Showing papers on "Domain (software engineering) published in 2002"

Recent improvements to the SMART domain-based sequence annotation resource

Abstract: SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains. Extensive annotation for each domain family is available, providing information relating to function, subcellular localization, phyletic distribution and tertiary structure. The January 2002 release has added more than 200 hand-curated domain models. This brings the total to over 600 domain families that are widely represented among nuclear, signalling and extracellular proteins. Annotation now includes links to the Online Mendelian Inheritance in Man (OMIM) database in cases where a human disease is associated with one or more mutations in a particular domain. We have implemented new analysis methods and updated others. New advanced queries provide direct access to the SMART relational database using SQL. This database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats. SMART output can now be easily included in users' documents. A SMART mirror has been created at http://smart.ox.ac.uk.

Toward Hierarchical Identity-Based Encryption

Abstract: We introduce the concept of hierarchical identity-based encryption (HIBE) schemes, give precise definitions of their security and mention some applications A two-level HIBE (2-HIBE) scheme consists of a root private key generator (PKG), domain PKGs and users, all of which are associated with primitive IDs (PIDs) that are arbitrary strings A user's public key consists of their PID and their domain's PID (in whole called an address) In a regular IBE (which corresponds to a 1-HIBE) scheme, there is only one PKG that distributes private keys to each user (whose public keys are their PID) In a 2-HIBE, users retrieve their private key from their domain PKG Domain PKGs can compute the private key of any user in their domain, provided they have previously requested their domain secret key from the root PKG (who possesses a master secret) We can go beyond two levels by adding subdomains, subsubdomains, and so on We present a two-level system with total collusion resistance at the upper (domain) level and partial collusion resistance at the lower (user) level, which has chosen-ciphertext security in the random-oracle model

Systematic identification of novel protein domain families associated with nuclear functions.

Abstract: A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic lineages, but 3 are species specific. For about 500 of the 1200 proteins that contain these new domains, nuclear localization could be inferred, and for 700, additional features could be predicted. For example, we identified a new domain, likely to have a role downstream of the unfolded protein response; a nematode-specific signalling domain; and a widespread domain, likely to be a noncatalytic homolog of ubiquitin-conjugating enzymes.

Identity Uncertainty and Citation Matching

Abstract: Identity uncertainty is a pervasive problem in real-world data analysis. It arises whenever objects are not labeled with unique identifiers or when those identifiers may not be perceived perfectly. In such cases, two observations may or may not correspond to the same object. In this paper, we consider the problem in the context of citation matching—the problem of deciding which citations correspond to the same publication. Our approach is based on the use of a relational probability model to define a generative model for the domain, including models of author and title corruption and a probabilistic citation grammar. Identity uncertainty is handled by extending standard models to incorporate probabilities over the possible mappings between terms in the language and objects in the domain. Inference is based on Markov chain Monte Carlo, augmented with specific methods for generating efficient proposals when the domain contains many objects. Results on several citation data sets show that the method outperforms current algorithms for citation matching. The declarative, relational nature of the model also means that our algorithm can determine object characteristics such as author names by combining multiple citations of multiple papers.

Predicate abstraction for software verification

Abstract: Software verification is an important and difficult problem. Many static checking techniques for software require annotations from the programmer in the form of method specifications and loop invariants. This annotation overhead, particularly of loop invariants, is a significant hurdle in the acceptance of static checking. We reduce the annotation burden by inferring loop invariants automatically.Our method is based on predicate abstraction, an abstract interpretation technique in which the abstract domain is constructed from a given set of predicates over program variables. A novel feature of our approach is that it infers universally-quantified loop invariants, which are crucial for verifying programs that manipulate unbounded data such as arrays. We present heuristics for generating appropriate predicates for each loop automatically; the programmer can specify additional predicates as well. We also present an efficient algorithm for computing the abstraction of a set of states in terms of a collection of predicates.Experiments on a 44KLOC program show that our approach can automatically infer the necessary predicates and invariants for all but 31 of the 396 routines that contain loops.

A system and method for secure and convenient management of digital electronic content

Abstract: A domain-based digital rights management (DRM) method and system. A domain has one or more communication devices, such as user devices that share a common cryptographic key of the domain. There may be a plurality of domains in a digital rights management environment and the domains may additionally be overlapping. A domain authority, in combination with a digital rights management module of a communication device, operates to selectively register and unregister the communication device to the one or more domains and to control access to encrypted digital content information.

Translating Named Entities Using Monolingual and Bilingual Resources

Abstract: Named entity phrases are some of the most difficult phrases to translate because new phrases can appear from nowhere, and because many are domain specific, not to be found in bilingual dictionaries. We present a novel algorithm for translating named entity phrases using easily obtainable monolingual and bilingual resources. We report on the application and evaluation of this algorithm in translating Arabic named entities to English. We also compare our results with the results obtained from human translations and a commercial system for the same task.

The role of concepts in program comprehension

Abstract: The paper presents an overview of the role of concepts in program comprehension. It discusses concept location, in which the implementation of a specific concept is located in the code. This process is very common and precedes a large proportion of code changes. The paper also discusses the process of learning about the domain from the code, which is a prerequisite of code reengineering. The paper notes the similarities and overlaps between program comprehension and human learning.

Domain-Specific Language Design Requires Feature Descriptions

Abstract: A domain-specific language (DSL) provides a notation tailored towards an application domain and is based on the relevant concepts and features of that domain. As such, a DSL is a means to describe and generate members of a family of programs in the domain. A prerequisite for the design of a DSL is a detailed analysis and structuring of the application domain. Graphical feature diagrams have been proposed to organize the dependencies between such features, and to indicate which ones are common to all family members and which ones vary. In this paper, we study feature diagrams in more details, as well as their relationship to domain-specific languages. We propose the Feature Description Language (FDL), a textual language to describe features. We explore automated manipulation of feature descriptions such as normalization, expansion to disjunctive normal form, variability computation and constraint satisfaction. Feature descriptions can be directly mapped to UML diagrams which in their turn can be used for Java code generation. The value of FDL is assessed via a case study in the use and expressiveness of feature descriptions for the area of documentation generators.

Stability analysis of linear time-delay systems subject to input saturation

Abstract: This paper is devoted to stability analysis of linear systems with state delay and input saturation. The domain of attraction resulting from an a priori designed state feedback law is analyzed using Lyapunov-Razumikhin and Lyapunov-Krasovskii functional approach. Both delay-independent and delay-dependent estimation of the domain of attraction are presented using the linear matrix inequality technique. The problem of designing linear state feedback laws such that the domain of attraction is enlarged is formulated and solved as an optimization problem with LMI constraints. Numerical examples are used to demonstrate the effectiveness of the proposed design technique.

Affect, Meta-Affect, and Mathematical Belief Structures

Abstract: Beliefs are defined here to be multiply-encoded, internal cognitive/affective configurations, to which the holder attributes truth value of some kind (e.g., empirical truth, validity, or applicability). This chapter offers some theoretical perspectives on mathematical beliefs drawn from analysis of the affective domain, especially the interplay between meta-affect and belief structures in sustaining each other in the individual.

The "Liquid Computer": A Novel Strategy for Real-Time Computing on Time Series

Abstract: We will discuss in this survey article a new framework for analysing computations on time series and in particular on spike trains, introduced in (Maass et. al. 2002). In contrast to common computational models this new framework does not require that information can be stored in some stable states of a computational system. It has recently been shown that such models where all events are transient can be successfully applied to analyse computations in neural systems and (independently) that the basic ideas can also be used to solve engineering tasks such as the design of nonlinear controllers. Using an illustrative example we will develop the main ideas of the proposed model. This illustrative example is generalized and cast into a rigorous mathematical model: the Liquid State Machine. A mathematical analysis shows that there are in principle no computational limitations of liquid state machines in the domain of time series computing. Finally we discuss several successful applications of the framework in the area of computational neuroscience and in the field of artificial neural networks.

