Dependency Directed Reasoning for Complex Program Understanding

Artificial Intelligence research involves the creation of extremely complex programs which must possess the capability to introspect, learn, and improve their expertise. Any truly intelligent program must be able to create procedures and to modify them as it gathers information from its experience. [Sussman, 1975] produced such a system for a 'mini-world'; but truly intelligent programs must be considerably more complex. A crucial stepping stone in AI research is the development of a system which can understand complex programs well enough to modify them. There is also a complexity barrier in the world of commercial software which is making the cost of software production and maintenance prohibitive. Here too a system which is capable of understanding complex programs is a necessary step. The Programmer's Apprentice Project [Rich and Shrobe, 76] is attempting to develop an interactive programming tool which will help expert programmers deal with the complexity involved in engineering a large software system. This report describes REASON, the deductive component of the programmer's apprentice. REASON is intended to help expert programmers in the process of evolutionary program design. REASON utilizes the engineering techniques of modelling, decomposition, and analysis by inspection to determine how modules interact to achieve the desired overall behavior of a program. REASON coordinates its various sources of knowledge by using a dependency-directed structure which records the justification for each deduction it makes. Once a program has been analyzed these justifications can be summarized into a teleological structure called a plan which helps the system understand the impact of a proposed program modification.

Using Analogy to Acquire Commonsense Knowledge from Human Contributors

The goal of the work reported here is to capture the commonsense knowledge of non-expert human contributors. Achieving this goal will enable more intelligent human-computer interfaces and pave the way for computers to reason about our world. In the domain of natural language processing, it will provide the world knowledge much needed for semantic processing of natural language. To acquire knowledge from contributors not trained in knowledge engineering, I take the following four steps: (i) develop a knowledge representation (KR) model for simple assertions in natural language, (ii) introduce cumulative analogy, a class of nearest-neighbor based analogical reasoning algorithms over this representation, (iii) argue that cumulative analogy is well suited for knowledge acquisition (KA) based on a theoretical analysis of effectiveness of KA with this approach, and (iv) test the KR model and the effectiveness of the cumulative analogy algorithms empirically. To investigate effectiveness of cumulative analogy for KA empirically, Learner, an open source system for KA by cumulative analogy has been implemented, deployed, and evaluated. (The site "1001 Questions," is available at http://teach-computers.org/learner.html). Learner acquires assertion-level knowledge by constructing shallow semantic analogies between a KA topic and its nearest neighbors and posing these analogies as natural language questions to human contributors. Suppose, for example, that based on the knowledge about "newspapers" already present in the knowledge base, Learner judges "newspaper" to be similar to "book" and "magazine." Further suppose that assertions "books contain information" and "magazines contain information" are also already in the knowledge base. Then Learner will use cumulative analogy from the similar topics to ask humans whether "newspapers contain information." Because similarity between topics is computed based on what is already known about them, Learner exhibits bootstrapping behavior --- the quality of its questions improves as it gathers more knowledge. By summing evidence for and against posing any given question, Learner also exhibits noise tolerance, limiting the effect of incorrect similarities. The KA power of shallow semantic analogy from nearest neighbors is one of the main findings of this thesis. I perform an analysis of commonsense knowledge collected by another research effort that did not rely on analogical reasoning and demonstrate that indeed there is sufficient amount of correlation in the knowledge base to motivate using cumulative analogy from nearest neighbors as a KA method. Empirically, evaluating the percentages of questions answered affirmatively, negatively and judged to be nonsensical in the cumulative analogy case compares favorably with the baseline, no-similarity case that relies on random objects rather than nearest neighbors. Of the questions generated by cumulative analogy, contributors answered 45% affirmatively, 28% negatively and marked 13% as nonsensical; in the control, no-similarity case 8% of questions were answered affirmatively, 60% negatively and 26% were marked as nonsensical.

The Use of Equality in Deduction and Knowledge Representation

This report describes a system which maintains canonical expressions for designators under a set of equalities. Substitution is used to maintain all knowledge in terms of these canonical expressions. A partial order on designators, termed the better-name relation, is used in the choice of canonical expressions. It is shown that with an appropriate better-name relation an important engineering reasoning technique, propagation of constraints, can be implemented as a special case of this substitution process. Special purpose algebraic simplification procedures are embedded such that they interact effectively with the equality system. An electrical circuit analysis system is developed which relies upon constraint propagation and algebraic simplification as primary reasoning techniques. The reasoning is guided by a better-name relation in which referentially transparent terms are preferred to referentially opaque ones. Multiple description of subcircuits are shown to interact strongly with the reasoning mechanism.

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.