TGVizTab: An ontology visualisation extension for Protégé

Ontologies are gaining a lot of interest and many are being developed to provide a variety of knowledge services. There is an increasing need for tools to graphically and in-teractively visualise such modelling structures to enhance their clarification, verification and analysis. Protégé 2000 is one of the most popular ontology modelling tools currently available. This paper introduces TGVizTab; a new Protégé plugin based on TouchGraph technology to graphically visualise Protégé?s ontologies

An Efficient Parallel Solver for SDD Linear Systems

We present the first parallel algorithm for solving systems of linear equations in symmetric, diagonally dominant (SDD) matrices that runs in polylogarithmic time and nearly-linear work. The heart of our algorithm is a construction of a sparse approximate inverse chain for the input matrix: a sequence of sparse matrices whose product approximates its inverse. Whereas other fast algorithms for solving systems of equations in SDD matrices exploit low-stretch spanning trees, our algorithm only requires spectral graph sparsifiers

Fully Dynamic Connectivity in O(log⁡n(log⁡log⁡n)2)O(\log n(\log\log n)^2) Amortized Expected Time

Dynamic connectivity is one of the most fundamental problems in dynamic graph algorithms. We present a randomized Las Vegas dynamic connectivity data structure with $O(\log n(\log\log n)^2)$ amortized expected update time and $O(\log n/\log\log\log n)$ worst case query time, which comes very close to the cell probe lower bounds of Patrascu and Demaine (2006) and Patrascu and Thorup (2011)

Web Mediators for Accessible Browsing

We present a highly accurate method for classifying web pages based on link percentage, which is the percentage of text characters that are parts of links normalized by the number of all text characters on a web page. K-means clustering is used to create unique thresholds to differentiate index pages and article pages on individual web sites. Index pages contain mostly links to articles and other indices, while article pages contain mostly text. We also present a novel link grouping algorithm using agglomerative hierarchical clustering that groups links in the same spatial neighborhood together while preserving link structure. Grouping allows users with severe disabilities to use a scan-based mechanism to tab through a web page and select items. In experiments, we saw up to a 40-fold reduction in the number of commands needed to click on a link with a scan-based interface, which shows that we can vastly improve the rate of communication for users with disabilities. We used web page classification and link grouping to alter web page display on an accessible web browser that we developed to make a usable browsing interface for users with disabilities. Our classification method consistently outperformed a baseline classifier even when using minimal data to generate article and index clusters, and achieved classification accuracy of 94.0% on web sites with well-formed or slightly malformed HTML, compared with 80.1% accuracy for the baseline classifier.National Science Foundation (IIS-0308213, IIS-039009, IIS-0093367, P200A01031, EIA-0202067

JGraphT -- A Java library for graph data structures and algorithms

Mathematical software and graph-theoretical algorithmic packages to efficiently model, analyze and query graphs are crucial in an era where large-scale spatial, societal and economic network data are abundantly available. One such package is JGraphT, a programming library which contains very efficient and generic graph data-structures along with a large collection of state-of-the-art algorithms. The library is written in Java with stability, interoperability and performance in mind. A distinctive feature of this library is the ability to model vertices and edges as arbitrary objects, thereby permitting natural representations of many common networks including transportation, social and biological networks. Besides classic graph algorithms such as shortest-paths and spanning-tree algorithms, the library contains numerous advanced algorithms: graph and subgraph isomorphism; matching and flow problems; approximation algorithms for NP-hard problems such as independent set and TSP; and several more exotic algorithms such as Berge graph detection. Due to its versatility and generic design, JGraphT is currently used in large-scale commercial, non-commercial and academic research projects. In this work we describe in detail the design and underlying structure of the library, and discuss its most important features and algorithms. A computational study is conducted to evaluate the performance of JGraphT versus a number of similar libraries. Experiments on a large number of graphs over a variety of popular algorithms show that JGraphT is highly competitive with other established libraries such as NetworkX or the BGL.Comment: Major Revisio

When the path is never shortest: a reality check on shortest path biocomputation

Shortest path problems are a touchstone for evaluating the computing performance and functional range of novel computing substrates. Much has been published in recent years regarding the use of biocomputers to solve minimal path problems such as route optimisation and labyrinth navigation, but their outputs are typically difficult to reproduce and somewhat abstract in nature, suggesting that both experimental design and analysis in the field require standardising. This chapter details laboratory experimental data which probe the path finding process in two single-celled protistic model organisms, Physarum polycephalum and Paramecium caudatum, comprising a shortest path problem and labyrinth navigation, respectively. The results presented illustrate several of the key difficulties that are encountered in categorising biological behaviours in the language of computing, including biological variability, non-halting operations and adverse reactions to experimental stimuli. It is concluded that neither organism examined are able to efficiently or reproducibly solve shortest path problems in the specific experimental conditions that were tested. Data presented are contextualised with biological theory and design principles for maximising the usefulness of experimental biocomputer prototypes.Comment: To appear in: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

Interactive, tree-based graph visualization

We introduce an interactive graph visualization scheme that allows users to explore graphs by viewing them as a sequence of spanning trees, rather than the entire graph all at once. The user determines which spanning trees are displayed by selecting a vertex from the graph to be the root. Our main contributions are a graph drawing algorithm that generates meaningful representations of graphs using extracted spanning trees, and a graph animation algorithm for creating smooth, continuous transitions between graph drawings. We conduct experiments to measure how well our algorithms visualize graphs and compare them to another visualization scheme

Universal Compressed Text Indexing

The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression scheme, several different indexing solutions have been proposed in the last two decades. To date, the fastest indexes for repetitive texts are based on the run-length compressed Burrows-Wheeler transform and on the Compact Directed Acyclic Word Graph. The most space-efficient indexes, on the other hand, are based on the Lempel-Ziv parsing and on grammar compression. Indexes for more universal schemes such as collage systems and macro schemes have not yet been proposed. Very recently, Kempa and Prezza [STOC 2018] showed that all dictionary compressors can be interpreted as approximation algorithms for the smallest string attractor, that is, a set of text positions capturing all distinct substrings. Starting from this observation, in this paper we develop the first universal compressed self-index, that is, the first indexing data structure based on string attractors, which can therefore be built on top of any dictionary-compressed text representation. Let $\gamma$ be the size of a string attractor for a text of length $n$. Our index takes $O(\gamma\log(n/\gamma))$ words of space and supports locating the $occ$ occurrences of any pattern of length $m$ in $O(m\log n + occ\log^{\epsilon}n)$ time, for any constant $\epsilon>0$. This is, in particular, the first index for general macro schemes and collage systems. Our result shows that the relation between indexing and compression is much deeper than what was previously thought: the simple property standing at the core of all dictionary compressors is sufficient to support fast indexed queries.Comment: Fixed with reviewer's comment