Walid Keirouz

A foundation for interoperability in next-generation product development systems

United States industry spends billions of dollars as a result of poor interoperability between computer-aided engineering software tools. While ongoing standards development efforts are attempting to address this problem in todays tools, the more significant demand in next-generation tools will be for representations that allow information used or generated during various product development activities to feed forward and backward into others by way of direct electronic interchange. Although the next generation of tools has the potential for greatly increased benefits, there is also a potential for the cost of poor interoperability to multiply. The goal of this work is to develop representations of information that are unavailable in traditional computer-aided engineering tools to support the exchange of product information in a distributed product development environment. This paper develops a vision of next-generation product development systems and provides a core representation for product development information on which future systems can be built.

A Model for the Flow of Design Information in Product Development

The complexity of modern products and design tools has made the exchange of design information more complex. It is widely recognised that the seamless capture, storage, and retrieval of design information is one of the major challenges for the next generation of computer aided design tools. This paper presents a model for the flow of design information that is sufficiently formal to eventually support a semantics-based approach for developing information exchange standards. The model classifies design information into various types, organises these types into information states and levels of abstraction, and identifies the various transformations that operate within and between the information states. The model’s ability to support a variety of design process models is illustrated by applying it to the Systems Integration of Manufacturing Applications (SIMA) design process model, and the model is then applied to a design example.

Prediction of protein-glucose binding sites using support vector machines.

Glucose is a simple sugar that plays an essential role in many basic metabolic and signaling pathways. Many proteins have binding sites that are highly specific to glucose. The exponential increase of genomic data has revealed the identity of many proteins that seem to be central to biological processes, but whose exact functions are unknown. Many of these proteins seem to be associated with disease processes. Being able to predict glucose‐specific binding sites in these proteins will greatly enhance our ability to annotate protein function and may significantly contribute to drug design. We hereby present the first glucose‐binding site classifier algorithm. We consider the sugar‐binding pocket as a spherical spatio‐chemical environment and represent it as a vector of geometric and chemical features. We then perform Random Forests feature selection to identify key features and analyze them using support vector machines classification. Our work shows that glucose binding sites can be modeled effectively using a limited number of basic chemical and residue features. Using a leave‐one‐out cross‐validation method, our classifier achieves a 8.11% error, a 89.66% sensitivity and a 93.33% specificity over our dataset. From a biochemical perspective, our results support the relevance of ordered water molecules and ions in determining glucose specificity. They also reveal the importance of carboxylate residues in glucose binding and the high concentration of negatively charged atoms in direct contact with the bound glucose molecule. Proteins 2009.

EVALUATION OF FINITE ELEMENT SYSTEM ARCHITECTURES

Abstract The finite element method is a powerful engineering analysis tool. However, the scope and size of the problems solved are limited by the capabilities and costs of computers currently used. New computer architectures with parallel processing capabilities can exploit the parallelism in the finite element method. Because of the large number of alternative hardware and software configurations and the high costs incurred in the development of such systems, a methodology is needed to compare proposed finite element systems without implementing either hardware or software. This paper presents such a methodology. System architectures are evaluated by simulating the execution of the finite element software on the hardware. Hardware is represented as a set of processors and resources, while the software is modeled as a set of computational tasks organized into an acyclic directed graph. The simulation is performed by scheduling routines. The result of the scheduling routines is a schedule consisting of task-processor assignments and task starting and finishing times. Also, processor and resource utilization levels are generated. These results provide a means of comparing proposed finite element systems.

An Abstract Model for Testing MVC and Workflow Based Web Applications

In this paper, we examine the classes of faults found in web applications that use development frameworks based on the MVC design pattern and the workflow paradigm. Our findings reveal opportunities to adapt state-based and code-based testing methodologies to test these faults. To support our proposed testing methodology, we propose an abstract workflow graph model and show, using an example, how state-based testing as well as structural-based testing methodologies can be applied to test MVC and workflow-based web applications.

An inductive logic programming approach to validate Hexose binding biochemical knowledge

Hexoses are simple sugars that play a key role in many cellular pathways, and in the regulation of development and disease mechanisms. Current protein-sugar computational models are based, at least partially, on prior biochemical findings and knowledge. They incorporate different parts of these findings in predictive black-box models. We investigate the empirical support for biochemical findings by comparing Inductive Logic Programming (ILP) induced rules to actual biochemical results. We mine the Protein Data Bank for a representative data set of hexose binding sites, non-hexose binding sites and surface grooves. We build an ILP model of hexose-binding sites and evaluate our results against several baseline machine learning classifiers. Our method achieves an accuracy similar to that of other black-box classifiers while providing insight into the discriminating process. In addition, it confirms wet-lab findings and reveals a previously unreported Trp-Glu amino acids dependency.

Geometry and Domain Modelling for Construction Robots

Construction robots operate in an environment very different from that of manufacturing robots. This environment is less structured, more complex and more dynamic than is the norm in manufacturing. In addition, construction robots are inherently mobile, as they are engaged in building or maintaining an immobile structure which is large compared to their dimensions. Another complicating factor is the uniqueness of actions that must he taken by a construction robot: the number of special conditions that may exist in buildings is large. All of diese differences provide arguments for two related capabilities that arc required of construction robots: the ability to reason about and to model their environment. In diis paper we present current work at Carnegie-Mellon University which addresses the problems of geometrie reasoning and domain modelling in the specific context of knowledge based expert systems.

A Topological Abstraction for Implementing Recursive Subdivision Surface Computations

AbstractWe present a new abstraction, association space, in the context of recursive subdivision surfaces. An association space relates elements in a recursive subdivision surface at a given refinement level to the elements of the surface at the previous refinement level. These associations allow a programmer to easily implement recursive subdivision algorithms and augment them with computations, such as multigrid techniques, that require inter-level traversals of the hierarchy of refined meshes. These associations also extend to distributed recursive subdivision surfaces. They underlie the mechanism for stitching the refined partitions of a mesh into a single refined mesh.

An architecture for conceptual mechanical modeling

Computer-Aided Design (CAD) systems have fallen short of their potential to improve the mechanical design process. CAD systems are actually used for activities that occur near the end of the design process: detailing the geometry of artifacts, analysis ( e.g., stress, thermal) of such artifacts, generating production drawings, etc. By this time most of the critical design decisions have been made already. One need only look at studies, revealing that 75

Computer method and apparatus for developing web pages and applications

%of the eventual costs of a product are determined before “full-scale development” begins, to realize the implications of this pattern of usage,