The space of ultrametric phylogenetic trees

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods.Comment: Minor changes. This version has been published in JTB. 27 pages, 9 figure

Heap Abstractions for Static Analysis

Heap data is potentially unbounded and seemingly arbitrary. As a consequence, unlike stack and static memory, heap memory cannot be abstracted directly in terms of a fixed set of source variable names appearing in the program being analysed. This makes it an interesting topic of study and there is an abundance of literature employing heap abstractions. Although most studies have addressed similar concerns, their formulations and formalisms often seem dissimilar and some times even unrelated. Thus, the insights gained in one description of heap abstraction may not directly carry over to some other description. This survey is a result of our quest for a unifying theme in the existing descriptions of heap abstractions. In particular, our interest lies in the abstractions and not in the algorithms that construct them. In our search of a unified theme, we view a heap abstraction as consisting of two features: a heap model to represent the heap memory and a summarization technique for bounding the heap representation. We classify the models as storeless, store based, and hybrid. We describe various summarization techniques based on k-limiting, allocation sites, patterns, variables, other generic instrumentation predicates, and higher-order logics. This approach allows us to compare the insights of a large number of seemingly dissimilar heap abstractions and also paves way for creating new abstractions by mix-and-match of models and summarization techniques.Comment: 49 pages, 20 figure

Parameter dependencies for reusable performance specifications of software components

To avoid design-related per­for­mance problems, model-driven performance prediction methods analyse the response times, throughputs, and re­source utilizations of software architectures before and during implementation. This thesis proposes new modeling languages and according model transformations, which allow a reusable description of usage profile dependencies to the performance of software components. Predictions based on this new methods can support performance-related design decisions

The Joys of Graph Transformation

We believe that the technique of graph transformation offers a very natural way to specify semantics for languages that have dynamic allocation and linking structure; for instance, object-oriented programming languages, but also languages for mobility. In this note we expose, on a rather informal level, the reasons for this belief. Our hope in doing this is to raise interest in this technique and so generate more interest in the fascinating possibilities and open questions of this area.\u

Refinement checking on parametric modal transition systems

Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS

An Object-Oriented Programming Environment for Parallel Genetic Algorithms

This thesis investigates an object-oriented programming environment for building parallel applications based on genetic algorithms (GAs). It describes the design of the Genetic Algorithms Manipulation Environment (GAME), which focuses on three major software development requirements: flexibility, expandability and portability. Flexibility is provided by GAME through a set of libraries containing pre-defined and parameterised components such as genetic operators and algorithms. Expandability is offered by GAME'S object-oriented design. It allows applications, algorithms and genetic operators to be easily modified and adapted to satisfy diverse problem's requirements. Lastly, portability is achieved through the use of the standard C++ language, and by isolating machine and operating system dependencies into low-level modules, which are hidden from the application developer by GAME'S application programming interfaces. The development of GAME is central to the Programming Environment for Applications of PArallel GENetic Algorithms project (PAPAGENA). This is the principal European Community (ESPRIT III) funded parallel genetic algorithms project. It has two main goals: to provide a general-purpose tool kit, supporting the development and analysis of large-scale parallel genetic algorithms (PGAs) applications, and to demonstrate the potential of applying evolutionary computing in diverse problem domains. The research reported in this thesis is divided in two parts: i) the analysis of GA models and the study of existing GA programming environments from an application developer perspective; ii) the description of a general-purpose programming environment designed to help with the development of GA and PGA-based computer programs. The studies carried out in the first part provide the necessary understanding of GAs' structure and operation to outline the requirements for the development of complex computer programs. The second part presents GAME as the result of combining development requirements, relevant features of existing environments and innovative ideas, into a powerful programming environment. The system is described in terms of its abstract data structures and sub-systems that allow the representation of problems independently of any particular GA model. GAME's programming model is also presented as general-purpose object-oriented framework for programming coarse-grained parallel applications. GAME has a modular architecture comprising five modules: the Virtual Machine, the Parallel Execution Module, the Genetic Libraries, the Monitoring Control Module, and the Graphic User Interface. GAME's genetic-oriented abstract data structures, and the Virtual Machine, isolates genetic operators and algorithms from low-level operations such as memory management, exception handling, etc. The Parallel Execution Module supports GAME's object- oriented parallel programming model. It defines an application programming interface and a runtime library that allow the same parallel application, created within the environment, to run on different hardware and operating system platforms. The Genetic Libraries outline a hierarchy of components implemented as parameterised versions of standard and custom genetic operators, algorithms and applications. The Monitoring Control Module supports dynamic control and monitoring of simulations, whereas the Graphic User Interface defines a basic framework and graphic 'widgets' for displaying and entering data. This thesis describes the design philosophy and rationale behind these modules, covering in more detail the Virtual Machine, the Parallel Execution Module and the Genetic Libraries. The assessment discusses the system's ability to satisfy the main requirements of GA and PGA software development, as well as the features that distinguish GAME from other programming environments