Formal Molecular Biology Done in CCS-R

We present CCS-R, a reversible variant of Milner's CCS offering a backtracking mechanism. Formalization of biological systems satisfying a “perfect mix” assumption within CCS-R is discussed.     

The Evolution of Concurrent Programs

Process algebra are formal languages used for the rigorous specification and analysis of concurrent systems. By using a process algebra as the target language of a genetic programming system, the derivation of concurrent programs satisfying given problem specifications is possible. A genetic programming system based on Koza's model has been implemented. The target language used is Milner's CCS process algebra, and is chosen for its conciseness and simplicity. The genetic programming environment needs a few adaptations to the computational characteristics of concurrent programs. In particular, means for efficiently controlling the exponentially large computation spaces that are common with process algebra must be addressed. Experimental runs of the system successfully evolved a number of non–iterative CCS systems, hence proving the potential of evolutionary approaches to concurrent system development.     

Self-assembling Trees

RCCS is a variant of Milner's CCS where processes are allowed a controlled form of backtracking. It turns out that the RCCS reinterpretation of a CCS process is equivalent, in the sense of weak bisimilarity, to its causal transition system in CCS. This can be used to develop an efficient method for designing distributed algorithms, which we illustrate here by deriving a distributed algorithm for assembling trees. Such a problem requires solving a highly distributed consensus, and a comparison with a traditional CCS-based solution shows that the code we obtain is shorter, easier to understand, and easier to prove correct by hand, or even to verify.     

Integrated environments for formally well-founded design andsimulation of concurrent systems

An ongoing project concerned with the development of environments that support the specification and design of concurrent systems is reported. The project has two key aspects: an existing and working system, Clara, that supports Milner's CCS as a specification and design language; and the development of general techniques for computer-aided generation of Clara-like environments for other concurrent languages. The Clara environment is emphasized. It has two main components: support for the usage of formal techniques in the design process, and a rich and highly interactive simulation facility. A further distinguishing feature is the environment's graphical user interface which is based on a pictorial version of CCS. The semantics of CCS is defined nonprocedurally in two phases: an operational semantics given as a set of inference rules, and an algebraic semantics represented by a set of equational rules     

Towards modeling user behavior in interactions mediated through an automated bidirectional speech translation system

This paper addresses modeling user behavior in interactions between two people who do not share a common spoken language and communicate with the aid of an automated bidirectional speech translation system. These interaction settings are complex. The translation machine attempts to bridge the language gap by mediating the verbal communication, noting however that the technology may not be always perfect. In a step toward understanding user behavior in this mediated communication scenario, usability data from doctor–patient dialogs involving a two way English–Persian speech translation system are analyzed. We specifically consider user behavior in light of potential uncertainty in the communication between the interlocutors. We analyze the Retry (Repeat and Rephrase) versus Accept behaviors in the mediated verbal channel and as a result identify three user types – Accommodating, Normal and Picky, and propose a dynamic Bayesian network model of user behavior. To validate the model, we performed offline and online experiments. The experimental results using offline data show that correct user type is clearly identified as a user keeps his/her consistent behavior in a given interaction condition. In the online experiment, agent feedback was presented to users according to the user types. We show high user satisfaction and interaction efficiency in the analysis of user interview, video data, questionnaire and log data.     

Executable structural operational semantics in Maude

This paper describes in detail how to bridge the gap between theory and practice when implementing in Maude structural operational semantics described in rewriting logic, where transitions become rewrites and inference rules become conditional rewrite rules with rewrites in the conditions, as made possible by the new features in Maude 2. We validate this technique using it in several case studies: a functional language Fpl (evaluation and computation semantics), an imperative language WhileL (evaluation and computation semantics), Kahn’s functional language Mini-ML (evaluation or natural semantics), Milner’s CCS (with strong and weak transitions), and Full LOTOS (including ACT ONE data type specifications). In addition, on top of CCS we develop an implementation of the Hennessy–Milner modal logic for describing local capabilities of processes, and for LOTOS we build an entire tool where Full LOTOS specifications can be entered and executed (without user knowledge of the underlying implementation of the semantics). We also compare this method based on transitions as rewrites with another one based on transitions as judgements.     

Secure Information Flow via Linear Continuations

Security-typed languages enforce secrecy or integrity policies by type-checking. This paper investigates continuation-passing style (CPS) as a means of proving that such languages enforce noninterference and as a first step towards understanding their compilation. We present a low-level, secure calculus with higher-order, imperative features and linear continuations.Linear continuations impose a stack discipline on the control flow of programs. This additional structure in the type system lets us establish a strong information-flow security property called noninterference. We prove that our CPS target language enjoys the noninterference property and we show how to translate secure high-level programs to this low-level language. This noninterference proof is the first of its kind for a language with higher-order functions and state.     

Lifting non-finite axiomatizability results to extensions of process algebras

This paper presents a general technique for obtaining new results pertaining to the non-finite axiomatizability of behavioural (pre)congruences over process algebras from old ones. The proposed technique is based on a variation on the classic idea of reduction mappings. In this setting, such reductions are translations between languages that preserve sound (in)equations and (in)equational provability over the source language, and reflect families of (in)equations responsible for the non-finite axiomatizability of the target language. The proposed technique is applied to obtain a number of new non-finite axiomatizability theorems in process algebra via reduction to Moller’s celebrated non-finite axiomatizability result for CCS. The limitations of the reduction technique are also studied. In particular, it is shown that prebisimilarity is not finitely based over CCS with the divergent process Ω, but that this result cannot be proved by a reduction to the non-finite axiomatizability of CCS modulo bisimilarity. This negative result is the inspiration for the development of a sharpened reduction method that is powerful enough to show that prebisimilarity is not finitely based over CCS with the divergent process Ω.     

Implicitly Heterogeneous Multi-Stage Programming

Previous work on semantics-based multi-stage programming (MSP) language design focused on homogeneous designs, where the generating and the generated languages are the same. Homogeneous designs simply add a hygienic quasi-quotation and evaluation mechanism to a base language. An apparent disadvantage of this approach is that the programmer is bound to both the expressivity and performance characteristics of the base language. This paper proposes a practical means to avoid this by providing specialized translations from subsets of the base language to different target languages. This approach preserves the homogeneous “look” of multi-stage programs, and, more importantly, the static guarantees about the generated code. In addition, compared to an explicitly heterogeneous approach, it promotes reuse of generator source code and systematic exploration of the performance characteristics of the target languages. To illustrate the proposed approach, we design and implement a translation to a subset of C suitable for numerical computation, and show that it preserves static typing. The translation is implemented, and evaluated with several benchmarks. The implementation is available in the online distribution of MetaOCaml.     

Space Complexity Vs. Query Complexity

Combinatorial property testing deals with the following relaxation of decision problems: Given a fixed property and an input x, one wants to decide whether x satisfies the property or is “far” from satisfying it. The main focus of property testing is in identifying large families of properties that can be tested with a certain number of queries to the input. In this paper we study the relation between the space complexity of a language and its query complexity. Our main result is that for any space complexity s(n) ≤ log n there is a language with space complexity O(s(n)) and query complexity 2^Ω(s(n)). Our result has implications with respect to testing languages accepted by certain restricted machines. Alon et al. [FOCS 1999] have shown that any regular language is testable with a constant number of queries. It is well known that any language in space o(log log n) is regular, thus implying that such languages can be so tested. It was previously known that there are languages in space O(log n) that are not testable with a constant number of queries and Newman [FOCS 2000] raised the question of closing the exponential gap between these two results. A special case of our main result resolves this problem as it implies that there is a language in space O(log log n) that is not testable with a constant number of queries. It was also previously known that the class of testable properties cannot be extended to all context-free languages. We further show that one cannot even extend the family of testable languages to the class of languages accepted by single counter machines.      

Symbolic-to-statistical hybridization: extending generation-heavy machine translation

The last few years have witnessed an increasing interest in hybridizing surface-based statistical approaches and rule-based symbolic approaches to machine translation (MT). Much of that work is focused on extending statistical MT systems with symbolic knowledge and components. In the brand of hybridization discussed here, we go in the opposite direction: adding statistical bilingual components to a symbolic system. Our base system is Generation-heavy machine translation (GHMT), a primarily symbolic asymmetrical approach that addresses the issue of Interlingual MT resource poverty in source-poor/target-rich language pairs by exploiting symbolic and statistical target-language resources. GHMT’s statistical components are limited to target-language models, which arguably makes it a simple form of a hybrid system. We extend the hybrid nature of GHMT by adding statistical bilingual components. We also describe the details of retargeting it to Arabic–English MT. The morphological richness of Arabic brings several challenges to the hybridization task. We conduct an extensive evaluation of multiple system variants. Our evaluation shows that this new variant of GHMT—a primarily symbolic system extended with monolingual and bilingual statistical components—has a higher degree of grammaticality than a phrase-based statistical MT system, where grammaticality is measured in terms of correct verb-argument realization and long-distance dependency translation.     

A semantics for Behavior Trees using CSP with specification commands

In this paper we give a formal definition of the requirements translation language Behavior Trees. This language has been used with success in industry to systematically translate large, complex, and often erroneous requirements documents into a structured model of the system. It contains a mixture of state-based manipulations, synchronisation, message passing, and parallel, conditional, and iterative control structures. The formal semantics of a Behavior Tree is given via a translation to a version of Hoare’s process algebra CSP, extended with state-based constructs such as guards and updates, and a message passing facility similar to that used in publish/subscribe protocols. We first provide the extension of CSP and its operational semantics, which preserves the meaning of the original CSP operators, and then the Behavior Tree notation and its translation into the extended version of CSP.     

Type theory and concurrency

This paper describes the use of an automated reasoning tool, the Nuprl system, to formalize Milner's Calculus of Communicating Systems (CCS). The goals of this work are two-fold: the first is to investigate the feasibility of using systems like Nuprl to handle the formal detail arising from reasoning about concurrency, while the second is to develop a framework in which various formalisms for reasoning about concurrency may be presented in an automated fashion. To these ends, an implementation in Nuprl of a formal theory of concurrency is described, an implementation of CCS in this mechanized semantic theory presented, and two means of analyzing CCS terms are investigated.     

Indian parallelism on unary ol systems

In this paper we impose the Indian parallelism restriction on the unary developmental system, i. e. on UOL system. We observe that corresponding to any P_aUL language we can get a unary language of Restricted parallel content free language (RP_aCLUL).

Section 1 deals with definitions and Section 2 deals with some propoerties of P_aUL systems. In Section 3, we compare P_aUL language with unary languages of parallel content free grammars and also characterize some subfamilies of P_aUL languages. In the last section, we state a few hierarchial and closure properties.     

A logic for the specification and proof of regular controllable processes of CCS

Summary This work has been motivated by the following general problem: find logics for the specification and proof of programs, described by terms of some algebra with given congruence relation. This relation is supposed to define a satisfactory concept for the behavioural comparison of programs. We require these logics to be adequate with respect to the term language, in the sense that two programs, behaviourally equivalent satisfy the same formulas and conversely. The term language considered is the subset of controllable, regular terms of CCS, on a vocabulary of actions A, with observational congruence. A term is said to be controllable if it is congruent to some term without occurrence of . We obtain an adequate logic whose language of formulas is obtained from constants true, false and ¦Nil¦ by using operators , , fixpoint operators, + and a for aA; the latter can be considered as extensions of the operators + and a for aA of CCS. As a result, controllable CCS terms can be considered as formulas of this logic and the problem of program verification is reduced to the proof of the validity of a formula.     

Encoding Distributed Areas and Local Communication into the π-Calculus

We show how the π-calculus can express local communications within a distributed system, through an encoding of the local area π-calculus, an enriched system that explicitly represents names which are known universally but always refer to local information. Our translation replaces point-to-point communication with a system of shared local ethers; we prove that this preserves and reflects process behaviour. We give an example based on an internet service dæmon, and investigate some limitations of the encoding.     

A Structured Synchronization and Communication Model Fitting Irregular Data Accesses

In this paper, we present a parallel programming and execution model based on alogicalordering of control flows. We show that it is possible to provide a unifying framework consisting of a synchronous programming model, thereby facilitating the mastery of programs, and an asynchronous execution model yielding efficient executions. Our approach is based on a SPMD and task parallel programming language, called –Chan. Communications take place through channels and rely on explicit send/receive instructions. In contrast to classical message passing models, synchronizations and communications are dissociated. We show that it is possible to perform a data-driven automatic translation of sequential and arbitrary DOACROSS loops into –Chan, by using nonmatching send/receive instructions. Our parallelization technique allows us to handle irregular control and leads to optimizations of communications in irregular computations.     

Static use-based object confinement

The confinement of object references is a significant security concern for modern programming languages. We define a language that serves as a uniform model for a variety of confined object reference systems. A use-based approach to confinement is adopted, which we argue is more expressive than previous communication-based approaches. We then develop a readable, expressive type system for static analysis of the language, along with a type safety result demonstrating that run-time checks can be eliminated. The language and type system thus serve as a reliable, declarative, and efficient foundation for secure capability-based programming and object confinement .     

On the regularity of circular splicing languages: a survey and new developments

Circular splicing has been introduced to model a specific recombinant behaviour of circular DNA, continuing the investigation initiated with linear splicing. In this paper we focus on the relationship between regular circular languages and languages generated by finite circular splicing systems. We survey the known results towards a characterization of the intersection between these two classes and provide new contributions on the open problem of finding this characterization. First, we exhibit a non-regular circular language generated by a circular simple system thus disproving a known result in this area. Then we give new results related to a restrictive class of circular splicing systems, the marked systems. Precisely, we review in a graph theoretical setting the recently obtained characterization of marked systems generating regular circular languages. In particular, we define a slight variant of marked systems, that is the g-marked systems, and we introduce the graph associated with a g-marked system. We show that a g-marked system generates a regular circular language if and only if its associated graph is a cograph. Furthermore, we prove that the class of g-marked systems generating regular circular languages is closed under a complement operation applied to systems. We also prove that marked systems with self-splicing generate only regular circular languages.     

Graph theoretic closure properties of the family of boundary NLC graph languages

Summary Node label controlled (NLC) grammars are graph grammars (operating on node labeled undirected graphs) which rewrite single nodes only and establish connections between the embedded graph and the neighbors of the rewritten node on the basis of the labels of the involved nodes only. They define (possibly infinite) languages of undirected node labeled graphs (or, if we just omit the labels, languages of unlabeled graphs). Boundary NLC (BNLC) grammars are NLC grammars with the property that whenever — in a graph already generated — two nodes may be rewritten, then these nodes are not adjacent. The graph languages generated by this type of grammars are called BNLC languages. The present paper continues the investigations of basic properties of BNLC grammars and languages where the central question is the following: If L is a BNLC language and P is a graph theoretic property, is the set of all graphs from L satisfying P again a BNLC language? We demonstrate that the class of BNLC languages is very stable in the sense that for almost all properties we consider the resulting languages are BNLC. In particular, the above question gets an affirmative answer, if the property P is: being k-colorable, being connected, having a subgraph homeomorphic to a given graph, and being nonplanar.This research was carried out during the second author's stay at the Rijksuniversiteit Leiden, The Netherlands