Other Computer Sciences Commons^™

Creating Optimal Conditions For Reproducible Data Analysis In R With ‘Fertile’, Audrey M. Bertin, Benjamin Baumer

Statistical and Data Sciences: Faculty Publications

The advancement of scientific knowledge increasingly depends on ensuring that data-driven research is reproducible: that two people with the same data obtain the same results. However, while the necessity of reproducibility is clear, there are significant behavioral and technical challenges that impede its widespread implementation and no clear consensus on standards of what constitutes reproducibility in published research. We present fertile, an R package that focuses on a series of common mistakes programmers make while conducting data science projects in R, primarily through the RStudio integrated development environment. fertile operates in two modes: proactively, to prevent reproducibility mistakes from happening …

Coevolution, Dynamics And Allostery Conspire In Shaping Cooperative Binding And Signal Transmission Of The Sars-Cov-2 Spike Protein With Human Angiotensin-Converting Enzyme 2, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Binding to the host receptor is a critical initial step for the coronavirus SARS-CoV-2 spike protein to enter into target cells and trigger virus transmission. A detailed dynamic and energetic view of the binding mechanisms underlying virus entry is not fully understood and the consensus around the molecular origins behind binding preferences of SARS-CoV-2 for binding with the angiotensin-converting enzyme 2 (ACE2) host receptor is yet to be established. In this work, we performed a comprehensive computational investigation in which sequence analysis and modeling of coevolutionary networks are combined with atomistic molecular simulations and comparative binding free energy analysis of …

Analyzing Yankees And Red Sox Sentiment Over The Course Of A Season, Connor Koch

Honors Projects in Data Science

This paper investigates data collected on twitter which references the Yankees or Red Sox during the 2020 Major League Baseball (MLB) season. The objective is to analyze the sentiment of tweets referencing the Yankees and Red Sox over the course of the season. In addition, an investigation of the networks within the data and the topics that were prevalent will be conducted. The 2020 MLB season was started late because of the COVID-19 pandemic and was a season like no other. The expectation of a dataset revolving around baseball is that the topics discussed would be about baseball. The findings …

Divide And Slide: Layer-Wise Refinement For Output Range Analysis Of Deep Neural Networks, Chao Huang, Jiameng Fan, Xin Chen, Wenchao Li, Qi Zhu

Computer Science Faculty Publications

In this article, we present a layer-wise refinement method for neural network output range analysis. While approaches such as nonlinear programming (NLP) can directly model the high nonlinearity brought by neural networks in output range analysis, they are known to be difficult to solve in general. We propose to use a convex polygonal relaxation (overapproximation) of the activation functions to cope with the nonlinearity. This allows us to encode the relaxed problem into a mixed-integer linear program (MILP), and control the tightness of the relaxation by adjusting the number of segments in the polygon. Starting with a segment number of …

Espade: An Efficient And Semantically Secure Shortest Path Discovery For Outsourced Location-Based Services, Bharath K. Samanthula, Divyadharshini Karthikeyan, Boxiang Dong, K. Anitha Kumari

Department of Computer Science Faculty Scholarship and Creative Works

With the rapid growth of smart devices and technological advancements in tracking geospatial data, the demand for Location-Based Services (LBS) is facing a constant rise in several domains, including military, healthcare and transportation. It is a natural step to migrate LBS to a cloud environment to achieve on-demand scalability and increased resiliency. Nonetheless, outsourcing sensitive location data to a third-party cloud provider raises a host of privacy concerns as the data owners have reduced visibility and control over the outsourced data. In this paper, we consider outsourced LBS where users want to retrieve map directions without disclosing their location information. …

Anatomy Of The Edelman: Measuring The World’S Best Analytics Projects, Michael F. Gorman, Lakshminarayana Nittala, Jeffrey M. Aldenb

MIS/OM/DS Faculty Publications

Each year, the INFORMS Edelman Award celebrates the best and most impactful implementations of operations research, management science, and analytics. As the Edelman Award approaches its 50-year mark, we provide a history and characterization of the award’s finalists and winners. We provide some basic descriptive analytics about the participating organizations and authors, the impact of their work, and the methods they employed. We also conduct predictive analytics on finalist submissions, gauging contributors to success in establishing winning entries. We find that predicting Edelman winners a priori is extremely difficult; however, given a set of finalists, predictive models based on monetary …

Forecasting Vegetation Health In The Mena Region By Predicting Vegetation Indicators With Machine Learning Models, Sachi Perera, Wenzhao Li, Erik Linstead, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

Machine learning (ML) techniques can be applied to predict and monitor drought conditions due to climate change. Predicting future vegetation health indicators (such as EVI, NDVI, and LAI) is one approach to forecast drought events for hotspots (e.g. Middle East and North Africa (MENA) regions). Recently, ML models were implemented to predict EVI values using parameters such as land types, time series, historical vegetation indices, land surface temperature, soil moisture, evapotranspiration etc. In this work, we collected the MODIS atmospherically corrected surface spectral reflectance imagery with multiple vegetation related indices for modeling and evaluation of drought conditions in the MENA …

Teaching Computational Machine Learning (Without Statistics), Katherine M. Kinnaird

Statistical and Data Sciences: Faculty Publications

This paper presents an undergraduate machine learning course that emphasizes algorithmic understanding and programming skills while assuming no statistical training. Emphasizing the development of good habits of mind, this course trains students to be independent machine learning practitioners through an iterative, cyclical framework for teaching concepts while adding increasing depth and nuance. Beginning with unsupervised learning, this course is sequenced as a series of machine learning ideas and concepts with specific algorithms acting as concrete examples. This paper also details course organization including evaluation practices and logistics.

Functional Morphology Of Gliding Flight Ii. Morphology Follows Predictions Of Gliding Performance, Jonathan Rader, Tyson L. Hedrick, Yanyan He, Lindsay D. Waldrop

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The evolution of wing morphology among birds, and its functional consequences, remains an open question, despite much attention. This is in part because the connection between form and function is difficult to test directly. To address this deficit, in prior work we used computational modeling and sensitivity analysis to interrogate the impact of altering wing aspect ratio, camber, and Reynolds number on aerodynamic performance, revealing the performance landscapes that avian evolution has explored. In the present work, we used a dataset of three-dimensionally scanned bird wings coupled with the performance landscapes to test two hypotheses regarding the evolutionary diversification of …

Exploring The Eating Disorder Examination Questionnaire, Clinical Impairment Assessment, And Autism Quotient To Identify Eating Disorder Vulnerability: A Cluster Analysis, Natalia Stewart Rosenfield, Erik Linstead

Engineering Faculty Articles and Research

Eating disorders are very complicated and many factors play a role in their manifestation. Furthermore, due to the variability in diagnosis and symptoms, treatment for an eating disorder is unique to the individual. As a result, there are numerous assessment tools available, which range from brief survey questionnaires to in-depth interviews conducted by a professional. One of the many benefits to using machine learning is that it offers new insight into datasets that researchers may not previously have, particularly when compared to traditional statistical methods. The aim of this paper was to employ k-means clustering to explore the Eating Disorder …

A Fortran-Keras Deep Learning Bridge For Scientific Computing, Jordan Ott, Mike Pritchard, Natalie Best, Erik Linstead, Milan Curcic, Pierre Baldi

Engineering Faculty Articles and Research

Implementing artificial neural networks is commonly achieved via high-level programming languages such as Python and easy-to-use deep learning libraries such as Keras. These software libraries come preloaded with a variety of network architectures, provide autodifferentiation, and support GPUs for fast and efficient computation. As a result, a deep learning practitioner will favor training a neural network model in Python, where these tools are readily available. However, many large-scale scientific computation projects are written in Fortran, making it difficult to integrate with modern deep learning methods. To alleviate this problem, we introduce a software library, the Fortran-Keras Bridge (FKB). This two-way …

A Multicenter Mixed-Effects Model For Inference And Prediction Of 72-H Return Visits To The Emergency Department For Adult Patients With Trauma-Related Diagnoses, Ehsan Yaghmaei, Louis Ehwerhemuepha, William Feaster, David Gibbs, Cyril Rakovski

Mathematics, Physics, and Computer Science Faculty Articles and Research

Objective

Emergency department (ED) return visits within 72 h may be a sign of poor quality of care and entail unnecessary use of healthcare resources. In this study, we compare the performance of two leading statistical and machine learning classification algorithms, and we use the best performing approach to identify novel risk factors of ED return visits.

