A lightweight, graph-theoretic model of class-based similarity to support object-oriented code reuse.

The work presented in this thesis is principally concerned with the development of a method and set of tools designed to support the identification of class-based similarity in collections of object-oriented code. Attention is focused on enhancing the potential for software reuse in situations where a reuse process is either absent or informal, and the characteristics of the organisation are unsuitable, or resources unavailable, to promote and sustain a systematic approach to reuse. The approach builds on the definition of a formal, attributed, relational model that captures the inherent structure of class-based, object-oriented code. Based on code-level analysis, it relies solely on the structural characteristics of the code and the peculiarly object-oriented features of the class as an organising principle: classes, those entities comprising a class, and the intra and inter-class relationships existing between them, are significant factors in defining a two-phase similarity measure as a basis for the comparison process. Established graph-theoretic techniques are adapted and applied via this model to the problem of determining similarity between classes. This thesis illustrates a successful transfer of techniques from the domains of molecular chemistry and computer vision. Both domains provide an existing template for the analysis and comparison of structures as graphs. The inspiration for representing classes as attributed relational graphs, and the application of graph-theoretic techniques and algorithms to their comparison, arose out of a well-founded intuition that a common basis in graph-theory was sufficient to enable a reasonable transfer of these techniques to the problem of determining similarity in object-oriented code. The practical application of this work relates to the identification and indexing of instances of recurring, class-based, common structure present in established and evolving collections of object-oriented code. A classification so generated additionally provides a framework for class-based matching over an existing code-base, both from the perspective of newly introduced classes, and search "templates" provided by those incomplete, iteratively constructed and refined classes associated with current and on-going development. The tools and techniques developed here provide support for enabling and improving shared awareness of reuse opportunity, based on analysing structural similarity in past and ongoing development, tools and techniques that can in turn be seen as part of a process of domain analysis, capable of stimulating the evolution of a systematic reuse ethic

A treatment of stereochemistry in computer aided organic synthesis

This thesis describes the author’s contributions to a new stereochemical processing module constructed for the ARChem retrosynthesis program. The purpose of the module is to add the ability to perform enantioselective and diastereoselective retrosynthetic disconnections and generate appropriate precursor molecules. The module uses evidence based rules generated from a large database of literature reactions. Chapter 1 provides an introduction and critical review of the published body of work for computer aided synthesis design. The role of computer perception of key structural features (rings, functions groups etc.) and the construction and use of reaction transforms for generating precursors is discussed. Emphasis is also given to the application of strategies in retrosynthetic analysis. The availability of large reaction databases has enabled a new generation of retrosynthesis design programs to be developed that use automatically generated transforms assembled from published reactions. A brief description of the transform generation method employed by ARChem is given. Chapter 2 describes the algorithms devised by the author for handling the computer recognition and representation of the stereochemical features found in molecule and reaction scheme diagrams. The approach is generalised and uses flexible recognition patterns to transform information found in chemical diagrams into concise stereo descriptors for computer processing. An algorithm for efficiently comparing and classifying pairs of stereo descriptors is described. This algorithm is central for solving the stereochemical constraints in a variety of substructure matching problems addressed in chapter 3. The concise representation of reactions and transform rules as hyperstructure graphs is described. Chapter 3 is concerned with the efficient and reliable detection of stereochemical symmetry in both molecules, reactions and rules. A novel symmetry perception algorithm, based on a constraints satisfaction problem (CSP) solver, is described. The use of a CSP solver to implement an isomorph‐free matching algorithm for stereochemical substructure matching is detailed. The prime function of this algorithm is to seek out unique retron locations in target molecules and then to generate precursor molecules without duplications due to symmetry. Novel algorithms for classifying asymmetric, pseudo‐asymmetric and symmetric stereocentres; meso, centro, and C2 symmetric molecules; and the stereotopicity of trigonal (sp2) centres are described. Chapter 4 introduces and formalises the annotated structural language used to create both retrosynthetic rules and the patterns used for functional group recognition. A novel functional group recognition package is described along with its use to detect important electronic features such as electron‐withdrawing or donating groups and leaving groups. The functional groups and electronic features are used as constraints in retron rules to improve transform relevance. Chapter 5 details the approach taken to design detailed stereoselective and substrate controlled transforms from organised hierarchies of rules. The rules employ a rich set of constraints annotations that concisely describe the keying retrons. The application of the transforms for collating evidence based scoring parameters from published reaction examples is described. A survey of available reaction databases and the techniques for mining stereoselective reactions is demonstrated. A data mining tool was developed for finding the best reputable stereoselective reaction types for coding as transforms. For various reasons it was not possible during the research period to fully integrate this work with the ARChem program. Instead, Chapter 6 introduces a novel one‐step retrosynthesis module to test the developed transforms. The retrosynthesis algorithms use the organisation of the transform rule hierarchy to efficiently locate the best retron matches using all applicable stereoselective transforms. This module was tested using a small set of selected target molecules and the generated routes were ranked using a series of measured parameters including: stereocentre clearance and bond cleavage; example reputation; estimated stereoselectivity with reliability; and evidence of tolerated functional groups. In addition a method for detecting regioselectivity issues is presented. This work presents a number of algorithms using common set and graph theory operations and notations. Appendix A lists the set theory symbols and meanings. Appendix B summarises and defines the common graph theory terminology used throughout this thesis

Topological Equivalence and Similarity in Multi-Representation Geographic Databases

Geographic databases contain collections of spatial data representing the variety of views for the real world at a specific time. Depending on the resolution or scale of the spatial data, spatial objects may have different spatial dimensions, and they may be represented by point, linear, or polygonal features, or combination of them. The diversity of data that are collected over the same area, often from different sources, imposes a question of how to integrate and to keep them consistent in order to provide correct answers for spatial queries. This thesis is concerned with the development of a tool to check topological equivalence and similarity for spatial objects in multi-representation databases. The main question is what are the components of a model to identify topological consistency, based on a set of possible transitions for the different types of spatial representations. This work develops a new formalism to model consistently spatial objects and spatial relations between several objects, each represented at multiple levels of detail. It focuses on the topological consistency constraints that must hold among the different representation of objects, but it is not concerned about generalization operations of how to derive one representation level from another. The result of this thesis is a?computational tool to evaluate topological equivalence and similarity across multiple representations. This thesis proposes to organize a spatial scene -a set of spatial objects and their embeddings in space- directly as a relation-based model that uses a hierarchical graph representation. The focus of the relation-based model is on relevant object representations. Only the highest-dimensional object representations are explicitly stored, while their parts are not represented in the graph

Creating Formal Specifications with Analogical Reasoning

We describe the Arís (Analogical Reasoning for Implementations and Specifications) system that uses analogical reasoning to create formal specifications for a given implementation. Arís is built on the hypothesis that structurally similar implementations often represent similar functionality. It leverages this similarity to create new specifications, by analogy to a retrieved similar example. Of course some similarly structured implementations provide different functionality, so a major focus of Arís is to discriminate between analogous and dis-analogous pairs of code. Examples are used to highlight Arís’ ability to create specifications, across a range of similar implementations and even similar algorithms. Results are presented on Arís ability to create verified specifications for a sample of ten textbook problems. We argue that Arís both emulates and supports the workaday little-c creativity of formal software developers

Consciosusness in Cognitive Architectures. A Principled Analysis of RCS, Soar and ACT-R

This report analyses the aplicability of the principles of consciousness developed in the ASys project to three of the most relevant cognitive architectures. This is done in relation to their aplicability to build integrated control systems and studying their support for general mechanisms of real-time consciousness.\ud To analyse these architectures the ASys Framework is employed. This is a conceptual framework based on an extension for cognitive autonomous systems of the General Systems Theory (GST).\ud A general qualitative evaluation criteria for cognitive architectures is established based upon: a) requirements for a cognitive architecture, b) the theoretical framework based on the GST and c) core design principles for integrated cognitive conscious control systems

Software bug management from bug reports to bug signatures

Ph.DDOCTOR OF PHILOSOPH

SIMILARITY METRICS APPLIED TO GRAPH BASED DESIGN MODEL AUTHORING

Model reuse is typically facilitated by search and retrieval tools, matching the sought model with models in a database. This research aims at providing similar assistance to users authoring design exemplars, a data structure to represent parametric and geometric design problems. The design exemplar represents design problems in the form of a bi-partite graph consisting of entities and relations. Authoring design exemplars for relatively complex design problems can be time consuming and error prone. This forms the motivation of developing a search and retrieval tool, capable of retrieving exemplars that are similar to the exemplar that a user is trying to author, from a database of previously authored exemplars. In order to develop such a tool, similarity measures have been developed to evaluate the similarity between the exemplar that a user is trying to author and target exemplars in the database. Two exemplars can be considered similar based on the number and types of entities and relations shared by them. However, exemplars meant for the same purpose can be authored using different entities and relations. Hence, the two main challenges in developing a search and retrieval tool are to evaluate the similarity between exemplars based on structure and semantics. In this research, four distinct similarity metrics are developed to evaluate the structural similarity between exemplars for exemplar retrieval: entity similarity, relation similarity, attribute similarity, and graph matching similarity. As well, a thorough understanding of semantics in engineering design has been developed. Different types of semantic information found in engineering design have been identified and classified. Design intent and rationale have been proposed as the two main types of semantic information necessary to evaluate the semantic similarity between exemplars. The semantic and structural similarity measures have been implemented as separate modules in an interactive modeling environment. Several experiments have been conducted in order to evaluate the accuracy and effectiveness of the proposed similarity measures. It is found that for most queries, the semantic retrieval module retrieves exemplars that are not retrieved by structural retrieval module and vice versa

Stereoscopic Sketchpad: 3D Digital Ink

--Context-- This project looked at the development of a stereoscopic 3D environment in which a user is able to draw freely in all three dimensions. The main focus was on the storage and manipulation of the ‘digital ink’ with which the user draws. For a drawing and sketching package to be effective it must not only have an easy to use user interface, it must be able to handle all input data quickly and efficiently so that the user is able to focus fully on their drawing. --Background-- When it comes to sketching in three dimensions the majority of applications currently available rely on vector based drawing methods. This is primarily because the applications are designed to take a users two dimensional input and transform this into a three dimensional model. Having the sketch represented as vectors makes it simpler for the program to act upon its geometry and thus convert it to a model. There are a number of methods to achieve this aim including Gesture Based Modelling, Reconstruction and Blobby Inflation. Other vector based applications focus on the creation of curves allowing the user to draw within or on existing 3D models. They also allow the user to create wire frame type models. These stroke based applications bring the user closer to traditional sketching rather than the more structured modelling methods detailed. While at present the field is inundated with vector based applications mainly focused upon sketch-based modelling there are significantly less voxel based applications. The majority of these applications focus on the deformation and sculpting of voxmaps, almost the opposite of drawing and sketching, and the creation of three dimensional voxmaps from standard two dimensional pixmaps. How to actually sketch freely within a scene represented by a voxmap has rarely been explored. This comes as a surprise when so many of the standard 2D drawing programs in use today are pixel based. --Method-- As part of this project a simple three dimensional drawing program was designed and implemented using C and C++. This tool is known as Sketch3D and was created using a Model View Controller (MVC) architecture. Due to the modular nature of Sketch3Ds system architecture it is possible to plug a range of different data structures into the program to represent the ink in a variety of ways. A series of data structures have been implemented and were tested for efficiency. These structures were a simple list, a 3D array, and an octree. They have been tested for: the time it takes to insert or remove points from the structure; how easy it is to manipulate points once they are stored; and also how the number of points stored effects the draw and rendering times. One of the key issues brought up by this project was devising a means by which a user is able to draw in three dimensions while using only two dimensional input devices. The method settled upon and implemented involves using the mouse or a digital pen to sketch as one would in a standard 2D drawing package but also linking the up and down keyboard keys to the current depth. This allows the user to move in and out of the scene as they draw. A couple of user interface tools were also developed to assist the user. A 3D cursor was implemented and also a toggle, which when on, highlights all of the points intersecting the depth plane on which the cursor currently resides. These tools allow the user to see exactly where they are drawing in relation to previously drawn lines. --Results-- The tests conducted on the data structures clearly revealed that the octree was the most effective data structure. While not the most efficient in every area, it manages to avoid the major pitfalls of the other structures. The list was extremely quick to render and draw to the screen but suffered severely when it comes to finding and manipulating points already stored. In contrast the three dimensional array was able to erase or manipulate points effectively while the draw time rendered the structure effectively useless, taking huge amounts of time to draw each frame. The focus of this research was on how a 3D sketching package would go about storing and accessing the digital ink. This is just a basis for further research in this area and many issues touched upon in this paper will require a more in depth analysis. The primary area of this future research would be the creation of an effective user interface and the introduction of regular sketching package features such as the saving and loading of images