Computer Sciences Commons^™

Exploring Factors Influencing Information Technology Portfolio Selection Process In Government-Funded Bioinformatics Projects, Braulio J. Cabral

Walden Dissertations and Doctoral Studies

In 2012, the National Cancer Institute's (NCI) Board of Scientific Advisors (BSA) conducted a review of the Center for Biomedical Informatics and Information Technology's (CBIIT) bioinformatics program. The BSA suggested that the lack of a formal project selection process made it difficult to determine the alignment of projects with the mission of the organization. The problem addressed by this study was that CBIIT did not have an in-depth understanding of the project selection process and the factors influencing the process. The purpose of this study was to understand the project selection process at CBIIT. The research methodology was an exploratory …

A Study Of Social Web Data On Buprenorphine Abuse Using Semantic Web Technology, Raminta Daniulaityte, Amit P. Sheth

Kno.e.sis Publications

The Specific Aims of this application are to use a paradigmatic approach that combines Semantic Web technology, Natural Language Processing and Machine Learning techniques to:

1) Describe drug users’ knowledge, attitudes, and behaviors related to the non-medical use of Suboxone and Subutex as discussed on Web-based forums.
2) Identify and describe temporal patterns of non-medical use of Suboxone and Subutex as discussed on Web-based forums.

The research was carried out by an interdisciplinary team of members of the Center for Interventions, Treatment and Addictions Research (CITAR) and the Ohio Center of Excellence in Knowledge- enabled Computing (Kno.e.sis) at Wright State …

Building The Web Of Knowledge With Smart Iot Applications, Amelie Gyrard, Pankesh Patel, Amit P. Sheth, Martin Serrano

Kno.e.sis Publications

The Internet of Things (IoT) is experiencing fast adoption because of its positive impact to change all aspects of our lives, from agriculture in rural areas, to health and wellness, to smart home and smart-x applications in cities. The development of IoT applications and deployment of smart IoT-based solutions is just starting; smart IoT applications will modify our physical world and our interaction with cyber spaces, from how we remotely control appliances at home to how we care for patients or elderly persons. The massive deployment of IoT devices represents a tremendous economic impact and at the same time offers …

Co-Evolution Of Rdf Datasets, Sidra Faisal, Kemele M. Endris, Saeedeh Shekarpour, Sören Auer, Maria-Esther Vidal

Kno.e.sis Publications

Linking Data initiatives have fostered the publication of large number of RDF datasets in the Linked Open Data (LOD) cloud, as well as the development of query processing infrastructures to access these data in a federated fashion. However, different experimental studies have shown that availability of LOD datasets cannot be always ensured, being RDF data replication required for envisioning reliable federated query frameworks. Albeit enhancing data availability, RDF data replication requires synchronization and conflict resolution when replicas and source datasets are allowed to change data over time, i.e., co-evolution management needs to be provided to ensure consistency. In this paper, …

Assessing Accuracies And Improving Efficiency For Segmentation-Based Rna Secondary Structure Prediction Methods, Gerardo A. Cardenas

Open Access Theses & Dissertations

RNA secondary structure prediction has become an important area of interest in biology and medicine because it helps in understanding the mechanisms of many biological processes such as gene regulation and viral replication, and in designing RNA-based therapies to treat various diseases such as cancers and AIDS. Different thermodynamics-based computational algorithms for RNA structure prediction exist, and have been used to help understand the disease mechanisms and design treatments. However, most of these computational tools that can predict complex pseudoknot structures have a sequence length limitation of few hundred nucleotide bases due to their high demands of computer resources. Yet, …

Evaluating And Improving The Efficiency Of Software And Algorithms For Sequence Data Analysis, Hugh L. Eaves

Theses and Dissertations

With the ever-growing size of sequence data sets, data processing and analysis are an increasingly large portion of the time and money spent on nucleic acid sequencing projects. Correspondingly, the performance of the software and algorithms used to perform that analysis has a direct effect on the time and expense involved. Although the analytical methods are widely varied, certain types of software and algorithms are applicable to a number of areas. Targeting improvements to these common elements has the potential for wide reaching rewards. This dissertation research consisted of several projects to characterize and improve upon the efficiency of several …

Deep Models For Brain Em Image Segmentation: Novel Insights And Improved Performance, Ahmed Fakhry, Hanchuan Peng, Shuiwang Ji

Computer Science Faculty Publications

Motivation: Accurate segmentation of brain electron microscopy (EM) images is a critical step in dense circuit reconstruction. Although deep neural networks (DNNs) have been widely used in a number of applications in computer vision, most of these models that proved to be effective on image classification tasks cannot be applied directly to EM image segmentation, due to the different objectives of these tasks. As a result, it is desirable to develop an optimized architecture that uses the full power of DNNs and tailored specifically for EM image segmentation.