Methods

We analyzed 3.2 million ED encounters with at least one diagnosis under “injury, poisoning and certain other consequences of external causes” and “external causes of morbidity.” These encounters included patients 18 years or older from across 128 emergency room facilities in the …

Functional Morphology Of Gliding Flight I. Modeling Reveals Distinct Performance Landscapes Based On Soaring Strategies, Lindsay D. Waldrop, Yanyan He, Tyson L. Hedrick, Jonathan Rader

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The physics of flight influences the morphology of bird wings through natural selection on flight performance. The connection between wing morphology and performance is unclear due to the complex relationships between various parameters of flight. In order to better understand this connection, we present a holistic analysis of gliding flight that preserves complex relationships between parameters. We use a computational model of gliding flight, along with analysis by uncertainty quantification, to 1) create performance landscapes of gliding based on output metrics (maximum lift-to-drag ratio, minimum gliding angle, minimum sinking speed, lift coefficient at minimum sinking speed); and 2) predict what …

Causality In Microbiomes, Md Musfiqur Rahman Sazal

FIU Electronic Theses and Dissertations

No abstract provided.

Children In 2077: Designing Children’S Technologies In The Age Of Transhumanism, Oğuz Oz Buruk, Oğuzhan Özcan, Gökçe Elif Baykal, Tilbe Göksun, Selçuk Acar, Güler Akduman, Mehmet Aydın Baytaş, Ceylan Beşevli, Joe Best, Aykut Coşkun, Hüseyin Uğur Genç, Baki Kocaballi, Samuli Laato, Cássia Mota, Konstantinos Papangelis, Marigo Raftopoulos, Richard Ramchurn, Juan Sádaba, Mattia Thibault, Annika Wolff, Mert Yıldız

Presentations and other scholarship

What for and how will we design children’s technologies in the transhumanism age, and what stance will we take as designers? This paper aims to answer this question with 13 fictional abstracts from sixteen authors of different countries, institutions and disciplines. Transhumanist thinking envisions enhancing human body and mind by blending human biology with technological augmentations. Fundamentally, it seeks to improve the human species, yet the impacts of such movement are unknown and the implications on children’s lives and technologies were not explored deeply. In an age, where technologies can clearly be defined as transhumanist, such as under-skin chips or …

A Machine Learning Approach To Delineating Neighborhoods From Geocoded Appraisal Data, Rao Hamza Ali, Josh Graves, Stanley Wu, Jenny Lee, Erik Linstead

Engineering Faculty Articles and Research

Identification of neighborhoods is an important, financially-driven topic in real estate. It is known that the real estate industry uses ZIP (postal) codes and Census tracts as a source of land demarcation to categorize properties with respect to their price. These demarcated boundaries are static and are inflexible to the shift in the real estate market and fail to represent its dynamics, such as in the case of an up-and-coming residential project. Delineated neighborhoods are also used in socioeconomic and demographic analyses where statistics are computed at a neighborhood level. Current practices of delineating neighborhoods have mostly ignored the information …

Automatic Recognition, Segmentation, And Sex Assignment Of Nocturnal Asthmatic Coughs And Cough Epochs In Smartphone Audio Recordings: Observational Field Study, Filipe Barata, Peter Tinschert, Frank Rassouli, Claudia Steurer-Stey, Elgar Fleisch, Milo Puhan, Martin Brutsche, David Kotz, Tobias Kowatsch

Dartmouth Scholarship

Background: Asthma is one of the most prevalent chronic respiratory diseases. Despite increased investment in treatment, little progress has been made in the early recognition and treatment of asthma exacerbations over the last decade. Nocturnal cough monitoring may provide an opportunity to identify patients at risk for imminent exacerbations. Recently developed approaches enable smartphone-based cough monitoring. These approaches, however, have not undergone longitudinal overnight testing nor have they been specifically evaluated in the context of asthma. Also, the problem of distinguishing partner coughs from patient coughs when two or more people are sleeping in the same room using contact-free audio …

Motivational Principles And Personalisation Needs For Geo-Crowdsourced Intangible Cultural Heritage Mobile Applications, Federica Lucia Vinella, Ioanna Lykourentzou, Konstantinos Papangelis

Presentations and other scholarship

Whether it’s for altruistic reasons, personal gains, or third party’s interests, users are influenced by different kinds of motivations when making use of mobile geo-crowdsourcing applications (geoCAs). These reasons, extrinsic and/or intrinsic, must be factored in when evaluating the use intention of these applications and how effective they are. A functional geoCA, particularly if designed for Volunteered Geographic Information (VGI), is the one that persuades and engages its users, by accounting for their diversity of needs across a period of time. This paper explores a number of proven and novel motivational factors destined for the preservation and collection of Intangible …

