Computer Sciences Commons^™

Trust Networks: Interpersonal, Social, And Sensor, Krishnaprasad Thirunarayan, Pramod Anantharam

Kno.e.sis Publications

Trust relationships occur naturally in many diverse contexts such as ecommerce, interpersonal interactions, social networks, sensor web, etc. As agents providing content and services become increasingly removed from the agents that consume them, the issue of robust trust inference and update become critical. Unfortunately, there is neither a universal notion of trust that is applicable to all domains nor a clear explication of its semantics or computation in many situations. In this beginner's level tutorial, we motivate the trust problem, explain the relevant concepts, summarize research in modeling trust and gleaning trustworthiness, and discuss challenges confronting us in this process.

Beespace Navigator: Exploratory Analysis Of Gene Function Using Semantic Indexing Of Biological Literature, Moushumi Sen Sarma, David Arcoleo, Radhika S. Khetani, Brant Chee, Xu Ling, Xin He, Jing Jiang, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz

Research Collection School Of Computing and Information Systems

With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software supports an automatic analogue of the curator process to extract functions, with a simple interface intended for all biologists. Since extraction is done on selected collections that are semantically indexed into conceptual spaces, the curation can be task specific. Biological literature containing references to gene lists from expression experiments …

Rna Secondary Structure Prediction Tool, Meenakshee Mali

Master's Projects

Ribonucleic Acid (RNA) is one of the major macromolecules essential to all forms of life. Apart from the important role played in protein synthesis, it performs several important functions such as gene regulation, catalyst of biochemical reactions and modification of other RNAs. In some viruses, instead of DNA, RNA serves as the carrier of genetic information. RNA is an interesting subject of research in the scientific community. It has lead to important biological discoveries. One of the major problems researchers are trying to solve is the RNA structure prediction problem. It has been found that the structure of RNA is …

Ab Initio Protein Structure Prediction Algorithms, Maciej Kicinski

Master's Projects

Genes that encode novel proteins are constantly being discovered and added to databases, but the speed with which their structures are being determined is not keeping up with this rate of discovery. Currently, homology and threading methods perform the best for protein structure prediction, but they are not appropriate to use for all proteins. Still, the best way to determine a protein's structure is through biological experimentation. This research looks into possible methods and relations that pertain to ab initio protein structure prediction. The study includes the use of positional and transitional probabilities of amino acids obtained from a non-redundant …

Computational Complexity Of Approximate And Precise Data With Constraint Automaton, Dipty Singh

School of Computing: Dissertations, Theses, and Student Research

The DNA molecules packaged in structures called chromosomes within the cells of living organisms encode hereditary information that is passed on to their offspring. Using transcription and translation, the genes within these DNA molecules help in protein synthesis. Thus chromosomal DNA serves as a blueprint for the chemical processes of life.

In order to analyze a DNA sequence by currently available technology, we have to cut it into small fragments, e.g. by using restriction enzymes. The application of different restriction enzymes to the multiple copies of the same DNA sequence generates many overlapping fragments. In order to construct the original …

Identifying And Implementing The Underlying Operators For Nuclear Magnetic Resonance Based Metabolomics Data Analysis, Ashwin Manjunatha, Ajith H. Ranabahu, Paul E. Anderson, Amit P. Sheth

Kno.e.sis Publications

The science of metabolomics is a relatively young field that requires intensive signal processing and multivariate data analysis for interpretation of experimental results. The lack of integration and standardization for metabolomics compounded by the complexity of the experimental data has lead to a fragmented research community. While efforts have been undertaken to approach these problems, the efforts to develop a set of standards for reporting processing and analysis procedures has stalled.

In this paper, we propose a set of fundamental operators for nuclear magnetic resonance(NMR) based metabolomics. These operators are implementation independent, and can be used to easily and precisely …

Aminormotiffinder - A Graph Grammar Based Tool To Effectively Search A Minor Motifs In 3d Rna Molecules, Ankur Malhotra

Theses

RNA Motifs are three dimensional folds that play important role in RNA folding and its interaction with other molecules. They basically have modular structure and are composed of conserved building blocks dependent upon the sequence. Their automated in silico identification remains a challenging task. Existing motif identification tools does not correctly identify motifs with large structure variations. Here a “graph rewriting” based method is proposed to identify motifs in real three dimensional structures. The unique encoding of A Minor Searcher takes into consideration the non canonical base pairs and also multipairing of RNA structural motifs. The accuracy is demonstrated by …

A Genetic Optimization Approach For Isolating Translational Efficiency Bias, Douglas W. Raiford, Dan E. Krane, Travis E. Doom, Michael L. Raymer

