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Power Of Clouds In Your Pocket: An Efficient Approach For Cloud Mobile Hybrid Application Development, Ashwin Manjunatha, Ajith Harshana Ranabahu, Amit P. Sheth, Krishnaprasad Thirunarayan 2010 Wright State University - Main Campus

Power Of Clouds In Your Pocket: An Efficient Approach For Cloud Mobile Hybrid Application Development, Ashwin Manjunatha, Ajith Harshana Ranabahu, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The advancements in computing have resulted in a boom of cheap, ubiquitous, connected mobile devices as well as seemingly unlimited, utility style, pay as you go computing resources, commonly referred to as Cloud computing. However, taking full advantage of this mobile and cloud computing landscape, especially for the data intensive domains has been hampered by the many heterogeneities that exist in the mobile space as well as the Cloud space. Our research focuses on exploiting the capabilities of the mobile and cloud landscape by defining a new class of applications called cloud mobile hybrid (CMH) applications and a Domain Specific ...


A Reasonable Semantic Web, Pascal Hitzler, Frank van Harmelen 2010 Wright State University - Main Campus

A Reasonable Semantic Web, Pascal Hitzler, Frank Van Harmelen

Computer Science and Engineering Faculty Publications

The realization of Semantic Web reasoning is central to substantiating the Semantic Web vision. However, current mainstream research on this topic faces serious challenges, which forces us to question established lines of research and to rethink the underlying approaches. We argue that reasoning for the Semantic Web should be understood as "shared inference," which is not necessarily based on deductive methods. Model-theoretic semantics (and sound and complete reasoning based on it) functions as a gold standard, but applications dealing with large-scale and noisy data usually cannot afford the required runtimes. Approximate methods, including deductive ones, but also approaches based on ...


Semantic Web – Interoperability, Usability, Applicability, Pascal Hitzler, Krzysztof Janowicz 2010 Wright State University - Main Campus

Semantic Web – Interoperability, Usability, Applicability, Pascal Hitzler, Krzysztof Janowicz

Computer Science and Engineering Faculty Publications

No abstract provided.


From Questions To Effective Answers: On The Utility Of Knowledge-Driven Querying Systems For Life Sciences Data, Amir H. Asiaee, Prashant Doshi, Todd Minning, Satya S. Sahoo, Priti Parikh, Amit P. Sheth, Rick L. Tarleton 2010 Wright State University - Main Campus

From Questions To Effective Answers: On The Utility Of Knowledge-Driven Querying Systems For Life Sciences Data, Amir H. Asiaee, Prashant Doshi, Todd Minning, Satya S. Sahoo, Priti Parikh, Amit P. Sheth, Rick L. Tarleton

Kno.e.sis Publications

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data. These interfaces could be seen as implementing a set of 'pre-canned' queries commonly used by the life science researchers that we study. The second approach is based on semantic Web technologies and is knowledge (model) driven. It utilizes a large OWL ontology and same datasets as before but associated as RDF instances of the ontology concepts. An intuitive interface is provided that allows the ...


A Study In Hadoop Streaming With Matlab For Nmr Data Processing, Kalpa Gunaratna, Paul E. Anderson, Ajith Harshana Ranabahu, Amit P. Sheth 2010 Wright State University - Main Campus

A Study In Hadoop Streaming With Matlab For Nmr Data Processing, Kalpa Gunaratna, Paul E. Anderson, Ajith Harshana Ranabahu, Amit P. Sheth

Kno.e.sis Publications

Applying Cloud computing techniques for analyzing large data sets has shown promise in many data-driven scientific applications. Our approach presented here is to use Cloud computing for Nuclear Magnetic Resonance (NMR)data analysis which normally consists of large amounts of data. Biologists often use third party or commercial software for ease of use. Enabling the capability to use this kind of software in a Cloud will be highly advantageous in many ways. Scripting languages especially designed for clouds may not have the flexibility biologists need for their purposes. Although this is true, they are familiar with special software packages that ...