Computer Go

Abstract: Computer Go is one of the biggest challenges faced by game programmers. This survey describes the typical components of a Go program, and discusses knowledge representation, search methods and techniques for solving specific subproblems in this domain. Along with a summary of the development of computer Go in recent years, areas for future research are pointed out.

A wireless universal personal access system

Abstract: The invention relates to a two-way bi-directional wireless-based access communication system that allows a user to access any one of multiple independent secured domain systems from a single handheld remote keyless entry device, whereupon activation of the remote keyless device by the user, an encoded request signal containing a predetermined access code is generated and transmitted by the remote keyless entry device to one of the multiple secure domain systems. And, based on the access code contained within the encoded request signal, the domain system determines the validity of the access code and transmits a corresponding encoded authorization signal to user at the transceiver device.

Domain visualization using VxInsight for science and technology management

Abstract: We present the application of our knowledge visualization tool, VxInsight, to enable domain analysis for science and technology management within the enterprise. Data mining from sources of bibliographic information is used to define subsets of information relevant to a technology domain. Relationships between the individual objects (e.g., articles) are identified using citations, descriptive terms, or textual similarities. Objects are then clustered using a force-directed placement algorithm to produce a terrain view of the many thousands of objects. A variety of features that allow exploration and manipulation of the landscapes and that give detail on demand, enable quick and powerful analysis of the resulting landscapes. Examples of domain analyses used in S&T management at Sandia are given.

A maximum entropy approach to information extraction from semi-structured and free text

Abstract: In this paper, we present a classification-based approach towards single-slot as well as multi-slot information extraction (IE). For single-slot IE, we worked on the domain of Seminar Announcements, where each document contains information on only one seminar. For multi-slot IE, we worked on the domain of Management Succession. For this domain, we restrict ourselves to extracting information sentence by sentence, in the same way as (Soderland 1999). Each sentence can contain information on several management succession events. By using a classification approach based on a maximum entropy framework, our system achieves higher accuracy than the best previously published results in both domains.

Occupational Therapy Practice Framework: Domain and Process

Abstract: The fourth edition of the Occupational Therapy Practice Framework: Domain and Process (hereinafter referred to as the OTPF-4), is an official document of the American Occupational Therapy Association (AOTA). Intended for occupational therapy practitioners and students, other health care professionals, educators, researchers, payers, policymakers, and consumers, the OTPF-4 presents a summary of interrelated constructs that describe occupational therapy practice.

The role of domain information in Word Sense Disambiguation

Abstract: This paper explores the role of domain information in word sense disambiguation. The underlying hypothesis is that domain labels, such as MEDICINE, ARCHITECTURE and SPORT, provide a useful way to establish semantic relations among word senses, which can be profitably used during the disambiguation process. Results obtained at the SENSEVAL-2 initiative confirm that for a significant subset of words domain information can be used to disambiguate with a very high level of precision.

An ontological approach to domain engineering

Abstract: Domain engineering aims to support systematic reuse, focusing on modeling common knowledge in a problem domain. Ontologies have also been pointed as holding great promise for software reuse. In this paper, we present ODE (Ontology-based Domain Engineering), an ontological approach for domain engineering that aims to join ontologies and object-oriented technology.

Generative Programming for Embedded Software: An Industrial Experience Report

Abstract: Physical products come in many variants, and so does the software embedded in them. The software embedded in a product variant usually has to be optimized to fit its limited memory and computing power. Generative programming is well suited for developing embedded software since it allows us to automatically produce variants of embedded software optimized for specific products. This paper reports on our experience in applying generative programming in the embedded domain. We propose an extended feature modeling notation, discuss tool support for feature modeling, describe a domain-independent system configuration editor, and comment on the applicability of static configuration in the area of embedded systems.

Rei : A Policy Language for the Me-Centric Project

Abstract: Policies guide the way entities within a domain act, by providing rules for their behavior. Most of the research in policies is within a certain application area, for example security for databases, and there are no general specifications for policies. Another problem with policies is that they require domain dependent information, forcing researchers to create policy languages that are bound to the domains for which they were developed. This prevents policy languages from being flexible and being usable across domains. This report describes the specifications of the Rei policy language, which provides constructs based on deontic concepts. These constructs are extremely flexible and allow different kinds of policies to be stated. This simple policy language is not tied to any specific application and allows domain dependent information to be added without any modification. The policy engine associated with Rei accepts policies in first order logic and RDF. The report also discusses the functionality of the policy engine that interprets and reasons over Rei policies.

System, method and computer program product for caching domain name system information on a network gateway

Abstract: A system, method and computer program product is provided for caching domain name system (DNS) information on a network gateway. In particular, a network gateway that interfaces one or more customer premises equipment (CPE) devices to an IP network maintains a centralized on-board cache for storing domain names and corresponding IP addresses. The domain names and IP addresses in the cache are used by the network gateway to resolve DNS queries generated by application programs running on the CPE devices in a manner that is transparent to the CPE devices and that does not expend CPE resources. The cache may be initially loaded by an attached CPE or an external network entity and is continuously populated with information extracted from DNS messages exchanged between a CPE device and the external IP network.

Predictome: a database of putative functional links between proteins

Abstract: The current deluge of genomic sequences has spawned the creation of tools capable of making sense of the data. Computational and high-throughput experimental methods for generating links between proteins have recently been emerging. These methods effectively act as hypothesis machines, allowing researchers to screen large sets of data to detect interesting patterns that can then be studied in greater detail. Although the potential use of these putative links in predicting gene function has been demonstrated, a central repository for all such links for many genomes would maximize their usefulness. Here we present Predictome, a database of predicted links between the proteins of 44 genomes based on the implementation of three computational methods--chromosomal proximity, phylogenetic profiling and domain fusion--and large-scale experimental screenings of protein-protein interaction data. The combination of data from various predictive methods in one database allows for their comparison with each other, as well as visualization of their correlation with known pathway information. As a repository for such data, Predictome is an ongoing resource for the community, providing functional relationships among proteins as new genomic data emerges. Predictome is available at http://predictome.bu.edu.

Method, system and program for associating a resource to be translated with a domain dictionary

Abstract: In a machine translation environment, a context-specific domain directory must sometimes be selected to provide a proper translation in context. A database for trigger patterns associated with specific domains is prepared. When a resource is to be translated, appearances of the pattern within the resource are detected. If appearance frequency for at least one domain exceeds a threshold value, the appearance frequency for that domain is compared to the appearance frequency for other domains. If the appearance frequency for the one domain is found to be significantly higher, the dictionary for that domain is selected for the translation.

Microarchitectural exploration with Liberty

Abstract: To find the best designs, architects must rapidly simulate many design alternatives and have confidence in the results. Unfortunately, the most prevalent simulator construction methodology, hand-writing monolithic simulators in sequential programming languages, yields simulators that are hard to retarget, limiting the number of designs explored, and hard to understand, instilling little confidence in the model. Simulator construction tools have been developed to address these problems, but analysis reveals that they do not address the root cause, the error-prone mapping between the concurrent, structural hardware domain and the sequential, functional software domain. This paper presents an analysis of these problems and their solution, the Liberty Simulation Environment (LSE). LSE automatically constructs a simulator from a machine description that closely resembles the hardware, ensuring fidelity in the model. Furthermore, through a strict but general component communication contract, LSE enables the creation of highly reusable component libraries, easing the task of rapidly exploring ever more exotic designs.

Parallel-in-time molecular-dynamics simulations.

Abstract: While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations.