Automatically Recovering Geometry and Texture from Large Sets of Calibrated Images

Three-dimensional models which contain both geometry and texture have numerous applications such as urban planning, physical simulation, and virtual environments. A major focus of computer vision (and recently graphics) research is the automatic recovery of three-dimensional models from two-dimensional images. After many years of research this goal is yet to be achieved. Most practical modeling systems require substantial human input and unlike automatic systems are not scalable. This thesis presents a novel method for automatically recovering dense surface patches using large sets (1000's) of calibrated images taken from arbitrary positions within the scene. Physical instruments, such as Global Positioning System (GPS), inertial sensors, and inclinometers, are used to estimate the position and orientation of each image. Essentially, the problem is to find corresponding points in each of the images. Once a correspondence has been established, calculating its three-dimensional position is simply a matter of geometry. Long baseline images improve the accuracy. Short baseline images and the large number of images greatly simplifies the correspondence problem. The initial stage of the algorithm is completely local and scales linearly with the number of images. Subsequent stages are global in nature, exploit geometric constraints, and scale quadratically with the complexity of the underlying scene. We describe techniques for: 1) detecting and localizing surface patches; 2) refining camera calibration estimates and rejecting false positive surfels; and 3) grouping surface patches into surfaces and growing the surface along a two-dimensional manifold. We also discuss a method for producing high quality, textured three-dimensional models from these surfaces. Some of the most important characteristics of this approach are that it: 1) uses and refines noisy calibration estimates; 2) compensates for large variations in illumination; 3) tolerates significant soft occlusion (e.g. tree branches); and 4) associates, at a fundamental level, an estimated normal (i.e. no frontal-planar assumption) and texture with each surface patch.

Understanding Subsystems in Biology through Dimensionality Reduction, Graph Partitioning and Analytical Modeling

Biological systems exhibit rich and complex behavior through the orchestrated interplay of a large array of components. It is hypothesized that separable subsystems with some degree of functional autonomy exist; deciphering their independent behavior and functionality would greatly facilitate understanding the system as a whole. Discovering and analyzing such subsystems are hence pivotal problems in the quest to gain a quantitative understanding of complex biological systems. In this work, using approaches from machine learning, physics and graph theory, methods for the identification and analysis of such subsystems were developed. A novel methodology, based on a recent machine learning algorithm known as non-negative matrix factorization (NMF), was developed to discover such subsystems in a set of large-scale gene expression data. This set of subsystems was then used to predict functional relationships between genes, and this approach was shown to score significantly higher than conventional methods when benchmarking them against existing databases. Moreover, a mathematical treatment was developed to treat simple network subsystems based only on their topology (independent of particular parameter values). Application to a problem of experimental interest demonstrated the need for extentions to the conventional model to fully explain the experimental data. Finally, the notion of a subsystem was evaluated from a topological perspective. A number of different protein networks were examined to analyze their topological properties with respect to separability, seeking to find separable subsystems. These networks were shown to exhibit separability in a nonintuitive fashion, while the separable subsystems were of strong biological significance. It was demonstrated that the separability property found was not due to incomplete or biased data, but is likely to reflect biological structure.

Towards Grid-Wide Modeling and Simulation

Modeling and simulation permeate all areas of business, science and engineering. With the increase in the scale and complexity of simulations, large amounts of computational resources are required, and collaborative model development is needed, as multiple parties could be involved in the development process. The Grid provides a platform for coordinated resource sharing and application development and execution. In this paper, we survey existing technologies in modeling and simulation, and we focus on interoperability and composability of simulation components for both simulation development and execution. We also present our recent work on an HLA-based simulation framework on the Grid, and discuss the issues to achieve composability.