Learning World Models in Environments with Manifest Causal Structure

This thesis examines the problem of an autonomous agent learning a causal world model of its environment. Previous approaches to learning causal world models have concentrated on environments that are too "easy" (deterministic finite state machines) or too "hard" (containing much hidden state). We describe a new domain --- environments with manifest causal structure --- for learning. In such environments the agent has an abundance of perceptions of its environment. Specifically, it perceives almost all the relevant information it needs to understand the environment. Many environments of interest have manifest causal structure and we show that an agent can learn the manifest aspects of these environments quickly using straightforward learning techniques. We present a new algorithm to learn a rule-based causal world model from observations in the environment. The learning algorithm includes (1) a low level rule-learning algorithm that converges on a good set of specific rules, (2) a concept learning algorithm that learns concepts by finding completely correlated perceptions, and (3) an algorithm that learns general rules. In addition this thesis examines the problem of finding a good expert from a sequence of experts. Each expert has an "error rate"; we wish to find an expert with a low error rate. However, each expert's error rate and the distribution of error rates are unknown. A new expert-finding algorithm is presented and an upper bound on the expected error rate of the expert is derived.

Inverse Metabolic Engineering of Synechocystis PCC 6803 for Improved Growth Rate and Poly-3-hydroxybutyrate Production

Synechocystis PCC 6803 is a photosynthetic bacterium that has the potential to make bioproducts from carbon dioxide and light. Biochemical production from photosynthetic organisms is attractive because it replaces the typical bioprocessing steps of crop growth, milling, and fermentation, with a one-step photosynthetic process. However, low yields and slow growth rates limit the economic potential of such endeavors. Rational metabolic engineering methods are hindered by limited cellular knowledge and inadequate models of Synechocystis. Instead, inverse metabolic engineering, a scheme based on combinatorial gene searches which does not require detailed cellular models, but can exploit sequence data and existing molecular biological techniques, was used to find genes that (1) improve the production of the biopolymer poly-3-hydroxybutyrate (PHB) and (2) increase the growth rate. A fluorescence activated cell sorting assay was developed to screen for high PHB producing clones. Separately, serial sub-culturing was used to select clones that improve growth rate. Novel gene knock-outs were identified that increase PHB production and others that increase the specific growth rate. These improvements make this system more attractive for industrial use and demonstrate the power of inverse metabolic engineering to identify novel phenotype-associated genes in poorly understood systems.