Automatic Selection of Statistical Model Checkers for Analysis of Biological Models

Statistical Model Checking (SMC) blends the speed of simulation with the rigorous analytical capabilities of model checking, and its success has prompted researchers to implement a number of SMC tools whose availability provides flexibility and fine-tuned control over model analysis. However, each tool has its own practical limitations, and different tools have different requirements and performance characteristics. The performance of different tools may also depend on the specific features of the input model or the type of query to be verified. Consequently, choosing the most suitable tool for verifying any given model requires a significant degree of experience, and in most cases, it is challenging to predict the right one. The aim of our research has been to simplify the model checking process for researchers in biological systems modelling by simplifying and rationalising the model selection process. This has been achieved through delivery of the various key contributions listed below. • We have developed a software component for verification of kernel P (kP) system models, using the NuSMV model checker. We integrated it into a larger software platform (www.kpworkbench.org). • We surveyed five popular SMC tools, comparing their modelling languages, external dependencies, expressibility of specification languages, and performance. To best of our knowledge, this is the first known attempt to categorise the performance of SMC tools based on the commonly used property specifications (property patterns) for model checking. • We have proposed a set of model features which can be used for predicting the fastest SMC for biological model verification, and have shown, moreover, that the proposed features both reduce computation time and increase predictive power. • We used machine learning algorithms for predicting the fastest SMC tool for verification of biological models, and have shown that this approach can successfully predict the fastest SMC tool with over 90% accuracy. • We have developed a software tool, SMC Predictor, that predicts the fastest SMC tool for a given model and property query, and have made this freely available to the wider research community (www.smcpredictor.com). Our results show that using our methodology can generate significant savings in the amount of time and resources required for model verification

Machine learning and its applications in reliability analysis systems

In this thesis, we are interested in exploring some aspects of Machine Learning (ML) and its application in the Reliability Analysis systems (RAs). We begin by investigating some ML paradigms and their- techniques, go on to discuss the possible applications of ML in improving RAs performance, and lastly give guidelines of the architecture of learning RAs. Our survey of ML covers both levels of Neural Network learning and Symbolic learning. In symbolic process learning, five types of learning and their applications are discussed: rote learning, learning from instruction, learning from analogy, learning from examples, and learning from observation and discovery. The Reliability Analysis systems (RAs) presented in this thesis are mainly designed for maintaining plant safety supported by two functions: risk analysis function, i.e., failure mode effect analysis (FMEA) ; and diagnosis function, i.e., real-time fault location (RTFL). Three approaches have been discussed in creating the RAs. According to the result of our survey, we suggest currently the best design of RAs is to embed model-based RAs, i.e., MORA (as software) in a neural network based computer system (as hardware). However, there are still some improvement which can be made through the applications of Machine Learning. By implanting the 'learning element', the MORA will become learning MORA (La MORA) system, a learning Reliability Analysis system with the power of automatic knowledge acquisition and inconsistency checking, and more. To conclude our thesis, we propose an architecture of La MORA

On minimising the maximum expected verification time

Cyber Physical Systems (CPSs) consist of hardware and software components. To verify that the whole (i.e., software + hardware) system meets the given specifications, exhaustive simulation-based approaches (Hardware In the Loop Simulation, HILS) can be effectively used by first generating all relevant simulation scenarios (i.e., sequences of disturbances) and then actually simulating all of them (verification phase). When considering the whole verification activity, we see that the above mentioned verification phase is repeated until no error is found. Accordingly, in order to minimise the time taken by the whole verification activity, in each verification phase we should, ideally, start by simulating scenarios witnessing errors (counterexamples). Of course, to know beforehand the set of such scenarios is not feasible. In this paper we show how to select scenarios so as to minimise the Worst Case Expected Verification Tim

Developing a distributed electronic health-record store for India

The DIGHT project is addressing the problem of building a scalable and highly available information store for the Electronic Health Records (EHRs) of the over one billion citizens of India

Development and validation of computational models of cellular interaction

In this paper we take the view that computational models of biological systems should satisfy two conditions – they should be able to predict function at a systems biology level, and robust techniques of validation against biological models must be available. A modelling paradigm for developing a predictive computational model of cellular interaction is described, and methods of providing robust validation against biological models are explored, followed by a consideration of software issues

Comparative Analysis of Statistical Model Checking Tools

Statistical model checking is a powerful and flexible approach for formal verification of computational models like P systems, which can have very large search spaces. Various statistical model checking tools have been developed, but choosing between them and using the most appropriate one requires a significant degree of experience, not only because different tools have different modelling and property specification languages, but also because they may be designed to support only a certain subset of property types. Furthermore, their performance can vary depending on the property types and membrane systems being verified. In this paper we evaluate the performance of various common statistical model checkers against a pool of biological models. Our aim is to help users select the most suitable SMC tools from among the available options, by comparing their modelling and property specification languages, capabilities and performances