Boundaries and Topological Algorithms

This thesis develops a model for the topological structure of situations. In this model, the topological structure of space is altered by the presence or absence of boundaries, such as those at the edges of objects. This allows the intuitive meaning of topological concepts such as region connectivity, function continuity, and preservation of topological structure to be modeled using the standard mathematical definitions. The thesis shows that these concepts are important in a wide range of artificial intelligence problems, including low-level vision, high-level vision, natural language semantics, and high-level reasoning.

Maximum Entropy Discrimination

We present a general framework for discriminative estimation based on the maximum entropy principle and its extensions. All calculations involve distributions over structures and/or parameters rather than specific settings and reduce to relative entropy projections. This holds even when the data is not separable within the chosen parametric class, in the context of anomaly detection rather than classification, or when the labels in the training set are uncertain or incomplete. Support vector machines are naturally subsumed under this class and we provide several extensions. We are also able to estimate exactly and efficiently discriminative distributions over tree structures of class-conditional models within this framework. Preliminary experimental results are indicative of the potential in these techniques.

Natural Object Categorization

This thesis addresses the problem of categorizing natural objects. To provide a criteria for categorization we propose that the purpose of a categorization is to support the inference of unobserved properties of objects from the observed properties. Because no such set of categories can be constructed in an arbitrary world, we present the Principle of Natural Modes as a claim about the structure of the world. We first define an evaluation function that measures how well a set of categories supports the inference goals of the observer. Entropy measures for property uncertainty and category uncertainty are combined through a free parameter that reflects the goals of the observer. Natural categorizations are shown to be those that are stable with respect to this free parameter. The evaluation function is tested in the domain of leaves and is found to be sensitive to the structure of the natural categories corresponding to the different species. We next develop a categorization paradigm that utilizes the categorization evaluation function in recovering natural categories. A statistical hypothesis generation algorithm is presented that is shown to be an effective categorization procedure. Examples drawn from several natural domains are presented, including data known to be a difficult test case for numerical categorization techniques. We next extend the categorization paradigm such that multiple levels of natural categories are recovered; by means of recursively invoking the categorization procedure both the genera and species are recovered in a population of anaerobic bacteria. Finally, a method is presented for evaluating the utility of features in recovering natural categories. This method also provides a mechanism for determining which features are constrained by the different processes present in a multiple modal world.

A Distributed Model for Mobile Robot Environment-Learning and Navigation

A distributed method for mobile robot navigation, spatial learning, and path planning is presented. It is implemented on a sonar-based physical robot, Toto, consisting of three competence layers: 1) Low-level navigation: a collection of reflex-like rules resulting in emergent boundary-tracing. 2) Landmark detection: dynamically extracts landmarks from the robot's motion. 3) Map learning: constructs a distributed map of landmarks. The parallel implementation allows for localization in constant time. Spreading of activation computes both topological and physical shortest paths in linear time. The main issues addressed are: distributed, procedural, and qualitative representation and computation, emergent behaviors, dynamic landmarks, minimized communication.

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.