Analytical Representation of Contours

The interpretation and recognition of noisy contours, such as silhouettes, have proven to be difficult. One obstacle to the solution of these problems has been the lack of a robust representation for contours. The contour is represented by a set of pairwise tangent circular arcs. The advantage of such an approach is that mathematical properties such as orientation and curvature are explicityly represented. We introduce a smoothing criterion for the contour tht optimizes the tradeoff between the complexity of the contour and proximity of the data points. The complexity measure is the number of extrema of curvature present in the contour. The smoothing criterion leads us to a true scale-space for contours. We describe the computation of the contour representation as well as the computation of relevant properties of the contour. We consider the potential application of the representation, the smoothing paradigm, and the scale-space to contour interpretation and recognition.

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.