Life Sciences Commons^™

Anonymized Video Analysis Methods And Systems, Marjorie Skubic, James M. Keller, Fang Wang, Derek T. Anderson, Erik Stone, Robert H. Luke Iii, Tanvi Banerjee, Marilyn J. Rantz

Kno.e.sis Publications

Methods and systems for anonymized video analysis are described. In one embodiment, a first silhouette image of a person in a living unit may be accessed. The first silhouette image may be based on a first video signal recorded by a first video camera. A second silhouette image of the person in the living unit may be accessed. The second silhouette image may be of a different view of the person than the first silhouette image. The second silhouette image may be based on a second video signal recorded by a second video camera. A three-dimensional model of the person …

Protecting Web Servers From Web Robot Traffic, Derek Doran

Kno.e.sis Publications

No abstract provided.

Triad-Based Role Discovery For Large Social Systems, Derek Doran

Kno.e.sis Publications

The social role of a participant in a social system conceptualizes the circumstances under which she chooses to interact with others, making their discovery and analysis important for theoretical and practical purposes. In this paper, we propose a methodology to detect such roles by utilizing the conditional triad censuses of ego-networks. These censuses are a promising tool for social role extraction because they capture the degree to which basic social forces push upon a user to interact with others in a system. Clusters of triad censuses, inferred from network samples that preserve local structural properties, define the social roles. The …

Gwatch: A Web Platform For Automated Gene Association Discovery Analysis, Anton Svitin, Sergey Malov, Nikolay Cherkasov, Paul Geerts, Mikhail Rotkevich, Pavel Dobrynin, Andrey Shevchenko, Li Guan, Jennifer L. Troyer, Sher L. Hendrickson, Holli Hutcheson Dilks, T. K. Oleksyk, Sharyne Donfield, Edward Gomperts, Douglas A. Jabs, Efe Sezgin, Mark Van Natta, P. Richard Harrigan, Zabrina L. Brumme, Stephen J. O'Brien

Biology Faculty Articles

Background: As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations.

Findings: Here we present a dynamic web-based platform – GWATCH – that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication …

Design Of Randomized Experiments In Networks, Dylan Walker, Lev Muchnik

Business Faculty Articles and Research

Over the last decade, the emergence of pervasive online and digitally enabled environments has created a rich source of detailed data on human behavior. Yet, the promise of big data has recently come under fire for its inability to separate correlation from causation-to derive actionable insights and yield effective policies. Fortunately, the same online platforms on which we interact on a day-to-day basis permit experimentation at large scales, ushering in a new movement toward big experiments. Randomized controlled trials are the heart of the scientific method and when designed correctly provide clean causal inferences that are robust and reproducible. However, …

An Analysis Of Mayo Clinic Search Query Logs For Cardiovascular Diseases, Ashutosh Sopan Jadhav, Amit P. Sheth, Jyotishman Pathak

Kno.e.sis Publications

Increasingly, individuals are taking active participation in learning and managing their health by leveraging online resources. Understanding online health information searching behavior can help us to study what health topics users search for and how search queries are formulated. In this work, we analyzed 10 million cardiovascular diseases (CVD) related search queries from MayoClinic.com. We performed semantic analysis on the queries using UMLS MetaMap and analyzed structural and textual properties as well as linguistic characteristics of the queries.

Discovering Perceptions In Online Social Media: A Probabilistic Approach, Derek Doran, Swapna S. Gokhale, Aldo Dagnino

Kno.e.sis Publications

People across the world habitually turn to online social media to share their experiences, thoughts, ideas, and opinions as they go about their daily lives. These posts collectively contain a wealth of insights into how masses perceive their surroundings. Therefore, extracting people’s perceptions from social media posts can provide valuable information about pertinent issues such as public transportation, emergency conditions, and even reactions to political actions or other activities. This paper proposes a novel approach to extract such perceptions from a corpus of social media posts originating from a given broad geographical region. The approach divides the broad region into …

Online Information Searching For Cardiovascular Diseases: An Analysis Of Mayo Clinic Search Query Logs, Ashutosh Sopan Jadhav, Amit P. Sheth, Jyotishman Pathak

