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- Semantic Web (7)
- Ontology (5)
- RDF (3)
- Semantic Analytics (3)
- Semantic Association (2)
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- Semantic Associations (2)
- Semantic Discovery (2)
- Semantic Metadata (2)
- Semantic Search (2)
- Adaptation (1)
- Aggregate Constraint (1)
- Autonomic Web Processes (1)
- Bootstrap (1)
- Business Processes (1)
- Classification (1)
- Clustering (1)
- Configuration and Execution Environment (1)
- Constrained Data Mining (1)
- Customer Identification and Risk Assessment Solution (1)
- Data Cube (1)
- Data Mediation (1)
- Dataset Generation (1)
- Differential expression; false discovery rate; q-values; shrinkage; significance analysis of microarrays (1)
- Dimensionality reduction (1)
- Distributed Semantic Association Search (1)
- Document Clustering (1)
- Domain-Based Registry (1)
- Domain-Specific Search (1)
- Dye-bias (1)
- Dye-swap (1)
Articles 1 - 30 of 58
Full-Text Articles in Physical Sciences and Mathematics
Bayesian Analysis Of Cell-Cycle Gene Expression Data, Chuan Zhou, Jon Wakefield, Linda Breeden
Bayesian Analysis Of Cell-Cycle Gene Expression Data, Chuan Zhou, Jon Wakefield, Linda Breeden
UW Biostatistics Working Paper Series
The study of the cell-cycle is important in order to aid in our understanding of the basic mechanisms of life, yet progress has been slow due to the complexity of the process and our lack of ability to study it at high resolution. Recent advances in microarray technology have enabled scientists to study the gene expression at the genome-scale with a manageable cost, and there has been an increasing effort to identify cell-cycle regulated genes. In this chapter, we discuss the analysis of cell-cycle gene expression data, focusing on a model-based Bayesian approaches. The majority of the models we describe …
Openws-Transaction: Enabling Reliable Web Service Transactions, Ivan Vasquez, John A. Miller, Kunal Verma, Amit P. Sheth
Openws-Transaction: Enabling Reliable Web Service Transactions, Ivan Vasquez, John A. Miller, Kunal Verma, Amit P. Sheth
Kno.e.sis Publications
OpenWS-Transaction is an open source middleware that enables Web services to participate in a distributed transaction as prescribed by the WS-Coordination and WS-Transaction set of specifications. Central to the framework are the Coordinator and Participant entities, which can be integrated into existing services by introducing minimal changes to application code. OpenWS-Transaction allows transaction members to recover their original state in case of operational failure by leveraging techniques in logical logging and recovery at the application level. Depending on transaction style, system recovery may involve restoring key application variables and replaying uncommitted database activity. Transactions are assumed to be defined in …
Demonstrating Dynamic Configuration And Execution Of Web Processes, Karthik Gomadam, Kunal Verma, Amit P. Sheth, John A. Miller
Demonstrating Dynamic Configuration And Execution Of Web Processes, Karthik Gomadam, Kunal Verma, Amit P. Sheth, John A. Miller
Kno.e.sis Publications
Web processes are next generation workflows on the web, created using Web services. In this paper we demonstrate the METEOR-S Configuration and Execution Environment (MCEE) system. It will illustrate the capabilities of the system to a) Discover partners b) Optimize partner selection using constraint analysis, c) Perform interaction protocol and data mediation. A graphical execution monitor to monitor the various phases of execution will be used to demonstrate various aspects of the system.
Discovering Informative Connection Subgraphs In Multi-Relational Graphs, Cartic Ramakrishnan, William Milnor, Matthew Perry, Amit P. Sheth
Discovering Informative Connection Subgraphs In Multi-Relational Graphs, Cartic Ramakrishnan, William Milnor, Matthew Perry, Amit P. Sheth
Kno.e.sis Publications
Discovering patterns in graphs has long been an area of interest. In most approaches to such pattern discovery either quantitative anomalies, frequency of substructure or maximum flow is used to measure the interestingness of a pattern. In this paper we introduce heuristics that guide a subgraph discovery algorithm away from banal paths towards more "informative" ones. Given an RDF graph a user might pose a question of the form: "What are the most relevant ways in which entity X is related to entity Y?" the response to which is a subgraph connecting X to Y. We use our heuristics to …
Optimal Feature Selection For Nearest Centroid Classifiers, With Applications To Gene Expression Microarrays, Alan R. Dabney, John D. Storey
Optimal Feature Selection For Nearest Centroid Classifiers, With Applications To Gene Expression Microarrays, Alan R. Dabney, John D. Storey
UW Biostatistics Working Paper Series
Nearest centroid classifiers have recently been successfully employed in high-dimensional applications. A necessary step when building a classifier for high-dimensional data is feature selection. Feature selection is typically carried out by computing univariate statistics for each feature individually, without consideration for how a subset of features performs as a whole. For subsets of a given size, we characterize the optimal choice of features, corresponding to those yielding the smallest misclassification rate. Furthermore, we propose an algorithm for estimating this optimal subset in practice. Finally, we investigate the applicability of shrinkage ideas to nearest centroid classifiers. We use gene-expression microarrays for …
A New Approach To Intensity-Dependent Normalization Of Two-Channel Microarrays, Alan R. Dabney, John D. Storey
A New Approach To Intensity-Dependent Normalization Of Two-Channel Microarrays, Alan R. Dabney, John D. Storey
UW Biostatistics Working Paper Series
A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within arrays, it is necessary to remove systematic errors that distort the biological signal of interest. The standard for accomplishing this is smoothing "MA-plots" to remove intensity-dependent dye bias and array-specific effects. However, MA methods require strong assumptions. We review these assumptions and derive several practical scenarios in which they fail. The "dye-swap" normalization method has been much less frequently used because it requires two arrays per pair of samples. We show …
Ontoqa: Metric-Based Ontology Quality Analysis, Samir Tartir, I. Budak Arpinar, Michael Moore, Amit P. Sheth, Boanerges Aleman-Meza
Ontoqa: Metric-Based Ontology Quality Analysis, Samir Tartir, I. Budak Arpinar, Michael Moore, Amit P. Sheth, Boanerges Aleman-Meza
Kno.e.sis Publications
As the Semantic Web gains importance for sharing knowledge on the Internet this has lead to the development and publishing of many ontologies in different domains. When trying to reuse existing ontologies into their applications, users are faced with the problem of determining if an ontology is suitable for their needs. In this paper, we introduce OntoQA, an approach that analyzes ontology schemas and their populations (i.e. knowledgebases) and describes them through a well defined set of metrics. These metrics can highlight key characteristics of an ontology schema as well as its population and enable users to make an informed …
Semantics For Scientific Experiments And The Web: The Implicit, The Formal And The Powerful, Amit P. Sheth
Semantics For Scientific Experiments And The Web: The Implicit, The Formal And The Powerful, Amit P. Sheth
Kno.e.sis Publications
No abstract provided.
Modeling Fuzzy Rules With Description Logics, Sudhir Agarwal, Pascal Hitzler
Modeling Fuzzy Rules With Description Logics, Sudhir Agarwal, Pascal Hitzler
Computer Science and Engineering Faculty Publications
In real application scenarios, input data and knowledge is often vague. Likewise, it is often the case that exact reasoning over data is impossible due to complex dependencies between input data and target outputs. For practical applications, however, good approximations often suffice, and efficient calculation of an approximate answer is often preferable over complex processing which may take a long time to come up with an exact answer. Fuzzy logic supports both features by providing fuzzy membership functions and fuzzy IF-THEN rule bases. In this paper, we show how fuzzy membership functions and fuzzy rules can be modeled by means …
Dlp Isn't So Bad After All, Peter Haase, Markus Krotzsch, York Sure, Rudi Studer, Pascal Hitzler
Dlp Isn't So Bad After All, Peter Haase, Markus Krotzsch, York Sure, Rudi Studer, Pascal Hitzler
Computer Science and Engineering Faculty Publications
We discuss some of the recent controversies concerning the DLP fragment of OWL. We argue that it is a meaningful fragment and can serve as a basic interoperability layer between OWL and logic programming-based ontology languages.
