RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.]

A Theory of Formal Synthesis via Inductive Learning

Formal synthesis is the process of generating a program satisfying a high-level formal specification. In recent times, effective formal synthesis methods have been proposed based on the use of inductive learning. We refer to this class of methods that learn programs from examples as formal inductive synthesis. In this paper, we present a theoretical framework for formal inductive synthesis. We discuss how formal inductive synthesis differs from traditional machine learning. We then describe oracle-guided inductive synthesis (OGIS), a framework that captures a family of synthesizers that operate by iteratively querying an oracle. An instance of OGIS that has had much practical impact is counterexample-guided inductive synthesis (CEGIS). We present a theoretical characterization of CEGIS for learning any program that computes a recursive language. In particular, we analyze the relative power of CEGIS variants where the types of counterexamples generated by the oracle varies. We also consider the impact of bounded versus unbounded memory available to the learning algorithm. In the special case where the universe of candidate programs is finite, we relate the speed of convergence to the notion of teaching dimension studied in machine learning theory. Altogether, the results of the paper take a first step towards a theoretical foundation for the emerging field of formal inductive synthesis

A System for Deduction-based Formal Verification of Workflow-oriented Software Models

The work concerns formal verification of workflow-oriented software models using deductive approach. The formal correctness of a model's behaviour is considered. Manually building logical specifications, which are considered as a set of temporal logic formulas, seems to be the significant obstacle for an inexperienced user when applying the deductive approach. A system, and its architecture, for the deduction-based verification of workflow-oriented models is proposed. The process of inference is based on the semantic tableaux method which has some advantages when compared to traditional deduction strategies. The algorithm for an automatic generation of logical specifications is proposed. The generation procedure is based on the predefined workflow patterns for BPMN, which is a standard and dominant notation for the modeling of business processes. The main idea for the approach is to consider patterns, defined in terms of temporal logic,as a kind of (logical) primitives which enable the transformation of models to temporal logic formulas constituting a logical specification. Automation of the generation process is crucial for bridging the gap between intuitiveness of the deductive reasoning and the difficulty of its practical application in the case when logical specifications are built manually. This approach has gone some way towards supporting, hopefully enhancing our understanding of, the deduction-based formal verification of workflow-oriented models.Comment: International Journal of Applied Mathematics and Computer Scienc

Transitioning Applications to Semantic Web Services: An Automated Formal Approach

Semantic Web Services have been recognized as a promising technology that exhibits huge commercial potential, and attract significant attention from both industry and the research community. Despite expectations being high, the industrial take-up of Semantic Web Service technologies has been slower than expected. One of the main reasons is that many systems have been developed without considering the potential of the web in integrating services and sharing resources. Without a systematic methodology and proper tool support, the migration from legacy systems to Semantic Web Service-based systems can be a very tedious and expensive process, which carries a definite risk of failure. There is an urgent need to provide strategies which allow the migration of legacy systems to Semantic Web Services platforms, and also tools to support such a strategy. In this paper we propose a methodology for transitioning these applications to Semantic Web Services by taking the advantage of rigorous mathematical methods. Our methodology allows users to migrate their applications to Semantic Web Services platform automatically or semi-automatically

A Historical Perspective on Runtime Assertion Checking in Software Development

This report presents initial results in the area of software testing and analysis produced as part of the Software Engineering Impact Project. The report describes the historical development of runtime assertion checking, including a description of the origins of and significant features associated with assertion checking mechanisms, and initial findings about current industrial use. A future report will provide a more comprehensive assessment of development practice, for which we invite readers of this report to contribute information