Background: Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences -ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation.
Abstract. We present an encoding of the semantics of the probabilistic guarded command language (pGCL) in the Unifying Theories of Programming (UTP) framework. Our contribution is a UTP encoding that captures pGCL programs as predicate-transformers, on predicates over probability distributions on before-and after-states: these predicates capture the same information as the models traditionally used to give semantics to pGCL; in addition our formulation allows us to define a generic choice construct, that covers conditional, probabilistic and non-deterministic choice. As an example we study the Monty Hall game in this framework.
We explore the interactions between programvariable state visibility and communication behaviour in state-rich CSP-like processes, using the Unifying Theories of Programming (UTP) framework. The key results of this work are: having variable state visible while a process is waiting to communicate, results in an operationally complex theory of behaviour; by contrast, considering state as unobservable during communication waitperiods results in an elegant theory, with much cleaner operational intuitions. The language constructs most affected by this observability choice are those of external choice and parallel composition. We also discuss situations where this state hiding can prevent the adoption of interesting operators that seize control from waiting processes.
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