A multi-resolution surface distance model for k-NN query processing
A spatial k-NN query returns k nearest points in a point dataset to a given query point. To measure the distance between two points, most of the literature focuses on the Euclidean distance or the network distance. For many applications, such as wildlife movement, it is necessary to consider the surface distance, which is computed from the shortest path along a terrain surface. In this paper, we investigate the problem of efficient surface k-NN (sk-NN) query processing. This is an important yet highly challenging problem because the underlying environment data can be very large and the computational cost of finding the shortest path on a surface can be very high. To minimize the amount of surface data to be used and the cost of surface distance computation, a multi-resolution surface distance model is proposed in this paper to take advantage of monotonic distance changes when the distances are computed at different resolution levels. Based on this innovative model, sk-NN queries can be processed efficiently by accessing and processing surface data at a just-enough resolution level within a just-enough search region. Our extensive performance evaluations using real world datasets confirm the efficiency of our proposed model.

title: GEOMI: GEOmetry for Maximum Insight
abstract: This paper describes the GEOMI system, a visual analysis tool for the visualisation and analysis of large and complex networks. GEOMI provides a collection of network analysis methods, graph layout algorithms and several graph navigation and interaction methods. GEOMI is part of a new generation of visual analysis tools combining graph visualisation techniques with network analysis methods. GEOMI is available from

title: Semi-bipartite Graph Visualization for Gene Ontology Networks
abstract: In this paper we propose three layout algorithms for semi-bipartite graphs—bipartite graphs with edges in one partition—that emerge from microarray experiment analysis. We also introduce a method that effectively reduces visual complexity by removing less informative nodes. The drawing quality and running time are evaluated with five real-world datasets, and the results show significant reduction in crossing number and total edge length. All the proposed methods are available in visualization package GEOMI , and are well received by domain users.

title: Direct mesh: a multiresolution approach to terrain visualization
abstract: Terrain can be approximated by a triangular mesh consisting millions of 3D points. Multiresolution triangular mesh (MTM) structures are designed to support applications that use terrain data at variable levels of detail (LOD). Typically, an MTM adopts a tree structure where a parent node represents a lower-resolution approximation of its descendants. Given a region of interest (ROI) and a LOD, the process of retrieving the required terrain data from the database is to traverse the MTM tree from the root to reach all the nodes satisfying the ROI and LOD conditions. This process, while being commonly used for multiresolution terrain visualization, is inefficient as either a large number of sequential I/O operations or fetching a large amount of extraneous data is incurred. Various spatial indexes have been proposed in the past to address this problem, however level-by-level tree traversal remains a common practice in order to obtain topological information among the retrieved terrain data. A new MTM data structure called direct mesh is proposed. We demonstrate that with direct mesh the amount of data retrieval can be substantially reduced. Comparing with existing MTM indexing methods, a significant performance improvement has been observed for real-life terrain data.

title: GraphScape: integrated multivariate network visualization
abstract: In this paper, we introduce a new method, GraphScape, to visualize multivariate networks, i.e., graphs with multivariate data associated with their nodes. GraphScape adopts a landscape metaphor with network structure displayed on a 2D plane and the surface height in the third dimension represents node attribute. More than one attribute can be visualized simultaneously by using multiple surfaces. In addition, GraphScape can be easily combined with existing methods to further increase the total number of attributes visualized. One of the major goals of GraphScape is to reveal multivariate graph clustering, which is based on both network structure and node attributes. This is achieved by a new layout algorithm and an innovative way of constructing attribute surface, which also allows visual clustering at different scales through interaction. A simplified attribute surface model is also proposed to reduce computation requirement when visualizing large networks. GraphScape is applied to networks of three different size (20, 100, and 1500) to demonstrate its effectiveness.

title: 2.5D Visualisation of Overlapping Biological Networks
abstract: Biological data is often structured in the form of complex interconnected networks such as protein interaction and metabolic networks. In this paper, we investigate a new problem of visualising such overlapping biological networks. Two networks overlap if they share some nodes and edges. We present an approach for constructing visualisations of two overlapping networks, based on a restricted three dimensional representation. More specifically, we use three parallel two dimensional planes placed in three dimensions to represent overlapping networks: one for each network (the top and the bottom planes) and one for the overlapping part (in the middle plane). Our method aims to achieve both drawing aesthetics (or conventions) for each individual network, and highlighting the intersection part by them. Using three biological datasets, we evaluate our visualisation design with the aim to test whether overlapping networks can support the visual analysis of heterogeneous and yet interconnected networks.

