Verification by Reduction to Functional Programs

In molecular programming, the Chemical Reaction Network model is often used to describe systems of interacting molecules. This model can describe either real systems, allowing us to analyze and determine their computational function; or describe hypothetical systems, with known computational function but perhaps no known physical example. One significant breakthrough in the field is that any Chemical Reaction Network can be approximated by a system using DNA Strand Displacement mechanisms. This allows the Chemical Reaction Network model to be treated like a programming language, where programs can be written in the abstract and then compiled into physical molecules. Given a programming language and a proof-of-concept compiler, one would want to take the compiler from the proof-of-concept stage into a more reliable, more systematic, and better understood process. This thesis is made up of my contributions to that effort. First, given a programming language and a compiler, it would be useful to formally verify that the compiler is correct. My collaborators, Qing Dong and Erik Winfree, and I defined a Chemical Reaction Network-specific form of bisimulation equivalence, which can compare two such networks and verify that one is (or is not) a correct implementation of the other. For example, the compiler-produced DNA circuit can be verified as an implementation of its abstract program, although this is not the only possible use. After defining this concept of equivalence, we show that it can be checked by algorithm; although various parts of the problem are NP-complete or PSPACE-complete, we give algorithms that meet these lower bounds. We also prove a number of interesting properties of Chemical Reaction Network bisimulation equivalence, including transitivity and modularity properties which are particularly useful for stepwise checking of large systems. We further extend this bisimulation method to linear Polymer Reaction Networks, a strictly more powerful abstraction which has been occasionally used in molecular programming. Again we prove complexity hardness results, which in this case are as expected uncomputable in the general case; however, many practical systems can still be verified, and we give one such example. Finally, we use bisimulation to identify a class of single-locus networks that are practical to implement. Thus we show a method of verification which can simplify use of the above-mentioned compiler by proving general statements of correctness about its results. Second, given a programming language and a concept of compiling it, it would be useful to optimize the result of the compilation. One particular area of optimization is the number of DNA strands per prepared complex; some experiments suggest that systems with no more than 2 strands per complex are more robust. Lulu Qian and I developed some proposed DNA Strand Displacement schemes for general Chemical Reaction Network implementations with no more than 2 strands per complex, and a number of other desirable properties. Meanwhile, having been shown to be useful for many reasons, the mechanisms of DNA Strand Displacement have recently been formalized, abstracted, and analyzed. I show that this formalization, combined with the bisimulation methods above, can prove various statements about the limits of DNA Strand Displacement systems. For example, a set of desirable conditions including the 2-strand limit cannot be achieved by any general Chemical Reaction Network implementation scheme. I also observe that two of the new schemes we discovered, each meeting all but one condition of the impossible set, were found in the process of coming up with this proof. I thus argue that through formalization of DNA Strand Displacement we can have a more systematic method of finding and designing molecular programs, and of knowing when the programs we want do not exist.

Generic programming is likely to become a new challenge for a critical mass of developers. Therefore, it is crucial to refine the support for generic programming in mainstream Object-Oriented languages — both at the design and at the implementation level — as well as to suggest novel ways to exploit the additional degree of expressiveness made available by genericity. This study is meant to provide a contribution towards bringing Java genericity to a more mature stage with respect to mainstream programming practice, by increasing the effectiveness of its implementation, and by revealing its full expressive power in real world scenario. With respect to the current research setting, the main contribution of the thesis is twofold. First, we propose a revised implementation for Java generics that greatly increases the expressiveness of the Java platform by adding reification support for generic types. Secondly, we show how Java genericity can be leveraged in a real world case-study in the context of the multi-paradigm language integration. Several approaches have been proposed in order to overcome the lack of reification of generic types in the Java programming language. Existing approaches tackle the problem of reification of generic types by defining new translation techniques which would allow for a runtime representation of generics and wildcards. Unfortunately most approaches suffer from several problems: heterogeneous translations are known to be problematic when considering reification of generic methods and wildcards. On the other hand, more sophisticated techniques requiring changes in the Java runtime, supports reified generics through a true language extension (where clauses) so that backward compatibility is compromised. In this thesis we develop a sophisticated type-passing technique for addressing the problem of reification of generic types in the Java programming language; this approach — first pioneered by the so called EGO translator — is here turned into a full-blown solution which reifies generic types inside the Java Virtual Machine (JVM) itself, thus overcoming both performance penalties and compatibility issues of the original EGO translator. Java-Prolog integration Integrating Object-Oriented and declarative programming has been the subject of several researches and corresponding technologies. Such proposals come in two flavours, either attempting at joining the two paradigms, or simply providing an interface library for accessing Prolog declarative features from a mainstream Object-Oriented languages such as Java. Both solutions have however drawbacks: in the case of hybrid languages featuring both Object-Oriented and logic traits, such resulting language is typically too complex, thus making mainstream application development an harder task; in the case of library-based integration approaches there is no true language integration, and some “boilerplate code” has to be implemented to fix the paradigm mismatch. In this thesis we develop a framework called PatJ which promotes seamless exploitation of Prolog programming in Java. A sophisticated usage of generics/wildcards allows to define a precise mapping between Object-Oriented and declarative features. PatJ defines a hierarchy of classes where the bidirectional semantics of Prolog terms is modelled directly at the level of the Java generic type-system.

