the plane in general position, that is, no three points of $P$ are on a common line. We say that a set $H$ of five points from $P$ is a $5$-hole in $P$ if $H$ is the vertex set of a convex $5$-gon containing no other points of $P$. For a positive integer $n$, let $h_5(n)$ be the minimum number of 5-holes among all sets of $n$ points in the plane in general position. Despite many efforts in the last 30 years, the best known asymptotic lower and upper bounds for $h_5(n)$ have been of order $\Omega(n)$ and $O(n^2)$, respectively. We show that $h_5(n) = \Omega(n\log^{4/5}{n})$, obtaining the first superlinear lower bound on $h_5(n)$. The following structural result, which might be of independent interest, is a crucial step in the proof of this lower bound. If a finite set $P$ of points in the plane in general position is partitioned by a line $\ell$ into two subsets, each of size at least 5 and not in convex position, then $\ell$ intersects the convex hull of some 5-hole in $P$. The proof of this result is computer-assisted.
The straight skeleton of a polygon is the geometric graph obtained by tracing the vertices during a mitered offsetting process. It is known that the straight skeleton of a simple polygon is a tree, and one can naturally derive directions on the edges of the tree from the propagation of the shrinking process. In this paper, we ask the reverse question: Given a tree with directed edges, can it be the straight skeleton of a polygon? And if so, can we find a suitable simple polygon? We answer these questions for all directed trees where the order of edges around each node is fixed.
We study a generalization of the classical problem of the illumination of polygons. Instead of modeling a light source we model a wireless device whose radio signal can penetrate a given number $k$ of walls. We call these objects $k$-modems and study the minimum number of $k$-modems sufficient and sometimes necessary to illuminate monotone and monotone orthogonal polygons. We show that every monotone polygon with $n$ vertices can be illuminated with $\big\lceil \frac{n-2}{2k+3} \big\rceil$ $k$-modems. In addition, we exhibit examples of monotone polygons requiring at least $\lceil \frac {n-2} {2k+3}\rceil$ $k$-modems to be illuminated. For monotone orthogonal polygons with $n$ vertices we show that for $k=1$ and for even $k$, every such polygon can be illuminated with $\big\lceil \frac{n-2}{2k+4} \big\rceil$ $k$-modems, while for odd $k\geq3$, $\big\lceil \frac{n-2}{2k+6} \big\rceil$ $k$-modems are always sufficient. Further, by presenting according examples of monotone orthogonal polygons, we show that both bounds are tight.
We consider a variation of the classical Erd\H{o}s-Szekeres problems on the existence and number of convex $k$-gons and $k$-holes (empty $k$-gons) in a set of $n$ points in the plane. Allowing the $k$-gons to be non-convex, we show bounds and structural results on maximizing and minimizing their numbers. Most noteworthy, for any $k$ and sufficiently large $n$, we give a quadratic lower bound for the number of $k$-holes, and show that this number is maximized by sets in convex position.
A directed path whose edges are assigned labels "up", "down", "right", or "left" is called \emph{four-directional}, and \emph{three-directional} if at most three out of the four labels are used. A \emph{direction-consistent embedding} of an \mbox{$n$-vertex} four-directional path $P$ on a set $S$ of $n$ points in the plane is a straight-line drawing of $P$ where each vertex of $P$ is mapped to a distinct point of $S$ and every edge points to the direction specified by its label. We study planar direction-consistent embeddings of three- and four-directional paths and provide a complete picture of the problem for convex point sets.
Let $P=B\cup R$ be a set of $2n$ points in general position, where $B$ is a set of $n$ blue points and $R$ a set of $n$ red points. A \emph{$BR$-matching} is a plane geometric perfect matching on $P$ such that each edge has one red endpoint and one blue endpoint. Two $BR$-matchings are compatible if their union is also plane. The \emph{transformation graph of $BR$-matchings} contains one node for each $BR$-matching and an edge joining two such nodes if and only if the corresponding two $BR$-matchings are compatible. In SoCG 2013 it has been shown by Aloupis, Barba, Langerman, and Souvaine that this transformation graph is always connected, but its diameter remained an open question. In this paper we provide an alternative proof for the connectivity of the transformation graph and prove an upper bound of $2n$ for its diameter, which is asymptotically tight.
