Quality encoding for tetrahedral mesh optimization
We define quality differential coordinates (QDC) for per-vertex encoding of the quality of a tetrahedral mesh. QDC measures the deviation of a mesh vertex from a position which maximizes the combined quality of the set of tetrahedra incident at that vertex. Our formulation allows the incorporation of different choices of element quality metrics into QDC construction to penalize badly shaped and inverted tetrahedra. We develop an algorithm for tetrahedral mesh optimization through energy minimization driven by QDC. The variational problem is solved efficiently and robustly using gradient flow based on a stable semi-implicit integration scheme. To ensure quality boundary of the resulting tetrahedral mesh, we propose a harmonic-guided optimization scheme which leads to consistent handling of both the interior and boundary tetrahedra.

title: Dynamic harmonic fields for surface processing
abstract: Harmonic fields have been shown to provide effective guidance for a number of geometry processing problems. In this paper, we propose a method for fast updating of harmonic fields defined on polygonal meshes, enabling real-time insertion and deletion of constraints. Our approach utilizes the penalty method to enforce constraints in harmonic field computation. It maintains the symmetry of the Laplacian system and takes advantage of fast multi-rank updating and downdating of Cholesky factorization, achieving both speed and numerical stability. We demonstrate how the interactivity induced by fast harmonic field update can be utilized in several applications, including harmonic-guided quadrilateral remeshing, vector field design, interactive geometric detail modeling, and handle-driven shape editing and animation transfer with a dynamic handle set.

title: A Mesh Meaningful Segmentation Algorithm Using Skeleton and Minima-Rule
abstract: In this paper, a hierarchical shape decomposition algorithm is proposed, which integrates the advantages of skeleton-based and minima-rule-based meaningful segmentation algorithms. The method makes use of new geometrical and topological functions of skeleton to define initial cutting critical points, and then employs salient contours with negative minimal principal curvature values to determine natural final boundary curves among parts. And sufficient experiments have been carried out on many meshes, and shown that our framework can provide more reasonable perceptual results than single skeleton-based [8] or minima-rule-based [15] algorithm. In addition, our algorithm not only can divide a mesh of any genus into a collection of genus zero, but also partition level-of-detail meshes into similar parts.

title: 2D shape deformation based on rigid square matching
abstract: In this paper, we propose a fast and stable method for 2D shape deformation based on rigid square matching. Our method utilizes uniform quadrangular control meshes for 2D shapes and tries to maintain the rigidity of each square in the control mesh during user manipulation. A rigid shape matching method is performed to find an optimal pure rotational transformation for each square in the control mesh. An iterative solver is proposed to compute the final deformation result for the entire control mesh by minimizing the difference between the deformed vertices and their counterparts in the neighboring rigid square. The deformation result on the 2D shape is as rigid as possible and the details of the shape are preserved well. As extensions, we present a shape-aware splitting method to improve the deformation effect for coarse meshes and a simple sketch-based clustering method for skeletal deformation. Experiments with various 2D shapes show that our method is efficient and easy to use, and can provide physically plausible result for shapes of objects in real world. Therefore, our shape deformation method is especially suitable for applications in cartoon character animation.

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: Non-rigid Registration in 3D Implicit Vector Space
abstract: We present an implicit approach for pair-wise non-rigid registration of moving and deforming objects. Shapes of interest are implicitly embedded in the 3D implicit vector space. In this implicit embedding space, registration is performed using a global-to-local framework. Firstly, a non-linear optimization functional defined on the vector distance function is used to find the global alignment between shapes. Secondly, an incremental cubic B-spline free form deformation is used to recover the non-rigid transformation parameters. Local non-rigid registration is posed in terms of minimising an energy functional, for which we give a closed-form linear system and solve it using an improved iterative Gauss-Seidel method. Our approach can consistently produce smooth and continuous registration fields, and correctly establish dense one-to-one correspondences. It can naturally deal with both open partial and closed shapes, and imperfect models with gaps and noise, through its use of the implicit vector representation. Experimental results on several datasets demonstrate the robustness of the proposed method.

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: 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 Multiresolution Terrain Model for Efficient Visualization Query Processing
abstract: Multiresolution triangular mesh (MTM) models are widely used to improve the performance of large terrain visualization by replacing the original model with a simplified one. MTM models, which consist of both original and simplified data, are commonly stored in spatial database systems due to their size. The relatively slow access speed of disks makes data retrieval the bottleneck of such terrain visualization systems. Existing spatial access methods proposed to address this problem rely on main-memory MTM models, which leads to significant overhead during query processing. In this paper, we approach the problem from a new perspective and propose a novel MTM called direct mesh that is designed specifically for secondary storage. It supports available indexing methods natively and requires no modification to MTM structure. Experiment results, which are based on two real-world data sets, show an average performance improvement of 5-10 times over the existing methods

title: An Investigation of the Intrinsic Force Sensing Capabilities of Continuum Robots
abstract: This paper presents the theoretical analysis and the experimental validation of the force sensing capabilities of continuum robots. These robots employ superelastic NiTi backbones and actuation redundancy. The paper uses screw theory to analyze the limitations and provide geometric interpretation to the sensible wrenches. The analysis is based on the singular value decomposition of the Jacobian mapping between the configuration space and the twist space of the end effector. The results show that the sensible wrenches belong to a 2-D screw system and the insensible wrenches belong to a 4-D screw system. The theory presented in this paper is validated through simulations and experiments. It is shown that the force sensing errors have an average of 0.34 g with a standard deviation of 0.83 g. Another experiment of generating the stiffness map of a silicone strip suggests possible medical application of palpation for tumor detection. The presented study allows force sensing in challenging environments where placing force sensors at the distal end of a robot is not possible due to limitations such as size and MRI compatibility.

title: Detecting Projected Outliers in High-Dimensional Data Streams
abstract: In this paper, we study the problem of projected outlier detection in high dimensional data streams and propose a new technique, called Stream Projected Ouliter deTector (SPOT), to identify outliers embedded in subspaces. Sparse Subspace Template (SST), a set of subspaces obtained by unsupervised and/or supervised learning processes, is constructed in SPOT to detect projected outliers effectively. Multi-Objective Genetic Algorithm (MOGA) is employed as an effective search method for finding outlying subspaces from training data to construct SST. SST is able to carry out online self-evolution in the detection stage to cope with dynamics of data streams. The experimental results demonstrate the efficiency and effectiveness of SPOT in detecting outliers in high-dimensional data streams.