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.

Type-omega DPLs

Type-omega DPLs (Denotational Proof Languages) are languages for proof presentation and search that offer strong soundness guarantees. LCF-type systems such as HOL offer similar guarantees, but their soundness relies heavily on static type systems. By contrast, DPLs ensure soundness dynamically, through their evaluation semantics; no type system is necessary. This is possible owing to a novel two-tier syntax that separates deductions from computations, and to the abstraction of assumption bases, which is factored into the semantics of the language and allows for sound evaluation. Every type-omega DPL properly contains a type-alpha DPL, which can be used to present proofs in a lucid and detailed form, exclusively in terms of primitive inference rules. Derived inference rules are expressed as user-defined methods, which are "proof recipes" that take arguments and dynamically perform appropriate deductions. Methods arise naturally via parametric abstraction over type-alpha proofs. In that light, the evaluation of a method call can be viewed as a computation that carries out a type-alpha deduction. The type-alpha proof "unwound" by such a method call is called the "certificate" of the call. Certificates can be checked by exceptionally simple type-alpha interpreters, and thus they are useful whenever we wish to minimize our trusted base. Methods are statically closed over lexical environments, but dynamically scoped over assumption bases. They can take other methods as arguments, they can iterate, and they can branch conditionally. These capabilities, in tandem with the bifurcated syntax of type-omega DPLs and their dynamic assumption-base semantics, allow the user to define methods in a style that is disciplined enough to ensure soundness yet fluid enough to permit succinct and perspicuous expression of arbitrarily sophisticated derived inference rules. We demonstrate every major feature of type-omega DPLs by defining and studying NDL-omega, a higher-order, lexically scoped, call-by-value type-omega DPL for classical zero-order natural deduction---a simple choice that allows us to focus on type-omega syntax and semantics rather than on the subtleties of the underlying logic. We start by illustrating how type-alpha DPLs naturally lead to type-omega DPLs by way of abstraction; present the formal syntax and semantics of NDL-omega; prove several results about it, including soundness; give numerous examples of methods; point out connections to the lambda-phi calculus, a very general framework for type-omega DPLs; introduce a notion of computational and deductive cost; define several instrumented interpreters for computing such costs and for generating certificates; explore the use of type-omega DPLs as general programming languages; show that DPLs do not have to be type-less by formulating a static Hindley-Milner polymorphic type system for NDL-omega; discuss some idiosyncrasies of type-omega DPLs such as the potential divergence of proof checking; and compare type-omega DPLs to other approaches to proof presentation and discovery. Finally, a complete implementation of NDL-omega in SML-NJ is given for users who want to run the examples and experiment with the language.

Coordinate-Independent Computations on Differential Equations

This project investigates the computational representation of differentiable manifolds, with the primary goal of solving partial differential equations using multiple coordinate systems on general n- dimensional spaces. In the process, this abstraction is used to perform accurate integrations of ordinary differential equations using multiple coordinate systems. In the case of linear partial differential equations, however, unexpected difficulties arise even with the simplest equations.

Inspection Methods in Programming

The work reported here lies in the area of overlap between artificial intelligence software engineering. As research in artificial intelligence, it is a step towards a model of problem solving in the domain of programming. In particular, this work focuses on the routine aspects of programming which involve the application of previous experience with similar programs. I call this programming by inspection. Programming is viewed here as a kind of engineering activity. Analysis and synthesis by inspection area prominent part of expert problem solving in many other engineering disciplines, such as electrical and mechanical engineering. The notion of inspections methods in programming developed in this work is motivated by similar notions in other areas of engineering. This work is also motivated by current practical concerns in the area of software engineering. The inadequacy of current programming technology is universally recognized. Part of the solution to this problem will be to increase the level of automation in programming. I believe that the next major step in the evolution of more automated programming will be interactive systems which provide a mixture of partially automated program analysis, synthesis and verification. One such system being developed at MIT, called the programmer's apprentice, is the immediate intended application of this work. This report concentrates on the knowledge are of the programmer's apprentice, which is the form of a taxonomy of commonly used algorithms and data structures. To the extent that a programmer is able to construct and manipulate programs in terms of the forms in such a taxonomy, he may relieve himself of many details and generally raise the conceptual level of his interaction with the system, as compared with present day programming environments. Also, since it is practical to expand a great deal of effort pre-analyzing the entries in a library, the difficulty of verifying the correctness of programs constructed this way is correspondingly reduced. The feasibility of this approach is demonstrated by the design of an initial library of common techniques for manipulating symbolic data. This document also reports on the further development of a formalism called the plan calculus for specifying computations in a programming language independent manner. This formalism combines both data and control abstraction in a uniform framework that has facilities for representing multiple points of view and side effects.