Kno.e.sis Publications

The study of codon usage bias is an important research area that contributes to our understanding of molecular evolution, phylogenetic relationships, respiratory lifestyle, and other characteristics. Translational efficiency bias is perhaps the most well studied codon usage bias, as it is frequently utilized to predict relative protein expression levels. We present a novel approach to isolating translational efficiency bias in microbial genomes. There are several existent methods for isolating translational efficiency bias. Previous approaches are susceptible to the confounding influences of other potentially dominant biases. Additionally, existing approaches to identifying translational efficiency bias generally require both genomic sequence information and …

A Systematic Property Mapping Using Category Hierarchy And Data, Kalpa Gunaratna, Sarasi Lalithsena, Prateek Jain, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

Relationships play a key role in Semantic Web to connect the dots between entities (concepts or instances in a way that enables to absorb the real sense of the entities. Even though relationships are important, it is difficult to categorize or identify them because they consist of complex knowledge in the schema. Therefore systematically identifying relationships yield many advantages and open doors for new research avenues. In this work, we try to identify a specific type of relationship (part of) in a multi-domain dataset and devised an algorithm using Wikipedia to identify patterns of part of relationships in the dataset. …

Cloudvista: Visual Cluster Exploration For Extreme Scale Data In The Could, Keke Chen, Huiqi Xi, Fengguang Tian, Shumin Guo

Kno.e.sis Publications

The problem of efficient and high-quality clustering of extreme scale datasets with complex clustering structures continues to be one of the most challenging data analysis problems. An innovate use of data cloud would provide unique opportunity to address this challenge. In this paper, we propose the CloudVista framework to address (1) the problems caused by using sampling in the existing approaches and (2) the problems with the latency caused by cloud-side processing on interactive cluster visualization. The CloudVista framework aims to explore the entire large data stored in the cloud with the help of the data structure visual frame and …

Analysis On Partial Relationship In Lod, Kalpa Gunaratna, Sarasi Lalithsena, Cory Andrew Henson, Prateek Jain

Kno.e.sis Publications

Relationships play a key role in Semantic Web to connect the dots between entities (concepts or instances) in a way that enables to absorb the real sense of the entities. Some interesting relationships would give proof for the existence of subject and object in triples which in tern can be defined as evidential relationships. Identifying evidential relationships will yield solutions to some existing inference problems and open doors for new applications and research. Part_of relationships are identified as a special kind of an evidential relationship out of membership, causality and etc. Linked Open data as a global data space would …

Contextual Ontology Alignment Of Lod With An Upper Ontology: A Case Study With Proton, Prateek Jain, Peter Z. Yeh, Kunal Verma, Reymonrod G. Vasquez, Mariana Darnorva, Pascal Hitzler, Amit P. Sheth

Kno.e.sis Publications

The Linked Open Data (LOD) is a major milestone towards realizing the Semantic Web vision, and can enable applications such as robust Question Answering (QA) systems that can answer queries requiring multiple, disparate information sources. However, realizing these applications requires relationships at both the schema and instance level, but currently the LOD only provides relationships for the latter. To address this limitation, we present a solution for automatically finding schema-level links between two LOD ontologies – in the sense of ontology alignment. Our solution, called BLOOMS+, extends our previous solution (i.e. BLOOMS) in two significant ways. BLOOMS+ 1) uses a …

Reconciling Owl And Rules, David Carral Martinez, Adila A. Krisnadhi, Frederick Maier, Kunal Sengupta, Pascal Hitzler

Computer Science and Engineering Faculty Publications

We report on a recent advance in integrating Rules and OWL. We discuss a recent proposal, known as nominal schemas, which realizes a seamless integration of Datalog rules into the description logic SROIQ which underlies OWL 2 DL. We present extensions of the standardized OWL syntaxes to incorporate nominal schemas, reasoning algorithms, and a first naive implementation. And we argue why this approach goes a long way towards overcoming the present paradigm split.

Privacy-Aware An Scalable Content Dissemination In Distributed Social Networks, Pavan Kapanipathi, Julia Anaya, Amit P. Sheth, Brett Slatkin, Alexandre Passant

Kno.e.sis Publications

Centralized social networking websites raise scalability issues - due to the growing number of participants - and, as well as, policy concerns - such as control, privacy and ownership over the user's published data. Distributed Social Networks aim to solve this issue by enabling architecture where people own their data and share it their own way. However, the privacy and scalability challenge is still to be tackled. This paper presents a privacy-aware extension to Google's PubSubHubbub protocol, using Semantic Web technologies, solving both the scalability and the privacy issues in Distributed Social Networks. We enhanced the traditional feature of PubSubHubbub …