Probabilistic programming refers to the idea of using standard programming constructs for specifying probabilistic models from machine learning and statistics, and employing generic inference algorithms for answering various queries on these models, such as posterior inference and estimation of model evidence. Although this idea itself is not new and was, in fact, explored by several programming-language and statistics researchers in the early 2000, it is only in the last few years that probabilistic programming has gained a large amount of attention among researchers in machine learning and programming languages, and that expressive and efficient probabilistic programming systems (such as Anglican, Church, Figaro, Infer.net, PSI, PyMC, Stan, and Venture) started to appear and have been taken up by a nontrivial number of users. The primary goal of my talk is to introduce probabilistic programming to the CONCUR/QUEST/FORMATS audience. At the end of my talk, I want the audience to understand basic results and techniques in probabilistic programming and to feel that these results and techniques are relevant or at least related to what she or he studies, although they typically come from foreign research areas, such as machine learning and statistics. My talk will contain both technical materials and lessons that I learnt from my machine-learning colleagues in Oxford, who are developing a highly-expressive higher-order probabilistic programming language, called Anglican. It will also include my work on the denotational semantics of higher-order probabilistic programming languages and their inference algorithms, which are jointly pursued with colleagues in Cambridge, Edinburgh, Oxford and Tubingen.

For systems which deal with serious or dangerous things (for example nuclear power plant), programs are constrained by legislation to be safe in any case, which requires verification process during the execution, in other words “Runtime Verification” (RV). The field of runtime verification has many different names: runtime monitoring, runtime checking, runtime result checking, runtime reflection, monitoring oriented programming, design by contract, runtime analysis, dynamic analysis, trace analysis, fault protection, etc. Aspect-oriented programming (AOP) is a useful paradigm for monitoring programs, even if it was not created for this purpose. Indeed, AOP tries to deal with crosscutting concerns (tangled and scattered codes) by “capturing” them within a new entity called aspect, and runtime verification properties are conceptually transversal to the code they verify, unavoidably resulting in such crosscutting codes. AOP is always used as an extension of an existing language. Hence it is necessary to design an aspect language extending the target language, and to use what is called a weaver, to realize a binding operation between the target program and the aspects. Thus, one can find many aspect-programming extensions (including an aspect language and an aspect weaver) for most programming languages. The first one to be developed was AspectJ, designed for Java, and which has been the best-known reference among aspect-oriented tools until now. We use an AspectJ-like tool, straight inspired from AspectJ but designed for C, called ACC, which is itself an improved version of AspectC. The purpose of this paper is to explore the possibility of implementing and monitoring generic (also called parameterized) verification properties, i.e. which could be used on any target code, with ACC through a basic example. As ACC, contrary to AspectJ, does not provide abstraction for aspects, which would have made generic monitoring an easy task, we tried to simulate abstraction by making use of macros in the aspect code, which boils down to monitor every parameterized property within one macro function. We will see that despite losses of expressiveness without complexification of the monitoring code, the method still allows monitoring generically any property which is already monitorable directly in ACC.