Optimal Adaptation In Autonomic Web Processes With Inter-Service Dependencies, Kunal Verma, Prashant Doshi, Karthik Gomadam, John A. Miller, Amit P. Sheth
Optimal Adaptation In Autonomic Web Processes With Inter-Service Dependencies, Kunal Verma, Prashant Doshi, Karthik Gomadam, John A. Miller, Amit P. Sheth
Kno.e.sis Publications
We present methods for optimally adapting Web processes to exogenous events while preserving inter-service dependencies. For example, in a supply chain process, orders placed by the manufacturer may get delayed in arriving. In response to this event, the manufacturer has the choice of either waiting out the delay or changing the supplier.
Computing For Human Experience And Wellness, Amit P. Sheth
Computing For Human Experience And Wellness, Amit P. Sheth
Kno.e.sis Publications
No abstract provided.
Work In Progress: The Wsu Model For Engineering Mathematics Education, Nathan W. Klingbeil, Richard Mercer, Kuldip S. Rattan, Michael L. Raymer, David B. Reynolds
Work In Progress: The Wsu Model For Engineering Mathematics Education, Nathan W. Klingbeil, Richard Mercer, Kuldip S. Rattan, Michael L. Raymer, David B. Reynolds
Kno.e.sis Publications
This paper summarizes progress to date on the WSU model for engineering mathematics education, an NSF funded curriculum reform initiative at Wright State University. The WSU model seeks to increase student retention, motivation and success in engineering through application-driven, just-in-time engineering math instruction. The WSU approach involves the development of a novel freshman-level engineering mathematics course EGR 101, as well as a large-scale restructuring of the engineering curriculum. By removing traditional math prerequisites and moving core engineering courses earlier in the program, the WSU model shifts the traditional emphasis on math prerequisite requirements to an emphasis on engineering motivation for …
The Optimal Discovery Procedure: A New Approach To Simultaneous Significance Testing, John D. Storey
The Optimal Discovery Procedure: A New Approach To Simultaneous Significance Testing, John D. Storey
UW Biostatistics Working Paper Series
Significance testing is one of the main objectives of statistics. The Neyman-Pearson lemma provides a simple rule for optimally testing a single hypothesis when the null and alternative distributions are known. This result has played a major role in the development of significance testing strategies that are used in practice. Most of the work extending single testing strategies to multiple tests has focused on formulating and estimating new types of significance measures, such as the false discovery rate. These methods tend to be based on p-values that are calculated from each test individually, ignoring information from the other tests. As …
The Optimal Discovery Procedure For Large-Scale Significance Testing, With Applications To Comparative Microarray Experiments, John D. Storey, James Y. Dai, Jeffrey T. Leek
The Optimal Discovery Procedure For Large-Scale Significance Testing, With Applications To Comparative Microarray Experiments, John D. Storey, James Y. Dai, Jeffrey T. Leek
UW Biostatistics Working Paper Series
As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of related measurements. The common property among these high-dimensional biological studies is that the measured features have a rich and largely unknown underlying structure. One example of much recent interest is identifying differentially expressed genes in comparative microarray experiments. We propose a new approach aimed at optimally performing many hypothesis tests in a high-dimensional study. This approach estimates the Optimal Discovery Procedure (ODP), which has recently been introduced and theoretically shown …
Ga-Facilitated Knn Classifier Optimization With Varying Similarity Measures, Michael R. Peterson, Travis E. Doom, Michael L. Raymer
Ga-Facilitated Knn Classifier Optimization With Varying Similarity Measures, Michael R. Peterson, Travis E. Doom, Michael L. Raymer
Kno.e.sis Publications
Genetic algorithms are powerful tools for k-nearest neighbors classifier optimization. While traditional knn classification techniques typically employ Euclidian distance to assess pattern similarity, other measures may also be utilized. Previous research demonstrates that GAs can improve predictive accuracy by searching for optimal feature weights and offsets for a cosine similarity-based knn classifier. GA-selected weights determine the classification relevance of each feature, while offsets provide alternative points of reference when assessing angular similarity. Such optimized classifiers perform competitively with other contemporary classification techniques. This paper explores the effectiveness of GA weight and offset optimization for knowledge discovery using knn classifiers with …
Extracting Reduced Logic Programs From Artificial Neural Networks, Jens Lehmann, Sebastian Bader, Pascal Hitzler
Extracting Reduced Logic Programs From Artificial Neural Networks, Jens Lehmann, Sebastian Bader, Pascal Hitzler
Computer Science and Engineering Faculty Publications
Artificial neural networks can be trained to perform excellently in many application areas. While they can learn from raw data to solve sophisticated recognition and analysis problems, the acquired knowledge remains hidden within the network architecture and is not readily accessible for analysis or further use: Trained networks are black boxes. Recent research efforts therefore investigate the possibility to extract symbolic knowledge from trained networks, in order to analyze, validate, and reuse the structural insights gained implicitly during the training process. In this paper, we will study how knowledge in form of propositional logic programs can be obtained in such …
Integrating First-Order Logic Programs And Connectionist Systems - A Constructive Approach, Sebastian Bader, Andreas Witzel, Pascal Hitzler
Integrating First-Order Logic Programs And Connectionist Systems - A Constructive Approach, Sebastian Bader, Andreas Witzel, Pascal Hitzler
Computer Science and Engineering Faculty Publications
Significant advances have recently been made concerning the integration of symbolic knowledge representation with artificial neural networks (also called connectionist systems). However, while the integration with propositional paradigms has resulted in applicable systems, the case of first-order knowledge representation has so far hardly proceeded beyond theoretical studies which prove the existence of connectionist systems for approximating first-order logic programs up to any chosen precision. Advances were hindered severely by the lack of concrete algorithms for obtaining the approximating networks which were known to exist: the corresponding proofs are not constructive in that they do not yield concrete methods for building …
Enterprise Applications Of Semantic Web: The Sweet Spot Of Risk And Compliance, Amit P. Sheth
Enterprise Applications Of Semantic Web: The Sweet Spot Of Risk And Compliance, Amit P. Sheth
Kno.e.sis Publications
Semantic Web is in the transition from vision and research to reality. In this early state, it is important to study the technical capabilities in the context of real-world applications, and how applications built using the Semantic Web technology meet the real market needs. Beyond push from research, it is the market pull and the ability of the technology to meet real business needs that is a key to ultimate success of any technology. In this paper, we discuss the market of Risk and Compliance which presents unique market opportunity combined with challenging technical requirements. We discuss how the Semantic …
Ontology Learning As A Use-Case For Neural-Symbolic Integration, Pascal Hitzler, Sebastian Bader, Artur Garcez
Ontology Learning As A Use-Case For Neural-Symbolic Integration, Pascal Hitzler, Sebastian Bader, Artur Garcez
Computer Science and Engineering Faculty Publications
We argue that the field of neural-symbolic integration is in need of identifying application scenarios for guiding further research. We furthermore argue that ontology learning - as occurring in the context of semantic technologies - provides such an application scenario with potential for success and high impact on neural-symbolic integration.
