Multiresolution Spatial Databases: Making Web-Based Spatial Applications Faster
Spatial data has now been used extensively in the Web environment, providing online customized maps and supporting map-based applications. The full potential of Web-based spatial applications, however, has yet to be achieved due to performance issues related to the large sizes and high complexity of spatial data. In this paper, we introduce a multiresolution approach to spatial data management and query processing such that the database server can choose spatial data at the right resolution level for different Web applications. One highly desirable property of the proposed approach is that the server-side processing cost and network traffic can be reduced when the level of resolution required by applications are low. Another advantage is that our approach pushes complex multiresolution structures and algorithms into the spatial database engine. That is, the developer of spatial Web applications needs not to be concerned with such complexity. This paper explains the basic idea, technical feasibility and applications of multiresolution spatial databases.

title: Biomedical Information Visualization
abstract: 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: 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 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: 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: Monitoring with behavior view diagrams for debugging
abstract: UML sequence diagrams are widely used during requirements analysis and design for specifying the expected message exchanges among a set of objects in various scenarios for the program to perform a certain task. In this paper, we present the behavior view diagrams, a type of extended sequence diagrams, to facilitate execution monitoring during debugging. Using a behavior view diagram, software developers can precisely specify the runtime objects whose behaviors will be monitored during debugging. Software developers can also specify the important message exchanges to be observed among these objects during the progress of various scenarios, and may further define the monitoring actions to be performed for inspecting the program state when a message exchange is observed. We also present a debugger that can automatically monitor the program execution using the information specified in a behavior view diagram. Through this monitoring, the debugger can not only check whether the scenarios are progressed as intended, but also check whether the actions performed by the program have the the desired effects on the program states. Therefore, it will be useful for detecting and localizing bugs.

title: Actuation compensation for flexible surgical snake-like robots with redundant remote actuation
abstract: This paper presents two actuation compensation methods for a snake-like robot implementing multi flexible backbones and actuation redundancy. This snake-like robot is designed for distal dexterity enhancement in MIS surgery of the throat. Actuation compensation is required to account for the flexibility of the actuation lines that connect this snake-like robot with its remote actuation units. The paper presents both a naive model-based compensation approach and a combined model-based recursive linear-estimation approach that uses data gathered from external measurements of the snake-like unit configuration such as vision. The kinematic and static model of this multi-backbone snake-like unit is reviewed and a simplified redundancy resolution is implemented in the error compensation model. The results show that the performance of the snake-like unit is significantly improved when compensation is implemented. The combined model-based recursive linear estimation method showed 1deg accuracy in path tracking. Finally, an updated Jacobian that accounts for the required compensation is presented. All the work done here strides the crucial step towards a successful clinical task such as suturing in the throat

title: Design, simulation and evaluation of kinematic alternatives for Insertable Robotic Effectors Platforms in Single Port Access Surgery
abstract: This paper presents the task specifications for designing a novel Insertable Robotic Effectors Platform (IREP) with integrated stereo vision and surgical intervention tools for Single Port Access Surgery (SPAS). This design provides a compact deployable mechanical architecture that may be inserted through a single Ø15 mm access port. Dexterous surgical intervention and stereo vision are achieved via the use of two snake-like continuum robots and two controllable CCD cameras. Simulations and dexterity evaluation of our proposed design are compared to several design alternatives with different kinematic arrangements. Results of these simulations show that dexterity is improved by using an independent revolute joint at the tip of a continuum robot instead of achieving distal rotation by transmission of rotation about the backbone of the continuum robot. Further, it is shown that designs with two robotic continuum robots as surgical arms have diminished dexterity if the bases of these arms are close to each other. This result justifies our design and points to ways of improving the performance of existing designs that use continuum robots as surgical arms.

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.