Jeff Magee and Jeff Kramer John Wiley and Sons, New York, NY, 1999, 374 pp. ISBN 0471987107, $64.99 The book is an introductory text to the ideas, concepts, and topics of concurrency. The text focuses on understanding concepts and techniques, and problems of concurrency, not on the implementation or language. The author's overall goal is that by a combination of learning and doing using Java should make the process of acquiring the skills relating to concurrency interesting, enjoyable, and challenging. The Java language is thus used only for illustration and programming experience of the reader. The book is intended for a computer science student or software developer. A background in programming is expected, as well as some familiarity with the essential concepts of object-oriented programming. Knowledge of the Java programming language and operating systems concepts is beneficial but not required. After reading the text, a reader can expect to have a broad understanding of the concepts of concurrency, the problems that arise, methods to emphasis desirable properties in a concurrent system, and ways to avoid the undesirable ones. The text provides a systematic treatment of concepts, as means to rigorously specify and model concurrent systems, with Java examples to animate and illustrate the concepts discussed. The book is organized into twelve chapters, with three appendices. The first eight chapters provide a concise and comprehensive foundation of concurrency, with the remaining four chapters focusing on more advanced concepts. The latter four chapters are somewhat supplemental and can be read at the discretion of the reader. The content of the text is self-contained, with no reliance upon external references. The authors provide a concluding set of notes and further topics which reference external works, but these are not used in the chapter contents. The introduction provides the foundation for the book, and an idea of what will follow in the rest of the text. The basics of modeling and Java are covered. Authors follow with the concepts of processes, threads and with the idea of concurrency. The emphasis is on using Java, and on the notation used to define a concurrent process or thread. The discussion continues covering interleaving and asynchronous concurrency. Various details about composition of parallel processes and finite state processing modeling are presented. The programming of concurrent execution using Java is then examined via the concept of multiple threads. Here, sharing objects among Java threads is also discussed. The concept of conditional synchronization is covered next, and is used to construct a monitor. The methods of the base object in Java is used, and a waiting queue associated with a Java object is discussed and implemented. This discussion is followed by introduction of deadlock. Authors show the conditions necessary for a deadlock to occur and present an analysis of a concurrent system establishing that such a system is deadlock-free. The classic Dining Philosopher's problem is used to illustrate the distinction between finding deadlocks in models and in programs. The presentation continues with the safety property (that asserts that nothing bad happens), and the liveliness property (that asserts that nothing good happens). Here, authors use the material on model-based design to consolidate many of the concepts previously discussed. No one modeling method or design methodology is emphasized. Then creation and elimination of threads in a running program is covered next. The dynamic starting and stopping of Java threads is presented. The discussion moves then to messaging passing. Asynchronous and synchronous messaging is presented with Java programming examples. The concept of a rendezvous, allowing for interaction in a messaging system, is also presented. Based on the concepts developed so far filter-pipeline, supervisor-worker, and announcer-listener concurrent architectures are examined. Java programs demonstrating how the elements of each model interact at runtime are developed. The presentation completes with modeling and implementing of timed systems. Time is signaled by the passage of successive time ticks. The authors then elaborate on a system that is event-based rather than thread-based. Java programs are used to illustrate in implementation the concepts discussed. The three appendices provide a reference, specification, and listing of semantics for the finite-state modeling algebra used by the authors throughout the book. The text is ideal for teaching in a classroom environment, or for a motivated reader to use for self-paced learning. Its organization follows a logical train of discussion and thought, with each chapter building successively on the other, with the more difficult concepts and topics withheld until later. This gradual approach makes the material flow smoothly and cohesively from the beginning to the end. The book is intended as a textbook, so does organize the material and discussion as one, but does not become too dry or bland to stifle the reader's interest in the material. The examples are inter-mixed with the discussion to highlight and emphasize essential points the authors make in each chapter. The text illustrates concepts well under discussion, and does not become a long-winded recital of theory. The topics examined are fundamental to concurrency, and are well illustrated and discussed, but no one topic is examined extensively. The code examples are well written concerning the programming style, indentation and comments. A CD is provided, containing the codes from the book. In addition supplementary material consisting of presentation slides and an errata is provided on the author's WWW site, as well as on the CD. The book is up to date both on the topics of concurrency, and with the Java applets, code, and programs used to illustrate them. Later, as the Java language evolves, the examples may need to be updated, but for the time being the text well represents that state of the Java language. William F. Gilreath, Micron Technology, Inc., Boise Idaho

