Computer Sciences Commons^™

A Time Series Analysis Method Using Hidden Variables For Gene Network Reconstruction, Xi Wu

Dissertations

The DNA microarray technology can be applied to obtain time series data which contains thousands of genes and tens of time points. When confront the great amount of data points a fast and effective method must be constructed to extract useful information. The assumption that the interactions between genes are static in the time series data is made. After made the assumption how to reconstruct those interactions becomes a difficulty problem. Since the underlying interactions between genes are complicated, which involve transcription, translation and protein-protein interaction, to construct a model from physicochemistry is almost impossible/effortless. The popular methods constructed from …

B-Cell Epitope Prediction Through A Graph Model, Liang Zhao, Limsoon Wong, Lanyuan Lu, Steven C. H. Hoi, Jinyan Li

Research Collection School Of Computing and Information Systems

Prediction of B-cell epitopes from antigens is useful to understand the immune basis of antibody-antigen recognition, and is helpful in vaccine design and drug development. Tremendous efforts have been devoted to this long-studied problem, however, existing methods have at least two common limitations. One is that they only favor prediction of those epitopes with protrusive conformations, but show poor performance in dealing with planar epitopes. The other limit is that they predict all of the antigenic residues of an antigen as belonging to one single epitope even when multiple non-overlapping epitopes of an antigen exist.

Demonstration: Dynamic Sensor Registration And Semantic Processing For Ad-Hoc Mobile Environments (Semmob), Pramod Anantharam, Gary Alan Smith, Josh Pschorr, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

SemMOB enables dynamic registration of sensors via mobile devices, search, and near real-time inference over sensor observations in ad-hoc mobile environments (e.g., fire fighting). We demonstrate SemMOB in the context of an emergency response use case that requires automatic and dynamic registrations of sensor devices and annotation of sensor observations, decoding of latitude-longitude information in terms of human sensible names, fusion and abstraction of sensor values using background knowledge, and their visualization using mash-up.

Using Social Influence To Predict Subscriber Churn, Derek Doran, Veena Mendiratta, Chitra Phadke, Dan Kushnir, Huseyin Uzunalioglu

Kno.e.sis Publications

The saturation of mobile phone markets has resulted in rising costs for operators to obtain new customers. These operators thus focus their energies on identifying users that will churn so they can be targeted for retention campaigns. Typical churn prediction algorithms identify churners based on service usage metrics, network performance indicators, and demographic information. Social and peer-influence to churn, however, is usually not considered. In this paper, we describe a new churn prediction algorithm that incorporates the influence churners spread to their social peers. Using data from a major service provider, we show that social influence improves churn prediction and …

Understanding User Triads On Facebook, Derek Doran, Alberta De La Rosa Algarin, Swapna S. Gokhale

Kno.e.sis Publications

Contemporary approaches that analyze user behavior on online social networks only consider interactions among dyads, which are pairs of directly connected users. A large body of sociological work, however, suggests that mutual connections among users can influence their activities, leading to differences between two- and three-way interactions. This paper explores the dynamics of triads among Facebook users based on the wall posts from the New Orleans regional network. Initially, each connection is categorized as a close friendship or an acquiantance, contingent on the number of wall posts exchanged. Subsequently, the impact of different types of connections comprising triads is examined …

How I Would Like Semantic Web To Be, For My Children., Raghava Mutharaju

Kno.e.sis Publications

Semantic Web, since its inception, has gone through lot of developments in its relatively nascent existence; right from people's perception, to the standards and to its adoption by the industry and more importantly by the scientific community. This impressive growth only seems to increase. In this paper, we project this growth to the next 10 years and highlight some of the facets on which Semantic Web could have a major impact on. We also present the challenges that Semantic Web and its community has to deal with in order to get there.

An Efficient Bit Vector Approach To Semantics-Based Machine Perception In Resource-Constrained Devices, Cory Andrew Henson, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

The primary challenge of machine perception is to define efficient computational methods to derive high-level knowledge from low-level sensor observation data. Emerging solutions are using ontologies for expressive representation of concepts in the domain of sensing and perception, which enable advanced integration and interpretation of heterogeneous sensor data. The computational complexity of OWL, however, seriously limits its applicability and use within resource-constrained environments, such as mobile devices. To overcome this issue, we employ OWL to formally define the inference tasks needed for machine perception – explanation and discrimination – and then provide efficient algorithms for these tasks, using bit-vector encodings …

