34497095
3D Protein Structure Matching by Patch Signatures
For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have one or more matching structural regions called patches. As 3D structures for proteins are large, complex and constantly evolving, it is computationally expensive and very time-consuming to identify possible locations and sizes of patches for a given protein against a large protein database. In this paper, we address a vector space based representation for protein structures, where a patch is formed by the vectors within the region. Based on our previews work, a compact representation of the patch named patch signature is applied here. A similarity measure of two patches is then derived based on their signatures. To achieve fast patch matching in large protein databases, a match-and-expand strategy is proposed. Given a query patch, a set of small k-sized matching patches, called candidate patches, is generated in match stage. The candidate patches are further filtered by enlarging k in expand stage. Our extensive experimental results demonstrate encouraging performances with respect to this biologically critical but previously computationally prohibitive problem.
16206286
Classifying Document Titles Based on Information Inference
We propose an intelligent document title classification agent based on a theory of information inference. The information is represented as vectorial spaces computed by a cognitively motivated model, namely Hyperspace Analogue to Language (HAL). A combination heuristic is used to combine a group of concepts into one single combination vector. Information inference can be performed on the HAL spaces via computing information flow between vectors or combination vectors. Based on this theory, a document title is treated as a combination vector by applying the combination heuristic to all the non-stop terms in the title. Two methodologies for learning and assigning categories to document titles are addressed. Experimental results on Reuters-21578 corpus show that our framework is promising and its performance achieves 71% of the upper bound (which is approximated by using whole documents).
1039548
Walking Through a Very Large Virtual Environment in Real-time
Users expect high and constant rendering frame rates when they interactively navigate in a Virtual Environment (VE). However, when the VE is too large to t into the main memory, the frame rates can become unacceptable. In this paper, we combine walkthrough semantics and database techniques, such as indexing, caching and prefetching, to improve the performance of walkthrough of a very large VE. We implemented a prototype walkthrough system called REVIEW (REaltime VIrtual Environment Walkthrough) and evaluated its performance on a 1 GB synthetic data-set generated to simulate a large cityscape. Our results show that the proposed techniques are e ective for generating constant frame rate and improving the visual e ects.
3144439
Fast rendering of foveated volumes in wavelet-based representation
A foveated volume can be viewed as a blending of multiple regions, each with a different level of resolution. It can be efficiently represented in the wavelet domain by retaining a small number of wavelet coefficients. We exploit the arrangement of those wavelet coefficients to achieve fast volume rendering. The running time is O(n2+m), where n is the width of the rendered image, and m is the number of wavelet coefficients retained for the foveated volume. Our algorithm consists of two phases. The first phase is a fast reconstruction of the super-voxels from the wavelet coefficients, and the second phase renders the super-voxels by carefully tracking rays with different thickness in the super-voxels. No expensive preprocessing on the wavelet coefficients is required. Hence, it is possible to interactively modify different viewing parameters like the transfer functions. A potential application of our algorithm is in remote visualization of large volume data-sets.
18313204
A taxonomy of web agents
We propose a taxonomy of Web agents, which encompasses agents that provide a text-based interface to, for example, information retrieval services as well as avatar-embodied guides that help visitors to navigate in virtual environments. Our taxonomy must be regarded as an instrument to delineate targets for research and the realization of prototype applications that demonstrate the usefulness of agent-based intelligence on the Web. In addition, we deploy our agent-taxonomy to establish the implications particular target applications have with respect to software architecture and computational resources.
17908385
The hierarchical degree-of-visibility tree
In this paper, we present a novel structure called the hierarchical degree-of-visibility tree (HDoV-tree) for visibility query processing in visualization systems. The HDoV-tree builds on and extends the R-tree such that 1) the search space is pruned based on the degree of visibility of objects and 2) internal nodes store level-of-details (LoDs) that represent a collection of objects in a coarser form. We propose two tree traversal algorithms that balance performance and visual fidelity, explore three storage structures for the HDoV-tree, and develop novel caching techniques for disk-based HDoV-tree. We implemented the HDoV-tree in a prototype walkthrough system called VISUAL. Our experimental study shows that VISUAL can lead to high frame rates without compromising visual fidelity.
14014109
Dynamic Goal Hierarchies
In this paper we introduce and formalise dynamic goal hierarchies. We begin with a formal definition of goals, according to which they are rational desires. In particular, we require that an agent's goals are coherent; that is, that the agent believes that each goal is jointly realisable with all of the goals which the agent considers to be more important. Thus an agent's goals form a hierarchy, and new goals are defined with reference to it. We then show how preferential entailment can be used to formalise the rational revision of goals and goal hierarchies.