Peer-To-Peer Discovery Of Semantic Associations, Matthew Perry, Maciej Janik, Cartic Ramakrishnan, Conrad Ibanez, I. Budak Arpinar, Amit P. Sheth
Peer-To-Peer Discovery Of Semantic Associations, Matthew Perry, Maciej Janik, Cartic Ramakrishnan, Conrad Ibanez, I. Budak Arpinar, Amit P. Sheth
Kno.e.sis Publications
The Semantic Web vision promises an extension of the current Web in which all data is annotated with machine understandable metadata. The relationship-centric nature of this data has led to the definition of Semantic Associations, which are complex relationships between resources. Semantic Associations attempt to answer queries of the form “how are resource A and resource B related?” Knowing how two entities are related is a crucial question in knowledge discovery applications. Much the same way humans collaborate and interact to form new knowledge, discovery of Semantic Associations across repositories on a peer-to-peer network can allow peers to share their …
A Semantic Template Based Designer For Semantic Web Processes, Ranjit Mulye, John A. Miller, Kunal Verma, Karthik Gomadam, Amit P. Sheth
A Semantic Template Based Designer For Semantic Web Processes, Ranjit Mulye, John A. Miller, Kunal Verma, Karthik Gomadam, Amit P. Sheth
Kno.e.sis Publications
The growing popularity of service oriented computing based on Web services standards is creating a need for paradigms to represent and design business processes. Significant work has been done in the representation aspects with regards to WSBPEL. However, design and modeling of business processes is still an open issue. In this paper, we present a novel designer for business processes, which allows for intuitive modeling of Web processes, as well as using a template based approach for semi-automatically integrating partners either at design time or at deployment time. This work has been done as part of the METEOR-S project, which …
On Embedding Machine-Processable Semantics Into Documents, Krishnaprasad Thirunarayan
On Embedding Machine-Processable Semantics Into Documents, Krishnaprasad Thirunarayan
Kno.e.sis Publications
Most Web and legacy paper-based documents are available in human comprehensible text form, not readily accessible to or understood by computer programs. Here, we investigate an approach to amalgamate XML technology with programming languages for representational purposes that can enhance traceability, thereby facilitating semiautomatic extraction and update. Specifically, we propose a modular technique to embed machine-processable semantics into a text document with tabular data via annotations, resulting sometimes in ill-formed XML fragments, and evaluate this technique vis a vis document querying, manipulation, and integration. The ultimate aim is to be able to author and extract human-readable and machine-comprehensible parts of …
Faster Owl Using Split Programs, Denny Vrandecic, Pascal Hitzler
Faster Owl Using Split Programs, Denny Vrandecic, Pascal Hitzler
Computer Science and Engineering Faculty Publications
Knowledge representation and reasoning on the Semantic Web is done by means of ontologies. While the quest for suitable ontology languages is still ongoing, OWL [5] has been established as a core standard. It comes in three flavours, as OWL Full, OWL DL and OWL Lite, where OWL Full contains OWL DL, which in turn contains OWL Lite. The latter two coincide semantically with certain description logics and can thus be considered fragments of first-order predicate logic.