Semantic Social Mashup Approach For Designing Citizen Diplomacy, Amit P. Sheth

Kno.e.sis Publications

Advancement in technology has brought exceptional connectivity, easy and open access to communication mediums via Internet. Everyday millions of people are interactively communicating to each other and sharing multimedia content through Social Media/Networks, Web-based and mobile-based technologies. Social media provides variety of interesting, engaging applications such as Twitter, Facebook, YouTube, Flicker, Blogs. People interested in contributing to global welfare and improving humanity are connected to various NGO's like Red Cross, Ushahidi (www.ushahidi.com), eMoksha (emoksha.org), etc. Social media and NGOs are acting as an excellent medium of communication and sharing, connected diverse people irrespective of their nationality, religion, culture, etc. Social …

Citizen Sensor Data Mining, Social Media Analytics And Development Centric Web Applications, Meenakshi Nagarajan, Amit P. Sheth, Selvam Velmuru

Kno.e.sis Publications

With the rapid rise in the popularity of social media (500M+ Facebook users, 100M+ twitter users), and near ubiquitous mobile access (4.1 billion actively-used mobile phones), the sharing of observations and opinions has become common-place (nearly 100M tweets a day, 1.8 trillion SMSs in US last year). This has given us an unprecedented access to the pulse of a populace and the ability to perform analytics on social data to support a variety of socially intelligent applications -- be it towards targeted online content delivery, crisis management, organizing revolutions or promoting social development in underdeveloped and developing countries. This tutorial …

A Unified Framework Fro Managing Provenance Information In Translational Research, Satya S. Sahoo, Vinh Nguyen, Olivier Bodenreider, Priti Parikh, Todd Minning, Amit P. Sheth

Kno.e.sis Publications

Background

A critical aspect of the NIH Translational Research roadmap, which seeks to accelerate the delivery of "bench-side" discoveries to patient's "bedside," is the management of the provenance metadata that keeps track of the origin and history of data resources as they traverse the path from the bench to the bedside and back. A comprehensive provenance framework is essential for researchers to verify the quality of data, reproduce scientific results published in peer-reviewed literature, validate scientific process, and associate trust value with data and results. Traditional approaches to provenance management have focused on only partial sections of the translational research …

The Cloud Agnostic E-Science Analysis Platform, Ajith Harshana Ranabahu, Paul E. Anderson, Amit P. Sheth

Kno.e.sis Publications

The amount of data being generated for e-Science domains has grown exponentially in the past decade, yet the adoption of new computational techniques in these fields hasn't seen similar improvements. The presented platform can exploit the power of cloud computing while providing abstractions for scientists to create highly scalable data processing workflows.

A Parallel Graph Sampling Algorithm For Analyzing Gene Correlation Networks, Kathryn Dempsey Cooper, Kanimathi Duraisamy, Hesham Ali, Sanjukta Bhowmick

Interdisciplinary Informatics Faculty Publications

Effcient analysis of complex networks is often a challenging task due to its large size and the noise inherent in the system. One popular method of overcoming this problem is through graph sampling, that is extracting a representative subgraph from the larger network. The accuracy of the sample is validated by comparing the combinatorial properties of the subgraph and the original network. However, there has been little study in comparing networks based on the applications that they represent. Furthermore, sampling methods are generally applied agnostically, without mapping to the requirements of the underlying analysis. In this paper,we introduce a parallel …

Prediction Of Ribonucleic Acid Secondary Structures Using A Heuristic Backtracking Search, Christopher Roman Cuellar

Open Access Theses & Dissertations

Ribonucleic acid (RNA) is essential for all forms of life. RNA is made up of a large chain of nucleotide bases: Guanine (G), Uracil (U), Cytosine (C), and Adenine (A). An RNA strand can fold on itself to allow G-C, A-U, and G-U bases to form hydrogen bonds, this is known as a secondary structure. Knowing the secondary structure of an RNA chain is very important because it will allow researchers to better understand its specific functions. RNA will create secondary structures that tend to minimize their free energy. RNA secondary structure prediction is the attempt to predict physical folding …

Demonstration: Real-Time Semantic Analysis Of Sensor Streams, Harshal Kamlesh Patni, Cory Andrew Henson, Michael Cooney, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The emergence of dynamic information sources - including sensor networks - has led to large streams of real-time data on the Web. Research studies suggest, these dynamic networks have created more data in the last three years than in the entire history of civilization, and this trend will only increase in the coming years. With this coming data explosion, real-time analytics software must either adapt or die. This paper focuses on the task of integrating and analyzing multiple heterogeneous streams of sensor data with the goal of creating meaningful abstractions, or features. These features are then temporally aggregated into feature …