Allosteric Regulation At The Crossroads Of New Technologies: Multiscale Modeling, Networks, And Machine Learning, Gennady M. Verkhivker, Steve Agajanian, Guang Hu, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Allosteric regulation is a common mechanism employed by complex biomolecular systems for regulation of activity and adaptability in the cellular environment, serving as an effective molecular tool for cellular communication. As an intrinsic but elusive property, allostery is a ubiquitous phenomenon where binding or disturbing of a distal site in a protein can functionally control its activity and is considered as the “second secret of life.” The fundamental biological importance and complexity of these processes require a multi-faceted platform of synergistically integrated approaches for prediction and characterization of allosteric functional states, atomistic reconstruction of allosteric regulatory mechanisms and discovery of …

Automatic Learning Of Document Section Structure For Ontology-Based Semantic Search, Deya Banisakher

FIU Electronic Theses and Dissertations

Modeling natural human behavior in understanding written language is crucial for developing true artificial intelligence. For people, words convey certain semantic concepts. While documents represent an abstract concept---they are collections of text organized in some logical structure, that is, sentences, paragraphs, sections, and so on. Similar to words, these document structures, are used to convey a logical flow of semantic concepts. Machines however, only view words as spans of characters and documents as mere collections of free-text, missing any underlying meanings behind words and the logical structure of those documents.

Automatic semantic concept detection is the process by which the …

Patterns Of Population Displacement During Mega-Fires In California Detected Using Facebook Disaster Maps, Shenyue Jia, Seung Hee Kim, Son V. Nghiem, Paul Doherty, Menas Kafatos

Mathematics, Physics, and Computer Science Faculty Articles and Research

The Facebook Disaster Maps (FBDM) work presented here is the first time this platform has been used to provide analysis-ready population change products derived from crowdsourced data targeting disaster relief practices. We evaluate the representativeness of FBDM data using the Mann-Kendall test and emerging hot and cold spots in an anomaly analysis to reveal the trend, magnitude, and agglommeration of population displacement during the Mendocino Complex and Woolsey fires in California, USA. Our results show that the distribution of FBDM pre-crisis users fits well with the total population from different sources. Due to usage habits, the elder population is underrepresented …

Summed Batch Lexicase Selection On Software Synthesis Problems, Joseph Deglman

Student Research, Papers, and Creative Works

Lexicase selection is one of the most successful parent selection methods in evolutionary computation. However, it has the drawback of being a more computationally involved process and thus taking more time compared to other selection methods, such as tournament selection. Here, we study a version of lexicase selection where test cases are combined into several composite errors, called summed batch lexicase selection; the hope being faster but still reasonable success. Runs on some software synthesis problems show that a larger batch size tends to reduce the success rate of runs, but the results are not very conclusive as the number …

Developing Open Source Software Using Version Control Systems: An Introduction To The Git Language For Documenting Your Computational Research, Jared D. Smith, Jonathan D. Herman

All ECSTATIC Materials

Version control systems track the history of code as it is committed (saved) by any number of developers. Have you made a coding error and cannot debug it? Version control systems allow for resetting code back to when it worked, and show what code has changed since previous commits.

The contents of this lecture provide an introduction to the git version control language, GitHub for cloud hosting open source code repositories, and tutorials that demonstrate common and useful git and GitHub practices. This lecture is intended to be coupled with a discussion on creating reproducible computational research.

The zipped folder …

Homo Ludens Moralis: Designing And Developing A Board Game To Teach Ethics For Ict Education, Damian Gordon, Dympna O'Sullivan, Ioannis Stavrakakis, Andrea Curley

Conference papers

The ICT ethical landscape is changing at an astonishing rate, as technologies become more complex, and people choose to interact with them in new and distinct ways, the resultant interactions are more novel and less easy to categorise using traditional ethical frameworks. It is vitally important that the developers of these technologies do not live in an ethical vacuum; that they think about the uses and abuses of their creations, and take some measures to prevent others being harmed by their work.