title: A mass-spring model for surface mesh deformation based on shape matching
abstract: In this paper, we propose a mass-spring model based on shape matching for real-time deformable modeling in virtual reality systems. By defining a rigid core for surface mesh model and adding a new generalized spring for each mass, our surface mesh model can preserve its original geometric features such as volume and shape. Then, we use shape matching approaches to update the rigid core of the model dynamically so as to simulate global deformations. At last, we adopt an inverse dynamics technique to deal with the resulting deformations. We correct the non-real "super-elastic" effect for linear elastic models so that the visual reality is improved.

title: Formally defining a graphical language for monitoring and checking object interactions
abstract: Monitoring and checking object interactions is an important activity for testing/debugging scenario implementation in an object-oriented system. In our previous work, we proposed behavior view diagrams (BVD) as a graphical language for writing programs that automate such monitoring and checking process. In this paper, we illustrate the formal definition of the syntax and the semantics of an extended version of BVD that can also be used to describe multi-threaded scenarios. This formal definition provides a critical foundation both for understanding the language and for building its tool support.

title: Design and Integration of a Telerobotic System for Minimally Invasive Surgery of the Throat
abstract: In this paper we present the clinical motivation, design specifications, kinematics, statics, and actuation compensation for a newly constructed telerobotic system for Minimally Invasive Surgery (MIS) of the throat. A hybrid dual-arm telesurgical slave, with 20 joint-space Degrees-of-Freedom (DoFs), is used in this telerobotic system to provide the necessary dexterity in deep surgical fields such as the throat. The telerobotic slave uses novel continuum robots that use multiple super-elastic backbones for actuation and structural integrity. We present the kinematics of the telesurgical slave and methods for actuation compensation to cancel the effects of backlash, friction, and flexibility of the actuation lines. A method for actuation compensation is presented in order to overcome uncertainties of modeling, friction, and backlash. This method uses a tiered hierarchy of two novel approaches of actuation compensation for remotely actuated snake-like robots. The tiered approach for actuation compensation uses compensation in both joint space and configuration space of the continuum robots. These hybrid actuation compensation schemes use intrinsic model information and external data through a recursive linear estimation algorithm and involve compensation using configuration space and joint space variables. Experimental results validate the ability of our integrated telemanipulation system through experiments of suturing and knot tying in confined spaces.

title: Test-Driven Component Integration with UML 2.0 Testing and Monitoring Profile
abstract: Test-driven development (TDD) is a software development methodology for achieving high reliability. However, the practice of TDD at the integration level is rare. In this paper, we propose a test-driven component integration approach with the support of UML 2.0 Testing and Monitoring Profile (U2TMP) that is also proposed in this paper. In our approach, automated integration-level test cases are specified using U2TMP before writing the glue-code that integrates components. U2TMP enhances UML 2.0 diagrams for specifying how test scenarios should be set up and how the integrated components are expected to interact under these scenarios. Test cases written in U2TMP can be automatically transformed into test artifacts that setup the test environment, generate test stimuli, and monitor the component interactions at runtime. These test cases serve as a guideline for writing the glue-code and a regression test- bed. With this approach, the software developers may produce glue-code of high reliability.

title: A Pilot Study of Robot-Assisted Cochlear Implant Surgery Using Steerable Electrode Arrays
abstract: This paper presents results of a pilot study evaluating the efficacy of robotic assistance using novel steerable electrode arrays for cochlear implant surgery. The current surgical setup of cochlear implant surgery is briefly reviewed and its limitations are highlighted. In an effort to reduce trauma to the structure of the cochlea, the kinematics and path planning for novel cochlear steerable electrodes are developed to minimize the interaction forces between the electrode and the cochlea. An experimental robotic system is used to compare the electrode insertion forces of steerable implants with those of nonsteerable electrodes. The results of these experiments show about 70% reduction in the insertion forces when steerable electrodes are used with our proposed path planning and control. A distance metric explaining this reduction in the insertion force is defined and experimentally validated. Although this is only a preliminary study, we believe that these results provide a strong indication to the potential of robot-assisted cochlear implant surgery to provide a significant reduction in trauma rates during cochlear implant surgery.