Entropy guided visualization and analysis of multivariate spatio-temporal data generated by physically based simulation

Flow fields produced by physically based simulations are subsets of multivariate spatiotemporal data, and have been in interest of many researchers for visualization, since the data complexity makes it difficult to extract representative views for the interpretation of fluid behavior. In this thesis, we utilize Information Theory to find entropy maps for vector flow fields, and use entropy maps to aid visualization and analysis of the flow fields. Our major contribution is to use Principal Component Analyses (PCA) to find a projection that has the maximal directional variation in polar coordinates for each sampling window in order to generate histograms according to the projected 3D vector field, producing results with fewer artifacts than the traditional methods. Entropy guided visualization of different data sets are presented to evaluate proposed method for the generation of entropy maps. High entropy regions and coherent directional components of the flow fields are visible without cluttering to reveal fluid behavior in rendered images. In addition to using data sets those are available for research purposes, we have developed a fluid simulation framework using Smoothed Particle Hydrodynamics (SPH) to produce flow fields. SPH is a widely used method for fluid simulations, and used to generate data sets that are difficult to interpret with direct visualization techniques. A moderate improvement for the performance and stability of SPH implementations is also proposed with the use of fractional derivatives, which are known to be useful for approximating particle behavior immersed in fluids

Real-time deformable objects in collaborative virtual environments

This thesis presents a method for deformations on closed surfaces in 3D over a network, which is suitable for simulation of tissue and organs for training purposes, as well as cloth simulation in collaborative virtual environments (CVE). CVE's are extensively used for training, design and gaming for several years. To demonstrate a deformable object on a CVE, we employ a real-time physical simulation of a uniformtension- membrane, based on linear finite-element-discretization of the surface yielding a sparse linear system of equations, which is solved using the Runge-Kutta Fehlberg method. The proposed method introduces an architecture that distributes the computational load of physical simulation between clients. As our approach requires a uniform-mesh representation of the simulated structure, we also designed and implemented an algorithm that converts irregularly triangulated genus zero surfaces into a uniform triangular mesh with regular connectivity. This algorithm uses springembedders for stretch optimization of the spherical parameterization step. The strength of our approach comes from the subdivision methodology that enables to use multi-resolution surfaces for graphical representation, physical simulation, and network transmission, without compromising simulation accuracy and visual quality

DockPro: A VR-Based Tool for Protein-Protein Docking Problem

Proteins are large molecules that are vital for all living organisms and they are essential components of many industrial products. The process of binding a protein to another is called protein-protein docking. Many automated algorithms have been proposed to find docking configurations that might yield promising protein-protein complexes. However, these automated methods are likely to come up with false positives and have high computational costs. Consequently, Virtual Reality has been used to take advantage of user's experience on the problem; and proposed applications can be further improved. Haptic devices have been used for molecular docking problems; but they are inappropriate for protein-protein docking due to their workspace limitations. Instead of haptic rendering of forces, we provide a novel visual feedback for simulating physicochemical forces of proteins. We propose an interactive 3D application, DockPro, which enables domain experts to come up with dockings of protein-protein couples by using magnetic trackers and gloves in front of a large display

Real-Time Deformable Objects IN COLLABORATIVE VIRTUAL ENVIRONMENTS

This thesis presents a method for deformations on closed surfaces in 3D over a network, which is suitable for simulation of tissue and organs for training purposes, as well as cloth simulation in collaborative virtual environments (CVE). CVE's are extensively used for training, design and gaming for several years. To demonstrate a deformable object on a CVE, we employ a real-time physical simulation of a uniformtension-membrane, based on linear finite-element-discretization of the surface yielding a sparse linear system of equations, which is solved using the Runge-Kutta Fehlberg method. The proposed method introduces an architecture that distributes the computational load of physical simulation between clients. As our approach requires a uniform-mesh representation of the simulated structure, we also designed and implemented an algorithm that converts irregularly triangulated genus zero surfaces into a uniform triangular mesh with regular connectivity. This algorithm uses springembedders for stretch optimization of the spherical parameterization step. The strength of our approach comes from the subdivision methodology that enables to us

Representational image generation for 3D objects

Finding good representational images for 3D object exploration is a highly subjective problem in the cognitive field. The “best” or “good” definitions do not depend on any metric. We have explained the VKL distance concept and introduced a novel view descriptor called vSKL distance for finding “good” representational images. The image generation is done by projecting the surfaces of 3D objects onto the screen or any planar surface. The projection process depends on parameters such as camera position, camera vector, up vector, and clipping plane positions. In this work we present a technique to find such camera positions that the 3D object is projected in “good” or “best” way where those subjective definitions are mapped to Information Theoretical distances. We compared greedy view selection integrated vSKL with two well known techniques: VKL and VMI. vSKL performs very close to the other two, hence face coverage perturbation is minimal, but it is 3 to 4 times faster. Furthermore, the saliency information is conveyed to users with generated images

Temporal dynamics of user interests in web search queries

Web search query logs contain valuable information which can be utilized for personalization and improvement of search engine performance. The aim in this paper(1) is to cluster users based on their interests, and analyze the temporal dynamics of these clusters. In the proposed approach, we first apply clustering techniques to group similar users with respect to their web searches. Anticipating that the small number of query terms used in search queries would not be sufficient to obtain a proper clustering scheme, we extracted the summary content of the clicked web page from the query log. In this way, we enriched the feature set more efficiently than the content crawling. We also provide preliminary survey results to evaluate clusters. Clusters may change with the user flow from one cluster to the other as time passes. This is due to the fact that users' interests may shift over time. We used statistical methods for the analysis of temporal changes in users' interests. As a case study, we experimented on the query logs of a search engine