Automatic Qualitative Modeling of Dynamic Physical Systems

This report describes MM, a computer program that can model a variety of mechanical and fluid systems. Given a system's structure and qualitative behavior, MM searches for models using an energy-based modeling framework. MM uses general facts about physical systems to relate behavioral and model properties. These facts enable a more focussed search for models than would be obtained by mere comparison of desired and predicted behaviors. When these facts do not apply, MM uses behavior-constrained qualitative simulation to verify candidate models efficiently. MM can also design experiments to distinguish among multiple candidate models.

Transition Space

Informal causal descriptions of physical systems abound in sources such as encyclopedias, reports and user's manuals. Yet these descriptions remain largely opaque to computer processing. This paper proposes a representational framework in which such descriptions are viewed as providing partial specifications of paths in a space of possible transitions, or transition space. In this framework, the task of comprehending informal causal descriptions emerges as one of completing the specifications of paths in transition space---filling causal gaps and relating accounts of activity varied by analogy and abstraction. The use of the representation and its operations is illustrated in the context of a simple description concerning rocket propulsion.

Automatic Qualitative Analysis of Ordinary Differential Equations Using Piecewise Linear Approximations

This paper explores automating the qualitative analysis of physical systems. It describes a program, called PLR, that takes parameterized ordinary differential equations as input and produces a qualitative description of the solutions for all initial values. PLR approximates intractable nonlinear systems with piecewise linear ones, analyzes the approximations, and draws conclusions about the original systems. It chooses approximations that are accurate enough to reproduce the essential properties of their nonlinear prototypes, yet simple enough to be analyzed completely and efficiently. It derives additional properties, such as boundedness or periodicity, by theoretical methods. I demonstrate PLR on several common nonlinear systems and on published examples from mechanical engineering.

Causal and Teleological Reasoning in Circuit Recognition

This thesis presents a theory of human-like reasoning in the general domain of designed physical systems, and in particular, electronic circuits. One aspect of the theory, causal analysis, describes how the behavior of individual components can be combined to explain the behavior of composite systems. Another aspect of the theory, teleological analysis, describes how the notion that the system has a purpose can be used to aid this causal analysis. The theory is implemented as a computer program, which, given a circuit topology, can construct by qualitative causal analysis a mechanism graph describing the functional topology of the system. This functional topology is then parsed by a grammar for common circuit functions. Ambiguities are introduced into the analysis by the approximate qualitative nature of the analysis. For example, there are often several possible mechanisms which might describe the circuit's function. These are disambiguated by teleological analysis. The requirement that each component be assigned an appropriate purpose in the functional topology imposes a severe constraint which eliminates all the ambiguities. Since both analyses are based on heuristics, the chosen mechanism is a rationalization of how the circuit functions, and does not guarantee that the circuit actually does function. This type of coarse understanding of circuits is useful for analysis, design and troubleshooting.

Automated Reasoning About Classical Mechanics

In recent years, researchers in artificial intelligence have become interested in replicating human physical reasoning talents in computers. One of the most important skills in this area is predicting how physical systems will behave. This thesis discusses an implemented program that generates algebraic descriptions of how systems of rigid bodies evolve over time. Discussion about the design of this program identifies a physical reasoning paradigm and knowledge representation approach based on mathematical model construction and algebraic reasoning. This paradigm offers several advantages over methods that have become popular in the field, and seems promising for reasoning about a wide variety of classical mechanics problems.

BioJADE: A Design and Simulation Tool for Synthetic Biological Systems

The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.