The emergence of Unified Modeling Language (UML) as a standard for modeling systems has encouraged the use of automated software tools that facilitate the development process from analysis through coding. The UML state machine diagram is used for modeling the dynamic aspects of systems and includes many concepts that are not present in most popular programming languages, like Java or C++. There exists a gap between high level modeling language and a programming language. This paper proposes an approach to narrow the gap between multiple UML models and an implemented system. The narrowing of gap is achieved by generating compact and efficient Java code directly from UML state machine having sequential and concurrent substates. The code generation is achieved by creating a mapping between UML behavior and the Java programming language. Our model can work as a basis for automatic code generation for object-oriented systems.

This thesis proposes a novel way of performing type checking, whose results are incremental, depending on the provided local information. This new way of type checking is called co-contextual, where all context information of expressions, methods, classes, etc., is removed. Instead, we introduce corresponding structures using requirements. Standard type systems are translated to the co-contextual ones systematically using dualism as technique. Type systems play an important role to prevent execution errors from occurring during runtime. They are used to check programs statically for potential errors. Programs are type checked against a given set of rules. Depending on these rules programs are well-typed or not. The set of these rules is called typing rules. Each type rule associates types to the constructs of a program given a certain context. There can be different forms of contexts, depending on the features of the typed programming language. Functional languages use a typing context of variables and their types; object-oriented (OO) languages use additional class tables. Class tables are used for example to ensure that method and class declarations are well-typed. Type checking is performed top-down. While traversing the syntax tree of a program, typing contexts are extended with information on the expressions and their types. In case of OO, class tables are extended with clauses from class declarations, including the class members, i.e., fields, methods, or constructors. Contexts are passed through the nodes of the syntax tree in order to coordinate type checking between them. Therefore, while traversing the syntax tree top-down, the type checker creates dependencies between otherwise independent subexpressions. This way, it inhibits incrementalization and parallelization of type checking. That is, a change to a node of the syntax tree would require to redo the type check of the whole syntax tree. In this thesis a novel formulation of type systems is proposed, in order to remove dependencies between subexpressions. We propose a co-contextual formulation of typing rules that depends only on the local program constructs, e.g., expressions, methods, classes. The co-contextual typing rules have as conclusion a type and sets of requirements. That is, contexts and class tables are replaced by the dual concept of context and class table requirements. In addition, operations on contexts and class tables are replaced by new dual operations on requirements. The co-contextual type checker traverses a syntax tree bottom-up and merges context requirements of independently checked subexpressions. We describe a method for systematically constructing a co-contextual formulation of type rules from a regular context-based formulation and we show how co-contextual type rules give rise to incremental type checking. We derive co-contextual type checkers for functional and OO languages. As a representative of functional languages we consider PCF and extensions of it: records, parametric polymorphism, structural subtyping and let-polymorphism. Also, we investigate featherweight java (FJ) as the basis of OO languages and extensions of it: method overloading and generics. We build a1 co-contextual type checker for FJ enabling key features of OO languages: subtype polymorphism, nominal typing and implementation inheritance. The dualism between the co-contextual and contextual type systems preserves the correctness of the contextual calculus. That is, we prove the correctness of the co-contextual calculus via the equivalence between contextual type rules and their co-contextual formulations. We implemented an incremental type checker for PCF along with a performance evaluation showing that co-contextual type checking has performance comparable to standard context-based type checking, and incrementalization can improve performance significantly. Regarding FJ, we implemented a co-contextual type checker with incrementalization and compared its performance against javac on a number of realistic programs. Our performance evaluation shows significant speedups for the co-contextual type checker with incrementalization in comparison to javac.

One of the important objectives of computer science (programming) education is to develop fundamental proficiency in the area of computer programming. Knowledge of programming is so important that almost all computer science programs include it in their curriculum. This important subject is widely reported as being challenging for novices especially in the very beginning early lessons. Study on bilingual language instructions shows that use of native language instructions help students to understand the subject better and use of secondary language instructions increase their social context of choice. When a learner learns through a language other than the mother tongue, learner faces problems because his task becomes two-fold. The first is that the learner has to make sense of the instructional tasks, which are presented in the second language or an interactive manner, and the second is Learner has to get linguistic competence that is required for effective learning to take place.

Proof assistants and the programming languages that implement them need to deal with a range of linguistic expressions that involve bindings. Since most mature proof assistants do not have built-in methods to treat this aspect of syntax, many of them have been extended with various packages and libraries that allow them to encode bindings using, for example, de Bruijn numerals and nominal logic features. I put forward the argument that bindings are such an intimate aspect of the structure of expressions that they should be accounted for directly in the underlying programming language support for proof assistants and not added later using packages and libraries. One possible approach to designing programming languages and proof assistants that directly supports such an approach to bindings in syntax is presented. The roots of such an approach can be found in the mobility of binders between term-level bindings, formula-level bindings (quantifiers), and proof-level bindings (eigenvariables). In particular, by combining Church's approach to terms and formulas (found in his Simple Theory of Types) and Gentzen's approach to sequent calculus proofs, we can learn how bindings can declaratively interact with the full range of logical connectives and quantifiers. I will also illustrate how that framework provides an intimate and semantically clean treatment of computation and reasoning with syntax containing bindings. Some implemented systems, which support this intimate and built-in treatment of bindings, will be briefly described.

A class dictionary defines all data structures that appear in a program as well as a language for describing data specified by the data structures. We demonstrate that class dictionaries are ideal for simplifying object-oriented programming. Our class dictionary-based approach to object-oriented programming is independent of any particular programming language, so it is applicable to a large variety of object-oriented systems. The experience in designing and using over one hundred class dictionaries has resulted in a set of useful design techniques. This novel approach to object-oriented programming makes interesting links between language design, data structure design, and data-base design.

Recursive function theory studies functions that can be evaluated by an algorithm based on some computing model such as a Turing machine or computer program. These functions are called partial recursive (p.r.) and are defined on subsets of N, where N = {0, 1,... }, with values in N. (A good introduction to the theory may be found in [2].) This paper explains the Parameter Theorem, illustrates some unusual computer programs, and explains their connection to recursive function theory. Basing our computing model on a modern high level language, we can construct programs whose existence is known through more formal means. Our functions will operate on strings rather than numbers, however. There is no loss in generality since strings can be viewed as members of N, and vice-versa. From a practical aspect, this approach is somewhat more desirable since conventional programming languages often allow making use of long strings, but place more restrictive limits on the size of integers. We first pose a problem: Does there exist a program (written in some conventional programming language) which halts if and only if its input is identical to the program's text (i.e., source code)? For the remainder of this note X is the set of ASCII characters 'a,' 'b, +,' space, line feed, and so forth, needed to write programs in most programming languages. We denote by X * the set of all strings (finite sequences) over X. Let P1 be the set of all one variable partial recursive functions on X *. A function I belongs to P1 if and only if there is a subset of S of X* and some algorithm which computes 't by associating with each element of S a well-defined element of X *. Similarly, 't belongs to P2 if and only if there is a set S c X * X X *, and an algorithm for 't which associates with each element of S a well-defined element of X *. A partial recursive function I in P1 (or in P2) is recursive if the algorithm is defined on all of X * (or X * X X *). This is equivalent to saying that the algorithm which evaluates I always halts. Our computing model will be based on Adat; its high-level string-handling properties simplify later examples. For readability, however, we will express algorithms in a more familiar Pascal-like style. Readers familiar with either programming language should find forthcoming algorithms sufficiently clear. A formal presentation in Ada is given in the Appendix. A string of ASCII characters, such as in FIGURE 1, represents a function in our language which takes strings to strings. Of course, strings of ASCII characters such as The quick brown fox and %*!! represent nothing at all in our programming language. Let A1 be the set of all strings in X * representing functions in our language of one input STRING which outputs a STRING. Similarly let A2 be the set of all strings in

The aim of this thesis is to construct toolsets that support the Synchronous Java programming language, an extension to the Java language that introduces a new method of synchronization between threads. The contributions of this thesis include a State Space Analyzer (SSAS) and a Deadlock Detector for Synchronous Java (DDSJ). As the first tool I developed an analyzer, the SSAS, that explores all the reachable states and all the possible execution paths of an sJava model. This exploration aims at the analysis of the communication between active threads and the detection of deadlocks in a given sJava model. When a deadlock is encountered, the toolset generates the error traces that help the developers to examine how the deadlocks were produced in the input model. The analyzer also generates the state space of the system model and a graphical representation of this state space. In the second toolset, the DDSJ, I developed an approach that reduces the number of states when verifying an sJava program in Bandera and Bogor, which are the toolsets that support the verification of Java models. If errors are detected when verifying an sJava model, DDSJ generates a counter-example that allows developers to simulate the execution of the given model to study how errors were produced. The outcomes of this thesis give the Synchronous Java developers more confidence in using this programming language. These toolsets provide a possibility to examine sJava programs and to refine them before they can be delivered as product.

Mark Watson Morgan Kaufmann Publishers, San Francisco, 1997, 377 pp. ISBN 1-55860-420-0, $44.95 This book is well written and organized to cover how to apply AI (Artificial Intelligence) techniques for practical Internet and Intranet tools by using the Java programming language. In the book, the author uses neural network and genetic algorithms to develop distributed systems that are applied for the Internet and Intranets, such as client/server model and information retrieval tool and so on. Part 1 begins with a good general introduction to AI. The history and survey of Artificial Intelligence research are given briefly. In addition, symbolic processing versus neural networks approaches are discussed. This author opts to use neural network to develop example Internet/Intranet systems in the book. Part 2 consists of Java programs developed for AI, neural networks, genetic algorithms, natural language processing, and expert systems. Chapter 2 illustrates Graphical User Interface (GUI) class that is derived from Applet and Canvas classes in Java, which is used in most example programs in the book. Chapter 3 introduces a frame data structure that is used as a message in distributed systems in the later chapters. Chapter 4 shows neural network classes developed in Java and its theory and implementation. Chapter 5 explains the genetic algorithms and the Java genetic algorithm classes. Chapter 6 describes how to develop and implement natural language processing classes using Java. Chapter 7 shows how to share data objects in distributed systems. For example, distributed AI agent classes are developed to share data objects, WWW data collection agent classes are shown to retrieve documents in the Internet, and small POP (Post Office Protocol) mail classes are developed to send and receive mails. Chapter 8 illustrates how to develop expert systems by using Java Jess, which is based on OPS5/CLIPS expert systems. Part 3 explains how to generate and implement the projects using the Java classes that are developed in Part 2. Chapter 9 shows the project that demonstrates the use of genetic algorithms in chapter 5 to control enemy ships in a scrolling arcade game. Chapter 10 describes the real-time handwriting recognition system developed by using the neural network classes in chapter 4. Chapter 11 illustrates a greedy algorithm to optimize neural networks that is based on the author’s hand-tuning neural training data. Chapter 12 improves neural network training data by applying genetic algorithms, to discard bad training data and to avoid discarding good training data. Chapter 13 describes the distributed natural language processing system that uses natural language processing classes in chapter 6. The data structures in chapter 2 are used to store historical data in a separate server application on any other computer in the Internet or Intranets. The final chapter provides the design and implementation of a complete agent-based information retrieval tool for the Internet. The retrieved documents are stored in ASCII or HTML format. This book is a very good reference book for anyone interested in developing systems using Java in distributed environments, especially applying AI techniques. Also, the author provides the CD-ROM that includes the source code for Java classes developed in the book. Haklin Kimm, University of Tennessee

Many interdisciplinary works have underlined the importance of lexical knowledge in terms of vocabulary knowledge. Lexical knowledge is an inseparable part in the knowledge of language. However, in the compilation of electronic dictionary, the technology can be involved in all the stages, because it is maximum utilized in both mental and mechanical works almost equally. The entire mechanical works can be easily carried out by computers using suitable programmes.The machine can also provide various processed information which actually helps the lexicographers to accomplish the most of the mental tasks with ease. Thus, this attempt is made to develop an e- dictionary for school children to enrich their vocabulary power through a technology-incorporated dictionary i.e. a virtual software (programme) written in a programming language (i.e. vb.net) as an asset to Tamil language and also its community.

First-order languages based on rewrite rules share many features with functional languages, but one difference is that matching and rewriting can be made much more expressive and powerful by incorp...