Robust and Scalable Transmission of Arbitrary 3D Models over Wireless Networks

We describe transmission of 3D objects represented by texture and mesh over unreliable networks, extending our earlier work for regular mesh structure to arbitrary meshes and considering linear versus cubic interpolation. Our approach to arbitrary meshes considers stripification of the mesh and distributing nearby vertices into different packets, combined with a strategy that does not need texture or mesh packets to be retransmitted. Only the valence (connectivity) packets need to be retransmitted; however, storage of valence information requires only 10% space compared to vertices and even less compared to photorealistic texture. Thus, less than 5% of the packets may need to be retransmitted in the worst case to allow our algorithm to successfully reconstruct an acceptable object under severe packet loss. Even though packet loss during transmission has received limited research attention in the past, this topic is important for improving quality under lossy conditions created by shadowing and interference. Results showing the implementation of the proposed approach using linear, cubic, and Laplacian interpolation are described, and the mesh reconstruction strategy is compared with other methods

Multi-scale geometry interpolation

Interpolating vertex positions among triangle meshes with identical vertex-edge graphs is a fundamental part of many geometric modelling systems. Linear vertex interpolation is robust but fails to preserve local shape. Most recent approaches identify local affine transformations for parts of the mesh, model desired interpolations of the affine transformations, and then optimize vertex positions to conform with the desired transformations. However, the local interpolation of the rotational part is non-trivial for more than two input configurations and ambiguous if the meshes are deformed significantly. We propose a solution to the vertex interpolation problem that starts from interpolating the local metric (edge lengths) and mean curvature (dihedral angles) and makes consistent choices of local affine transformations using shape matching applied to successively larger parts of the mesh. The local interpolation can be applied to any number of input vertex configurations and due to the hierarchical scheme for generating consolidated vertex positions, the approach is fast and can be applied to very large meshes

Spherical harmonics coeffcients for ligand-based virtual screening of cyclooxygenase inhibitors

Background: Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening. Methodology/Principal Findings: We introduce and validate a partially rotation-invariant three-dimensional molecular shape descriptor based on the norm of spherical harmonics expansion coefficients. Using this molecular representation, we parameterize molecular surfaces, i.e., isosurfaces of spatial molecular property distributions. We validate the shape descriptor in a comprehensive retrospective virtual screening experiment. In a prospective study, we virtually screen a large compound library for cyclooxygenase inhibitors, using a self-organizing map as a pre-filter and the shape descriptor for candidate prioritization. Conclusions/Significance: 12 compounds were tested in vitro for direct enzyme inhibition and in a whole blood assay. Active compounds containing a triazole scaffold were identified as direct cyclooxygenase-1 inhibitors. This outcome corroborates the usefulness of spherical harmonics for representation of molecular shape in virtual screening of large compound collections. The combination of pharmacophore and shape-based filtering of screening candidates proved to be a straightforward approach to finding novel bioactive chemotypes with minimal experimental effort

Automatic 3D facial modelling with deformable models.

Facial modelling and animation has been an active research subject in computer graphics since the 1970s. Due to extremely complex biomechanical structures of human faces and peoples visual familiarity with human faces, modelling and animating realistic human faces is still one of greatest challenges in computer graphics. Since we are so familiar with human faces and very sensitive to unnatural subtle changes in human faces, it usually requires a tremendous amount of artistry and manual work to create a convincing facial model and animation. There is a clear need of developing automatic techniques for facial modelling in order to reduce manual labouring. In order to obtain a realistic facial model of an individual, it is now common to make use of 3D scanners to capture range scans from the individual and then fit a template to the range scans. However, most existing template-fitting methods require manually selected landmarks to warp the template to the range scans. It would be tedious to select landmarks by hand over a large set of range scans. Another way to reduce repeated work is synthesis by reusing existing data. One example is expression cloning, which copies facial expression from one face to another instead of creating them from scratch. This aim of this study is to develop a fully automatic framework for template-based facial modelling, facial expression transferring and facial expression tracking from range scans. In this thesis, the author developed an extension of the iterative closest points (ICP) algorithm, which is able to match a template with range scans in different scales, and a deformable model, which can be used to recover the shapes of range scans and to establish correspondences between facial models. With the registration method and the deformable model, the author proposed a fully automatic approach to reconstructing facial models and textures from range scans without re-quiring any manual interventions. In order to reuse existing data for facial modelling, the author formulated and solved the problem of facial expression transferring in the framework of discrete differential geometry. The author also applied his methods to face tracking for 4D range scans. The results demonstrated the robustness of the registration method and the capabilities of the deformable model. A number of possible directions for future work were pointed out

Spherical Harmonics Coefficients for Ligand-Based Virtual Screening of Cyclooxygenase Inhibitors

Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening.We introduce and validate a partially rotation-invariant three-dimensional molecular shape descriptor based on the norm of spherical harmonics expansion coefficients. Using this molecular representation, we parameterize molecular surfaces, i.e., isosurfaces of spatial molecular property distributions. We validate the shape descriptor in a comprehensive retrospective virtual screening experiment. In a prospective study, we virtually screen a large compound library for cyclooxygenase inhibitors, using a self-organizing map as a pre-filter and the shape descriptor for candidate prioritization.12 compounds were tested in vitro for direct enzyme inhibition and in a whole blood assay. Active compounds containing a triazole scaffold were identified as direct cyclooxygenase-1 inhibitors. This outcome corroborates the usefulness of spherical harmonics for representation of molecular shape in virtual screening of large compound collections. The combination of pharmacophore and shape-based filtering of screening candidates proved to be a straightforward approach to finding novel bioactive chemotypes with minimal experimental effort

Interactive global illumination on the CPU

Computing realistic physically-based global illumination in real-time remains one of the major goals in the fields of rendering and visualisation; one that has not yet been achieved due to its inherent computational complexity. This thesis focuses on CPU-based interactive global illumination approaches with an aim to develop generalisable hardware-agnostic algorithms. Interactive ray tracing is reliant on spatial and cache coherency to achieve interactive rates which conflicts with needs of global illumination solutions which require a large number of incoherent secondary rays to be computed. Methods that reduce the total number of rays that need to be processed, such as Selective rendering, were investigated to determine how best they can be utilised. The impact that selective rendering has on interactive ray tracing was analysed and quantified and two novel global illumination algorithms were developed, with the structured methodology used presented as a framework. Adaptive Inter- leaved Sampling, is a generalisable approach that combines interleaved sampling with an adaptive approach, which uses efficient component-specific adaptive guidance methods to drive the computation. Results of up to 11 frames per second were demonstrated for multiple components including participating media. Temporal Instant Caching, is a caching scheme for accelerating the computation of diffuse interreflections to interactive rates. This approach achieved frame rates exceeding 9 frames per second for the majority of scenes. Validation of the results for both approaches showed little perceptual difference when comparing against a gold-standard path-traced image. Further research into caching led to the development of a new wait-free data access control mechanism for sharing the irradiance cache among multiple rendering threads on a shared memory parallel system. By not serialising accesses to the shared data structure the irradiance values were shared among all the threads without any overhead or contention, when reading and writing simultaneously. This new approach achieved efficiencies between 77% and 92% for 8 threads when calculating static images and animations. This work demonstrates that, due to the flexibility of the CPU, CPU-based algorithms remain a valid and competitive choice for achieving global illumination interactively, and an alternative to the generally brute-force GPU-centric algorithms