GPU-Based Parallel Particle Swarm Optimization Methods for Graph Drawing

Particle Swarm Optimization (PSO) is a population-based stochastic search technique for solving optimization problems, which has been proven to be effective in a wide range of applications. However, the computational efficiency on large-scale problems is still unsatisfactory. A graph drawing is a pictorial representation of the vertices and edges of a graph. Two PSO heuristic procedures, one serial and the other parallel, are developed for undirected graph drawing. Each particle corresponds to a different layout of the graph. The particle fitness is defined based on the concept of the energy in the force-directed method. The serial PSO procedure is executed on a CPU and the parallel PSO procedure is executed on a GPU. Two PSO procedures have different data structures and strategies. The performance of the proposed methods is evaluated through several different graphs. The experimental results show that the two PSO procedures are both as effective as the force-directed method, and the parallel procedure is more advantageous than the serial procedure for larger graphs

FieldPlacer - A flexible, fast and unconstrained force-directed placement method for heterogeneous reconfigurable logic architectures

The field of placement methods for components of integrated circuits, especially in the domain of reconfigurable chip architectures, is mainly dominated by a handful of concepts. While some of these are easy to apply but difficult to adapt to new situations, others are more flexible but rather complex to realize. This work presents the FieldPlacer framework, a flexible, fast and unconstrained force-directed placement method for heterogeneous reconfigurable logic architectures, in particular for the ever important heterogeneous FPGAs. In contrast to many other force-directed placers, this approach is called ‘unconstrained’ as it does not require a priori fixed logic elements in order to calculate a force equilibrium as the solution to a system of equations. Instead, it is based on a free spring embedder simulation of a graph representation which includes all logic block types of a design simultaneously. The FieldPlacer framework offers a huge amount of flexibility in applying different distance norms (e. g., the Manhattan distance) for the force-directed layout and aims at creating adapted layouts for various objective functions, e. g., highest performance or improved routability. Depending on the individual situation, a runtime-quality trade-off can be considered to either produce a decent placement in a very short time or to generate an exceptionally good placement, which takes longer. An extensive comparison with the latest simulated annealing placement method from the well-known Versatile Place and Route (VPR) framework shows that the FieldPlacer approach can create placements of comparable quality much faster than VPR or, alternatively, generate better placements in the same time. The flexibility in defining arbitrary objective functions and the intuitive adaptability of the method, which, among others, includes different concepts from the field of graph drawing, should facilitate further developments with this framework, e. g., for new upcoming optimization targets like the energy consumption of an implemented design

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

Visual analytics for relationships in scientific data

Domain scientists hope to address grand scientific challenges by exploring the abundance of data generated and made available through modern high-throughput techniques. Typical scientific investigations can make use of novel visualization tools that enable dynamic formulation and fine-tuning of hypotheses to aid the process of evaluating sensitivity of key parameters. These general tools should be applicable to many disciplines: allowing biologists to develop an intuitive understanding of the structure of coexpression networks and discover genes that reside in critical positions of biological pathways, intelligence analysts to decompose social networks, and climate scientists to model extrapolate future climate conditions. By using a graph as a universal data representation of correlation, our novel visualization tool employs several techniques that when used in an integrated manner provide innovative analytical capabilities. Our tool integrates techniques such as graph layout, qualitative subgraph extraction through a novel 2D user interface, quantitative subgraph extraction using graph-theoretic algorithms or by querying an optimized B-tree, dynamic level-of-detail graph abstraction, and template-based fuzzy classification using neural networks. We demonstrate our system using real-world workflows from several large-scale studies. Parallel coordinates has proven to be a scalable visualization and navigation framework for multivariate data. However, when data with thousands of variables are at hand, we do not have a comprehensive solution to select the right set of variables and order them to uncover important or potentially insightful patterns. We present algorithms to rank axes based upon the importance of bivariate relationships among the variables and showcase the efficacy of the proposed system by demonstrating autonomous detection of patterns in a modern large-scale dataset of time-varying climate simulation

09061 Abstracts Collection -- Combinatorial Scientific Computing

From 01.02.2009 to 06.02.2009, the Dagstuhl Seminar 09061 ``Combinatorial Scientific Computing \u27\u27 was held in Schloss Dagstuhl -- Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Preventing premature convergence and proving the optimality in evolutionary algorithms

http://ea2013.inria.fr//proceedings.pdfInternational audienceEvolutionary Algorithms (EA) usually carry out an efficient exploration of the search-space, but get often trapped in local minima and do not prove the optimality of the solution. Interval-based techniques, on the other hand, yield a numerical proof of optimality of the solution. However, they may fail to converge within a reasonable time due to their inability to quickly compute a good approximation of the global minimum and their exponential complexity. The contribution of this paper is a hybrid algorithm called Charibde in which a particular EA, Differential Evolution, cooperates with a Branch and Bound algorithm endowed with interval propagation techniques. It prevents premature convergence toward local optima and outperforms both deterministic and stochastic existing approaches. We demonstrate its efficiency on a benchmark of highly multimodal problems, for which we provide previously unknown global minima and certification of optimality

Computational Methods for Learning and Inference on Dynamic Networks.

Networks are ubiquitous in science, serving as a natural representation for many complex physical, biological, and social phenomena. Significant efforts have been dedicated to analyzing such network representations to reveal their structure and provide some insight towards the phenomena of interest. Computational methods for analyzing networks have typically been designed for static networks, which cannot capture the time-varying nature of many complex phenomena. In this dissertation, I propose new computational methods for machine learning and statistical inference on dynamic networks with time-evolving structures. Specifically, I develop methods for visualization, tracking, clustering, and prediction of dynamic networks. The proposed methods take advantage of the dynamic nature of the network by intelligently combining observations at multiple time steps. This involves the development of novel statistical models and state-space representations of dynamic networks. Using the methods proposed in this dissertation, I identify long-term trends and structural changes in a variety of dynamic network data sets including a social network of spammers and a network of physical proximity among employees and students at a university campus.PHDElectrical Engineering-SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/94022/1/xukevin_1.pd