Computer Sciences Commons^™

Trust Networks, Krishnaprasad Thirunarayan, Pramod Anantharam, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

Trust relationships occur naturally in many diverse contexts such as collaborative systems, e-commerce, interpersonal interactions, social networks, semantic sensor web, etc. As collaborating agents providing content and services become increasingly removed from the agents that consume them, the issue of robust trust inference and update become critical. There is a need to find online substitutes for traditional (direct or face-to-face) cues to derive measures of trust, and create efficient and secure system for managing trust, to support decision-making. Unfortunately, there is neither a universal notion of trust that is applicable to all domains nor a clear explication of its semantics …

Extending Description Logic Rules, David Carral Martinez, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Description Logics – the logics underpinning the Web Ontology Language OWL – and rules are currently the most prominent paradigms used for modeling knowledge for the Semantic Web. While both of these approaches are based on classical logic, the paradigms also differ significantly, so that naive combinations result in undesirable properties such as undecidability. Recent work has shown that many rules can in fact be expressed in OWL. In this paper we extend this work to include some types of rules previously excluded. We formally define a set of first order logic rules, C-Rules, which can be expressed within OWL …

Challenging Disciplinary Boundaries In The First Year: A New Introductory Integrated Science Course For Stem Majors, Lisa Gentile, Lester Caudill, Mirela Fetea, April L. Hill, Kathy Hoke, Barry Lawson, Ovidiu Z. Lipan, Michael Kerckhove, Carol A. Parish, Krista J. Stenger, Doug Szajda

Department of Math & Statistics Faculty Publications

To help undergraduates make connections among disciplines so they are able to approach, evaluate, and contribute to the solutions of important global problems, our campus has been focused on interdisciplinary research and education opportunities across the science, technology, engineering, and mathematics (STEM) disciplines. This paper describes the mobilization, planning, and implementation of a first-year interdisciplinary course for STEM majors that integrates key concepts found in traditional first-semester biology, chemistry, computer science, mathematics, and physics courses. This team-taught course, Integrated Quantitative Science (IQS), is half of a first-year student’s schedule in both semesters and is composed of a double lecture and …

Challenging Disciplinary Boundaries In The First Year: A New Introductory Integrated Science Course For Stem Majors, Lisa Gentile, Lester Caudill, Mirela Fetea, April L. Hill, Kathy Hoke, Barry Lawson, Ovidiu Z. Lipan, Michael Kerckhove, Carol A. Parish, Krista J. Stenger, Doug Szajda

Biology Faculty Publications

To help undergraduates make connections among disciplines so they are able to approach, evaluate, and contribute to the solutions of important global problems, our campus has been focused on interdisciplinary research and education opportunities across the science, technology, engineering, and mathematics (STEM) disciplines. This paper describes the mobilization, planning, and implementation of a first-year interdisciplinary course for STEM majors that integrates key concepts found in traditional first-semester biology, chemistry, computer science, mathematics, and physics courses. This team-taught course, Integrated Quantitative Science (IQS), is half of a first-year student’s schedule in both semesters and is composed of a double lecture and …

Using Bioinformatics To Efficiently Organize And Analyze Significant Immunogenic Epitope Sequences In Various Stages Of Trypanosoma Cruzi, Karla Singh^, Andrea Wurm, Clemente Aguilar, Alexandre Marques, M-Y Leung*, Igor Almeida*

COURI Symposium Abstracts, Spring 2012

No abstract provided.

A Spatially Explicit Agent Based Model Of Muscovy Duck Home Range Behavior, James Howard Anderson

USF Tampa Graduate Theses and Dissertations

ABSTRACT

Research in GIScience has identified agent-based simulation methodologies as effective in the study of complex adaptive spatial systems (CASS). CASS are characterized by the emergent nature of their spatial expressions and by the changing relationships between their constituent variables and how those variables act on the system's spatial expression over time. Here, emergence refers to a CASS property where small-scale, individual action results in macroscopic or system-level patterns over time. This research develops and executes a spatially-explicit agent based model of Muscovy Duck home range behavior. Muscovy duck home range behavior is regarded as a complex adaptive spatial system …

Binding Efficacy Of Different Polyphenolic Phytochemicals With Β-Lactoglobulin And Human Serum Albumin: Implication For Therapeutics Against Neurodegenerative Diseases, Rene Duran^, Andres Ortiz^, Mahesh Narayan*, Vladik Kreinovich*

COURI Symposium Abstracts, Spring 2012

No abstract provided.

Derivation Of Hill's Equation From Scale Invariance, Andres Ortiz^, Vladik Kreinovich*

COURI Symposium Abstracts, Spring 2012

No abstract provided.

Entropy And The Complexity Of Graphs Revisited, Abbe Mowshowitz, Matthias Dehmer

Publications and Research

This paper presents a taxonomy and overview of approaches to the measurement of graph and network complexity. The taxonomy distinguishes between deterministic (e.g., Kolmogorov complexity) and probabilistic approaches with a view to placing entropy-based probabilistic measurement in context. Entropy-based measurement is the main focus of the paper. Relationships between the different entropy functions used to measure complexity are examined; and intrinsic (e.g., classical measures) and extrinsic (e.g., Körner entropy) variants of entropy-based models are discussed in some detail.

Localized Deconvolution: Characterizing Nmr-Based Metabolomics Spectroscopic Data Using Localized High-Throughput Deconvolution, Paul E. Anderson, Ajith H. Ranabahu, Deirdre A. Mahle, Nicholas V. Reo, Michael L. Raymer, Amit P. Sheth, Nicholas J. Delraso

Kno.e.sis Publications

The interpretation of nuclear magnetic resonance (NMR) experimental results for metabolomics studies requires intensive signal processing and multivariate data analysis techniques. Standard quantification techniques attempt to minimize effects from variations in peak positions caused by sample pH, ionic strength, and composition. These techniques fail to account for adjacent signals which can lead to drastic quantification errors. Attempts at full spectrum deconvolution have been limited in adoption and development due to the computational resources required. Herein, we develop a novel localized deconvolution algorithm for general purpose quantification of NMR-based metabolomics studies. Localized deconvolution decreases average absolute quantification error by 97% and …

Framework For The Analysis Of Coordination In Crisis Response, Hemant Purohit, Andrew Hampton, Valerie L. Shalin, Amit P. Sheth, John M. Flach

Kno.e.sis Publications

Social Media play a critical role during crisis events, revealing a natural coordination dynamic. We propose a computational framework guided by social science principles to measure, analyze, and understand coordination among the different types of organizations and actors in crisis response. The analysis informs both the scientific account of cooperative behavior and the design of applications and protocols to support crisis management.

Structural Characterization Of Human Uch37, E. S. Burgie, C. Bingman, Ameet Soni, G. N. Phillips Jr.

Computer Science Faculty Works

Uch37 is a de-ubiquitylating enzyme that is functionally linked with the 26S proteasome via Rpn13, and is essential for metazoan development. Here, we report the X-ray crystal structure of full-length human Uch37 at 2.95 Å resolution. Uch37's catalytic domain is similar to those of all UCH enzymes characterized to date. The C-terminal extension is elongated, predominantly helical and contains coiled coil interactions. Additionally, we provide an initial characterization of Uch37's oligomeric state and identify a systematic error in previous analyses of Uch37 activity. Taken together, these data provide a strong foundation for further analysis of Uch37's several functions.

Probabilistic Ensembles For Improved Inference In Protein-Structure Determination, Ameet Soni, J. Shavlik

Computer Science Faculty Works

Protein X-ray crystallography — the most popular method for determining protein structures — remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality protein images. Automating this process is critical in creating a high-throughput protein-structure determination pipeline. Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography. ACMI uses a Markov Random Field to model the three-dimensional (3D) location of each non-hydrogen atom in a protein. Calculating the best structure in this model is intractable, so ACMI uses approximate inference methods to estimate the optimal structure. …

Discovering Fine-Grained Sentiment In Suicide Notes, Wenbo Wang, Lu Chen, Ming Tan, Shaojun Wang, Amit P. Sheth

Kno.e.sis Publications

This paper presents our solution for the i2b2 sentiment classification challenge. Our hybrid system consists of machine learning and rule-based classifiers. For the machine learning classifier, we investigate a variety of lexical, syntactic and knowledge-based features, and show how much these features contribute to the performance of the classifier through experiments. For the rule-based classifier, we propose an algorithm to automatically extract effective syntactic and lexical patterns from training examples. The experimental results show that the rule-based classifier outperforms the baseline machine learning classifier using unigram features. By combining the machine learning classifier and the rule-based classifier, the hybrid system …

A Semantic Problem Solving Environment For Integrative Parasite Research: Identification Of Intervention Targets For Trypanosoma Cruzi, Priti Parikh, Todd Minning, Vinh Nguyen, Sarasi Lalithsena, Amir H. Asiaee, Satya S. Sahoo, Prashant Doshi, Rick L. Tarleton, Amit P. Sheth

Kno.e.sis Publications

Background: Research on the biology of parasites requires a sophisticated and integrated computational platform to query and analyze large volumes of data, representing both unpublished (internal) and public (external) data sources. Effective analysis of an integrated data resource using knowledge discovery tools would significantly aid biologists in conducting their research, for example, through identifying various intervention targets in parasites, and in deciding the future direction of ongoing as well as planned projects. A key challenge in achieving this objective is the heterogeneity between the internal lab data, usually stored as flat files, Excel spreadsheets or custom-built databases, and the external …

