Algorithms for Visualizing Phylogenetic Networks

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we restrict our attention to galled trees and galled networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Crossing Minimization for 1-page and 2-page Drawings of Graphs with Bounded Treewidth

We investigate crossing minimization for 1-page and 2-page book drawings. We show that computing the 1-page crossing number is fixed-parameter tractable with respect to the number of crossings, that testing 2-page planarity is fixed-parameter tractable with respect to treewidth, and that computing the 2-page crossing number is fixed-parameter tractable with respect to the sum of the number of crossings and the treewidth of the input graph. We prove these results via Courcelle's theorem on the fixed-parameter tractability of properties expressible in monadic second order logic for graphs of bounded treewidth.Comment: Graph Drawing 201

Clustered 3-Colouring Graphs of Bounded Degree

A (not necessarily proper) vertex colouring of a graph has "clustering" $c$ if every monochromatic component has at most $c$ vertices. We prove that planar graphs with maximum degree $\Delta$ are 3-colourable with clustering $O(\Delta^2)$. The previous best bound was $O(\Delta^{37})$. This result for planar graphs generalises to graphs that can be drawn on a surface of bounded Euler genus with a bounded number of crossings per edge. We then prove that graphs with maximum degree $\Delta$ that exclude a fixed minor are 3-colourable with clustering $O(\Delta^5)$. The best previous bound for this result was exponential in $\Delta$.Comment: arXiv admin note: text overlap with arXiv:1904.0479

Drawing Activity Diagrams

Activity diagrams experience an increasing importance in the design and description of software systems. Unfortunately, previous approaches for automatic layout support fail or are just insufficient to capture the complexity of the related requirements. We propose a new approach tailored to the needs of activity diagrams which combines the advantages of two fundamental layout concepts called "Sugiyama's approach" and "topology-shape-metrics approach", originally developed for layered layouts of directed graphs and for orthogonal layout of undirected graphs respectively

Connecting the dots (with minimum crossings)

We study a prototype Crossing Minimization problem, defined as follows. Let F be an infinite family of (possibly vertex-labeled) graphs. Then, given a set P of (possibly labeled) n points in the Euclidean plane, a collection L subseteq Lines(P)={l: l is a line segment with both endpoints in P}, and a non-negative integer k, decide if there is a subcollection L'subseteq L such that the graph G=(P,L') is isomorphic to a graph in F and L' has at most k crossings. By G=(P,L'), we refer to the graph on vertex set P, where two vertices are adjacent if and only if there is a line segment that connects them in L'. Intuitively, in Crossing Minimization, we have a set of locations of interest, and we want to build/draw/exhibit connections between them (where L indicates where it is feasible to have these connections) so that we obtain a structure in F. Natural choices for F are the collections of perfect matchings, Hamiltonian paths, and graphs that contain an (s,t)-path (a path whose endpoints are labeled). While the objective of seeking a solution with few crossings is of interest from a theoretical point of view, it is also well motivated by a wide range of practical considerations. For example, links/roads (such as highways) may be cheaper to build and faster to traverse, and signals/moving objects would collide/interrupt each other less often. Further, graphs with fewer crossings are preferred for graphic user interfaces. As a starting point for a systematic study, we consider a special case of Crossing Minimization. Already for this case, we obtain NP-hardness and W[1]-hardness results, and ETH-based lower bounds. Specifically, suppose that the input also contains a collection D of d non-crossing line segments such that each point in P belongs to exactly one line in D, and L does not contain line segments between points on the same line in D. Clearly, Crossing Minimization is the case where d=n - then, P is in general position. The case of d=2 is of interest not only because it is the most restricted non-trivial case, but also since it corresponds to a class of graphs that has been well studied - specifically, it is Crossing Minimization where G=(P,L) is a (bipartite) graph with a so called two-layer drawing. For d=2, we consider three basic choices of F. For perfect matchings, we show (i) NP-hardness with an ETH-based lower bound, (ii) solvability in subexponential parameterized time, and (iii) existence of an O(k^2)-vertex kernel. Second, for Hamiltonian paths, we show (i) solvability in subexponential parameterized time, and (ii) existence of an O(k^2)-vertex kernel. Lastly, for graphs that contain an (s,t)-path, we show (i) NP-hardness and W[1]-hardness, and (ii) membership in XP

Reduced-Dimension Linear Transform Coding of Correlated Signals in Networks

A model, called the linear transform network (LTN), is proposed to analyze the compression and estimation of correlated signals transmitted over directed acyclic graphs (DAGs). An LTN is a DAG network with multiple source and receiver nodes. Source nodes transmit subspace projections of random correlated signals by applying reduced-dimension linear transforms. The subspace projections are linearly processed by multiple relays and routed to intended receivers. Each receiver applies a linear estimator to approximate a subset of the sources with minimum mean squared error (MSE) distortion. The model is extended to include noisy networks with power constraints on transmitters. A key task is to compute all local compression matrices and linear estimators in the network to minimize end-to-end distortion. The non-convex problem is solved iteratively within an optimization framework using constrained quadratic programs (QPs). The proposed algorithm recovers as special cases the regular and distributed Karhunen-Loeve transforms (KLTs). Cut-set lower bounds on the distortion region of multi-source, multi-receiver networks are given for linear coding based on convex relaxations. Cut-set lower bounds are also given for any coding strategy based on information theory. The distortion region and compression-estimation tradeoffs are illustrated for different communication demands (e.g. multiple unicast), and graph structures.Comment: 33 pages, 7 figures, To appear in IEEE Transactions on Signal Processin

Connecting the Dots (with Minimum Crossings)

We study a prototype Crossing Minimization problem, defined as follows. Let F be an infinite family of (possibly vertex-labeled) graphs. Then, given a set P of (possibly labeled) n points in the Euclidean plane, a collection L subseteq Lines(P)={l: l is a line segment with both endpoints in P}, and a non-negative integer k, decide if there is a subcollection L\u27subseteq L such that the graph G=(P,L\u27) is isomorphic to a graph in F and L\u27 has at most k crossings. By G=(P,L\u27), we refer to the graph on vertex set P, where two vertices are adjacent if and only if there is a line segment that connects them in L\u27. Intuitively, in Crossing Minimization, we have a set of locations of interest, and we want to build/draw/exhibit connections between them (where L indicates where it is feasible to have these connections) so that we obtain a structure in F. Natural choices for F are the collections of perfect matchings, Hamiltonian paths, and graphs that contain an (s,t)-path (a path whose endpoints are labeled). While the objective of seeking a solution with few crossings is of interest from a theoretical point of view, it is also well motivated by a wide range of practical considerations. For example, links/roads (such as highways) may be cheaper to build and faster to traverse, and signals/moving objects would collide/interrupt each other less often. Further, graphs with fewer crossings are preferred for graphic user interfaces. As a starting point for a systematic study, we consider a special case of Crossing Minimization. Already for this case, we obtain NP-hardness and W[1]-hardness results, and ETH-based lower bounds. Specifically, suppose that the input also contains a collection D of d non-crossing line segments such that each point in P belongs to exactly one line in D, and L does not contain line segments between points on the same line in D. Clearly, Crossing Minimization is the case where d=n - then, P is in general position. The case of d=2 is of interest not only because it is the most restricted non-trivial case, but also since it corresponds to a class of graphs that has been well studied - specifically, it is Crossing Minimization where G=(P,L) is a (bipartite) graph with a so called two-layer drawing. For d=2, we consider three basic choices of F. For perfect matchings, we show (i) NP-hardness with an ETH-based lower bound, (ii) solvability in subexponential parameterized time, and (iii) existence of an O(k^2)-vertex kernel. Second, for Hamiltonian paths, we show (i) solvability in subexponential parameterized time, and (ii) existence of an O(k^2)-vertex kernel. Lastly, for graphs that contain an (s,t)-path, we show (i) NP-hardness and W[1]-hardness, and (ii) membership in XP