Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology

Fine-Grained Parallel and Distributed Spatial Stochastic Simulation of Biological Reactions

This volume contains the proceedings of the First International Workshop of Formal Techniques for Safety-Critical Systems (FTSCS 2012), held in Kyoto on November 12, 2012, as a satellite event of the ICFEM conference. The aim of this workshop is to bring together researchers and engineers interested in the application of (semi-)formal methods to improve the quality of safety-critical computer systems. FTSCS is particularly interested in industrial applications of formal methods. Topics include: - the use of formal methods for safety-critical and QoS-critical systems, including avionics, automotive, and medical systems; - methods, techniques and tools to support automated analysis, certification, debugging, etc.; - analysis methods that address the limitations of formal methods in industry; - formal analysis support for modeling languages used in industry, such as AADL, Ptolemy, SysML, SCADE, Modelica, etc.; and - code generation from validated models. The workshop received 25 submissions; 21 of these were regular papers and 4 were tool/work-in-progress/position papers. Each submission was reviewed by three referees; based on the reviews and extensive discussions, the program committee selected nine regular papers, which are included in this volume. Our program also included an invited talk by Ralf Huuck.

Formal methods for software development receive much attention in research centres, but are rarely used in industry for the development of (large) software systems. One of the reasons is that little is known about the integration of formal methods in the software process, and the exact role of formal methods in the software life-cycle is still unclear. In this paper, a detailed examination is made of the application of, and the benefits resulting from, a generally applicable formal method (VDM) in a standard model for software development (DoD-STD-2167A). Currently, there is no general agreement on how formal methods should be used, but in order to analyse the use of formal methods in the software process, a clear view of such use is essential. Therefore, we show what is meant by ‘using a formal method’. The different activities of DoD-STD-2167A are analysed with regard to their suitability for applying VDM and the benefits that may result from applying VDM for that activity. Based on this analysis, an overall view on the usage of formal methods in the software process is formulated.

Nanometer-scale structures suitable for computing have been investigated by several research groups in recent years. A common feature of these structures is their dynamic evolution through cascaded local interactions embedded on a discrete grid. Finding configurations capable of conducting computations is a task that often requires tedious experiments in laboratories. Formal methods—though used extensively for the specification and verification of software and hardware computing systems—are virtually unexplored with respect to computational structures at atomic scales. This paper presents a systematic approach toward the application of formal methods in this context, using techniques like abstraction, model-checking, and symbolic representations of states to explore and discover computational structures. The proposed techniques are applied to a system of CO molecules on a grid of Copper atoms, resulting in the design of a complete library of combinational logic gates based on this molecular system. The techniques are also applied on (more general) systems of cellular automata that employ an asynchronous mode of timing. The use of formal methods may narrow the gap between Physical Chemistry and Computer Science, allowing the description of interactions of nanometer scale systems on a level of abstraction suitable to devise computing devices.

The accuracy and credibility of model is the most important determinant of development of Modeling and Simulation (M&S). There is a desperate need for an immediate practical solution to the problem of VV&A (Validation, Verification and Accreditation) of simulation systems. A discussion and experiment of the relative merits of informal methods and formal methods are provided in this paper. In spite of increasing simulation speed via parallelization, the number of problem cases that can be covered is not highly increased. On the other hand, formal methods have proven to be valuable techniques, but they require detailed specifications of systems and requirements, therefore they are not very accessible in practical simulation systems development. According to the exhaustiveness of formal methods, a Model Driven Architecture (MDA) based simulation VV&A framework guided by model checking is presented in this paper. This framework combines scalability of simulation with exhaustiveness of formal methods in order to get the best of both worlds for simulation model verification. It can provide more confidence in simulation models and increase the use of formal methods in the context of M&S by people that are not trained in formal techniques.