Iexplore: Interactive Browsing And Exploring Biomedical Knowledge, Vinh Nguyen, Olivier Bodenreider, Jagannathan Srinivasan, Todd Minning, Thomas Rindflesch, Bastien Rance, Ramakanth Kavuluru, Himi Yalamanchili, Krishnaprasad Thirunarayan, Satya S. Sahoo, Amit P. Sheth

Kno.e.sis Publications

We present iExplore, a Semantic Web based application that helps biomedical researchers study and explore biomedical knowledge interactively. iExplore uses the Biomedical Knowledge Repository (BKR), which integrates knowledge from various sources ranging from information extracted from biomedical literature (from PubMed) to many structured vocabularies in the Unified Medical Language System (UMLS). The current version of BKR provides a unified provenance representation for 12 million semantic predications (triples with a predicate connecting a subject and an object) derived from 87 vocabulary families in the UMLS and 14 million predications extracted from 21 million PubMed abstracts. To engage the domain experts in …

Computing Perception From Sensor Data, Payam Barnaghi, Frieder Ganz, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

This paper describes a framework for perception creation from sensor data. We propose using data abstraction techniques, in particular Symbolic Aggregate Approximation (SAX), to analyse and create patterns from sensor data. The created patterns are then linked to semantic descriptions that define thematic, spatial and temporal features, providing highly granular abstract representation of the raw sensor data. This helps to reduce the size of the data that needs to be communicated from the sensor nodes to the gateways or highlevel processing components. We then discuss a method that uses abstract patterns created by SAX method and occurrences of different observations …

Privacy Preserving Boosting In The Cloud With Secure Half-Space Queries, Shumin Guo, Keke Chen

Kno.e.sis Publications

This paper presents a preliminary study on the PerturBoost approach that aims to provide efficient and secure classifier learning in the cloud with both data and model privacy preserved.

Recent Advances In Integrating Owl And Rules, Matthias Knorr, David Carral Martinez, Pascal Hitzler, Adila A. Krisnadhi, Frederick Maier, Cong Wang

Computer Science and Engineering Faculty Publications

As part of the quest for a unifying logic for the Semantic Web Technology Stack, a central issue is finding suitable ways of integrating description logics based on the Web Ontology Language (OWL) with rule-based approaches based on logic programming. Such integration is difficult since naive approaches typically result in the violation of one or more desirable design principles. For example, while both OWL 2 DL and RIF Core (a dialect of the Rule Interchange Format RIF) are decidable, their naive union is not, unless carefully chosen syntactic restrictions are applied.

We report on recent advances and ongoing work by …

A Tableau Algorithm For Description Logics With Nominal Schema, Adila Krisnadhi, Pascal Hitzler

Computer Science and Engineering Faculty Publications

We present a tableau algorithm for the description logic ALCOV. This description logic is obtained by extending the description logic ALCO with the expressive nominal schema construct that enables DL-safe datalog with predicates of arbitrary arity to be covered within the description logic framework. The tableau algorithm provides a basis to implement a delayed grounding strategy which was not facilitated by earlier versions of decision procedures for satisfiability in expressive description logics with nominal schemas.

Achieving High Accuracy Prediction Of Minimotifs, Tian Mi, Sanguthevar Rajasekaran, Jerlin Camilus Merlin, Michael R. Gryk, Martin Schiller

Life Sciences Faculty Research

The low complexity of minimotif patterns results in a high false-positive prediction rate, hampering protein function prediction. A multi-filter algorithm, trained and tested on a linear regression model, support vector machine model, and neural network model, using a large dataset of verified minimotifs, vastly improves minimotif prediction accuracy while generating few false positives. An optimal threshold for the best accuracy reaches an overall accuracy above 90%, while a stringent threshold for the best specificity generates less than 1% false positives or even no false positives and still produces more than 90% true positives for the linear regression and neural network …

Reconciling Owl And Non-Monotonic Rules For The Semantic Web, Matthias Knorr, Pascal Hitzler, Frederick Maier

Computer Science and Engineering Faculty Publications

We propose a description logic extending SROIQ (the description logic underlying OWL 2 DL) and at the same time encompassing some of the most prominent monotonic and nonmonotonic rule languages, in particular Datalog extended with the answer set semantics. Our proposal could be considered a substantial contribution towards fulfilling the quest for a unifying logic for the Semantic Web. As a case in point, two non-monotonic extensions of description logics considered to be of distinct expressiveness until now are covered in our proposal. In contrast to earlier such proposals, our language has the 'look and feel' of a description logic …

Using Attribute Behavior Diversity To Build Accurate Decision Tree Committees For Microarray Data, Qian Han, Guozhu Dong