Kno.e.sis Publications

Since the early 2000’s, Internet usage for health information searching has increased significantly. Studying search queries can help us to understand users “information need” and how do they formulate search queries (“expression of information need”). Although cardiovascular diseases (CVD) affect a large percentage of the population, few studies have investigated how and what users search for CVD. We address this knowledge gap in the community by analyzing a large corpus of 10 million CVD related search queries from MayoClinic.com. Using UMLS MetaMap and UMLS semantic types/concepts, we developed a rule-based approach to categorize the queries into 14 health categories. We …

Improving The Efficacy Of Web-Based Educational Outreach In Ecology, Gregory R. Goldsmith, Andrew D. Fulton, Colin D. Witherill, Javier F. Espeleta

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Scientists are increasingly engaging the web to provide formal and informal science education opportunities. Despite the prolific growth of web-based resources, systematic evaluation and assessment of their efficacy remains limited. We used clickstream analytics, a widely available method for tracking website visitors and their behavior, to evaluate 60,000 visits over three years to an educational website focused on ecology. Visits originating from search engine queries were a small proportion of the traffic, suggesting the need to actively promote websites to drive visitation. However, the number of visits referred to the website per social media post varied depending on the social …

Generalized Theoretical Criteria For Annihilation Of Hiv-1 Virions During Haart, Frank Nani, Mingxian Jin

Math and Computer Science Faculty Working Papers

Aims: This paper is an elaborate and quantitative attempt to construct medically applicable mathematical models and derive criteria for efficacious Highly Active Anti-Retroviral Therapy (HAART) protocol for an AIDS patient. The patho-physiological dynamics of Human Immuno-deficiency Virus type 1 (HIV-1) induced AIDS during HAART is modeled by a system of non-linear deterministic differential equations. The physiologically relevant and clinically plausible equations depict the dynamics of uninfected CD4+ T cells (x1), HIV-1 infected CD4+ T cells (x2), HIV-1 virions in the blood plasma (x3), HIV-1 specific CD8+ T cells (x4), and the concentration of HAART drug molecules (x5). The major objective …

Data Analytics For Power Utility Storm Planning, Lan Lin, Aldo Dagnino, Derek Doran, Swapna S. Gokhale

Kno.e.sis Publications

As the world population grows, recent climatic changes seem to bring powerful storms to populated areas. The impact of these storms on utility services is devastating. Hurricane Sandy is a recent example of the enormous damages that storms can inflict on infrastructure, society, and the economy. Quick response to these emergencies represents a big challenge to electric power utilities. Traditionally utilities develop preparedness plans for storm emergency situations based on the experience of utility experts and with limited use of historical data. With the advent of the Smart Grid, utilities are incorporating automation and sensing technologies in their grids and …

Evaluation Of Microarray-Based Dna Methylation Measurement Using Technical Replicates: The Atherosclerosis Risk In Communities (Aric) Study, Maitreyee Bose, Chong Wu, James S. Pankow, Ellen W. Demerath, Jan Bressler, Myriam Fornage, Megan L. Grove, Thomas H. Mosley, Chindo Hicks, Kari North, Wen Hong Kao, Yu Zhang, Eric Boerwinkle, Weihua Guan

Computer Science Faculty Publications

Background: DNA methylation is a widely studied epigenetic phenomenon; alterations in methylation patterns influence human phenotypes and risk of disease. As part of the Atherosclerosis Risk in Communities (ARIC) study, the Illumina Infinium HumanMethylation450 (HM450) BeadChip was used to measure DNA methylation in peripheral blood obtained from ~3000 African American study participants. Over 480,000 cytosine-guanine (CpG) dinucleotide sites were surveyed on the HM450 BeadChip. To evaluate the impact of technical variation, 265 technical replicates from 130 participants were included in the study.

Results: For each CpG site, we calculated the intraclass correlation coefficient (ICC) to compare variation of methylation levels …

A Keyword Sense Disambiguation Based Approach For Noise Filtering In Twitter, Sanjaya Wijeratne, Bahareh R. Heravi

Kno.e.sis Publications

In this paper, we describe an approach to filter out noisy data generated by keywords-based tweet filtering methods by performing Word Sense Disambiguation on those keywords used to collect tweets. We present the noise filtering problem as a binary classification problem and discuss our evaluation strategy which is to be carried out in future.