Sensor Data And Perception: Can Sensors Play 20 Questions, Cory Andrew Henson 2010 Wright State University - Main Campus

Sensor Data And Perception: Can Sensors Play 20 Questions, Cory Andrew Henson

Kno.e.sis Publications

Currently, there are many sensors collecting information about our environment, leading to an overwhelming number of observations that must be analyzed and explained in order to achieve situation awareness. As perceptual beings, we are also constantly inundated with sensory data, yet we are able to make sense of our environment with relative ease. Why is the task of perception so easy for us, and so hard for machines; and could this have anything to do with how we play the game 20 Questions?


Getting Code Near The Data: A Study Of Generating Customized Data Intensive Scientific Workflows With Domain Specific Language, Ashwin Manjunatha, Ajith Harshana Ranabahu, Paul E. Anderson, Amit P. Sheth 2010 Wright State University - Main Campus

Getting Code Near The Data: A Study Of Generating Customized Data Intensive Scientific Workflows With Domain Specific Language, Ashwin Manjunatha, Ajith Harshana Ranabahu, Paul E. Anderson, Amit P. Sheth

Kno.e.sis Publications

The amount of data produced in modern biological experiments such as Nuclear Magnetic Resonance (NMR) analysis far exceeds the processing capability of a single machine. The present state-of-the-art is taking the ”data to code”, the philosophy followed by many of the current service oriented workflow systems. However this is not feasible in some cases such as NMR data analysis, primarily due to the large scale of data.

The objective of this research is to bring ”code to data”, preferred in the cases when the data is extremely large. We present a DSL based approach to develop customized data intensive scientific ...


Provenance Context Entity (Pace): Scalable Provenance Tracking For Scientific Rdf Data, Satya S. Sahoo, Olivier Bodenreider, Pascal Hitzler, Amit P. Sheth, Krishnaprasad Thirunarayan 2010 Wright State University - Main Campus

Provenance Context Entity (Pace): Scalable Provenance Tracking For Scientific Rdf Data, Satya S. Sahoo, Olivier Bodenreider, Pascal Hitzler, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The Resource Description Framework (RDF) format is being used by a large number of scientific applications to store and disseminate their datasets. The provenance information, describing the source or lineage of the datasets, is playing an increasingly significant role in ensuring data quality, computing trust value of the datasets, and ranking query results. Current provenance tracking approaches using the RDF reification vocabulary suffer from a number of known issues, including lack of formal semantics, use of blank nodes, and application-dependent interpretation of reified RDF triples. In this paper, we introduce a new approach called Provenance Context Entity (PaCE) that uses ...


Sensor Discovery On Linked Data, Josh Pschorr, Cory Andrew Henson, Harshal Kamlesh Patni, Amit P. Sheth 2010 Wright State University - Main Campus

Sensor Discovery On Linked Data, Josh Pschorr, Cory Andrew Henson, Harshal Kamlesh Patni, Amit P. Sheth

Kno.e.sis Publications

There has been a drive recently to make sensor data accessible on the Web. However, because of the vast number of sensors collecting data about our environment, finding relevant sensors on the Web is a non-trivial challenge. In this paper, we present an approach to discovering sensors through a standard service interface over Linked Data. This is accomplished with a semantic sensor network middleware that includes a sensor registry on Linked Data and a sensor discovery service that extends the OGC Sensor Web Enablement. With this approach, we are able to access and discover sensors that are positioned near named-locations ...


Twitris 2.0 : Semantically Empowered System For Understanding Perceptions From Social Data, Ashutosh Sopan Jadhav, Hemant Purohit, Pavan Kapanipathi, Pramod Anantharam, Ajith H. Ranabahu, Vinh Nguyen, Pablo N. Mendes, Alan Gary Smith, Michael Cooney, Amit P. Sheth 2010 Wright State University - Main Campus

Twitris 2.0 : Semantically Empowered System For Understanding Perceptions From Social Data, Ashutosh Sopan Jadhav, Hemant Purohit, Pavan Kapanipathi, Pramod Anantharam, Ajith H. Ranabahu, Vinh Nguyen, Pablo N. Mendes, Alan Gary Smith, Michael Cooney, Amit P. Sheth

Kno.e.sis Publications

We present Twitris 2.0, a Semantic Web application that facilitates understanding of social perceptions by Semantics-based processing of massive amounts of event-centric data. Twitris 2.0 addresses challenges in large scale processing of social data, preserving spatio-temporal-thematic properties. Twitris 2.0 also covers context based semantic integration of multiple Web resources and expose semantically enriched social data to the public domain. Semantic Web technologies enable the systematic integration and analysis abilities.


Graph Connectivity: Approximation Algorithms And Applications To Protein-Protein Interaction Networks, Suzanne Renick Gallagher 2010 University of Colorado at Boulder

Graph Connectivity: Approximation Algorithms And Applications To Protein-Protein Interaction Networks, Suzanne Renick Gallagher

Computer Science Graduate Theses & Dissertations

A graph is connected if there is a path between any two of its vertices and k-connected if there are at least k disjoint paths between any two vertices. A graph is k-edge-connected if none of the k paths share any edges and k-vertex-connected (or k-connected) if they do not share any intermediate vertices. We examine some problems related to k-connectivity and an application.

We have looked at the k-edge-connected spanning subgraph problem: given a k-edge-connected graph, find the smallest subgraph that includes all vertices and is still k-edge-connected. We improved two algorithms for approximating solutions to this problem. The ...


Bayesmotif: De Novo Protein Sorting Motif Discovery From Impure Datasets, Jianjun Hu, F. Zhang 2010 University of South Carolina - Columbia

Bayesmotif: De Novo Protein Sorting Motif Discovery From Impure Datasets, Jianjun Hu, F. Zhang

Faculty Publications

Background

Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms.

Methods

We formulated the protein sorting motif discovery problem as a classification problem ...


An Intelligent Data-Centric Approach Toward Identification Of Conserved Motifs In Protein Sequences, Kathryn Dempsey Cooper, Benjamin Currall, Richard Hallworth, Hesham Ali 2010 University of Nebraska at Omaha

An Intelligent Data-Centric Approach Toward Identification Of Conserved Motifs In Protein Sequences, Kathryn Dempsey Cooper, Benjamin Currall, Richard Hallworth, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

The continued integration of the computational and biological sciences has revolutionized genomic and proteomic studies. However, efficient collaboration between these fields requires the creation of shared standards. A common problem arises when biological input does not properly fit the expectations of the algorithm, which can result in misinterpretation of the output. This potential confounding of input/output is a drawback especially when regarding motif finding software. Here we propose a method for improving output by selecting input based upon evolutionary distance, domain architecture, and known function. This method improved detection of both known and unknown motifs in two separate case ...


Biochemical Profiling Of Histone Binding Selectivity Of The Yeast Bromodomain Family, Qiang Zhang, Suvobrata Chakravarty, Dario Ghersi, Lei Zeng, Alexander N. Plotnikov, Roberto Sanchez, Ming-Ming Zhou 2010 University of Nebraska at Omaha

Biochemical Profiling Of Histone Binding Selectivity Of The Yeast Bromodomain Family, Qiang Zhang, Suvobrata Chakravarty, Dario Ghersi, Lei Zeng, Alexander N. Plotnikov, Roberto Sanchez, Ming-Ming Zhou

Interdisciplinary Informatics Faculty Publications

Background: It has been shown that molecular interactions between site-specific chemical modifications such as acetylation and methylation on DNA-packing histones and conserved structural modules present in transcriptional proteins are closely associated with chromatin structural changes and gene activation. Unlike methyl-lysine that can interact with different protein modules including chromodomains, Tudor and MBT domains, as well as PHD fingers, acetyl-lysine (Kac) is known thus far to be recognized only by bromodomains. While histone lysine acetylation plays a crucial role in regulation of chromatin-mediated gene transcription, a high degree of sequence variation of the acetyl-lysine binding site in the bromodomains has limited ...


Computing For The Human Experience: Semantics-Empowered Sensors, Services, And Social Computing On The Ubiquitous Web, Amit P. Sheth 2010 Wright State University - Main Campus

Computing For The Human Experience: Semantics-Empowered Sensors, Services, And Social Computing On The Ubiquitous Web, Amit P. Sheth

Kno.e.sis Publications

People are on the verge of an era in which the human experience can be enriched in ways they couldn't have imagined two decades ago. Rather than depending on a single technology, people progressed with several whose semantics-empowered convergence and integration will enable us to capture, understand, and reapply human knowledge and intellect. Such capabilities will consequently elevate our technological ability to deal with the abstractions, concepts, and actions that characterize human experiences. This will herald computing for human experience (CHE). The CHE vision is built on a suite of technologies that serves, assists, and cooperates with humans to ...