Results: In this work, we proposed a novel design of DNNs for …

Intent Classification Of Short-Text On Social Media, Hemant Purohit, Guozhu Dong, Valerie L. Shalin, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

Social media platforms facilitate the emergence of citizen communities that discuss real-world events. Their content reflects a variety of intent ranging from social good (e.g., volunteering to help) to commercial interest (e.g., criticizing product features). Hence, mining intent from social data can aid in filtering social media to support organizations, such as an emergency management unit for resource planning. However, effective intent mining is inherently challenging due to ambiguity in interpretation, and sparsity of relevant behaviors in social data. In this paper, we address the problem of multiclass classification of intent with a use-case of social data generated during crisis …

Computational Methods For Biomarker Identification In Complex Disease, Amin Ahmadi Adl

USF Tampa Graduate Theses and Dissertations

In a modern systematic view of biology, cell functions arise from the interaction between molecular components. One of the challenging problems in systems biology with high-throughput measurements is discovering the important components involved in the development and progression of complex diseases, which may serve as biomarkers for accurate predictive modeling and as targets for therapeutic purposes. Due to the non-linearity and heterogeneity of these complex diseases, traditional biomarker identification approaches have had limited success at finding clinically useful biomarkers. In this dissertation we propose novel methods for biomarker identification that explicitly take into account the non-linearity and heterogeneity of complex …

Feedback-Driven Radiology Exam Report Retrieval With Semantics, Sarasi Lalithsena, Luis Tari, Anna Von Reden, Benjamin Wilson, Brian J. Kolowitz, John Kalafut, Steven Gustafson, Amit P. Sheth

Kno.e.sis Publications

Clinical documents are vital resources for radiologists to have a better understanding of patient history. The use of clinical documents can complement the often brief reasons for exams that are provided by physicians in order to perform more informed diagnoses. With the large number of study exams that radiologists have to perform on a daily basis, it becomes too time-consuming for radiologists to sift through each patient's clinical documents. It is therefore important to provide a capability that can present contextually relevant clinical documents, and at the same time satisfy the diverse information needs among radiologists from different specialties. In …

Social Health Signals, Ashutosh Sopan Jadhav, Swapnil Soni, Amit P. Sheth

Kno.e.sis Publications

Recently Twitter, has emerged as one of the primary medium for sharing and seeking of the latest information related to variety of the topics including health information. Recently, Twitter has emerged as one of the primary mediums for sharing and seeking the latest information related to a variety of topics, including health information. Although Twitter is an excellent information source, identification of useful information from the deluge of tweets is one of the major challenge. Twitter search is limited to keyword based techniques to retrieve information for a given query and sometimes the results do not contain real-time information. Moreover, …

Implicit Information Extraction From Clinical Notes, Sujan Perera

Kno.e.sis Publications

We address the problem of extracting implicit information from the unstructured clinical notes. Here we introduce the problem of 'implicit entity recognition in clinical notes', propose a knowledge driven approach to address this problem and demonstrate the results of our initial experiments.

An Incremental Phylogenetic Tree Algorithm Based On Repeated Insertions Of Species, Peter Revesz, Zhiqiang Li

School of Computing: Conference and Workshop Papers

In this paper, we introduce a new phylogenetic tree algorithm that generates phylogenetic trees by repeatedly inserting species one-by-one. The incremental phylogenetic tree algorithm can work on proteins or DNA sequences. Computer experiments show that the new algorithm is better than the commonly used UPGMA and Neighbor Joining algorithms.

