Life Sciences Commons^™

On Computing Condensed Frequent Pattern Bases, Jian Pei, Guozhu Dong, Wei Zou, Jiawei Han

Kno.e.sis Publications

Frequent pattern mining has been studied extensively. However, the effectiveness and efficiency of this mining is often limited, since the number of frequent patterns generated is often too large. In many applications it is sufficient to generate and examine only frequent patterns with support frequency in close-enough approximation instead of in full precision. Such a compact but close-enough frequent pattern base is called a condensed frequent patterns-base.

In this paper, we propose and examine several alternatives at the design, representation, and implementation of such condensed frequent pattern-bases. A few algorithms for computing such pattern-bases are proposed. Their effectiveness at pattern …

A Neural Network Method For Protein Classification, Arie D. Jones

All-Inclusive List of Electronic Theses and Dissertations

The investigation detailed in this paper attempts to utilize a Leaming Vector Quantization network in order to classify a set of mitochondrial proteins based upon their amino acid sequence. The Learning Vector Quantization network uses a nearest neighbor approach to classification. Input vectors are fed into the network, which produces output vectors. Those output vectors are then matched by means of a distance bias to a corresponding classification vector. The learning and test sets consisted of thirteen similar mitochodrial proteins from seventy-two different species. This provided a pool of over nine hundred proteins to use. Half of the species were …

Semantic Web Services And Processes: Semantic Composition And Quality Of Service, Jorge Cardoso, Chistoph Bussler, Amit P. Sheth, Dieter Fensel

Kno.e.sis Publications

Web Services are increasingly being adapted by Enterprises as the new approach to component-based solutions for enterprise applications. They hold potential to transform Web from a collection of information resources to a distributed computing platform. Many enterprise applications, including those supporting e-commerce take a form of processes, which need to be created from individual Web Services and other software components.

Implementing Qos Management For Workflow Systems, Jorge Cardoso, Amit P. Sheth, Krzysztof J. Kochut

Kno.e.sis Publications

Workflow management systems (WfMSs) have been used to support various types of business processes. As organizations adopt new working models, such as e-commerce, new challenges arise for workflow systems. One such challenge is that of quality of service (QoS) management. QoS management includes mechanisms that specify, compute, monitor, and control the quality of service of the products or services to be delivered. A good management of QoS directly impacts the success of organizations participating in e-commerce activities by better fulfilling customer expectations and achieving customer satisfaction. In this paper we present an implementation of a comprehensive QoS model for workflows …

Applying Xml/Xslt Technology: A Case Study, Krishnaprasad Thirunarayan

Kno.e.sis Publications

Typically, paper-based semi-structured documents are used to communicate technical requirements in the industry. One approach to improving the efficiency and flexibility of searching and manipulating these documents is to obtain them in electronic form, and then make explicit the technical content in a form amenable to pattern matching and symbol manipulation. This paper explores the role of XML Technology for these purposes: the use of XML language to make explicit the content of a document in a standard fashion, and the use of XSLT to manipulate the content and mediate between applications that need this content. In order to recognize …

Semi-Automatic Content Extraction From Specifications, Krishnaprasad Thirunarayan, Aaron Berkovich, Dan Z. Sokol

Kno.e.sis Publications

Specifications are critical to companies involved in complex manufacturing. The constant reading, reviewing, and analysis of materials and process specifications is extremely labor-intensive, quality impacting, and time-consuming. A conceptual design for a tool that provides computer-assistance in the interpretation of specification requirements has been created and a strategy for semantic-markup, which is the overlaying of abstract syntax (“the essence”) on the text, has been developed. The solution is based on the techniques for Information Extraction and the XML technology, and it captures the specification content within a semantic ontology. The working prototype of the tool being built will serve as …

Towards Peer-To-Peer Semantic Web: A Distributed Environment For Sharing Semantic Knowledge On The Web, Madhan Arumugam, Amit P. Sheth, I. Budak Arpinar

Kno.e.sis Publications

The real value of Semantic Web vision can be demonstrated if people and applications can create and discover new and interesting knowledge and share this knowledge in a transparent manner similar to the way data is exchanged today. Therefore, we believe that Semantic Web will consist of a distributed environment of shared and interoperable ontologies, which have emerged as common formalisms for knowledge representation. The users will need to discover new ontologies, which are not known to them before and use them to either annotate the content or to formulate their information requests. This requires an environment that supports creating, …

Modeling Quality Of Service For Workflows And Web Service Processes, Jorge Cardoso, John A. Miller, Amit P. Sheth, Jonathan Arnold

Kno.e.sis Publications

Workflow management systems (WfMSs) have been used to support various types of business processes for more than a decade now. In workflows for e-commerce and Web-services applications, suppliers and customers define a binding agreement or contract between the two parties, specifying Quality of Service (QoS) items such as products or services to be delivered, deadlines, quality of products, and cost of services. The management of QoS metrics directly impacts the success of organizations participating in e-commerce. Therefore, when services or products are created or managed using workflows, the underlying workflow system must accept the specifications and be able to estimate, …

Breast Cancer On The World Wide Web: Cross Sectional Survey Of Quality Of Information And Popularity Of Websites, Funda Meric, Elmer V Bernstam, Nadeem Q Mirza, Kelly K Hunt, Frederick C Ames, Merrick I Ross, Henry M Kuerer, Raphael E Pollock, Mark A Musen, S Eva Singletary

Faculty, Staff and Student Publications

OBJECTIVES: To determine the characteristics of popular breast cancer related websites and whether more popular sites are of higher quality.

DESIGN: The search engine Google was used to generate a list of websites about breast cancer. Google ranks search results by measures of link popularity---the number of links to a site from other sites. The top 200 sites returned in response to the query "breast cancer" were divided into "more popular" and "less popular" subgroups by three different measures of link popularity: Google rank and number of links reported independently by Google and by AltaVista (another search engine).

MAIN OUTCOME …

Process Composition: Quality Of Service Specification, Semantics And Adaptation, Jorge Cardoso, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Characterizing Logic Programming Semantics With Level Mappings, Pascal Hitzler, Matthias Wendt

Computer Science and Engineering Faculty Publications

Declarative semantics in logic programming and nonmonotonic reasoning are often defined via fixed points of semantic operators. While many relationships between different semantics known from the literature have been studied, a uniform treatment is still missing. In this paper, we provide uniform operator-free characterizations for some of the most important semantics, more precisely, for the stable, the well-founded, and the Fitting semantics, for the weakly-perfect model semantics, and for the least model semantics for negation-free programs.

The Fixed-Point Theorems Of Priess-Crampe And Ribenboim In Logic Programming, Pascal Hitzler, Anthony K. Seda

Computer Science and Engineering Faculty Publications

Sibylla Priess-Crampe and Paulo Ribenboim recently established a general fixed-point theorem for multivalued mappings defined on generalized ultrametric spaces, and introduced it to the area of logic programming semantics. We discuss, in this context, the applications which have been made so far of this theorem and of its corollaries. In particular, we will relate these results to Scott-Ershov domains, familiar in programming language semantics, and to the generalized metrics of Khamsi, Kreinovich, and Misane which have been applied, by these latter authors, to logic programming. Amongst other things, we will also show that a unified treatment of the fixed-point theory …

Managing Semantic Content For The Web, Amit P. Sheth, Clemens Bertram, David Avant, Brian Hammond, Krzysztof Kochut, Yashodhan Warke

Kno.e.sis Publications

By associating meaning with content, the Semantic Web will facilitate search, interoperability, and the composition of complex applications. A recent Scientific American article described the Semantic Web as 'an extension of the current Web in which information is given well-defined meaning, better enabling computers and people to work in cooperation.' Not long ago, researchers at a Stanford University symposium predicted that this second phase of the Web would be as revolutionary as the Web itself.

Predicting Oral Reading Miscues, Jack Mostow, Joseph Beck, S. Vanessa Winter, Shaojun Wang

Kno.e.sis Publications

This paper explores the problem of predicting specific reading mistakes, called miscues, on a given word. Characterizing likely miscues tells an automated reading tutor what to anticipate, detect, and remediate. As training and test data, we use a database of over 100,000 miscues transcribed by University of Colorado researchers. We explore approaches that exploit different sources of predictive power: the uneven distribution of words in text, and the fact that most miscues are real words. We compare the approaches’ ability to predict miscues of other readers on other text. A simple rote method does best on the most frequent 100 …

Workflow Quality Of Service, Jorge Cardoso, Amit P. Sheth, John A. Miller

Kno.e.sis Publications

Workflow management systems (WfMSs) have been used to support various types of business processes for more than a decade now. In ecommerce processes, suppliers and customers define a binding agreement or contract between the two parties, specifying quality of service (QoS) items such as products or services to be delivered, deadlines, quality of products, and cost of service. Management of such QoS directly impacts success of organizations participating in e-commerce. Organizations operating in modern markets require an excellent degree of quality of service management. Products and services must be available to customers with well-defined specifications. A good management of quality …

Ilp Operators For Propositional Connectionist Networks, Miguel Angel Gutierrez-Naranjo, Pascal Hitzler

Computer Science and Engineering Faculty Publications

No abstract provided.

Towards Nonmonotonic Reasoning On Hierarchical Knowledge, Pascal Hitzler

Computer Science and Engineering Faculty Publications

W.C. Rounds and G.Q. Zhang have recently proposed to study a form of disjunctive logic programming generalized to algebraic domains [RZ01]. This system allows reasoning with information which is hierarchically structured and forms a (suitable) domain. We extend this framework to include reasoning with negative information, i.e. the implicit or explicit absence of bits of information. These investigations will naturally lead to a form of default reasoning which is strongly related to programming with answer sets to stable models, which has recently created much interest amongst artificial intelligence researchers concerned with knowledge representation and reasoning.

Focusing Feedback On Interpersonal Skills: Practice Makes Perfect A Web-Based Tutorial For Standardized Patients, Tamara Owens, Zhong Xie, Peggy Gregg, Cynthia Phelps, Craig W. Johnson

Faculty, Staff and Student Publications

Focusing Feedback on Interpersonal Skills: Practice Makes Perfect is a Web-Based learning environment enabling standardized patients (SPs) to develop, practice and enhance constructive feedback skills. The Web-based training environment for SPs features realistic professional healthcare provider/patient video scenarios, graphics, audio and immediate feedback in a student-centered self-instructional environment. SPs, who are trained to simulate an illness and portray a patient in a realistic and consistent way, subsequently provide feedback from a patient's perspective to students undergoing communication and interpersonal skills training in health science fields like medicine and nursing.

A Proposed Undergraduate Bioinformatics Curriculum For Computer Scientists, Travis E. Doom, Michael L. Raymer, Dan E. Krane, Oscar Garcia

Kno.e.sis Publications

Bioinformatics is a new and rapidly evolving discipline that has emerged from the fields of experimental molecular biology and biochemistry, and from the the artificial intelligence, database, and algorithms disciplines of computer science. Largely because of the inherently interdisciplinary nature of bioinformatics research, academia has been slow to respond to strong industry and government demands for trained scientists to develop and apply novel bioinformatics techniques to the rapidly-growing, freely-available repositories of genetic and proteomic data. While some institutions are responding to this demand by establishing graduate programs in bioinformatics, the entrance barriers for these programs are high, largely due to …

Multi-Dimensional Regression Analysis Of Time-Series Data Streams, Yixin Chen, Guozhu Dong, Jiawei Han, Benjamin W. Wah, Jianyong Wang

Kno.e.sis Publications

Real-time production systems and other dynamic environments often generate tremendous (potentially infinite) amount of stream data; the volume of data is too huge to be stored on disks or scanned multiple times. Can we perform on-line, multi-dimensional analysis and data mining of such data to alert people about dramatic changes of situations and to initiate timely, high-quality responses? This is a challenging task.

In this paper, we investigate methods for online, multi-dimensional regression analysis of time-series stream data, with the following contributions: (1) our analysis shows that only a small number of compressed regression measures instead of the complete stream …

Xml-Based Modeling And Simulation: Web Service Technologies And Their Synergy With Simulation, Senthilanand Chandrasekaran, Gregory S. Silver, John A. Miller, Jorge Cardoso, Amit P. Sheth

Kno.e.sis Publications

The World Wide Web has had an huge influence on the computing field in general as well as simulation in particular (e.g., Web-based simulation). A new wave of development based upon XML has started. Two of the most interesting aspects of this development are the Semantic Web and Web services. This paper examines the synergy between Web service technology and simulation. In one direction, Web service processes can be simulated for the purpose of correcting/improving the design. In the other direction, simulation models/components can be built out of Web services. Work on seamlessly using simulation as a part of Web …

Authorization And Access Control Of Application Data In Workflow Systems, Shengli Wu, Amit P. Sheth, John A. Miller, Zongwei Luo

Kno.e.sis Publications

Workflow Management Systems (WfMSs) are used to support the modeling and coordinated execution of business processes within an organization or across organizational boundaries. Although some research efforts have addressed requirements for authorization and access control for workflow systems, little attention has been paid to the requirements as they apply to application data accessed or managed by WfMSs. In this paper, we discuss key access control requirements for application data in workflow applications using examples from the healthcare domain, introduce a classification of application data used in workflow systems by analyzing their sources, and then propose a comprehensive data authorization and …

The Latent Maximum Entropy Principle, Shaojun Wang, Ronald Rosenfeld, Yunxin Zhao, Dale Schuurmans

Kno.e.sis Publications

We present an extension of Jaynes' maximum entropy principle to handle latent variables. We use an EM algorithm that incorporates nested iterative scaling to approximately calculate maximum entropy solutions for this principle, and give a proof of its convergence.

Evaluating The Prevalence, Content And Readability Of Complementary And Alternative Medicine (Cam) Web Pages On The Internet, Smitha Sagaram, Muhammad Walji, Elmer Bernstam

Faculty, Staff and Student Publications

Complementary and alternative medicine (CAM) use is growing rapidly. As CAM is relatively unregulated, it is important to evaluate the type and availability of CAM information. The goal of this study is to deter-mine the prevalence, content and readability of online CAM information based on searches for arthritis, diabetes and fibromyalgia using four common search engines. Fifty-eight of 599 web pages retrieved by a "condition search" (9.6%) were CAM-oriented. Of 216 CAM pages found by the "condition" and "condition + herbs" searches, 78% were authored by commercial organizations, whose pur-pose involved commerce 69% of the time and 52.3% had no …

Evaluating A Medical Error Taxonomy, Juliana Brixey, Todd R. Johnson, Jiajie Zhang

Faculty, Staff and Student Publications

Healthcare has been slow in using human factors principles to reduce medical errors. The Center for Devices and Radiological Health (CDRH) recognizes that a lack of attention to human factors during product development may lead to errors that have the potential for patient injury, or even death. In response to the need for reducing medication errors, the National Coordinating Council for Medication Errors Reporting and Prevention (NCC MERP) released the NCC MERP taxonomy that provides a standard language for reporting medication errors. This project maps the NCC MERP taxonomy of medication error to MedWatch medical errors involving infusion pumps. Of …

Foundations For An Integrative Parasitology: Collections, Archives, And Biodiversity Informatics, Eric P. Hoberg

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Burgeoning awareness about biodiversity emphasizes the fundamental importance of museum collections and the contributions of systematists and taxonomists in documenting the structure and history of the biosphere. An essential role is served by this infrastructure in collecting, preparing, analyzing, and disseminating information about the specimens that represent species, document a range of complex biological associations from symbioses to parasitism, and form the tapestry and the myriad facets of biodiversity (e.g., Wilson, 2000). As parasitologists we can examine how we may contribute to this broader documentation and understanding of global biodiversity, and we can articulate and communicate our role as vital …

Prognostic Model For Terminally Ill Cancer Patients On Laboratory Data, Kenji Hira, Noriaki Aoki, Akitoshi Hayashi, Janez Demsar, Blaz Zupan, Kim Dunn, William Jack Schull, Tsuguya Fukui

Faculty, Staff and Student Publications

No abstract provided.

Toward A Cognitive Taxonomy Of Medical Errors, Jiajie Zhang, Vimla L Patel, Todd R Johnson, Edward H Shortliffe

Faculty, Staff and Student Publications

One critical step in addressing and resolving the problems associated with human errors is the development of a cognitive taxonomy of such errors. In the case of errors, such a taxonomy may be developed (1) to categorize all types of errors along cognitive dimensions, (2) to associate each type of error with a specific underlying cognitive mechanism, (3) to explain why, and even predict when and where, a specific error will occur, and (4) to generate intervention strategies for each type of error. Based on Reason's (1992) definition of human errors and Norman's (1986) cognitive theory of human action, we …

Comparing Communication Technology On Chinese, English, And Spanish Diabetes Web Sites, Yanko F Michea, Karen Pancheri, Yang Gong, Elmer Bernstam

Faculty, Staff and Student Publications

Technological and cultural factors influence access to health information on the web in multifarious ways. We evaluated structural differences and availability of communication services on the web in three diverse language and cultural groups: Chinese, English, and Spanish. A total of 382 web sites were analyzed: 144 were English language sites (38%), 129 were Chinese language sites (34%), and 108 were Spanish language sites (28%). We did not find technical differences in the number of outgoing links per domain or the total availability of communication services between the three groups. There were differences in the distribution of available services between …

The Semantic Web And The Integration Of Health Data Resources, Rachel L. Richesson, James P. Turley, Mark S. Tuttle

Faculty, Staff and Student Publications

No abstract provided.