A Qualitative Examination Of Topical Tweet And Retweet Practices, Meenakshi Nagarajan, Hemant Purohit, Amit P. Sheth 2010 Wright State University - Main Campus

A Qualitative Examination Of Topical Tweet And Retweet Practices, Meenakshi Nagarajan, Hemant Purohit, Amit P. Sheth

Kno.e.sis Publications

This work contributes to the study of retweet behavior on Twitter surrounding real-world events. We analyze over a million tweets pertaining to three events, present general tweet properties in such topical datasets and qualitatively analyze the properties of the retweet behavior surrounding the most tweeted/viral content pieces. Findings include a clear relationship between sparse/dense retweet patterns and the content and type of a tweet itself; suggesting the need to study content properties in link-based diffusion models.


Provenance Aware Linked Sensor Data, Harshal Kamlesh Patni, Satya S. Sahoo, Cory Andrew Henson, Amit P. Sheth 2010 Wright State University - Main Campus

Provenance Aware Linked Sensor Data, Harshal Kamlesh Patni, Satya S. Sahoo, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

Provenance, from the French word “provenir”, describes the lineage or history of a data entity. Provenance is critical information in the sensors domain to identify a sensor and analyze the observation data over time and geographical space. In this paper, we present a framework to model and query the provenance information associated with the sensor data exposed as part of the Web of Data using the Linked Open Data conventions. This is accomplished by developing an ontology-driven provenance management infrastructure that includes a representation model and query infrastructure. This provenance infrastructure, called Sensor Provenance Management System (PMS), is underpinned by ...


Loqus: Linked Open Data Sparql Querying System, Prateek Jain, Kunal Verma, Peter Z. Yeh, Pascal Hitzler, Amit P. Sheth 2010 Wright State University - Main Campus

Loqus: Linked Open Data Sparql Querying System, Prateek Jain, Kunal Verma, Peter Z. Yeh, Pascal Hitzler, Amit P. Sheth

Kno.e.sis Publications

The LOD cloud is gathering a lot of momentum, with the number of contributors growing manifold. Many prominent data providers have submitted and linked their data to other dataset with the help of manual mappings. The potential of the LOD cloud is enormous ranging from challenging AI issues such as open domain question answering to automated knowledge discovery. We believe that there is not enough technology support available to effectively query the LOD cloud. To this effect, we present a system called Linked Open Data SPARQL Querying System (LOQUS), which automatically maps users queries written in terms of a conceptual ...


Understanding Events Through Analysis Of Social Media, Amit P. Sheth, Hemant Purohit, Ashutosh Sopan Jadhav, Pavan Kapanipathi, Lu Chen 2010 Wright State University - Main Campus

Understanding Events Through Analysis Of Social Media, Amit P. Sheth, Hemant Purohit, Ashutosh Sopan Jadhav, Pavan Kapanipathi, Lu Chen

Kno.e.sis Publications

Users are sharing vast amounts of social data through social networking platforms accessible by Web and increasingly via mobile devices. This opens an exciting opportunity to extract social perceptions as well as obtain insights relevant to events around us. We discuss the significant need and opportunity for analyzing event-centric user generated content on social networks, present some of the technical challenges and our approach to address them. This includes aggregating social data related to events of interest, along with Web resources (news, Wikipedia pages, multimedia) related to an event of interest, and supporting analysis along spatial, temporal, thematic, and sentiment ...


Automated Isolation Of Translational Efficiency Bias That Resists The Confounding Effect Of Gc(At)-Content, Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer 2010 Wright State University - Main Campus

Automated Isolation Of Translational Efficiency Bias That Resists The Confounding Effect Of Gc(At)-Content, Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

Genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale; however, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons is preferred. Detection of this bias is an important ...


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