Incremental Grid-like Layout Using Soft and Hard Constraints

We explore various techniques to incorporate grid-like layout conventions into a force-directed, constraint-based graph layout framework. In doing so we are able to provide high-quality layout---with predominantly axis-aligned edges---that is more flexible than previous grid-like layout methods and which can capture layout conventions in notations such as SBGN (Systems Biology Graphical Notation). Furthermore, the layout is easily able to respect user-defined constraints and adapt to interaction in online systems and diagram editors such as Dunnart.Comment: Accepted to Graph Drawing 201

An open source rule induction tool for transfer-based SMT

In this paper we describe an open source tool for automatic induction of transfer rules. Transfer rule induction is carried out on pairs of dependency structures and their node alignment to produce all rules consistent with the node alignment. We describe an efficient algorithm for rule induction and give a detailed description of how to use the tool

Particle alignments and shape change in 66^{66}Ge and 68^{68}Ge

The structure of the $N \approx Z$ nuclei $^{66}$Ge and $^{68}$Ge is studied by the shell model on a spherical basis. The calculations with an extended $P+QQ$ Hamiltonian in the configuration space ($2p_{3/2}$, $1f_{5/2}$, $2p_{1/2}$, $1g_{9/2}$) succeed in reproducing experimental energy levels, moments of inertia and $Q$ moments in Ge isotopes. Using the reliable wave functions, this paper investigates particle alignments and nuclear shapes in $^{66}$Ge and $^{68}$Ge. It is shown that structural changes in the four sequences of the positive- and negative-parity yrast states with even $J$ and odd $J$ are caused by various types of particle alignments in the $g_{9/2}$ orbit. The nuclear shape is investigated by calculating spectroscopic $Q$ moments of the first and second $2^+$ states, and moreover the triaxiality is examined by the constrained Hatree-Fock method. The changes of the first band crossing and the nuclear deformation depending on the neutron number are discussed.Comment: 18 pages, 21 figures; submitted to Phys. Rev.

Structure of conflict graphs in constraint alignment problems and algorithms

We consider the constrained graph alignment problem which has applications in biological network analysis. Given two input graphs $G_1=(V_1,E_1), G_2=(V_2,E_2)$, a pair of vertex mappings induces an {\it edge conservation} if the vertex pairs are adjacent in their respective graphs. %In general terms The goal is to provide a one-to-one mapping between the vertices of the input graphs in order to maximize edge conservation. However the allowed mappings are restricted since each vertex from $V_1$ (resp. $V_2$) is allowed to be mapped to at most $m_1$ (resp. $m_2$) specified vertices in $V_2$ (resp. $V_1$). Most of results in this paper deal with the case $m_2=1$ which attracted most attention in the related literature. We formulate the problem as a maximum independent set problem in a related {\em conflict graph} and investigate structural properties of this graph in terms of forbidden subgraphs. We are interested, in particular, in excluding certain wheals, fans, cliques or claws (all terms are defined in the paper), which corresponds in excluding certain cycles, paths, cliques or independent sets in the neighborhood of each vertex. Then, we investigate algorithmic consequences of some of these properties, which illustrates the potential of this approach and raises new horizons for further works. In particular this approach allows us to reinterpret a known polynomial case in terms of conflict graph and to improve known approximation and fixed-parameter tractability results through efficiently solving the maximum independent set problem in conflict graphs. Some of our new approximation results involve approximation ratios that are function of the optimal value, in particular its square root; this kind of results cannot be achieved for maximum independent set in general graphs.Comment: 22 pages, 6 figure

Stress-Minimizing Orthogonal Layout of Data Flow Diagrams with Ports

We present a fundamentally different approach to orthogonal layout of data flow diagrams with ports. This is based on extending constrained stress majorization to cater for ports and flow layout. Because we are minimizing stress we are able to better display global structure, as measured by several criteria such as stress, edge-length variance, and aspect ratio. Compared to the layered approach, our layouts tend to exhibit symmetries, and eliminate inter-layer whitespace, making the diagrams more compact