Kno.e.sis Publications

DNA microarrays (gene chips), frequently used in biological and medical studies, measure the expressions of thousands of genes per sample. Using microarray data to build accurate classifiers for diseases is an important task. This paper introduces an algorithm, called Committee of Decision Trees by Attribute Behavior Diversity (CABD), to build highly accurate ensembles of decision trees for such data. Since a committee's accuracy is greatly influenced by the diversity among its member classifiers, CABD uses two new ideas to "optimize" that diversity, namely (1) the concept of attribute behavior–based similarity between attributes, and (2) …

Twitris+: Social Media Analytics Platform For Effective Coordination, Gary Alan Smith, Amit P. Sheth, Ashutosh Sopan Jadhav, Hemant Purohit, Lu Chen, Michael Cooney, Pavan Kapanipathi, Pramod Anantharam, Pramod Koneru, Wenbo Wang

Kno.e.sis Publications

Twitris+ is a Semantic Social Media analytics platform to provide technologies for analyzing large-scale social media streams across Spatio-Temporal-Thematic (STT) and People-Content-Network (PCN) dimensions. It provides holistic situational awareness from one interface and enables organizational actors to engage in well-coordinated ways for desired tasks during emergency response.

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

Kno.e.sis Publications

We present an extension to Jaynes’ maximum entropy principle that incorporates latent variables. The principle of latent maximum entropy we propose is different from both Jaynes’ maximum entropy principle and maximum likelihood estimation, but can yield better estimates in the presence of hidden variables and limited training data. We first show that solving for a latent maximum entropy model poses a hard nonlinear constrained optimization problem in general. However, we then show that feasible solutions to this problem can be obtained efficiently for the special case of log-linear models---which forms the basis for an efficient approximation to the latent maximum …

What Kind Of #Communication Is Twitter? A Psycholinguistic Perspective On Communication In Twitter For The Purpose Of Emergency Coordination, Hemant Purohit, Andrew Hampton, Valerie L. Shalin, Amit P. Sheth, John Flach

Kno.e.sis Publications

The present research aims to detect coordinated citizen response within social media traffic to assist emergency response. We use domain-independent linguistic properties as the first step in narrowing the candidate set of messages for domain-dependent and computationally intensive analysis.

Exploring The Impact Of Knowledge And Social Environment On Influenza Prevention And Transmission In Midwestern United States High School Students, William L. Romine, Tanvi Banerjee, William S. Barrow, William R. Folk

Kno.e.sis Publications

We used data from a convenience sample of 410 Midwestern United States students from six secondary schools to develop parsimonious models for explaining and predicting precautions and illness related to influenza. Scores for knowledge and perceptions were obtained using two-parameter Item Response Theory (IRT) models. Relationships between outcome variables and predictors were verified using Pearson and Spearman correlations, and nested [student within school] fixed effects multinomial logistic regression models were specified from these using Akaike’s Information Criterion (AIC). Neural network models were then formulated as classifiers using 10-fold cross validation to predict precautions and illness. Perceived barriers against taking precautions …

De Novo Protein Structure Modeling From Cryoem Data Through A Dynamic Programming Algorithm In The Secondary Structure Topology Graph, Kamal H. Al Nasr

Computer Science Theses & Dissertations

Proteins are the molecules carry out the vital functions and make more than the half of dry weight in every cell. Protein in nature folds into a unique and energetically favorable 3-Dimensional (3-D) structure which is critical and unique to its biological function. In contrast to other methods for protein structure determination, Electron Cryorricroscopy (CryoEM) is able to produce volumetric maps of proteins that are poorly soluble, large and hard to crystallize. Furthermore, it studies the proteins in their native environment. Unfortunately, the volumetric maps generated by current advances in CryoEM technique produces protein maps at medium resolution about (~5 …

Iexplore: A Provenance-Based Application For Exploring Biomedical Knowledge, Vinh Nguyen, Olivier Bodenreider, Thomas Rindflesch, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

W3c Semantic Sensor Networks: Ontologies, Applications, And Future Directions, Cory Andrew Henson

Kno.e.sis Publications

Plenary Talk discussing the W3C Semantic Sensor Network, including the ontology, applications, and future directions.