The study of biological systems is complex and of great importance. There exist numerous approaches to signal transduction processes, including symbolic modeling of cellular adaptation. The use of formal methods for computational systems biology eases the analysis of cellular models and the establishment of the causes and consequences of certain cellular situations associated to diseases. In this paper, we define an application of logic modeling with rewriting logic and soft set theory. Our approach to decision making with soft sets offers a novel strategy that complements standard strategies. We implement a metalevel strategy to control and guide the rewriting process of the Maude rewriting engine. In particular, we adapt mathematical methods to capture imprecision, vagueness, and uncertainty in the available data. Using this new strategy, we propose an extension in the biological symbolic models of Pathway Logic. Our ultimate aim is to automatically determine the rules that are most appropriate and adjusted to reality in dynamic systems using decision making with incomplete soft sets.

The title of this paper provides an answer to the question posed by Larry King in his panel paper titled "Do formal methods really belong in the toolbox of the practicing engineer?" Yes, formal methods do indeed belong to the toolbox of the practicing engineer. The capabilities of today's computers are truly impressive and as a result have opened door to the design and development of increasingly ambitious systems. An almost unavoidable by-product of these systems is the growing consequences associated with their failure. Another attribute shared by most of these systems is that their complexity is of an unprecedented nature. Thus, these systems live in the cross section (or shall I say cross-hairs) of high consequence and high complexity. For these reasons, attaining and developing the ability to construct highly reliable software is be coming a significant concern. Furthermore, software manufacturers as well as consumers are getting more and more fed-up with missed deadlines, bugs crashing and freezing hardware, and in the worst case, causing havoc to organizations, as bugs/incompleteness lead to allowing trojan horses for hackers through viruses and attacks. This is leading to attempts to replace ad hoc techniques in system design by more systematic methods. What is the role that formal methods, as a field of study, can play in addressing these issues? If by formal methods, one is exclusively referring to formal verification methods for software, such tools will probably not be part of a practicing engineer's tool in the near future. King's note reflects the prevailing confusion about formal methods, what can be achieved using them, and what cannot be achieved using them, and their overall role in system design and development.

Designing protocols for multi-agent interaction that achieve the desired behavior is a challenging and error-prone process. The standard practice is to manually develop proofs of protocol correctness that rely on human intuition and require significant effort to develop. Even then, proofs can have mistakes that may go unnoticed after peer review, modeling and simulation, and testing. The use of formal methods can reduce the potential for such errors. In this paper, we discuss our experience applying model checking to a previously published multi-agent protocol for unmanned air vehicles. The original publication provides a compelling proof of correctness, along with extensive simulation results to support it. However, analysis through model checking found an error in one of the proof’s main lemmas. In this paper, we start by providing an overview of the protocol and its original “proof” of correctness, which represents the standard practice in multi-agent protocol design. We then describe how we modeled the protocol for a three-vehicle system in a model checker, the counterexample it returned, and the insight this counterexample provided. We also discuss benefits, limitations, and lessons learned from this exercise, as well as what future efforts would be needed to fully verify the protocol for an arbitrary number of vehicles.

Early prediction of the evolution and prognosis of mild acute pancreatitis through Dual Source-CT and Formal Methods.

Formal methods tools have been shown to be effective at finding defects in and verifying the correctness of safety-critical systems such as avionics systems. The recent release of DO-178C and the accompanying Formal Methods Supplement DO-333 will make it easier for developers of software for commercial aircraft to obtain certification credit for the use of formal methods. However, most developers of avionics systems are unfamiliar with formal methods, and most developers of formal methods tools are unfamiliar with certification requirements and processes. This article provides a brief overview of the certification process for commercial aircraft, as well as some of the issues related to the use of formal methods tools in this context.

The use of formal methods is often recommended to guarantee the provision of necessary services and to assess the correctness of critical properties, such as functional safety, cybersecurity, and reliability, in medical and health care devices. In the past, several formal and rigorous methods have been proposed and consequently applied for trustworthy development of medical software and systems. In this paper, we perform a systematic literature review on the available state of the art in this domain. We collect the relevant literature on the use of formal methods for modeling, design, development, verification, and validation of software‐intensive medical systems. We apply standard systematic literature review techniques and run several queries in well‐known repositories to obtain information that can be useful for people who are either already working in this field or planning to start. Our study covers both quantitative and qualitative aspects of the subject.

