Design, simulation and evaluation of kinematic alternatives for Insertable Robotic Effectors Platforms in Single Port Access Surgery
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: 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 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: 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: Surface k-NN Query Processing
abstract: A k-NN query finds the k nearest-neighbors of a given point from a point database. When it is sufficient to measure object distance using the Euclidian distance, the key to efficient k-NN query processing is to fetch and check the distances of a minimum number of points from the database. For many applications, such as vehicle movement along road networks or rover and animal movement along terrain surfaces, the distance is only meaningful when it is along a valid movement path. For this type of k-NN queries, the focus of efficient query processing is to minimize the cost of computing distances using the environment data (such as the road network data and the terrain data), which can be several orders of magnitude larger than that of the point data. Efficient processing of k-NN queries based on the Euclidian distance or the road network distance has been investigated extensively in the past. In this paper, we investigate the problem of surface k-NN query processing, where the distance is calculated from the shortest path along a terrain surface. This problem is very challenging, as the terrain data can be very large and the computational cost of finding shortest paths is very high. We propose an efficient solution based on multiresolution terrain models. Our approach eliminates the need of costly process of finding shortest paths by ranking objects using estimated lower and upper bounds of distance on multiresolution terrain models.

title: Gene Specific Co-regulation Discovery: An Improved Approach
abstract: Discovering gene co-regulatory relationships is a new but important research problem in DNA microarray data analysis. The problem of gene specific co-regulation discovery is to, for a particular gene of interest, called the target gene , identify its strongly co-regulated genes and the condition subsets where such strong gene co-regulations are observed. The study on this problem can contribute to a better understanding and characterization of the target gene. The existing method, using the genetic algorithm (GA), is slow due to its expensive fitness evaluation and long individual representation. In this paper, we propose an improved method for finding gene specific co-regulations. Compared with the current method, our method features a notably improved efficiency. We employ k NN Search Table to substantially speed up fitness evaluation in the GA. We also propose a more compact representation scheme for encoding individuals in the GA, which contributes to faster crossover and mutation operations. Experimental results with a real-life gene microarray data set demonstrate the improved efficiency of our technique compared with the current method.

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: 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.