To equip these developers to rise to this challenge and to create a positive future for the use …

Reducing Run-Time Adaptation Space Via Analysis Of Possible Utility Bounds, Clay Stevens, Hamid Bagheri

CSE Conference and Workshop Papers

Self-adaptive systems often employ dynamic programming or similar techniques to select optimal adaptations at run-time. These techniques suffer from the “curse of dimensionality", increasing the cost of run-time adaptation decisions. We propose a novel approach that improves upon the state-of-the-art proactive self-adaptation techniques to reduce the number of possible adaptations that need be considered for each run-time adaptation decision. The approach, realized in a tool called Thallium, employs a combination of automated formal modeling techniques to (i) analyze a structural model of the system showing which configurations are reachable from other configurations and (ii) compute the utility that can be …

An Inventory Of Existing Neuroprivacy Controls, Dustin Steinhagen, Houssain Kettani

Research & Publications

Brain-Computer Interfaces (BCIs) facilitate communication between brains and computers. As these devices become increasingly popular outside of the medical context, research interest in brain privacy risks and countermeasures has bloomed. Several neuroprivacy threats have been identified in the literature, including brain malware, personal data being contained in collected brainwaves and the inadequacy of legal regimes with regards to neural data protection. Dozens of controls have been proposed or implemented for protecting neuroprivacy, although it has not been immediately apparent what the landscape of neuroprivacy controls consists of. This paper inventories the implemented and proposed neuroprivacy risk mitigation techniques from open …

Synergistic Use Of Remote Sensing And Modeling For Estimating Net Primary Productivity In The Red Sea With Vgpm, Eppley-Vgpm, And Cbpm Models Intercomparison, Wenzhao Li, Surya Prakash Tiwari, Hesham El-Askary, Mohamed Ali Qurban, Vassilis Amiridis, K. P. Manikandan, Michael J. Garay, Olga V. Kalashnikova, Thomas C. Piechota, Daniele C. Struppa

Mathematics, Physics, and Computer Science Faculty Articles and Research

Primary productivity (PP) has been recently investigated using remote sensing-based models over quite limited geographical areas of the Red Sea. This work sheds light on how phytoplankton and primary production would react to the effects of global warming in the extreme environment of the Red Sea and, hence, illuminates how similar regions may behave in the context of climate variability. study focuses on using satellite observations to conduct an intercomparison of three net primary production (NPP) models--the vertically generalized production model (VGPM), the Eppley-VGPM, and the carbon-based production model (CbPM)--produced over the Red Sea domain for the 1998-2018 time period. …

Ml-Medic: A Preliminary Study Of An Interactive Visual Analysis Tool Facilitating Clinical Applications Of Machine Learning For Precision Medicine, Laura Stevens, David Kao, Jennifer Hall, Carsten Görg, Kaitlyn Abdo, Erik Linstead

Engineering Faculty Articles and Research

Accessible interactive tools that integrate machine learning methods with clinical research and reduce the programming experience required are needed to move science forward. Here, we present Machine Learning for Medical Exploration and Data-Inspired Care (ML-MEDIC), a point-and-click, interactive tool with a visual interface for facilitating machine learning and statistical analyses in clinical research. We deployed ML-MEDIC in the American Heart Association (AHA) Precision Medicine Platform to provide secure internet access and facilitate collaboration. ML-MEDIC’s efficacy for facilitating the adoption of machine learning was evaluated through two case studies in collaboration with clinical domain experts. A domain expert review was also …

A Model For The Spread Of Infectious Diseases In A Region, Elizabeth Hunter, Brian Mac Namee, John D. Kelleher

Articles

In understanding the dynamics of the spread of an infectious disease, it is important to understand how a town’s place in a network of towns within a region will impact how the disease spreads to that town and from that town. In this article, we take a model for the spread of an infectious disease in a single town and scale it up to simulate a region containing multiple towns. The model is validated by looking at how adding additional towns and commuters influences the outbreak in a single town. We then look at how the centrality of a town …

A Vertical Cooperation Model To Manage Digital Collections And Institutional Resources, Jack M. Maness, Kim Pham, Fernando Reyes, Jeff Rynhart

University Libraries: Faculty Scholarship

The technology space of the University of Denver Libraries to manage digital collections and institutional resources isn’t relegated to one department on campus – rather, it distributed across a network of collaborators with the skills and expertise to provide that support. The infrastructure, which is comprised of an archival metadata management system (Archivespace), a digital repository (Node.js + ElasticSearch), preservation storage (ArchivesDirect), and a streaming server (Kaltura) is independently but cooperatively managed across IT, library departments and vendors. The coordinated eort of digital curation activities still allows each group to focus on the service they have the most vested interest …