Rasp-Qs: Efficient And Confidential Query Services In The Cloud, Zohreh S. Alavi, Lu Zhou, James L. Powers, Keke Chen

Kno.e.sis Publications

Hosting data query services in public clouds is an attractive solution for its great scalability and significant cost savings. However, data owners also have concerns on data privacy due to the lost control of the infrastructure. This demonstration shows a prototype for efficient and confidential range/kNN query services built on top of the random space perturbation (RASP) method. The RASP approach provides a privacy guarantee practical to the setting of cloudbased computing, while enabling much faster query processing compared to the encryption-based approach. This demonstration will allow users to more intuitively understand the technical merits of the RASP approach via …

Document Retrieval Using Predication Similarity, Kalpa Gunaratna

Kno.e.sis Publications

Document retrieval has been an important research problem over many years in the information retrieval community. State-of-the-art techniques utilize various methods in matching documents to a given document including keywords, phrases, and annotations. In this paper, we propose a new approach for document retrieval that utilizes predications (subject-predicate-object triples) extracted from the documents. We represent documents as sets of predications. We measure the similarity between predications to compute the similarity between documents. Our approach utilizes the hierarchical information available in ontologies in computing concept-concept similarity, making the approach flexible. Predication-based document similarity is more precise and forms the basis for …

Development Of A Methodology That Couples Satellite Remote Sensing Measurements To Spatial-Temporal Distribution Of Soil Moisture In The Vadose Zone Of The Everglades National Park, Luis G. Perez

FIU Electronic Theses and Dissertations

Spatial-temporal distribution of soil moisture in the vadose zone is an important aspect of the hydrological cycle that plays a fundamental role in water resources management, including modeling of water flow and mass transport. The vadose zone is a critical transfer and storage compartment, which controls the partitioning of energy and mass linked to surface runoff, evapotranspiration and infiltration. This dissertation focuses on integrating hydraulic characterization methods with remote sensing technologies to estimate the soil moisture distribution by modeling the spatial coverage of soil moisture in the horizontal and vertical dimensions with high temporal resolution.

The methodology consists of using …

A Novel Web-Based Depth Video Rewind Approach Toward Fall Preventive Interventions In Hospitals, Moein Enayati, Tanvi Banerjee, Mihail Popescu, Marjorie Skubic, Marilyn J. Rantz

Kno.e.sis Publications

Falls in the hospital rooms are considered a huge burden on healthcare costs. They can lead to injuries, extended length of stay, and increase in cost for both the patients and the hospital. It can also lead to emotional trauma for the patients and their families [1]. Having Microsoft Kinects installed in the hospital rooms to capture and process every movement in the room, we deployed our previously developed fall-detection system to detect naturally occurring falls, generate a real-time fall alarm and broadcast it to hospital nurses for immediate intervention. These systems also store a processed and reduced version …

Assisting Coordination During Crisis: A Domain Ontology Based Approach To Infer Resource Needs From Tweets, Shreyansh Bhatt, Hemant Purohit, Andrew J. Hampton, Valerie L. Shalin, Amit P. Sheth, John Flach

Kno.e.sis Publications

Ubiquitous social media during crises provides citizen reports on the situation, needs and supplies. Previous research extracts resource needs directly from the text (e.g. "Power cut to Coney Island and Brighton beach" indicates a power need). This approach assumes that citizens derive and write about specific needs from their observations, properly specified for the emergency response system, an assumption that is not consistent with general conversational behavior. In our study, Twitter messages (tweets) from Hurricane Sandy in 2012 clearly indicate power blackouts, but not their probable implications (e.g. loss of power to hospital life support systems). We use a domain …

Semantics-Enhanced Geoscience Interoperability, Analytics, And Applications, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

We present our research ideas for developing cyberinfrastructure for Geoscience applications developed in the context of the EarthCube initiative, and our NSF-sponsored work on incorporating spatial-temporal-thematic semantics for enhanced querying and feature extraction from sensor data streams.