Ezdi's Semantics-Enhanced Linguistic, Nlp, And Ml Approach For Health Informatics, Raxit Goswami, Neil Shah, Amit P. Sheth

Kno.e.sis Publications

ezDI uses large and extensive knowledge graph to enhance linguistics, NLP and ML techniques to improve structured data extraction from millions of EMR records. It then normalizes it, and maps it with various computer-processable nomenclature such as SNOMED-CT, RxNorm, ICD-9, ICD-10, CPT, and LOINC. Furthermore, it applies advanced reasoning that exploited domain-specific and hierarchical relationships among entities in the knowledge graph to make the data actionable. These capabilities are part of its highly scalable AWS deployed heath intelligence platform that support healthcare informatics applications, including Computer Assisted Coding (CAC), Computerized Document Improvement (CDI), compliance and audit, and core measures and …

Mutations Of Adjacent Amino Acid Pairs Are Not Always Independent, Jyotsna Ramanan, Peter Revesz

School of Computing: Conference and Workshop Papers

Evolutionary studies usually assume that the genetic mutations are independent of each other. This paper tests the independence hypothesis for genetic mutations with regard to protein coding regions. According to the new experimental results the independence assumption generally holds, but there are certain exceptions. In particular, the coding regions that represent two adjacent amino acids seem to change in ways that sometimes deviate significantly from the expected theoretical probability under the independence assumption.

Efficient Algorithms For Prokaryotic Whole Genome Assembly And Finishing, Abhishek Biswas

Computer Science Theses & Dissertations

De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) using both overlapping reads and linked reads until the assembly runs into an ambiguous repeat region. These contigs are further bridged into scaffolds using linked read information. However, errors can be made in both phases of assembly due to high error threshold of overlap acceptance and linking based on too few mate reads. Identical as well as similar repeat regions can …

A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im

Bioinformatics Faculty Publications

Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates ‘imputed’ gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys …

Automatic Emotion Identification From Text, Wenbo Wang

Kno.e.sis Publications

Emotions are both prevalent in and essential to most aspects of our lives. They in- fluence our decision-making, affect our social relationships and shape our daily behavior. With the rapid growth of emotion-rich textual content, such as microblog posts, blog posts, and forum discussions, there is a growing need to develop algorithms and techniques for identifying people’s emotions expressed in text. It has valuable implications for the studies of suicide prevention, employee productivity, well-being of people, customer relationship management, etc. However, emotion identification is quite challenging partly due to the following reasons: i) It is a multi-class classification problem that …

Scalable Euclidean Embedding For Big Data, Zohreh S. Alavi, Sagar Sharma, Lu Zhou, Keke Chen

Kno.e.sis Publications

Euclidean embedding algorithms transform data defined in an arbitrary metric space to the Euclidean space, which is critical to many visualization techniques. At big-data scale, these algorithms need to be scalable to massive dataparallel infrastructures. Designing such scalable algorithms and understanding the factors affecting the algorithms are important research problems for visually analyzing big data. We propose a framework that extends the existing Euclidean embedding algorithms to scalable ones. Specifically, it decomposes an existing algorithm into naturally parallel components and non-parallelizable components. Then, data parallel implementations such as MapReduce and data reduction techniques are applied to the two categories of …

Evaluating A Potential Commercial Tool For Healthcare Application For People With Dementia, Tanvi Banerjee, Pramod Anantharam, William L. Romine, Larry Wayne Lawhorne

Kno.e.sis Publications

The widespread use of smartphones and sensors has made physiology, environment, and public health notifications amenable to continuous monitoring. Personalized digital health and patient empowerment can become a reality only if the complex multisensory and multimodal data is processed within the patient context, converting relevant medical knowledge into actionable information for better and timely decisions. We apply these principles in the healthcare domain of dementia. Specifically, in this study we validate one of our sensor platforms to ascertain whether it will be suitable for detecting physiological changes that may help us detect changes in people with dementia. This study shows …

Domain Specific Document Retrieval Framework For Real-Time Social Health Data, Swapnil Soni

Kno.e.sis Publications

With the advent of the web search and microblogging, the percentage of Online Health Information Seekers (OHIS) using these online services to share and seek health real-time information has in- creased exponentially. OHIS use web search engines or microblogging search services to seek out latest, relevant as well as reliable health in- formation. When OHIS turn to microblogging search services to search real-time content, trends and breaking news, etc. the search results are not promising. Two major challenges exist in the current microblogging search engines are keyword based techniques and results do not contain real-time information. To address these challenges, …

"Time For Dabs": Analyzing Twitter Data On Butane Hash Oil Use, Raminta Daniulaityte, Robert G. Carlson, Farahnaz Golroo, Sanjaya Wijeratne, Edward W. Boyer, Silvia S. Martins, Ramzi W. Nahhas, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Trust Management: Multimodal Data Perspective, Krishnaprasad Thirunarayan

Kno.e.sis Publications

No abstract provided.

