Hierarchical Object Recognition Using Libraries of Parameterized Model Sub-Parts

This thesis describes the development of a model-based vision system that exploits hierarchies of both object structure and object scale. The focus of the research is to use these hierarchies to achieve robust recognition based on effective organization and indexing schemes for model libraries. The goal of the system is to recognize parameterized instances of non-rigid model objects contained in a large knowledge base despite the presence of noise and occlusion. Robustness is achieved by developing a system that can recognize viewed objects that are scaled or mirror-image instances of the known models or that contain components sub-parts with different relative scaling, rotation, or translation than in models. The approach taken in this thesis is to develop an object shape representation that incorporates a component sub-part hierarchy- to allow for efficient and correct indexing into an automatically generated model library as well as for relative parameterization among sub-parts, and a scale hierarchy- to allow for a general to specific recognition procedure. After analysis of the issues and inherent tradeoffs in the recognition process, a system is implemented using a representation based on significant contour curvature changes and a recognition engine based on geometric constraints of feature properties. Examples of the system's performance are given, followed by an analysis of the results. In conclusion, the system's benefits and limitations are presented.

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.