Semantic Modelling Of Smart City Data, Stefan Bischof, Athanasios Karapantelakis, Cosmin-Septimiu Nechifor, Amit P. Sheth, Alessandra Mileo, Payam Barnaghi

Kno.e.sis Publications

Cities present an opportunity for rendering Web of Things-enabled services. According to the World Health Organization, population in cities will double by the middle of this century, while cities deal with increasingly pressing issues such as environmental sustainability, economic growth and citizen mobility. In this paper, we propose a discussion around the need for common semantic descriptions for smart city data to facilitate future services in "smart cities". We present examples of data that can be collected from cities, discuss issues around this data and put forward some preliminary thoughts for creating a semantic description model to describe and help …

Active Learning With Efficient Feature Weighting Methods For Improving Data Quality And Classification Accuracy, Justin Martineau, Lu Chen, Doreen Cheng, Amit P. Sheth

Kno.e.sis Publications

Many machine learning datasets are noisy with a substantial number of mislabeled instances. This noise yields sub-optimal classification performance. In this paper we study a large, low quality annotated dataset, created quickly and cheaply using Amazon Mechanical Turk to crowdsource annotations. We describe computationally cheap feature weighting techniques and a novel non-linear distribution spreading algorithm that can be used to iteratively and interactively correcting mislabeled instances to significantly improve annotation quality at low cost. Eight different emotion extraction experiments on Twitter data demonstrate that our approach is just as effective as more computationally expensive techniques. Our techniques save a considerable …

Mining Contrast Subspaces, Lei Duan, Guanting Tang, Jian Pei, James Bailey, Guozhu Dong, Akiko Campbell, Changjie Tang

Kno.e.sis Publications

In this paper, we tackle a novel problem of mining contrast subspaces. Given a set of multidimensional objects in two classes C₊  and C₋ and a query object o, we want to find top-k subspaces S that maximize the ratio of likelihood of o in C₊  against that in C₋. We demonstrate that this problem has important applications, and at the same time, is very challenging. It even does not allow polynomial time approximation. We present CSMiner, a mining method with various pruning techniques. CSMiner is substantially faster than the baseline method. Our …

With Whom To Coordinate, Why And How In Ad-Hoc Social Media Communications During Crisis Response, Hemant Purohit, Shreyansh Bhatt, Andrew Hampton, Valerie L. Shalin, Amit P. Sheth, John M. Flach

Kno.e.sis Publications

During crises affected people, well-wishers, and observers join social media communities to discuss the event. They often share useful information relevant to response coordination, for example, specific resource needs. However, responders face the challenge of massive data overload and lack the time to monitor social media traffic for important information. Analysis shows that only a small number of event related conversations are actionable. Moreover, responders do not know which sources are trustworthy. To address these challenges, response teams may apply manual filtering methods, resulting in limited coverage and quality. We propose a framework and interface for extracting specific resource-related information …

Hierarchical Interest Graph From Tweets, Pavan Kapanipathi, Prateek Jain, Chitra Venkataramani, Amit P. Sheth

Kno.e.sis Publications

Industry and researchers have identified numerous ways to monetize microblogs for personalization and recommendation. A common challenge across these different works is the identification of user interests. Although techniques have been developed to address this challenge, a flexible approach that spans multiple levels of granularity in user interests has not been forthcoming. In this work, we focus on exploiting hierarchical semantics of concepts to infer richer user interests expressed as a Hierarchical Interest Graph. To create such graphs, we utilize users' tweets to first ground potential user interests to structured background knowledge such as Wikipedia Category Graph. We then adapt …

Leveraging Social Media And Web Of Data For Crisis Response Coordination, Carlos Castillo, Fernando Diaz, Hemant Purohit

Kno.e.sis Publications

There is an ever increasing number of users in social media (1B+ Facebook users, 500M+ Twitter users) and ubiquitous mobile access (6B+ mobile phone subscribers) who share their observations and opinions. In addition, the Web of Data and existing knowledge bases keep on growing at a rapid pace. In this scenario, we have unprecedented opportunities to improve crisis response by extracting social signals, creating spatio-temporal mappings, performing analytics on social and Web of Data, and supporting a variety of applications. Such applications can help provide situational awareness during an emergency, improve preparedness, and assist during the rebuilding/recovery phase of a …

