18962931
Analyzing xfig using the Rigi tool suite
An experiment is conducted on how well expert users of program comprehension tools are able to perform specific program understanding and maintenance tasks on the xfig drawing program using these tools. The paper reports on the experiences of the users of the Rigi reverse engineering tool suite. Rigi is an interactive, visual tool designed to help developers better understand and redocument their software. Rigi includes parsers to read the source code of the subject software and produce a graph of extracted artifacts such as procedures, variables, calls, and data accesses. To manage the complexity of the graph, an editor allows the software engineer to automatically or manually collapse related artifacts into subsystems. These subsystems typically represent concepts such as abstract data types or personnel assignments. The created hierarchy can be navigated, analyzed, and presented using various automatic or user-guided graphical layouts.
14705463
C to Java migration experiences
With the growing popularity of the Java programming language for both client and server side applications in network-centric computing, there is a rising need for programming libraries that can be easily integrated into Java programs. In a previous paper, we surveyed current strategies for integrating C source code into Java programs, pointed out their weaknesses and presented goals for an improved migration approach. In this paper, we present the Ephedra approach to software migration and report on the results of three case studies transliterating C source code to Java using the Ephedra environment.
222672
Development and maintenance of a Web site for a Bachelor program
This paper describes our experiences with the development and maintenance of the BSENG Web site, which provides information about a new Bachelor program for software engineering at the University of Victoria. The site's requirements lead to a design that emphasizes simplicity to ease maintenance. We used Macromedia Dreamweaver to develop the site. During development, we identified two important maintenance tasks: detection of dead links and preservation of the site's navigational structure, that are not well supported by Dreamweaver. We discuss how we use the Rigi reverse engineering environment to aid the Web site developer with these maintenance tasks.
6534012
PreBIND and Textomy – mining the biomedical literature for protein-protein interactions using a support vector machine
BackgroundThe majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the formidable task-size of backfilling the database could be reduced by using Support Vector Machine technology to first locate interaction information in the literature. We present an information extraction system that was designed to locate protein-protein interaction data in the literature and present these data to curators and the public for review and entry into BIND.ResultsCross-validation estimated the support vector machine's test-set precision, accuracy and recall for classifying abstracts describing interaction information was 92%, 90% and 92% respectively. We estimated that the system would be able to recall up to 60% of all non-high throughput interactions present in another yeast-protein interaction database. Finally, this system was applied to a real-world curation problem and its use was found to reduce the task duration by 70% thus saving 176 days.ConclusionsMachine learning methods are useful as tools to direct interaction and pathway database back-filling; however, this potential can only be realized if these techniques are coupled with human review and entry into a factual database such as BIND. The PreBIND system described here is available to the public at http://bind.ca. Current capabilities allow searching for human, mouse and yeast protein-interaction information.
28154888
Architecture of a Framework for Generic Assisting Conversational Agents
In this paper, we focus on the notion of Assisting Conversational Agents (ACA) that are embodied agents dedicated to the function of assistance for novice users of software components and/or web services. We discuss the main requirements of such agents and we emphasize the genericity issue arising in the dialogical part of such architectures. This prompts us to propose a mediator-based framework, using a dynamic symbolic representation of the runtime of the assisted components. Then we define three strategies for the development of the mediators that are validated by the implementation of experiences taken in various situations.
61042466
The berkeley UNIX consultant project
UC (UNIX Consultant) is an intelligent, natural language interface that allows naive users to learn about the UNIX2 operating system. UC was undertaken because the task was thought to be both a fertile domain for artificial intelligence (AI) research and a useful application of AI work in planning, reasoning, natural language processing, and knowledge representation.The current implementation of UC comprises the following components: a language analyzer, called ALANA, produces a representation of the content contained in an utterance; an inference component, called a concretion mechanism, that further refines this content; a goal analyzer, PAGAN, that hypothesizes the plans and goals under which the user is operating; an agent, called UCEgo, that decides on UC's goals and proposes plans for them; a domain planner, called KIP, that computes a plan to address the user's request; an expression mechanism, UCExpress, that determines the content to be communicated to the user, and a language production mechanism, UCGen, that expresses UC's response in English.UC also contains a component, called KNOME, that builds a model of the user's knowledge state with respect to UNIX. Another mechanism, UCTeacher, allows a user to add knowledge of both English vocabulary and facts about UNIX to UC's knowledge base. This is done by interacting with the user in natural language.All these aspects of UC make use of knowledge represented in a knowledge representation system called KODIAK. KODIAK is a relation-oriented system that is intended to have wide representational range and a clear semantics, while maintaining a cognitive appeal. All of UC's knowledge, ranging from its most general concepts to the content of a particular utterance, is represented in KODIAK.
8053050
Characterization of Neuropathological Shape Deformations
We present a framework for analyzing the shape deformation of structures within the human brain. A mathematical model is developed describing the deformation of any brain structure whose shape is affected by both gross and detailed physical processes. Using our technique, the total shape deformation is decomposed into analytic modes of variation obtained from finite element modeling, and statistical modes of variation obtained from sample data. Our method is general, and can be applied to many problems where the goal is to separate out important from unimportant shape variation across a class of objects. In this paper, we focus on the analysis of diseases that affect the shape of brain structures. Because the shape of these structures is affected not only by pathology but also by overall brain shape, disease discrimination is difficult. By modeling the brain's elastic properties, we are able to compensate for some of the nonpathological modes of shape variation. This allows us to experimentally characterize modes of variation that are indicative of disease processes. We apply our technique to magnetic resonance images of the brains of individuals with schizophrenia, Alzheimer's disease, and normal-pressure hydrocephalus, as well as to healthy volunteers. Classification results are presented.
15015024
Annotating Multimodal Behaviors Occurring During Non Basic Emotions
The design of affective interfaces such as credible expressive characters in story-telling applications requires the understanding and the modeling of relations between realistic emotions and behaviors in different modalities such as facial expressions, speech, hand gestures and body movements. Yet, research on emotional multimodal behaviors has focused on individual modalities during acted basic emotions. In this paper we describe the coding scheme that we have designed for annotating multimodal behaviors observed during mixed and non acted emotions. We explain how we used it for the annotation of videos from a corpus of emotionally rich TV interviews. We illustrate how the annotations can be used to compute expressive profiles of videos and relations between non basic emotions and multimodal behaviors.