On Clonal Selection.

Clonal selection has been a dominant theme in many immune-inspired algorithms applied to machine learning and optimisation. We examine existing clonal selections algorithms for learning from a theoertical and empirical perspective and assert that the widely accepted computational interpretation of clonal selection is compromised both algorithmically andbiologically. We suggest a more capable abstraction of the clonal selection principle grounded in probabilistic estimation and approximation and demonstrate how it addresses some of the shortcomings in existing algorithms. We further show that by recasting black-box optimisation as a learning problem, the same abstraction may be re-employed; thereby taking steps toward unifying the clonal selection principle and distinguishing it from natural selection.

On the use of qualitative reasoning to simulate and identify metabolic pathways

King, R.D., Garrett, S.M., Coghill, G.M. (2005). On the use of qualitative reasoning to simulate and identify metabolic pathways. Bioinformatics 21(9):2017-2026 RAE2008

Data mining the yeast genome in a lazy functional language

Clare, A. and King R.D. (2003) Data mining the yeast genome in a lazy functional language. In Practical Aspects of Declarative Languages (PADL'03) (won Best/Most Practical Paper award).

From Limen to Lumen: computing students in liminal spaces.From Limen to Lumen: computing students in liminal spaces

Eckerdal, A., McCartney, R., Mostr?m, J. E., Sanders, K., Thomas, L., and Zander, C. 2007. From Limen to Lumen: computing students in liminal spaces. In Proceedings of the Third international Workshop on Computing Education Research (Atlanta, Georgia, USA, September 15 - 16, 2007). ICER '07. ACM, New York, NY, 123-132.

Systematic Verification of Safety Properties of Arbitrary Network Protocol Compositions Using CHAIN

Formal correctness of complex multi-party network protocols can be difficult to verify. While models of specific fixed compositions of agents can be checked against design constraints, protocols which lend themselves to arbitrarily many compositions of agents-such as the chaining of proxies or the peering of routers-are more difficult to verify because they represent potentially infinite state spaces and may exhibit emergent behaviors which may not materialize under particular fixed compositions. We address this challenge by developing an algebraic approach that enables us to reduce arbitrary compositions of network agents into a behaviorally-equivalent (with respect to some correctness property) compact, canonical representation, which is amenable to mechanical verification. Our approach consists of an algebra and a set of property-preserving rewrite rules for the Canonical Homomorphic Abstraction of Infinite Network protocol compositions (CHAIN). Using CHAIN, an expression over our algebra (i.e., a set of configurations of network protocol agents) can be reduced to another behaviorally-equivalent expression (i.e., a smaller set of configurations). Repeated applications of such rewrite rules produces a canonical expression which can be checked mechanically. We demonstrate our approach by characterizing deadlock-prone configurations of HTTP agents, as well as establishing useful properties of an overlay protocol for scheduling MPEG frames, and of a protocol for Web intra-cache consistency.

Distributed Parallel Computing in Mermera: Mixing Noncoherent Shared Memories

Programmers of parallel processes that communicate through shared globally distributed data structures (DDS) face a difficult choice. Either they must explicitly program DDS management, by partitioning or replicating it over multiple distributed memory modules, or be content with a high latency coherent (sequentially consistent) memory abstraction that hides the DDS' distribution. We present Mermera, a new formalism and system that enable a smooth spectrum of noncoherent shared memory behaviors to coexist between the above two extremes. Our approach allows us to define known noncoherent memories in a new simple way, to identify new memory behaviors, and to characterize generic mixed-behavior computations. The latter are useful for programming using multiple behaviors that complement each others' advantages. On the practical side, we show that the large class of programs that use asynchronous iterative methods (AIM) can run correctly on slow memory, one of the weakest, and hence most efficient and fault-tolerant, noncoherence conditions. An example AIM program to solve linear equations, is developed to illustrate: (1) the need for concurrently mixing memory behaviors, and, (2) the performance gains attainable via noncoherence. Other program classes tolerate weak memory consistency by synchronizing in such a way as to yield executions indistinguishable from coherent ones. AIM computations on noncoherent memory yield noncoherent, yet correct, computations. We report performance data that exemplifies the potential benefits of noncoherence, in terms of raw memory performance, as well as application speed.

A Linearization of the Lambda-Calculus and Consequences

If every lambda-abstraction in a lambda-term M binds at most one variable occurrence, then M is said to be "linear". Many questions about linear lambda-terms are relatively easy to answer, e.g. they all are beta-strongly normalizing and all are simply-typable. We extend the syntax of the standard lambda-calculus L to a non-standard lambda-calculus L^ satisfying a linearity condition generalizing the notion in the standard case. Specifically, in L^ a subterm Q of a term M can be applied to several subterms R1,...,Rk in parallel, which we write as (Q. R1 \wedge ... \wedge Rk). The appropriate notion of beta-reduction beta^ for the calculus L^ is such that, if Q is the lambda-abstraction (\lambda x.P) with m\geq 0 bound occurrences of x, the reduction can be carried out provided k = max(m,1). Every M in L^ is thus beta^-SN. We relate standard beta-reduction and non-standard beta^-reduction in several different ways, and draw several consequences, e.g. a new simple proof for the fact that a standard term M is beta-SN iff M can be assigned a so-called "intersection" type ("top" type disallowed).

Program Representation Size in an Intermediate Language with Intersection and Union Types

The CIL compiler for core Standard ML compiles whole programs using a novel typed intermediate language (TIL) with intersection and union types and flow labels on both terms and types. The CIL term representation duplicates portions of the program where intersection types are introduced and union types are eliminated. This duplication makes it easier to represent type information and to introduce customized data representations. However, duplication incurs compile-time space costs that are potentially much greater than are incurred in TILs employing type-level abstraction or quantification. In this paper, we present empirical data on the compile-time space costs of using CIL as an intermediate language. The data shows that these costs can be made tractable by using sufficiently fine-grained flow analyses together with standard hash-consing techniques. The data also suggests that non-duplicating formulations of intersection (and union) types would not achieve significantly better space complexity.

Hidden Type Variables and Conditional Extension for More Expressive Generic Programs

Generic object-oriented programming languages combine parametric polymorphism and nominal subtype polymorphism, thereby providing better data abstraction, greater code reuse, and fewer run-time errors. However, most generic object-oriented languages provide a straightforward combination of the two kinds of polymorphism, which prevents the expression of advanced type relationships. Furthermore, most generic object-oriented languages have a type-erasure semantics: instantiations of type parameters are not available at run time, and thus may not be used by type-dependent operations. This dissertation shows that two features, which allow the expression of many advanced type relationships, can be added to a generic object-oriented programming language without type erasure: 1. type variables that are not parameters of the class that declares them, and 2. extension that is dependent on the satisfiability of one or more constraints. We refer to the first feature as hidden type variables and the second feature as conditional extension. Hidden type variables allow: covariance and contravariance without variance annotations or special type arguments such as wildcards; a single type to extend, and inherit methods from, infinitely many instantiations of another type; a limited capacity to augment the set of superclasses after that class is defined; and the omission of redundant type arguments. Conditional extension allows the properties of a collection type to be dependent on the properties of its element type. This dissertation describes the semantics and implementation of hidden type variables and conditional extension. A sound type system is presented. In addition, a sound and terminating type checking algorithm is presented. Although designed for the Fortress programming language, hidden type variables and conditional extension can be incorporated into other generic object-oriented languages. Many of the same problems would arise, and solutions analogous to those we present would apply.