Volume 06, Kristen Gains, Amanda Willis, Holly Backer, Monika Gutierrez, Cara O'Neal, Sara Nelson, Sasha Silberman, Jessica Beardsley, Jamie Gardner, Edward Peeples, Matthew Sakach, Tess Lione, Emily Wilkins, Kelsey Holt, Jessica Page, Jamie Clift, Charles Vancampen, Gilbert Hall, Jenny Nehrt, Kasey Dye, Amanda Tharp, Jamie Leeuwrik, Ashley Mcgee, Emily Poulin, Michael Kropf, Nick Pastore, Austin Polasky, Morgan Glasco, Laura L. Kahler, Melinda L. Edwards, Brandon C. Smith, Mariah Asbell, Cabell Edmunds, Amelia D. Perry, Alyssa Hayes, Irina Boothe, Perry Bason, James Early

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Caught Between Folklore and the Cold War: The Americanization of Russian Children's Literature by Kristen Gains

Graphic Design by Amanda Willis

Graphic Design by Holly Backer

Prejudices in Swiss German Accents by Monika Gutierrez

Photography by Cara O'Neal

Photography by Sara Nelson

Edmund Tyrone's Long Journey through Night by Sasha Silberman

Photography by Jessica Beardsley

Photography by Jamie Gardner and Edward Peeples

The Republican Razor: The Guillotine as a Symbol of Equality by Jamie Clift

Graphic Design by Matthew Sakach

Genocide: The Lasting Effects of Gender Stratification in Rwanda By Tess Lione and Emily …

Theoretical Analysis And Simulation Of Acute And Chronic Phase Hiv-1 Dynamics, Frank Nani, Mingxian Jin

Math and Computer Science Faculty Working Papers

Aims: The dynamics of HIV-1 induced AIDS is attributed to several biological variables, which characterize the stage, virulence and morbidity of the disease. The aim of this research is to use a necessary and sufficient subset of these immunological variables to construct a clinically plausible mathematical model of the patho-physiological dynamics of HIV-1 induced AIDS during the acute and chronic phases. This model incorporates the interactions between uninfected CD4+ T cells, HIV-1 infected CD4+ T cells, HIV-1 virions in the blood plasma, and specific cytotoxic CD8+ T cells. The major objective is to derive mathematical criteria depicting conditions under which …

Integrating Water Exclusion Theory Into Β Contacts To Predict Binding Free Energy Changes And Binding Hot Spots, Qian Liu, Steven C. H. Hoi, Chee Keong Kwoh, Limsoon Wong, Jinyan Li

Research Collection School Of Computing and Information Systems

Binding free energy and binding hot spots at protein-protein interfaces are two important research areas for understanding protein interactions. Computational methods have been developed previously for accurate prediction of binding free energy change upon mutation for interfacial residues. However, a large number of interrupted and unimportant atomic contacts are used in the training phase which caused accuracy loss. Results: This work proposes a new method, β ACV ASA , to predict the change of binding free energy after alanine mutations. β ACV ASA integrates accessible surface area (ASA) and our newly defined β contacts together into an atomic contact vector …

Integrating Water Exclusion Theory Into Β Contacts To Predict Binding Free Energy Changes And Binding Hot Spots, Qian Liu, Steven C. H. Hoi, Chee Keong Kwoh, Limsoon Wong, Jinyan Li

Research Collection School Of Computing and Information Systems

Binding free energy and binding hot spots at protein-protein interfaces are two important research areas for understanding protein interactions. Computational methods have been developed previously for accurate prediction of binding free energy change upon mutation for interfacial residues. However, a large number of interrupted and unimportant atomic contacts are used in the training phase which caused accuracy loss. Results: This work proposes a new method, β ACV ASA , to predict the change of binding free energy after alanine mutations. β ACV ASA integrates accessible surface area (ASA) and our newly defined β contacts together into an atomic contact vector …

Comparative Trust Management With Applications: Bayesian Approaches Emphasis, 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, and semantic sensor web. As agents providing content and services become increasingly removed from the agents that consume them, the issue of robust trust inference and update becomes 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 robust systems for managing trust in order 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 …