Biomedical Information Visualization
The ongoing developments in the fields of molecular biology, genetics, and medical sciences have recently generated an explosion of information collected from living organisms. For the scientist who analyzes these huge amounts of data, information visualization can be a very useful tool.

title: PathBank: Web-Based Querying and Visualziation of an Integrated Biological Pathway Database
abstract: PathBank is a Web-based query and visualization system for biological pathways using an integrated pathway database. To address the needs for biologists to visualize and analyze biological pathways, PathBank is designed to be user-friendly, flexible and extensible. It is, to the best of our knowledge, the first Web-based system that allows biological pathways to be visualized in three dimensions. PathBank demonstrates the ability to automatically generate and layout biological pathways in response to Web-based database query about proteins, genes, gene ontology and small molecules. Using a novel OWL-to-relational database schema generation approach, it can automatically integrate biological data from different sources that support the BioPAX exchange format (e.g. KEGG, Bio- Cyc). The systems Web interface allows both simple keyword and complex query-based searches in the database. The pathway visualization component provides fast and interactive data access by using asynchronous data retrieval. Due to its modular implementation, it can be easily extended with new visualization algorithms

title: A multi-resolution surface distance model for k-NN query processing
abstract: 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: Visual Analysis of Overlapping Biological Networks
abstract: This paper investigates a new problem of visualizing a set of overlapping networks. We present two methods for constructing visualization of two and three overlapping networks in three dimensions. Our methods aim to achieve both drawing aesthetics (or conventions) for each individual network and exposing the common nodes between the overlapping networks. We evaluated our approaches using biological networks including protein interaction network, metabolic network, and gene regulatory network, from the bacterium Escherichia coli and crop plants to demonstrate their usefulness to support biological analysis.

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: 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: Partial intrinsic reflectional symmetry of 3D shapes
abstract: While many 3D objects exhibit various forms of global symmetries, prominent intrinsic symmetries which exist only on parts of an object are also well recognized. Such partial symmetries are often seen as more natural than a global one, even when the symmetric parts are under complex pose. We introduce an algorithm to extract partial intrinsic reflectional symmetries (PIRS) of a 3D shape. Given a closed 2-manifold mesh, we develop a voting scheme to obtain an intrinsic reflectional symmetry axis (IRSA) transform, which is a scalar field over the mesh that accentuates prominent IRSAs of the shape. We then extract a set of explicit IRSA curves on the shape based on a refined measure of local reflectional symmetry support along a curve. The iterative refinement procedure combines IRSA-induced region growing and region-constrained symmetry support refinement to improve accuracy and address potential issues arising from rotational symmetries in the shape. We show how the extracted IRSA curves can be incorporated into a conventional mesh segmentation scheme so that the implied symmetry cues can be utilized to obtain more meaningful results. We also demonstrate the use of IRSA curves for symmetry-driven part repair.

title: Testing Scenario Implementation with Behavior Contracts
abstract: This paper presents behavior contracts as a new assertion mechanism and a tool that uses such contracts to support the testing of object-oriented (OO) systems. A behavior contract models how the scenarios for performing a designated task are expected to be implemented. Based on this contract, our tool can automatically monitor the program execution for checking important properties related to these scenarios. This capability can help testers to determine whether the scenarios have been implemented correctly. Our tool can also collect test coverage information w.r.t. the scenarios modeled by a behavior contract. Such information can be used to direct the testing efforts towards the less-covered scenarios, and to determine whether the implementation of these scenarios has been adequately tested. Therefore, using this tool should improve both the efficiency and effectiveness of testing OO systems

title: Debugging object-oriented programs with behavior views
abstract: A complex software system may perform many program tasks during execution to provide the required functionalities. To detect and localize bugs related to the implementation of these tasks, the software developers must be able to monitor the progress of the tasks during execution and check whether the actions for these tasks have been performed correctly. This paper presents a debugger to facilitate this monitoring. The debugger introduces a new kind of abstraction, the behavior views, that can be used to specify how the actions for a program task are expected to occur in various scenarios. Enhanced with statements that can check properties at various steps during the progress of the task, a behavior view can be used to monitor whether the actions for the tasks have been performed at the right time, on the right set of data, and with the right effects on the program states. Our initial case study indicates that the debugger can be useful for localizing bugs.