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Articles 1891 - 1920 of 2074

Full-Text Articles in Computer Sciences

Towards (Semi-) Automatic Generation Of Bio-Medical Ontologies, Vipul Kashyap, Cartic Ramakrishnan, Thomas Rindflesch Nov 2003

Towards (Semi-) Automatic Generation Of Bio-Medical Ontologies, Vipul Kashyap, Cartic Ramakrishnan, Thomas Rindflesch

Kno.e.sis Publications

The design and construction of domain specific ontologies and taxonomies requires allocation of huge resources in terms of cost and time. These efforts are human intensive and we need to explore ways of minimizing human involvement and other resources. In the biomedical domain, we seek to leverage resources such as the UMLS1 Metathesaurus and NLP-based applications such as MetaMap2 in conjunction with statistical clustering techniques, to (partially) automate the process. This is expected to be useful to the team involved in developing MeSH and other biomedical taxonomies to identify gaps in the existing taxonomies, and to be able to quickly …

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What Can Semantics Do For Bioinformatics?, Amit P. Sheth Oct 2003

What Can Semantics Do For Bioinformatics?, Amit P. Sheth

Kno.e.sis Publications

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Modeling Of The Inverse Heat -Conduction Problem With Application To Laser Chemical Vapor Deposition And Bioheat Transfer, Peng Zhen Oct 2003

Modeling Of The Inverse Heat -Conduction Problem With Application To Laser Chemical Vapor Deposition And Bioheat Transfer, Peng Zhen

Doctoral Dissertations

This dissertation consists of two parts. Part one deals with three-dimensional laser induced chemical vapor deposition (3D-LCVD), whereas part two deals with a Pennes model of a 3D skin structure. LCVD is an important technique in manufacturing complex micro-structures with high aspect ratio. In part one, a numerical model was developed for simulating kinetically-limited growth of an axisymmetric cylindrical rod by pre-specifying the surface temperature distribution required for growing the rod and then by obtaining optimized laser power that gives rise to the pre-specified temperature distribution. The temperature distribution at the surface of the rod was assumed to be at …

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Semantic Web In Action: Ontology-Driven Information Search, Integration And Analysis, Amit P. Sheth Sep 2003

Semantic Web In Action: Ontology-Driven Information Search, Integration And Analysis, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

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Context-Aware Semantic Association Ranking, Boanerges Aleman-Meza, Christian Halaschek-Wiener, I. Budak Arpinar, Amit P. Sheth Sep 2003

Context-Aware Semantic Association Ranking, Boanerges Aleman-Meza, Christian Halaschek-Wiener, I. Budak Arpinar, Amit P. Sheth

Kno.e.sis Publications

Discovering complex and meaningful relationships, which we call Semantic Associations, is an important challenge. Just as ranking of documents is a critical component of today's search engines, ranking of relationships will be essential in tomorrow's semantic search engines that would support discovery and mining of the Semantic Web. Building upon our recent work on specifying types of Semantic Associations in RDF graphs, which are possible to create through semantic metadata extraction and annotation, we discuss a framework where ranking techniques can be used to identify more interesting and more relevant Semantic Associations. Our techniques utilize alternative ways of specifying the …

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Continuity Of Semantic Operators In Logic Programming And Their Approximation By Artificial Neural Networks, Pascal Hitzler, Anthony K. Seda Sep 2003

Continuity Of Semantic Operators In Logic Programming And Their Approximation By Artificial Neural Networks, Pascal Hitzler, Anthony K. Seda

Computer Science and Engineering Faculty Publications

One approach to integrating first-order logic programming and neural network systems employs the approximation of semantic operators by feedforward networks. For this purpose, it is necessary to view these semantic operators as continuous functions on the reals. This can be accomplished by endowing the space of all interpretations of a logic program with topologies obtained from suitable embeddings. We will present such topologies which arise naturally out of the theory of logic programming, discuss continuity issues of several well-known semantic operators, and derive some results concerning the approximation of these operators by feedforward neural networks.