Morphisms In Context, Markus Krotzsch, Guo-Qiang Zhang, Pascal Hitzler
Morphisms In Context, Markus Krotzsch, Guo-Qiang Zhang, Pascal Hitzler
Computer Science and Engineering Faculty Publications
Morphisms constitute a general tool for modelling complex relationships between mathematical objects in a disciplined fashion. In Formal Concept Analysis (FCA), morphisms can be used for the study of structural properties of knowledge represented in formal contexts, with applications to data transformation and merging. In this paper we present a comprehensive treatment of some of the most important morphisms in FCA and their relationships, including dual bonds, scale measures, infomorphisms, and their respective relations to Galois connections. We summarize our results in a concept lattice that cumulates the relationships among the considered morphisms. The purpose of this work is to …
A Modular Approach To Document Indexing And Semantic Search, Dhanya Ravishankar, Krishnaprasad Thirunarayan, Trivikram Immaneni
A Modular Approach To Document Indexing And Semantic Search, Dhanya Ravishankar, Krishnaprasad Thirunarayan, Trivikram Immaneni
Kno.e.sis Publications
This paper develops a modular approach to improving effectiveness of searching documents for information by reusing and integrating mature software components such as Lucene APIs, WORDNET, LSA techniques, and domain-specific controlled vocabulary. To evaluate the practical benefits, the prototype was used to query MEDLINE database, and to locate domain-specific controlled vocabulary terms in Materials and Process Specifications. Its extensibility has been demonstrated by incorporating a spell-checker for the input query, and by structuring the retrieved output into hierarchical collections for quicker assimilation. It is also being used to experimentally explore the relationship between LSA and document clustering using 20-mini-newsgroups and …
Lifecycle Of Semantic Web Processes, Jorge Cardoso, Chistoph Bussler, Amit P. Sheth
Lifecycle Of Semantic Web Processes, Jorge Cardoso, Chistoph Bussler, Amit P. Sheth
Kno.e.sis Publications
This tutorial presents what can be achieved by symbiotic synthesis of two of the most important research and technology application areas: Web Services and the Semantic Web. It presents the more recent evolution of the Web Service platform towards rich Web Service and process model annotation, and explores some of the promises and challenges in applying semantics to each of the steps in the Semantic Web Process lifecycle.
Web Service Semantics - Wsdl-S, Rama Akkiraju, Joel Farrell, John A. Miller, Meenakshi Nagarajan, Amit P. Sheth, Kunal Verma
Web Service Semantics - Wsdl-S, Rama Akkiraju, Joel Farrell, John A. Miller, Meenakshi Nagarajan, Amit P. Sheth, Kunal Verma
Kno.e.sis Publications
Web services have primarily been designed for providing inter-operability between business applications. Current technologies assume a large amount of human interaction, for integrating two applications. This is primarily due to the fact that business process integration requires understanding of data and functions of the involved entities. Semantic Web technologies, powered by description logic based languages like OWL[1], aim to add greater meaning to Web content, by annotating the data with ontologies. Ontologies provide a mechanism of providing shared conceptualizations of domains. This allows agents to get an understanding of users’ Web content and greatly reduces human interaction for meaningful Web …
Ga-Facilitated Classifier Optimization With Varying Similarity Measures, Michael R. Peterson, Travis E. Doom, Michael L. Raymer
Ga-Facilitated Classifier Optimization With Varying Similarity Measures, Michael R. Peterson, Travis E. Doom, Michael L. Raymer
Kno.e.sis Publications
Genetic algorithms are powerful tools for k-nearest neighbors classification. Traditional knn classifiers employ Euclidian distance to assess neighbor similarity, though other measures may also be used. GAs can search for optimal linear weights of features to improve knn performance using both Euclidian distance and cosine similarity. GAs also optimize additive feature offsets in search of an optimal point of reference for assessing angular similarity using the cosine measure. This poster explores weight and offset optimization for knn with varying similarity measures, including Euclidian distance (weights only), cosine similarity, and Pearson correlation. The use of offset optimization …
Description Logic Programs: A Practical Choice For The Modelling Of Ontologies, Rudi Studer, York Sure, Pascal Hitzler
Description Logic Programs: A Practical Choice For The Modelling Of Ontologies, Rudi Studer, York Sure, Pascal Hitzler
Computer Science and Engineering Faculty Publications
Knowledge representation using ontologies constitutes the heart of semantic technologies. Despite successful standardization efforts by the W3C, however, there are still numerous different ontology representation languages being used, and interoperability between them is in general not given. The problem is aggrevated by the fact that current standards lay foundations only and are well-known to be insufficient for the modelling of finer details. Thus, a plethora of extensions of the basic languages is being proposed, rendering the picture of ontology representation languages to be chaotic, to say the least. While semantic technologies start to become applicable and are being applied in …