Derivation Of A Novel Efficient Supervised Learning Algorithm From Cortical-Subcortical Loops, Ashok Chandrashekar, Richard Granger

Dartmouth Scholarship

Although brain circuits presumably carry out powerful perceptual algorithms, few instances of derived biological methods have been found to compete favorably against algorithms that have been engineered for specific applications. We forward a novel analysis of a subset of functions of cortical-subcortical loops, which constitute more than 80% of the human brain, thus likely underlying a broad range of cognitive functions. We describe a family of operations performed by the derived method, including a non-standard method for supervised classification, which may underlie some forms of cortically dependent associative learning. The novel supervised classifier is compared against widely used algorithms for …

Cognitive Approaches For The Semantic Web, Dedre Gentner, Frank Van Harmelen, Pascal Hitzler, Krzysztof Janowicz, Kai-Uwe Kuhnberger

Computer Science and Engineering Faculty Publications

A major focus in the design of Semantic Web ontology languages used to be on finding a suitable balance between the expressivity of the language and the tractability of reasoning services defined over this language. This focus mirrors the original vision of a Web composed of machine readable and understandable data. Similarly to the classical Web a few years ago, the attention is recently shifting towards a user-centric vision of the Semantic Web. Essentially, the information stored on the Web is from and for humans. This new focus is not only reflected in the fast growing Linked Data Web but …

A Natural Language Interface Plug-In For Cooperative Query Answering In Biological Databases, Hasan M. Jamil

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, queries are not always best posed using a structured language. By this we mean that approximate and flexible responses to natural language like queries are well suited for this domain. This is partly due to biologists' tendency to seek simpler interfaces and partly due to the fact that questions in biology involve high level concepts that are open to interpretations computed …

Semantics Of Perception: Towards A Semantic Web Approach To Machine Perception, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

The acts of observation and perception provide the building blocks for all human knowledge (Locke, 1690); they are the processes from which all ideas are born; and the sole bond connecting ourselves to the world around us. Now, with the advent of sensor networks capable of observation, this world may be directly accessible to machines. Missing from this vision, however, is the ability of machines to glean semantics from observation; to apprehend entities from detected qualities; to perceive. The systematic automation of this ability is the focus of machine perception -- the ability of computing machines to sense and interpret …

Minimotif Miner 3.0: Database Expansion And Significantly Improved Reduction Of False-Positive Predictions From Consensus Sequences., Tian Mi, Jerlin Camilus Merlin, Sandeep Deverasetty, Michael R. Gryk, Travis J. Bill, Andrew W. Brooks, Logan Lee, Viraj Rathnayake, Christian A. Ross, David P. Sargeant, Christy L. Strong, Paula Watts, Sanguthevar Rajasekaran, Martin Schiller

Life Sciences Faculty Research

Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300,000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins …

A Scalable Distributed Syntactic, Semantic And Lexical Language Model, Ming Tan, Wenli Zhou, Lei Zheng, Shaojun Wang

Kno.e.sis Publications

This paper presents an attempt at building a large scale distributed composite language model that is formed by seamlessly integrating an n-gram model, a structured language model, and probabilistic latent semantic analysis under a directed Markov random field paradigm to simultaneously account for local word lexical information, mid-range sentence syntactic structure, and long-span document semantic content. The composite language model has been trained by performing a convergent N-best list approximate EM algorithm and a follow-up EM algorithm to improve word prediction power on corpora with up to a billion tokens and stored on a supercomputer. The large scale distributed composite …

Alignment-Based Querying Of Linked Open Data, Amit Krishna Joshi, Prateek Jain, Pascal Hitzler, Peter Z. Yeh, Kunal Verma, Amit P. Sheth, Mariana Damova

Kno.e.sis Publications

The Linked Open Data (LOD) cloud is rapidly becoming the largest interconnected source of structured data on diverse domains. The potential of the LOD cloud is enormous, ranging from solving challenging AI issues such as open domain question answering to automated knowledge discovery. However, due to an inherent distributed nature of LOD and a growing number of ontologies and vocabularies used in LOD datasets, querying over multiple datasets and retrieving LOD data remains a challenging task. In this paper, we propose a novel approach to querying linked data by using alignments for processing queries whose constituent data come from heterogeneous …

On The Design Of Advanced Filters For Biological Networks Using Graph Theoretic Properties, Kathryn Dempsey Cooper, Tzu-Yi Chen, Sanjukta Bhowmick, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Network modeling of biological systems is a powerful tool for analysis of high-throughput datasets by computational systems biologists. Integration of networks to form a heterogeneous model requires that each network be as noise-free as possible while still containing relevant biological information. In earlier work, we have shown that the graph theoretic properties of gene correlation networks can be used to highlight and maintain important structures such as high degree nodes, clusters, and critical links between sparse network branches while reducing noise. In this paper, we propose the design of advanced network filters using structurally related graph theoretic properties. While spanning …

