A Breezing Proof of the KMW Bound

In their seminal paper from 2004, Kuhn, Moscibroda, and Wattenhofer (KMW) proved a hardness result for several fundamental graph problems in the LOCAL model: For any (randomized) algorithm, there are input graphs with $n$ nodes and maximum degree $\Delta$ on which $\Omega(\min\{\sqrt{\log n/\log \log n},\log \Delta/\log \log \Delta\})$ (expected) communication rounds are required to obtain polylogarithmic approximations to a minimum vertex cover, minimum dominating set, or maximum matching. Via reduction, this hardness extends to symmetry breaking tasks like finding maximal independent sets or maximal matchings. Today, more than $15$ years later, there is still no proof of this result that is easy on the reader. Setting out to change this, in this work, we provide a fully self-contained and $\mathit{simple}$ proof of the KMW lower bound. The key argument is algorithmic, and it relies on an invariant that can be readily verified from the generation rules of the lower bound graphs.Comment: 21 pages, 6 figure

Structural parameterizations for boxicity

The boxicity of a graph $G$ is the least integer $d$ such that $G$ has an intersection model of axis-aligned $d$-dimensional boxes. Boxicity, the problem of deciding whether a given graph $G$ has boxicity at most $d$, is NP-complete for every fixed $d \ge 2$. We show that boxicity is fixed-parameter tractable when parameterized by the cluster vertex deletion number of the input graph. This generalizes the result of Adiga et al., that boxicity is fixed-parameter tractable in the vertex cover number. Moreover, we show that boxicity admits an additive $1$-approximation when parameterized by the pathwidth of the input graph. Finally, we provide evidence in favor of a conjecture of Adiga et al. that boxicity remains NP-complete when parameterized by the treewidth.Comment: 19 page

Contours in Visualization

This thesis studies the visualization of set collections either via or defines as the relations among contours. In the first part, dynamic Euler diagrams are used to communicate and improve semimanually the result of clustering methods which allow clusters to overlap arbitrarily. The contours of the Euler diagram are rendered as implicit surfaces called blobs in computer graphics. The interaction metaphor is the moving of items into or out of these blobs. The utility of the method is demonstrated on data arising from the analysis of gene expressions. The method works well for small datasets of up to one hundred items and few clusters. In the second part, these limitations are mitigated employing a GPU-based rendering of Euler diagrams and mixing textures and colors to resolve overlapping regions better. The GPU-based approach subdivides the screen into triangles on which it performs a contour interpolation, i.e. a fragment shader determines for each pixel which zones of an Euler diagram it belongs to. The rendering speed is thus increased to allow multiple hundred items. The method is applied to an example comparing different document clustering results. The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Adapting popular graph drawing approaches to the problem of contour tree drawing it is found that they are unable to convey this information. Five aesthetic criteria for drawing contour trees are proposed and a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria is presented. The implementation is fast and effective for contour tree sizes usually used in interactive systems and also produces readable pictures for larger trees. Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods to analyze these model\''s validity. The fourth part of the thesis focuses on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; they are huge and high dimensional. Their most salient features are described by their so-called barrier tree -- a contour tree for discrete observation spaces. The changing folding landscapes of a growing RNA chain are visualized as an animation of the corresponding barrier tree sequence. The animation is created as an adaption of the foresight layout with tolerance algorithm for dynamic graph layout. The adaptation requires changes to the concept of supergraph and it layout. The thesis finishes with some thoughts on how these approaches can be combined and how the task the application should support can help inform the choice of visualization modality

Structural Data Recognition with Graph Model Boosting

This paper presents a novel method for structural data recognition using a large number of graph models. In general, prevalent methods for structural data recognition have two shortcomings: 1) Only a single model is used to capture structural variation. 2) Naive recognition methods are used, such as the nearest neighbor method. In this paper, we propose strengthening the recognition performance of these models as well as their ability to capture structural variation. The proposed method constructs a large number of graph models and trains decision trees using the models. This paper makes two main contributions. The first is a novel graph model that can quickly perform calculations, which allows us to construct several models in a feasible amount of time. The second contribution is a novel approach to structural data recognition: graph model boosting. Comprehensive structural variations can be captured with a large number of graph models constructed in a boosting framework, and a sophisticated classifier can be formed by aggregating the decision trees. Consequently, we can carry out structural data recognition with powerful recognition capability in the face of comprehensive structural variation. The experiments shows that the proposed method achieves impressive results and outperforms existing methods on datasets of IAM graph database repository.Comment: 8 page

Local Unitarity: a representation of differential cross-sections that is locally free of infrared singularities at any order

We propose a novel representation of differential scattering cross-sections that locally realises the direct cancellation of infrared singularities exhibited by its so-called real-emission and virtual degrees of freedom. We take advantage of the Loop-Tree Duality representation of each individual forward-scattering diagram and we prove that the ensuing expression is locally free of infrared divergences, applies at any perturbative order and for any process without initial-state collinear singularities. Divergences for loop momenta with large magnitudes are regulated using local ultraviolet counterterms that reproduce the usual Lagrangian renormalisation procedure of quantum field theories. Our representation is especially suited for a numerical implementation and we demonstrate its practical potential by computing fully numerically and without any IR counterterm the next-to-leading order accurate differential cross-section for the process $e^+ e^- \rightarrow d \bar{d}$. We also show first results beyond next-to-leading order by computing interference terms part of the N4LO-accurate inclusive cross-section of a $1\rightarrow 2+X$ scalar scattering process.Comment: 88 page

Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments