SHIM is a concurrent deterministic programming language for embedded systems built on rendezvous communication. It abstracts away many details to give the developer a high-level view that includes virtual shared variables, threads as orthogonal statements, and deterministic concurrent exceptions.
In this paper, we present a new way to compile a SHIM-like language into a set of asynchronous guarded actions, a well-established intermediate representation for concurrent systems. By doing so, we build a bridge to many other tools, including hardware synthesis and formal verification. We present our translation in detail, illustrate it through examples, and show how the result can be used by various other tools.
One of the fundamental problems in computational structural biology is the prediction of RNA secondary structures from a single sequence. To solve this problem, mainly two different approaches have been used over the past decades: the free energy minimization (MFE) approach which is still considered the most popular and successful method and the competing stochastic context-free grammar (SCFG) approach. While the accuracy of the MFE based algorithms is limited by the quality of underlying thermodynamic models, the SCFG method abstracts from free energies and instead tries to learn about the structural behavior of the molecules by training the grammars on known real RNA structures, making it highly dependent on the availability of a rich high quality training set. However, due to the respective problems associated with both methods, new statistics based approaches towards RNA structure prediction have become increasingly appreciated. For instance, over the last years, several statistical sampling methods and clustering techniques have been invented that are based on the computation of partition functions (PFs) and base pair probabilities according to thermodynamic models. A corresponding SCFG based statistical sampling algorithm for RNA secondary structures has been studied just recently. Notably, this probabilistic method is capable of producing accurate (prediction) results, where its worst-case time and space requirements are equal to those of common RNA folding algorithms for single sequences.
The aim of this work is to present a comprehensive study on how enriching the underlying SCFG by additional information on the lengths of generated substructures (i.e. by incorporating length-dependencies into the SCFG based sampling algorithm, which is actually possible without significant losses in performance) affects the reliability of the induced RNA model and the accuracy of sampled secondary structures. As we will see, significant differences with respect to the overall quality of generated sample sets and the resulting predictive accuracy are typically implied. In principle, when considering the more specialized length-dependent SCFG model as basis for statistical sampling, a higher accuracy of predicted foldings can be reached at the price of a lower diversity of generated candidate structures (compared to the more general traditional SCFG variant or sampling based on PFs that rely on free energies).
Ownership Domains generalize ownership types. They support programming patterns like iterators that are not possible with ordinary ownership types. However, they are still too restrictive for cases in which an object X wants to access the public domains of an arbitrary number of other objects, which often happens in observer scenarios. To overcome this restriction, we developed so-called loose domains which abstract over several precise domains. That is, similar to the relation between supertypes and subtypes we have a relation between loose and precise domains. In addition, we simplified ownership domains by reducing the number of domains per object to two and hard-wiring the access permissions between domains. We formalized the resulting type system for an OO core language and proved type soundness and a fundamental accessibility property.
This report gives an overview of the separate translation of synchronous imperative programs to synchronous guarded actions. In particular, we consider problems to be solved for separate compilation that stem from preemption statements and local variable declarations. We explain how we solved these problems and sketch our solutions implemented in the our Averest framework to implement a compiler that allows a separate compilation of imperative synchronous programs with local variables and unrestricted preemption statements. The focus of the report is the big picture of our entire design flow.
Over a period of 30 years, ITU-T’s Specification and Description Language (SDL) has matured to a sophisticated formal modelling language for distributed systems and communication protocols. The language definition of SDL-2000, the latest version of SDL, is complex and difficult to maintain. Full tool support for SDL is costly to implement. Therefore, only subsets of SDL are currently supported by tools. These SDL subsets - called SDL profiles - already cover a wide range of systems, and are often suffcient in practice. In this report, we present our approach for extracting the formal semantics for SDL profiles from the complete SDL semantics. We then formalise the approach, present our SDL-profile tool, and report on our experiences.
There is a well known relationship between alternating automata on finite words and symbolically represented nondeterministic automata on finite words. This relationship is of practical relevance because it allows to combine the advantages of alternating and symbolically represented nondeterministic automata on finite words. However, for infinite words the situation is unclear. Therefore, this work investigates the relationship between alternating omega-automata and symbolically represented nondeterministic omega-automata. Thereby, we identify classes of alternating omega-automata that are as expressive as safety, liveness and deterministic prefix automata, respectively. Moreover, some very simple symbolic nondeterminisation procedures are developed for the classes corresponding to safety and liveness properties.
Katja is a tool generating order-sorted recursive data types as well as position types for Java, from specifications using an enhanced ML like notation. Katja’s main features are its conciseness of specifications, the rich interface provided by the generated code and the Java atypical immutability of types. After several stages of extending and maintaining the Katja project, it became apparent many changes had to be done. The original design of Katja wasn’t prepared for the introduction of several backends, the introduction of position sorts and constant feature enhancements and bug fixes. By supplying this report Katja reaches release status for the first time.
Web-based authentication is a popular mechanism implemented by Wireless Internet Service Providers (WISPs) because it allows a simple registration and authentication of customers, while avoiding the high resource requirements of the new IEEE 802.11i security standard and the backward compatibility issues of legacy devices. In this work we demonstrate two different and novel attacks against web-based authentication. One attack exploits operational anomalies of low- and middle-priced devices in order to hijack wireless clients, while the other exploits an already known vulnerability within wired-networks, which in dynamic wireless environments turns out to be even harder to detect and protect against.
Abstraction is intensively used in the verification of large, complex or infinite-state systems. With abstractions getting more complex it is often difficult to see whether they are valid. However, for using abstraction in model checking it has to be ensured that properties are preserved. In this paper, we use a translation validation approach to verify property preservation of system abstractions. We formulate a correctness criterion based on simulation between concrete and abstract system for a property to be verified. For each distinct run of the abstraction procedure the correctness is verified in the theorem prover Isabelle/HOL. This technique is applied in the verification of embedded adaptive systems. This paper is an extended version a previously published work.
This article focuses on the analytical analysis of the free energy in a realistic model for RNA secondary structures. In fact, the free energy in a stochastic model derived from a database of small and large subunit ribosomal RNA (SSU and LSU rRNA) data is studied. A common thermody-namic model for computing the free energy of a given RNA secondary structure, as well as stochastic context-free grammars and generating functions are used to derive the desired results. These results include asymptotics for the expected free energy and for the corresponding variance of a random RNA secondary structure. The quality of our model is judged by comparing the derived results to the used database of SSU and LSU rRNA data. At the end of this article, it is discussed how our results could be used to help on identifying good predictions of RNA secondary structure.