A Novel Correlation Networks Approach For The Identification Of Gene Targets, Kathryn Dempsey Cooper, Stephen Bonasera, Dhundy Raj Bastola, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks are emerging as a powerful tool for modeling temporal mechanisms within the cell. Particularly useful in examining coexpression within microarray data, studies have determined that correlation networks follow a power law degree distribution and thus manifest properties such as the existence of “hub” nodes and semicliques that potentially correspond to critical cellular structures. Difficulty lies in filtering coincidental relationships from causative structures in these large, noise-heavy networks. As such, computational expenses and algorithm availability limit accurate comparison, making it difficult to identify changes between networks. In this vein, we present our work identifying temporal relationships from microarray data …

A Noise Reducing Sampling Approach For Uncovering Critical Properties In Large Scale Biological Networks, Karthik Duraisamy, Kathryn Dempsey Cooper, Hesham Ali, Sanjukta Bhowmick

Interdisciplinary Informatics Faculty Proceedings & Presentations

A correlation network is a graph-based representation of relationships among genes or gene products, such as proteins. The advent of high-throughput bioinformatics has resulted in the generation of volumes of data that require sophisticated in silico models, such as the correlation network, for in-depth analysis. Each element in our network represents expression levels of multiple samples of one gene and an edge connecting two nodes reflects the correlation level between the two corresponding genes in the network according to the Pearson correlation coefficient. Biological networks made in this manner are generally found to adhere to a scale-free structural nature, that …

Modeling And Quantitative Analysis Of White Matter Fiber Tracts In Diffusion Tensor Imaging, Xuwei Liang

University of Kentucky Doctoral Dissertations

Diffusion tensor imaging (DTI) is a structural magnetic resonance imaging (MRI) technique to record incoherent motion of water molecules and has been used to detect micro structural white matter alterations in clinical studies to explore certain brain disorders. A variety of DTI based techniques for detecting brain disorders and facilitating clinical group analysis have been developed in the past few years. However, there are two crucial issues that have great impacts on the performance of those algorithms. One is that brain neural pathways appear in complicated 3D structures which are inappropriate and inaccurate to be approximated by simple 2D structures, …

Spatial Semantics For Better Interoperability And Analysis: Challenges And Experiences In Building Semantically Rich Applications In Web 3.0, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

A Microrna Target Prediction Algorithm, Rupinder Singh

Master's Projects

MicroRNA target prediction using the experimental methods is a challenging task. To accelerate the process of miRNA target validation, many computational methods are used. Computational methods yield many potential candidates for experimental validation. This project is about developing a new computational method using dynamic programming to predict miRNA targets with more accuracy. The project discusses the currently available computational methods and develops a new algorithm using the currently available knowledge about miRNA interactions.

Flexible Bootstrapping-Based Ontology Alignment, Prateek Jain, Pascal Hitzler, Amit P. Sheth

Kno.e.sis Publications

BLOOMS (Jain et al, ISWC2010) is an ontology alignment system which, in its core, utilizes the Wikipedia category hierarchy for establishing alignments. In this paper, we present a Plug-and-Play extension to BLOOMS, which allows to flexibly replace or complement the use of Wikipedia by other online or offline resources, including domain-specific ontologies or taxonomies. By making use of automated translation services and of Wikipedia in languages other than English, it makes it possible to apply BLOOMS to alignment tasks where the input ontologies are written in different languages.

Ontology Alignment For Linked Open Data, Prateek Jain, Pascal Hitzler, Amit P. Sheth, Kunal Verma, Peter Z. Yeh

Kno.e.sis Publications

The Web of Data currently coming into existence through the Linked Open Data (LOD) effort is a major milestone in realizing the Semantic Web vision. However, the development of applications based on LOD faces difficulties due to the fact that the different LOD datasets are rather loosely connected pieces of information. In particular, links between LOD datasets are almost exclusively on the level of instances, and schema-level information is being ignored. In this paper, we therefore present a system for finding schema-level links between LOD datasets in the sense of ontology alignment. Our system, called BLOOMS, is based on the …

(1e,3e)-1,4-Bis(4-Methoxyphenyl)Buta1,3-Diene, Gopinathan Narayan, Nigam Rath, Suresh Das

Chemistry & Biochemistry Faculty Works

The title compound, C18H18O2, which exhibits blue emission in the solid state, is an inter­mediate in the preparation of liquid crystals and polymers. The mol­ecule is located on an inversion centre. In the crystal, mol­ecules are arranged in a herringbone motif.

2,2′,5,5′-Tetra­Chloro­Benzidine, Onome Ugono, Marcel Douglas, Nigam Rath, Alicia Beatty

Chemistry & Biochemistry Faculty Works

In the crystal structure of the title compound, C12H8Cl4N2, mol­ecules lie on crystallographic twofold axes at the centre of the C-C bonds linking the benzene rings, such that the asymmetric unit consists of a half-mol­ecule. The individual mol­ecules participate in inter­molecular N-H...N, N-H...Cl, C-H...Cl and Cl...Cl [3.4503 (3) Å] inter­actions.