Extracting Diverse Sentiment Expressions With Target-Dependent Polarity From Twitter, Lu Chen, Wenbo Wang, Meenakshi Nagarajan, Shaojun Wang, Amit P. Sheth

Kno.e.sis Publications

This study focuses on automatic extraction of sentiment expressions associated with given targets from Twitter. It addresses one of the key challenges in this work: Wide diversity and informal nature of sentiment expressions that cannot be trivially enumerated or captured using predefined lexical patterns.

On The Role Of Social Identity And Cohesion In Characterizing Online Social Communities, Hemant Purohit, Yiye Ruan, David Fuhry, Srinivasan Parthasarathy, Amit P. Sheth

Kno.e.sis Publications

Two prevailing theories for explaining social group or community structure are cohesion and identity. The social cohesion approach posits that social groups arise out of an aggregation of individuals that have mutual interpersonal attraction as they share common characteristics. These characteristics can range from common interests to kinship ties and from social values to ethnic backgrounds. In contrast, the social identity approach posits that an individual is likely to join a group based on an intrinsic self-evaluation at a cognitive or perceptual level. In other words group members typically share an awareness of a common category membership. In this work …

Role Of Semantic Web In Health Informatics, Satya S. Sahoo, Guo-Qiang Zhang, Amit P. Sheth

Kno.e.sis Publications

This tutorial weaves together three themes and the associated topics: [1] The role of biomedical ontologies [2] Key Semantic Web technologies with focus on Semantic provenance and integration [3] In-practice tools and real world use cases built to serve the needs of sleep medicine researchers, cardiologists involved in clinical practice, and work on vaccine development for human pathogens.

Semantics And Ontologies For Earthcube, Gary Berg-Cross, Isabel F. Cruz, Michael Dean, Timothy Finin, Mark Gahegan, Pascal Hitzler, Hook Hau, Krzysztof Janowicz, Naicong Li, Philip Murphy, Bryce Nordgren, Leo Obrst, Mark Schildhauer, Amit P. Sheth, Krishna Sinha, Anne Thessen, Nancy Wiegand, Ilya Zaslavasky

Kno.e.sis Publications

Semantic technologies and ontologies play an increasing role in scientific workflow systems and knowledge infrastructures. While ontologies are mostly used for the semantic annotation of metadata, semantic technologies enable searching metadata catalogs beyond simple keywords, with some early evidence of semantics used for data translation. However, the next generation of distributed and interdisciplinary knowledge infrastructures will require capabilities beyond simple subsumption reasoning over subclass relations. In this work, we report from the EarthCube Semantics Community by highlighting which role semantics and ontologies should play in the EarthCube knowledge infrastructure. We target the interested domain scientist and, thus, introduce the value …

Key Ingredients For Your Next Semantics Elevator Talk, Krzysztof Janowicz, Pascal Hitzler

Computer Science and Engineering Faculty Publications

2012 brought a major change to the semantics research community. Discussions on the use and benefits of semantic technologies are shifting away from the why to the how. Surprisingly this more in stakeholder interest is not accompanied by a more detailed understanding of what semantics research is about. Instead of blaming others for their (wrong) expectations, we need to learn how to emphasize the paradigm shift proposed by semantics research while abstracting from technical details and advocate the added value in a way that relates to the immediate needs of individual stakeholders without overselling. This paper highlights some of …

Hierarchical Multi-Label Classification For Protein Function Prediction Going Beyond Traditional Approaches, Noor Al Aydie

Wayne State University Dissertations

Hierarchical multi-label classification is a variant of traditional classification in which the

instances can belong to several labels, that are in turn organized in a hierarchy. Functional classification of genes is a challenging problem in functional genomics due to several reasons. First, each gene participates in multiple biological activities. Hence, prediction models should support multi-label classification. Second, the genes are organized and classified according to a hierarchical classification scheme that represents the relationships between the functions of the genes. These relationships should be maintained by the prediction models. In addition, various bimolecular data sources, such as gene expression data and …

Open And Transparent: The Review Process Of The Semantic Web Journal, Krzysztof Janowicz, Pascal Hitzler

Computer Science and Engineering Faculty Publications

While open access is established in the world of academic publishing, open reviews are rare. The Semantic Web journal goes further than just open review by implementing an open and transparent review process in which reviews are publicly available, and the assigned editors and reviewers are known by name, and are published together with accepted manuscripts. In this article we introduce the steps to realize such a process from the conceptual design, over the implementation, a overview of the results so far, and up to lessons learned.