Topical Anomaly Detection From Twitter Streams, Pramod Anantharam, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Prediction Of Topic Volume On Twitter, Yiye Ruan, Hemant Purohit, David Fuhry, Srinivasan Parthasarathy, Amit P. Sheth

Kno.e.sis Publications

We discuss an approach for predicting microscopic (individual) and macroscopic (collective) user behavioral patterns with respect to specific trending topics on Twitter. Going beyond previous efforts that have analyzed driving factors in whether and when a user will publish topic-relevant tweets, here we seek to predict the strength of content generation which allows more accurate understanding of Twitter users' behavior and more effective utilization of the online social network for diffusing information. Unlike traditional approaches, we consider multiple dimensions into one regression-based prediction framework covering network structure, user interaction, content characteristics and past activity. Experimental results on three large Twitter …

A Web-Based Study Of Self-Treatment Of Opioid Withdrawal Symptoms With Loperamide, Raminta Daniulaityte, Robert G. Carlson, Russel S. Falck, Delroy H. Cameron, Sujan Udayanaga, Lu Chen, Amit P. Sheth

Kno.e.sis Publications

Aims: Many websites provide a medium for individuals to freely share their experiences and knowledge about different drugs. Such user-generated content can be used as a rich data source to study emerging drug use practices and trends. The study aims to examine web-based reports of loperamide use practices among non-medical opioid users. Loperamide, a piperidine derivative, is an opioid agonist approved for the control of diarrhea symptoms. Because of its general inability to cross the blood-brain barrier, it is considered to have no abuse potential and is available without a prescription. Methods: A website that allows free discussion of illicit …

Phenotype Prediction And Feature Selection In Genome-Wide Association Studies, Andrew Roberts

Theses

Genome wide association studies (GWAS) search for correlations between single nucleotide polymorphisms (SNPs) in a subject genome and an observed phenotype. GWAS can be used to generate models for predicting phenotype based on genotype, as well as aiding in identification of specific genes affecting the biological mechanism underlying the phenotype.

In this investigation, phenotype prediction models are constructed from GWAS training data and are evaluated for performance on test data. Three methods are used to rank SNPs by their correlation with the phenotype: the univariate Wald test, a multivariate, support vector machine (SVM) based technique, and a hybrid method where …

A Comparative Analysis Of Machine Learning Algorithms For Genome Wide Association Studies, Neha Singh

Theses

Variations present in human genome play a vital role in the emergence of genetic disorders and abnormal traits. Single Nucleotide Polymorphism (SNP) is considered as the most common source of genetic variations. Genome Wide Association Studies (GWAS) probe these variations present in human population and find their association with complex genetic disorders. Now these days, recent advances in technology and drastic reduction in costs of Genome Wide Association Studies provide the opportunity to have a plethora of genomic data that delivers huge information of these variations to analyze. In fact, there is significant difference in pace of data generation and …

Data Mining Of Tetraloop-Tetraloop Receptors In Rna Xml Files, Sinan Ramazanoglu

Theses

RNA (Ribonucleic acid) Motifs are tertiary structures that play an important role in the folding mechanism of the RNA molecule. The overall function of a RNA Motif depends on its specific bp (base pairs) sequence that constitutes the secondary structure. Data mining is a novel method in both discovering potential tertiary structures within DNA (Deoxyribonucleic acid), RNA, and protein molecules and storing the information in databases. The RNA Motif of interest is the tetraloop-tetraloop receptor, which is composed of a highly conserved 11 nt (nucleotide) sequence and a tetraloop with the generic form of GNRA (where N = any base …

Integrating Owl And Rules: A Syntax Proposal For Nominal Schemas, David Carral Martinez, Adila Krisnadhi, Pascal Hitzler

Computer Science and Engineering Faculty Publications

This paper proposes an addition to OWL 2 syntax to incorporate nominal schemas, which is a new description-logic style extension of OWL 2 which was recently proposed, and which makes is possible to express "variable nominal classes" within axioms in an OWL 2 ontology. Nominal schemas make it possible to express DL-safe rules of arbitrary arity within the extended OWL paradigm, hence covering the well-known DL-safe SWRL language. To express this feature, we extend OWL 2 syntax to include necessary and minimal modifications to both Functional and Manchester syntax grammars and mappings from these two syntaxes to Turtle/RDF. We also …

Semantic Aspects Of Earthcube, Pascal Hitzler, Krzysztof Janowicz, Gary Berg-Cross, Leo Obrst, Amit P. Sheth, Timothy Finin, Isabel F. Cruz

Kno.e.sis Publications

In this document, we give a high-level overview of selected Semantic (Web) technologies, methods, and other important considerations, that are relevant for the success of EarthCube. The goal of this initial document is to provide entry points and references for discussions between the Semantic Technologies experts and the domain experts within EarthCube. The selected topics are intended to ground the EarthCube roadmap in the state of the art in semantics research and ontology engineering.

We anticipate that this document will evolve as EarthCube progresses. Indeed, all EarthCube parties are asked to provide topics of importance that should be treated in …