Formal methods should be taught as part of any degree in computing science or software engineering. We believe that discrete mathematics is the foundation upon which software development can be lifted up to the heights of a true engineering discipline. The transfer of formal methods to industry cannot be expected to occur without first transferring, from academia to industry, graduates who are well grounded in suchmathematical techniques. These graduatesmust bring a positive, yet realistic, view on the application of formal methods. Our goal is to produce software engineers who will go out into industry understanding the principles of specification, design and implementation. As these graduates develop their engineering skills, in an industrial setting, they should have the means, and the motivation, to integrate formality and rigour into any environment in which they are found. In this way, the formal methods should start to 'sell themselves'. This paper reports on our first attempt to teach a formal methods course as part of a degree in software engineering. Rather than concentrating on one particular method, we worked on a set of small case studies, using the mathematics in a flexible and intuitive manner, where the students could appreciate the need for formality. Each case study was intended to illustrate, in turn, the need for some fundamental formalism. An unexpected result was that we also identified weaknesses in our understanding of formal methods: students' naive questioning helped us to identify how the methods, and the teaching of these methods, could be improved. In brief, it was not just the students who were learning!

We present an overview of our observations and experiences of applying formal methods in industry. Our approach combines two existing and complimentary formal methods, namely the Cleanroom method [H. D. Mills et al., (1987), S. J. Prowell et al. (1998)] and the CSP framework [C. A. R. Hoare (1985), A. W. Roscoe (1998)] together with its model checker FDR. The problem we are interested in is the use of formal methods to develop software systems of a business-critical and untestable nature, where the software forms an essential part of some core product or service offered by a business. We argue that the successful implementation of such systems needs a more formal approach and reflect on why formal methods are rarely used in practice. We discuss the combination of Cleanroom and CSP, and show how they can be applied to develop the control software that is embedded in a complex manufacturing machine.

Microprocessors increasingly control and monitor our most critical systems, including automobiles, airliners, medical systems, transportation grids, and defense systems. The relentless march of semiconductor process technology has given engineers exponentially increasing transistor budgets at constant recurring cost. This has encouraged increased functional integration onto a single die, as well as increased architectural sophistication of the functional units themselves. Additionally, design cycle times are decreasing, thus putting increased schedule pressure on engineers. Not surprisingly, this environment has led to a number of uncaught design flaws. Traditional simulation-based design verification has not kept up with the scale or pace of modern microprocessor system design. Formal verification methods offer the promise of improved bug-finding capability, as well as the ability to establish functional correctness of a detailed design relative to a high-level specification. However, widespread use of formal methods has had to await breakthroughs in automated reasoning, integration with engineering design languages and processes, scalability, and usability. This book presents several breakthrough design and verification techniques that allow these powerful formal methods to be employed in the real world of high-assurance microprocessor system design.

Recently, formal methods have been used in large industrial organisations (including AWS, Facebook/Meta, and Microsoft) and have proved to be an effective part of a software engineering process finding important bugs. Perhaps because of that, practitioners are interested in using them more often. Nevertheless, formal methods are far less applied than expected, particularly for safety-critical systems where they are strongly recommended and have the most significant potential. We hypothesise that formal methods still seem not applicable enough or ready for their intended use in such areas. In critical software engineering, what do we mean when we speak of a formal method? And what does it mean for such a method to be applicable both from a scientific and practical viewpoint? Based on what the literature tells about the first question, with this manifesto, we identify key challenges and lay out a set of guiding principles that, when followed by a formal method, give rise to its mature applicability in a given scope. Rather than exercising criticism of past developments, this manifesto strives to foster increased use of formal methods in any appropriate context to the maximum benefit.