Entity Recommendations Using Hierarchical Knowledge Bases, Siva Kumar Cheekula, Pavan Kapanipathi, Derek Doran, Prateek Jain, Amit P. Sheth

Kno.e.sis Publications

Recent developments in recommendation algorithms have focused on integrating Linked Open Data to augment traditional algorithms with background knowledge. These developments recognize that the integration of Linked Open Data may or better performance, particularly in cold start cases. In this paper, we explore if and how a specific type of Linked Open Data, namely hierarchical knowledge, may be utilized for recommendation systems. We propose a content-based recommendation approaches that adapts a spreading activation algorithm over the DBpedia category structure to identify entities of interest to the user. Evaluation of the algorithm over the Movielens dataset demonstrates that our method yields …

Exact Genome Alignment, Nandini Ghosh

Theses

The increase in the volume of genomic data due to the decrease in the cost of whole genome sequencing techniques has opened up new avenues of research in the field of Bioinformatics, like comparative genomics and evolutionary dynamics. The fundamental task in these studies is to align the genome sequences accurately. Sequence alignment helps to identify regions of similarity between the sequences to establish their functional, evolutionary and structural relationship. The thesis investigates the performance of two sequence alignment programs LASTZ, a hash table based faster method and SSEARCH, a slower but more rigorous Smith-Waterman based approach, on whole genome …

Unsupervised Gene Regulatory Network Inference On Microarray Data, Nidhi Radia

Theses

Obtaining gene regulatory networks (GRNs) from expression data is a challenging and crucial task. Many computational methods and algorithms have been developed to infer gene networks for gene expression data, which are usually obtained from microarray experiments. A gene network is a method to depict the relation among clusters of genes. To infer gene networks, the unsupervised method is used in this study. The two types of data used are time-series data and steady-state data. The data is analyzed using various tools containing different algorithms and concepts. GRNs from time-series data tools are obtained using the Time-delayed Algorithm for the …

Identifying Modifier Genes In Sma Model Mice, Weiting Xu

Theses

Spinal Muscular Atrophy (SMA) involves the loss of nerve cells called motor neurons in the spinal cord and is classified as a motor neuron disease, it affects 1 in 5000-10000 newborns, one of the leading genetic causes of infant death in USA. Mutations in the SMN1, UBA1, DYNC1H1 and VAPB genes cause spinal muscular atrophy. Extra copies of the SMN2 gene modify the severity of spinal muscular atrophy. Mutations in SMN1 (Motor Neuron 1) mainly causes SMA (Autosomal recessive inheritance). SMN1 gene mutations lead to a shortage of the SMN protein and SMN protein forms SMN complex …

Domain Specific Document Retrieval Framework On Near Real-Time Social Health Data, Swapnil Soni

Kno.e.sis Publications

With the advent of web search and microblogging, the percentage of Online Health Information Seekers (OHIS) using these services to share and seek health information in real-time has increased exponentially. Recently, Twitter has emerged as one of the primary mediums for sharing and seeking of the latest information related to a variety of topics, including health information. Although Twitter is an excellent information source, the identification of useful information from the deluge of tweets is one of the major challenges. Twitter search is limited to keyword-based techniques to retrieve information for a given query and sometimes the results do not …

Analyzing The Social Media Footprint Of Street Gangs, Sanjaya Wijeratne, Derek Doran, Amit P. Sheth, Jack Dustin

Kno.e.sis Publications

Gangs utilize social media as a way to maintain threatening virtual presences, to communicate about their activities, and to intimidate others. Such usage has gained the attention of many justice service agencies that wish to create better crime prevention and judicial services. However, these agencies use analysis methods that are labor intensive and only lead to basic, qualitative data interpretations. This paper presents the architecture of a modern platform to discover the structure, function, and operation of gangs through the lens of social media. Preliminary analysis of social media posts shared in the greater Chicago, IL region demonstrate the platform’s …

A Dynamic Behavioral Biometric Approach To Authenticate Users Employing Their Fingers To Interact With Touchscreen Devices, Arturo Ponce

CCAC Theses and Dissertations

The use of mobile devices has extended to all areas of human life and has changed the way people work and socialize. Mobile devices are susceptible to getting lost, stolen, or compromised. Several approaches have been adopted to protect the information stored on these devices. One of these approaches is user authentication. The two most popular methods of user authentication are knowledge based and token based methods but they present different kinds of problems.

Biometric authentication methods have emerged in recent years as a way to deal with these problems. They use an individual’s unique characteristics for identification and have …