The Sensor Network Workbench: Towards Functional Specification, Verification and Deployment of Constrained Distributed Systems

As the commoditization of sensing, actuation and communication hardware increases, so does the potential for dynamically tasked sense and respond networked systems (i.e., Sensor Networks or SNs) to replace existing disjoint and inflexible special-purpose deployments (closed-circuit security video, anti-theft sensors, etc.). While various solutions have emerged to many individual SN-centric challenges (e.g., power management, communication protocols, role assignment), perhaps the largest remaining obstacle to widespread SN deployment is that those who wish to deploy, utilize, and maintain a programmable Sensor Network lack the programming and systems expertise to do so. The contributions of this thesis centers on the design, development and deployment of the SN Workbench (snBench). snBench embodies an accessible, modular programming platform coupled with a flexible and extensible run-time system that, together, support the entire life-cycle of distributed sensory services. As it is impossible to find a one-size-fits-all programming interface, this work advocates the use of tiered layers of abstraction that enable a variety of high-level, domain specific languages to be compiled to a common (thin-waist) tasking language; this common tasking language is statically verified and can be subsequently re-translated, if needed, for execution on a wide variety of hardware platforms. snBench provides: (1) a common sensory tasking language (Instruction Set Architecture) powerful enough to express complex SN services, yet simple enough to be executed by highly constrained resources with soft, real-time constraints, (2) a prototype high-level language (and corresponding compiler) to illustrate the utility of the common tasking language and the tiered programming approach in this domain, (3) an execution environment and a run-time support infrastructure that abstract a collection of heterogeneous resources into a single virtual Sensor Network, tasked via this common tasking language, and (4) novel formal methods (i.e., static analysis techniques) that verify safety properties and infer implicit resource constraints to facilitate resource allocation for new services. This thesis presents these components in detail, as well as two specific case-studies: the use of snBench to integrate physical and wireless network security, and the use of snBench as the foundation for semester-long student projects in a graduate-level Software Engineering course.

Safe Compositional Network Sketches: Tool & Use Cases

NetSketch is a tool that enables the specification of network-flow applications and the certification of desirable safety properties imposed thereon. NetSketch is conceived to assist system integrators in two types of activities: modeling and design. As a modeling tool, it enables the abstraction of an existing system so as to retain sufficient enough details to enable future analysis of safety properties. As a design tool, NetSketch enables the exploration of alternative safe designs as well as the identification of minimal requirements for outsourced subsystems. NetSketch embodies a lightweight formal verification philosophy, whereby the power (but not the heavy machinery) of a rigorous formalism is made accessible to users via a friendly interface. NetSketch does so by exposing tradeoffs between exactness of analysis and scalability, and by combining traditional whole-system analysis with a more flexible compositional analysis approach based on a strongly-typed, Domain-Specific Language (DSL) to specify network configurations at various levels of sketchiness along with invariants that need to be enforced thereupon. In this paper, we overview NetSketch, highlight its salient features, and illustrate how it could be used in applications, including the management/shaping of traffic flows in a vehicular network (as a proxy for CPS applications) and in a streaming media network (as a proxy for Internet applications). In a companion paper, we define the formal system underlying the operation of NetSketch, in particular the DSL behind NetSketch's user-interface when used in "sketch mode", and prove its soundness relative to appropriately-defined notions of validity.