We study monotone simultaneous embeddings of upward planar digraphs, which are simultaneous embeddings where the drawing of each digraph is upward planar, and the directions of the upwardness of different graphs can differ. We first consider the special case where each digraph is a directed path. In contrast to the known result that any two directed paths admit a monotone simultaneous embedding, there exist examples of three paths that do not admit such an embedding for any possible choice of directions of monotonicity. We prove that if a monotone simultaneous embedding of three paths exists then it also exists for any possible choice of directions of monotonicity. We provide a polynomial-time algorithm that, given three paths, decides whether a monotone simultaneous embedding exists and, in the case of existence, also constructs such an embedding. On the other hand, we show that already for three paths, any monotone simultaneous embedding might need a grid of exponential (w.r.t. the number of vertices) size. For more than three paths, we present a polynomial-time algorithm that, given any number of paths and predefined directions of monotonicity, decides whether the paths admit a monotone simultaneous embedding with respect to the given directions, including the construction of a solution if it exists. Further, we show several implications of our results on monotone simultaneous embeddings of general upward planar digraphs. Finally, we discuss complexity issues related to our problems.
In this paper we consider the flip operation for combinatorial pointed pseudo-triangulations where faces have size 3 or 4, so-called combinatorial 4-PPTs. We show that every combinatorial 4-PPT is stretchable to a geometric pseudo-triangulation, which in general is not the case if faces may have size larger than 4. Moreover, we prove that the flip graph of combinatorial 4-PPTs is connected and has diameter $O(n^2)$, even in the case of labeled vertices with fixed outer face. For this case we provide an $\Omega(n\log n)$ lower bound.
Polygons are a paramount data structure in computational geometry. While the complexity of many algorithms on simple polygons or polygons with holes depends on the size of the input polygon, the intrinsic complexity of the problems these algorithms solve is often related to the reflex vertices of the polygon. In this paper, we give an easy-to-describe linear-time method to replace an input polygon $\mathcal{P}$ by a polygon $\mathcal{P}'$ such that (1) $\mathcal{P}'$ contains $\mathcal{P}$, (2) $\mathcal{P}'$ has its reflex vertices at the same positions as $\mathcal{P}$, and (3) the number of vertices of $\mathcal{P}'$ is linear in the number of reflex vertices. Since the solutions of numerous problems on polygons (including shortest paths, geodesic hulls, separating point sets, and Voronoi diagrams) are equivalent for both $\mathcal{P}$ and $\mathcal{P}'$, our algorithm can be used as a preprocessing step for several algorithms and makes their running time dependent on the number of reflex vertices rather than on the size of $\mathcal{P}$.
A good drawing of a simple graph is a drawing on the sphere or, equivalently, in the plane in which vertices are drawn as distinct points, edges are drawn as Jordan arcs connecting their end vertices, and any pair of edges intersects at most once. In any good drawing, the edges of three pairwise connected vertices form a Jordan curve which we call a triangle. We say that a triangle is empty if one of the two connected components it induces does not contain any of the remaining vertices of the drawing of the graph. We show that the number of empty triangles in any good drawing of the complete graph $K_n$ with $n$ vertices is at least $n$.
We consider a coloring problem on dynamic, one-dimensional point sets: points appearing and disappearing on a line at given times. We wish to color them with k colors so that at any time, any sequence of p(k) consecutive points, for some function p, contains at least one point of each color. We prove that no such function p(k) exists in general. However, in the restricted case in which points appear gradually, but never disappear, we give a coloring algorithm guaranteeing the property at any time with p(k)=3k-2. This can be interpreted as coloring point sets in R^2 with k colors such that any bottomless rectangle containing at least 3k-2 points contains at least one point of each color. Here a bottomless rectangle is an axis-aligned rectangle whose bottom edge is below the lowest point of the set. For this problem, we also prove a lower bound p(k)>ck, where c>1.67. Hence for every k there exists a point set, every k-coloring of which is such that there exists a bottomless rectangle containing ck points and missing at least one of the k colors. Chen et al. (2009) proved that no such function $p(k)$ exists in the case of general axis-aligned rectangles. Our result also complements recent results from Keszegh and Palvolgyi on cover-decomposability of octants (2011, 2012).
Let $S$ be a $k$-colored (finite) set of $n$ points in $\mathbb{R}^d$, $d\geq 3$, in general position, that is, no {$(d + 1)$} points of $S$ lie in a common $(d - 1)$}-dimensional hyperplane. We count the number of empty monochromatic $d$-simplices determined by $S$, that is, simplices which have only points from one color class of $S$ as vertices and no points of $S$ in their interior. For $3 \leq k \leq d$ we provide a lower bound of $\Omega(n^{d-k+1+2^{-d}})$ and strengthen this to $\Omega(n^{d-2/3})$ for $k=2$. On the way we provide various results on triangulations of point sets in $\mathbb{R}^d$. In particular, for any constant dimension $d\geq3$, we prove that every set of $n$ points ($n$ sufficiently large), in general position in $\mathbb{R}^d$, admits a triangulation with at least $dn+\Omega(\log n)$ simplices.