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Context-Aware Semantic Association Ranking, Boanerges Aleman-Meza, Chris Halaschek, I. Budak Arpinar, Amit P. Sheth Aug 2003

Context-Aware Semantic Association Ranking, Boanerges Aleman-Meza, Chris Halaschek, I. Budak Arpinar, Amit P. Sheth

Kno.e.sis Publications

Discovering complex and meaningful relationships, which we call Semantic Associations, is an important challenge. Just as ranking of documents is a critical component of today's search engines, ranking of relationships will be essential in tomorrow's semantic search engines that would support discovery and mining of the Semantic Web. Building upon our recent work on specifying types of Semantic Associations in RDF graphs, which are possible to create through semantic metadata extraction and annotation, we discuss a framework where ranking techniques can be used to identify more interesting and more relevant Semantic Associations. Our techniques utilize alternative ways of specifying the …

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Boltzmann Machine Learning With The Latent Maximum Entropy Principle, Shaojun Wang, Dale Schuurmans, Fuchun Peng, Yunxin Zhao Aug 2003

Boltzmann Machine Learning With The Latent Maximum Entropy Principle, Shaojun Wang, Dale Schuurmans, Fuchun Peng, Yunxin Zhao

Kno.e.sis Publications

We present a new statistical learning paradigm for Boltzmann machines based on a new inference principle we have proposed: the latent maximum entropy principle (LME). LME is different both from Jaynes maximum entropy principle and from standard maximum likelihood estimation. We demonstrate the LME principle BY deriving new algorithms for Boltzmann machine parameter estimation, and show how robust and fast new variant of the EM algorithm can be developed. Our experiments show that estimation based on LME generally yields better results than maximum likelihood estimation, particularly when inferring hidden units from small amounts of data.

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Learning Mixture Models With The Latent Maximum Entropy Principle, Shaojun Wang, Dale Schuurmans, Fuchun Peng, Yunxin Zhao Aug 2003

Learning Mixture Models With The Latent Maximum Entropy Principle, Shaojun Wang, Dale Schuurmans, Fuchun Peng, Yunxin Zhao

Kno.e.sis Publications

We present a new approach to estimating mixture models based on a new inference principle we have proposed: the latent maximum entropy principle (LME). LME is different both from Jaynes’ maximum entropy principle and from standard maximum likelihood estimation. We demonstrate the LME principle by deriving new algorithms for mixture model estimation, and show how robust new variants of the EM algorithm can be developed. Our experiments show that estimation based on LME generally yields better results than maximum likelihood estimation, particularly when inferring latent variable models from small amounts of data.

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A Visual Framework Invites Human Into The Clustering Process, Keke Chen, Ling Liu Jul 2003

A Visual Framework Invites Human Into The Clustering Process, Keke Chen, Ling Liu

Kno.e.sis Publications

Clustering is a technique commonly used in scientific research. The task of clustering inevitably involves human participation - the clustering is not finished when the computer/algorithm finishes but the user has evaluated, understood and accepted the patterns. This defines a human involved "clustering-analysis/evaluation" iteration. Instead of neglecting this human involvement, we provide a visual framework (VISTA) with all power of algorithmic approaches (since their result can be visualized), and in addition we allow the user to steer/monitor/refine the clustering process with domain knowledge. The visual-rendering result also provides a precise pattern for fast post-processing.

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Toward A Comprehensive Supplement For Language Courses, Krishnaprasad Thirunarayan, Stephen P. Carl Jul 2003

Toward A Comprehensive Supplement For Language Courses, Krishnaprasad Thirunarayan, Stephen P. Carl

Kno.e.sis Publications

No abstract provided.

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Fast And Space-Efficient Location Of Heavy Or Dense Segments In Run-Length Encoded Sequences, Ronald I. Greenberg Jul 2003

Fast And Space-Efficient Location Of Heavy Or Dense Segments In Run-Length Encoded Sequences, Ronald I. Greenberg

Computer Science: Faculty Publications and Other Works

This paper considers several variations of an optimization problem with potential applications in such areas as biomolecular sequence analysis and image processing. Given a sequence of items, each with a weight and a length, the goal is to find a subsequence of consecutive items of optimal value, where value is either total weight or total weight divided by total length. There may also be a specified lower and/or upper bound on the acceptable length of subsequences. This paper shows that all the variations of the problem are solvable in linear time and space even with non-uniform item lengths and divisible …

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Adding Semantics To Web Services Standards, Kaarthik Sivashanmugam, Kunal Verma, Amit P. Sheth, John Miller Jun 2003

Adding Semantics To Web Services Standards, Kaarthik Sivashanmugam, Kunal Verma, Amit P. Sheth, John Miller

Kno.e.sis Publications

With the increasing growth in popularity of Web services, discovery of relevant Web services becomes a significant challenge. One approach is to develop semantic Web services where by the Web services are annotated based on shared ontologies, and use these annotations for semantics-based discovery of relevant Web services. We discuss one such approach that involves adding semantics to WSDL using DAML+OIL ontologies. Our approach also uses UDDI to store these semantic annotations and search for Web services based on them. We compare our approach with another initiative to add semantics to support Web service discovery, and show how our approach …

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Semantic Web Process Lifecycle: Role Of Semantics In Annotation, Discovery, Composition And Orchestration, Amit P. Sheth May 2003

Semantic Web Process Lifecycle: Role Of Semantics In Annotation, Discovery, Composition And Orchestration, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

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Healthcare Enterprise Process Development And Integration, Kemafor Anyanwu, Amit P. Sheth, Jorge Cardoso, John A. Miller, Krzysztof J. Kochut May 2003

Healthcare Enterprise Process Development And Integration, Kemafor Anyanwu, Amit P. Sheth, Jorge Cardoso, John A. Miller, Krzysztof J. Kochut

Kno.e.sis Publications

Healthcare enterprises involve complex processes that span diverse groups and organisations. These processes involve clinical and administrative tasks, large volumes of data, and large numbers of patients and personnel. The tasks can be performed either by humans or by automated systems. In the latter case, the tasks are supported by a variety of software applications and information systems which are very often heterogeneous, autonomous, and distributed. The development of systems to manage and automate these processes has increasingly played an important role in improving the efficiency of healthcare enterprises. In this paper we look at four healthcare and medical applications …

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Ρ-Queries: Enabling Querying For Semantic Associations On The Semantic Web, Kemafor Anyanwu, Amit P. Sheth May 2003

Ρ-Queries: Enabling Querying For Semantic Associations On The Semantic Web, Kemafor Anyanwu, Amit P. Sheth

Kno.e.sis Publications

This paper presents the notion of Semantic Associations as complex relationships between resource entities. These relationships capture both a connectivity of entities as well as similarity of entities based on a specific notion of similarity called ρ-isomorphism. It formalizes these notions for the RDF data model, by introducing a notion of a Property Sequence as a type. In the context of a graph model such as that for RDF, Semantic Associations amount to specific certain graph signatures. Specifically, they refer to sequences (i.e. directed paths) here called Property Sequences, between entities, networks of Property Sequences (i.e. undirected paths), or subgraphs …

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Exception Handling For Conflict Resolution In Cross-Organizational Workflows, Zongwei Luo, Amit P. Sheth, Krzysztof Kochut, I. Budak Arpinar May 2003

Exception Handling For Conflict Resolution In Cross-Organizational Workflows, Zongwei Luo, Amit P. Sheth, Krzysztof Kochut, I. Budak Arpinar

Kno.e.sis Publications

Workflow management systems (WfMSs) are being increasingly deployed to deliver e-business transactions across organizational boundaries. To ensure a high service quality in such transactions, exception-handling schemes for conflict resolution are needed. The conflicts primarily arise due to failure of a task in workflow execution because of underlying application, or controlling WfMS component failures or insufficient user input. So far, little progress has been reported in addressing conflict resolution in cross-organizational business processes, though its importance has been recognized. In this paper, we identify the exception handling techniques that support conflict resolution in cross-organizational settings. In particular, we propose a novel, …

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Identifying Patterns In Dna Change, Jason R. Gilder, Dan E. Krane, Travis E. Doom, Michael L. Raymer Apr 2003

Identifying Patterns In Dna Change, Jason R. Gilder, Dan E. Krane, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

Now that a draft sequence of the human genome is nearly complete, questions regarding both the information contained within our genetic blueprints as well as the manner in which that information content changes over time can be addressed in ways that had not previously been possible. By their very nature, some of the nucleotide sequences present within our genome allow detailed examination of the mode and pattern of evolution that has shaped our genetic instructions over time spans of tens of millions of years. Alu repeats are one example. Using these relatively short, ubiquitous DNA sequences we explore the problem …

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Ontology Driven Information Systems In Action (Capturing And Applying Existing Knowledge To Semantic Applications), Amit P. Sheth Mar 2003

Ontology Driven Information Systems In Action (Capturing And Applying Existing Knowledge To Semantic Applications), Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

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Deterministic Intracellular Modeling, Jacqueline B. Young Mar 2003

Deterministic Intracellular Modeling, Jacqueline B. Young

Theses and Dissertations

The United States Air Force is interested in the potential side effects at the cellular level from exposure to mission-essential chemicals. Presently, Air Force toxicology studies are conducted to help shed light in identifying potential hazards to workers. However, it takes a considerable amount of money, resources, and time to obtain and analyze experimental results from toxicology studies. The necessity for innovative methods that enable researchers to more effectively generate and analyze data is apparent.

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Pc–Based Data Acquisition For A Solid Substrate Cultivation Deep Bed Reactor, Mari S. Chinn, Sue E. Nokes, Richard S. Gates Mar 2003

Pc–Based Data Acquisition For A Solid Substrate Cultivation Deep Bed Reactor, Mari S. Chinn, Sue E. Nokes, Richard S. Gates

Biosystems and Agricultural Engineering Faculty Publications

This work describes an instrumentation and data acquisition system designed for a deep bed reactor used to cultivate Trichoderma longibrachiatum on wheat bran. The system allowed on–line measurements of substrate temperature, oxygen concentration within the reactor headspace, relative humidity and temperature of the inlet air, and inlet airflow rates while maintaining aseptic conditions and without disturbing the cultivation process. An error analysis for the instrumentation and data acquisition equipment was completed and provided insight into the reliability of the sensor readings. The collected data provided quantitative information about the reactor system dynamics which can be used to evaluate and apply …

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Generalized Metrics And Uniquely Determined Logic Programs, Pascal Hitzler, Anthony K. Seda Jan 2003

Generalized Metrics And Uniquely Determined Logic Programs, Pascal Hitzler, Anthony K. Seda

Computer Science and Engineering Faculty Publications

The introduction of negation into logic programming brings the benefit of enhanced syntax and expressibility, but creates some semantical problems. Specifically, certain operators which are monotonic in the absence of negation become non-monotonic when it is introduced, with the result that standard approaches to denotational semantics then become inapplicable. In this paper, we show how generalized metric spaces can be used to obtain fixed-point semantics for several classes of programs relative to the supported model semantics, and investigate relationships between the underlying spaces we employ. Our methods allow the analysis of classes of programs which include the acyclic, locally hierarchical, …

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Semantic N-Gram Language Modeling With The Latent Maximum Entropy Principle, Shaojun Wang, Dale Schuurmans, Fuchun Peng, Yunxin Zhao Jan 2003

Semantic N-Gram Language Modeling With The Latent Maximum Entropy Principle, Shaojun Wang, Dale Schuurmans, Fuchun Peng, Yunxin Zhao

Kno.e.sis Publications

We describe a unified probabilistic framework for statistical language modeling-the latent maximum entropy principle-which can effectively incorporate various aspects of natural language, such as local word interaction, syntactic structure and semantic document information. Unlike previous work on maximum entropy methods for language modeling, which only allow explicit features to be modeled, our framework also allows relationships over hidden features to be captured, resulting in a more expressive language model. We describe efficient algorithms for marginalization, inference and normalization in our extended models. We then present experimental results for our approach on the Wall Street Journal corpus.

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Web Service: Been There, Done That?, Steffen Staab, Will Van Der Aalst, V. Richard Benjamins, Amit P. Sheth, John A. Miller, Chistoph Bussler, Alexander Maedche, Dieter Fensel, Dennis Gannon Jan 2003

Web Service: Been There, Done That?, Steffen Staab, Will Van Der Aalst, V. Richard Benjamins, Amit P. Sheth, John A. Miller, Chistoph Bussler, Alexander Maedche, Dieter Fensel, Dennis Gannon

Kno.e.sis Publications

Web services can be defined as loosely coupled, reusable software components that semantically encapsulate discrete functionality and are distributed and programmatically accessible over standard Internet protocols. Web services have received a lot of hype, the reasons for which are not easily determined. Some of their benefits might even seem to waste away, once we touch on the nitty-gritty details, because Web services per se do not offer a solution to underlying problems. The contributions included in this section delve into some of these issues, including: pitfalls of workflow issues; structuring procedural knowledge into problem-solving methods; discussing how a low initial …

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Semantic Web Processes, Jorge Cardoso, Amit P. Sheth Jan 2003

Semantic Web Processes, Jorge Cardoso, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

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Sedimentological And Plant Taphonomic Evaluation Of The Early Middle Devonian Trout Valley Formation, Jonathan Allen Jan 2003

Sedimentological And Plant Taphonomic Evaluation Of The Early Middle Devonian Trout Valley Formation, Jonathan Allen

Honors Theses

The Trout Valley Formation of Emsian-Eifelian age, outcropped in Baxter State Park, Maine, consists offluvial and coastal deposits preserving early land plants. Massive, crudely bedded conglomerate represents deposits of proximal braided channels on an alluvial fan complex. Lithic sandstone bodies in channel-form geometries represent deposits of river channels draining the Acadian highlands whereas associated siltstones represent overbank deposits, intertidal flats, and tidal channels. Localized lenticular quartz arenites represent nearshore shelf bar deposits that were storm influenced. The majority of plant assemblages preserved mainly in siltstone lithologies are allochthonous and parautochthonous, with only one autochthonous assemblage identified in the sequence. Plant …

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Formal Concept Analysis And Resolution On Algebraic Domains - Preliminary Report, Matthias Wendt, Pascal Hitzler Jan 2003

Formal Concept Analysis And Resolution On Algebraic Domains - Preliminary Report, Matthias Wendt, Pascal Hitzler

Computer Science and Engineering Faculty Publications

We relate two formerly independent areas: Formal concept analysis and logic of domains. We will establish a correspondence between contextual attribute logic on formal contexts resp. concept lattices and a clausal logic on coherent algebraic cpos. We show how to identify the notion of formal concept in the domain theoretic setting. In particular, we show that a special instance of the resolution rule from the domain logic coincides with the concept closure operator from formal concept analysis. The results shed light on the use of contexts and domains for knowledge representation and reasoning purposes.

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Learning Continuous Latent Variable Models With Bregman Divergences, Shaojun Wang, Dale Schuurmans Jan 2003

Learning Continuous Latent Variable Models With Bregman Divergences, Shaojun Wang, Dale Schuurmans

Kno.e.sis Publications

We present a class of unsupervised statistical learning algorithms that are formulated in terms of minimizing Bregman divergences— a family of generalized entropy measures defined by convex functions. We obtain novel training algorithms that extract hidden latent structure by minimizing a Bregman divergence on training data, subject to a set of non-linear constraints which consider hidden variables. An alternating minimization procedure with nested iterative scaling is proposed to find feasible solutions for the resulting constrained optimization problem. The convergence of this algorithm along with its information geometric properties are characterized.

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Protocols For Disease Classification From Mass Spectrometry Data, Michael Wagner, Dayanand Naik, Alex Pothen Jan 2003

Protocols For Disease Classification From Mass Spectrometry Data, Michael Wagner, Dayanand Naik, Alex Pothen

Mathematics & Statistics Faculty Publications

We report our results in classifying protein matrix-assisted laser desorption/ionizationtime of flight mass spectra obtained from serum samples into diseased and healthy groups. We discuss in detail five of the steps in preprocessing the mass spectral data for biomarker discovery, as well as our criterion for choosing a small set of peaks for classifying the samples. Cross-validation studies with four selected proteins yielded misclassification rates in the 10-15% range for all the classification methods. Three of these proteins or protein fragments are down-regulated and one up-regulated in lung cancer, the disease under consideration in this data set. When cross-validation studies …

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Ordering Genetic Algorithm Genomes With Reconstructability Analysis, Stephen Shervais, Martin Zwick Jan 2003

Ordering Genetic Algorithm Genomes With Reconstructability Analysis, Stephen Shervais, Martin Zwick

Complex Systems Faculty Publications and Presentations

The building block hypothesis implies that genetic algorithm effectiveness is influenced by the relative location of epistatic genes on the chromosome. We find that this influence exists, but depends on the generation in which it is measured. Early in the search process it may be more effective to have epistatic genes widely separated. Late in the search process, effectiveness is improved when they are close together. The early search effect is weak but still statistically significant; the late search effect is much stronger and plainly visible. We demonstrate both effects with a set of simple problems, and show that infonnation-theoretic …

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