Other Computer Sciences Commons^™

Vrsensory: Designing Inclusive Virtual Games With Neurodiverse Children, Ben Wasserman, Derek Prate, Bryce Purnell, Alex Muse, Kaitlyn Abdo, Kendra Day, Louanne Boyd

Engineering Faculty Articles and Research

We explore virtual environments and accompanying interaction styles to enable inclusive play. In designing games for three neurodiverse children, we explore how designing for sensory diversity can be understood through a formal game design framework. Our process reveals that by using sensory processing needs as requirements we can make sensory and social accessible play spaces. We contribute empirical findings for accommodating sensory differences for neurodiverse children in a way that supports inclusive play. Specifically, we detail the sensory driven design choices that not only support the enjoyability of the leisure activities, but that also support the social inclusion of sensory-diverse …

Editorial: Machine Learning In Biomolecular Simulations, Gennady M. Verkhivker, Vojtech Spiwok, Francesco Luigi Gervasio

Mathematics, Physics, and Computer Science Faculty Articles and Research

"Interest in machine learning is growing in all fields of science, industry, and business. This interest was not primarily initiated by new theoretical findings. Interestingly, the theoretical basis of the majority of machine learning techniques, such as artificial neural networks, decision trees, or kernel methods, have been known for a relatively long time. Instead, there are other effects that triggered the recent boom of machine learning."

Identifying Depression In The National Health And Nutrition Examination Survey Data Using A Deep Learning Algorithm, Jihoon Oh, Kyongsik Yun, Uri Maoz, Tae-Suk Kim, Jeong-Ho Chae

Psychology Faculty Articles and Research

Background

As depression is the leading cause of disability worldwide, large-scale surveys have been conducted to establish the occurrence and risk factors of depression. However, accurately estimating epidemiological factors leading up to depression has remained challenging. Deep-learning algorithms can be applied to assess the factors leading up to prevalence and clinical manifestations of depression.

Methods

Customized deep-neural-network and machine-learning classifiers were assessed using survey data from 19,725 participants from the NHANES database (from 1999 through 2014) and 4949 from the South Korea NHANES (K-NHANES) database in 2014.

Results

A deep-learning algorithm showed area under the receiver operating characteristic curve (AUCs) …

Integration Of Random Forest Classifiers And Deep Convolutional Neural Networks For Classification And Biomolecular Modeling Of Cancer Driver Mutations, Steve Agajanian, Odeyemi Oluyemi, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Development of machine learning solutions for prediction of functional and clinical significance of cancer driver genes and mutations are paramount in modern biomedical research and have gained a significant momentum in a recent decade. In this work, we integrate different machine learning approaches, including tree based methods, random forest and gradient boosted tree (GBT) classifiers along with deep convolutional neural networks (CNN) for prediction of cancer driver mutations in the genomic datasets. The feasibility of CNN in using raw nucleotide sequences for classification of cancer driver mutations was initially explored by employing label encoding, one hot encoding, and embedding to …

Low-Energy Acceleration Of Binarized Convolutional Neural Networks Using A Spin Hall Effect Based Logic-In-Memory Architecture, Ashkan Samiee, Payal Borulkar, Ronald F. Demara, Peiyi Zhao, Yu Bai

Engineering Faculty Articles and Research

Deep Learning (DL) offers the advantages of high accuracy performance at tasks such as image recognition, learning of complex intelligent behaviors, and large-scale information retrieval problems such as intelligent web search. To attain the benefits of DL, the high computational and energy-consumption demands imposed by the underlying processing, interconnect, and memory devices on which software-based DL executes can benefit substantially from innovative hardware implementations. Logic-in-Memory (LIM) architectures offer potential approaches to attaining such throughput goals within area and energy constraints starting with the lowest layers of the hardware stack. In this paper, we develop a Spintronic Logic-in-Memory (S-LIM) XNOR neural …

Hartree-Fock Implementation For Pedagogical & Research Purposes, Gary Zeri, Jerry Larue

Student Scholar Symposium Abstracts and Posters

Often during the process of innovation and scientific advancement, experimentation is the key to increasing the current knowledge of body. Unfortunately, experimentation can often require extended periods of time as well as monetary resources to perform. The use of computational chemistry can increase the rate of scientific advancement by simulating experimental results, allowing researchers to focus on experiments whose computational counterparts show the greatest promise. Students new to the sciences are often not exposed to these methods due to their complexities. The purpose of this project is to implement the Hartree-Fock method, one type of computational chemistry method, whose programming …

A Virtual Reality System For Practicing Conversation Skills For Children With Autism, Natalia Stewart Rosenfield, Kathleen Lamkin, Jennifer Re, Kendra Day, Louanne E. Boyd, Erik J. Linstead

Engineering Faculty Articles and Research

We describe a virtual reality environment, Bob’s Fish Shop, which provides a system where users diagnosed with Autism Spectrum Disorder (ASD) can practice social interactions in a safe and controlled environment. A case study is presented which suggests such an environment can provide the opportunity for users to build the skills necessary to carry out a conversation without the fear of negative social consequences present in the physical world. Through the repetition and analysis of these virtual interactions, users can improve social and conversational understanding.

Applications Of Supervised Machine Learning In Autism Spectrum Disorder Research: A Review, Kayleigh K. Hyde, Marlena N. Novack, Nicholas Lahaye, Chelsea Parlett-Pelleriti, Raymond Anden, Dennis R. Dixon, Erik Linstead

Engineering Faculty Articles and Research

Autism spectrum disorder (ASD) research has yet to leverage "big data" on the same scale as other fields; however, advancements in easy, affordable data collection and analysis may soon make this a reality. Indeed, there has been a notable increase in research literature evaluating the effectiveness of machine learning for diagnosing ASD, exploring its genetic underpinnings, and designing effective interventions. This paper provides a comprehensive review of 45 papers utilizing supervised machine learning in ASD, including algorithms for classification and text analysis. The goal of the paper is to identify and describe supervised machine learning trends in ASD literature as …

Extending Set Functors To Generalised Metric Spaces, Adriana Balan, Alexander Kurz, Jiří Velebil

Mathematics, Physics, and Computer Science Faculty Articles and Research

For a commutative quantale V, the category V-cat can be perceived as a category of generalised metric spaces and non-expanding maps. We show that any type constructor T (formalised as an endofunctor on sets) can be extended in a canonical way to a type constructor T_V on V-cat. The proof yields methods of explicitly calculating the extension in concrete examples, which cover well-known notions such as the Pompeiu-Hausdorff metric as well as new ones.

Conceptually, this allows us to to solve the same recursive domain equation X ≅ TX in different categories (such as sets and metric spaces) and …

Exploring Age-Related Metamemory Differences Using Modified Brier Scores And Hierarchical Clustering, Chelsea Parlett-Pelleriti, Grace C. Lin, Masha R. Jones, Erik Linstead, Susanne M. Jaeggi

Engineering Faculty Articles and Research

Older adults (OAs) typically experience memory failures as they age. However, with some exceptions, studies of OAs’ ability to assess their own memory functions—Metamemory (MM)— find little evidence that this function is susceptible to age-related decline. Our study examines OAs’ and young adults’ (YAs) MM performance and strategy use. Groups of YAs (N = 138) and OAs (N = 79) performed a MM task that required participants to place bets on how likely they were to remember words in a list. Our analytical approach includes hierarchical clustering, and we introduce a new measure of MM—the modified Brier—in order to adjust …

Leveling The Playing Field: Supporting Neurodiversity Via Virtual Realities, Louanne E. Boyd, Kendra Day, Natalia Stewart, Kaitlyn Abdo, Kathleen Lamkin, Erik J. Linstead

Mathematics, Physics, and Computer Science Faculty Articles and Research

Neurodiversity is a term that encapsulates the diverse expression of human neurology. By thinking in broad terms about neurological development, we can become focused on delivering a diverse set of design features to meet the needs of the human condition. In this work, we move toward developing virtual environments that support variations in sensory processing. If we understand that people have differences in sensory perception that result in their own unique sensory traits, many of which are clustered by diagnostic labels such as Autism Spectrum Disorder (ASD), Sensory Processing Disorder, Attention-Deficit/Hyperactivity Disorder, Rett syndrome, dyslexia, and so on, then we …

The Chapman Bone Algorithm: A Diagnostic Alternative For The Evaluation Of Osteoporosis, Elise Levesque, Anton Ketterer, Wajiha Memon, Cameron James, Noah Barrett, Cyril Rakovski, Frank Frisch

Mathematics, Physics, and Computer Science Faculty Articles and Research

Osteoporosis is the most common metabolic bone disease and goes largely undiagnosed throughout the world, due to the inaccessibility of DXA machines. Multivariate analyses of serum bone turnover markers were evaluated in 226 Orange County, California, residents with the intent to determine if serum osteocalcin and serum pyridinoline cross-links could be used to detect the onset of osteoporosis as effectively as a DXA scan. Descriptive analyses of the demographic and lab characteristics of the participants were performed through frequency, means and standard deviation estimations. We implemented logistic regression modeling to find the best classification algorithm for osteoporosis. All calculations and …

Investigating On Through Glass Via Based Rf Passives For 3-D Integration, Libo Qian, Jifei Sang, Yinshui Xia, Jian Wang, Peiyi Zhao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Due to low dielectric loss and low cost, glass is developed as a promising material for advanced interposers in 2.5-D and 3-D integration. In this paper, through glass vias (TGVs) are used to implement inductors for minimal footprint and large quality factor. Based on the proposed physical structure, the impact of various process and design parameters on the electrical characteristics of TGV inductors is investigated with 3-D electromagnetic simulator HFSS. It is observed that TGV inductors have identical inductance and larger quality factor in comparison with their through silicon via counterparts. Using TGV inductors and parallel plate capacitors, a compact …

Player-Response: On The Nature Of Interactive Narratives As Literature, Lee Feldman

English (MA) Theses

In recent years, having evolved beyond solely play-based interactions, it is now possible to analyze video games alongside other narrative forms, such as novels and films. Video games now involve rich stories that require input and interaction on behalf of the player. This level of agency likens video games to a kind of modern hypertext, networking and weaving various narrative threads together, something which traditional modes of media lack. When examined from the lens of reader-response criticism, this interaction deepens even further, acknowledging the player’s experience as a valid interpretation of a video game’s plot. The wide freedom of choice …

Automating Data Analysis For Two-Dimensional Gas Chromatography/Time-Of-Flight Mass Spectrometry Non-Targeted Analysis Of Comparative Samples, Ivan A. Titaley, O. Maduka Ogba, Leah Chibwe, Eunha Hoh, Paul H.-Y. Cheong, Staci L. Massey Simonich

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Non-targeted analysis of environmental samples, using comprehensive two‐dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO^® ChromaTOF^® software and facilitates selection of analytes of interest based on peak area …

Atomistic Simulations And Network-Based Modeling Of The Hsp90-Cdc37 Chaperone Binding With Cdk4 Client Protein: A Mechanism Of Chaperoning Kinase Clients By Exploiting Weak Spots Of Intrinsically Dynamic Kinase Domains, John Czemeres, Kurt Buse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37- Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic …

Virtual Reality As A Training Tool To Treat Physical Inactivity In Children, Adam W. Kiefer, David Pincus, Michael J. Richardson, Gregory D. Myer

Psychology Faculty Articles and Research

Lack of adequate physical activity in children is an epidemic that can result in obesity and other poor health outcomes across the lifespan. Physical activity interventions focused on motor skill competence continue to be developed, but some interventions, such as neuromuscular training (NMT), may be limited in how early they can be implemented due to dependence on the child’s level of cognitive and perceptual-motor development. Early implementation of motor-rich activities that support motor skill development in children is critical for the development of healthy levels of physical activity that carry through into adulthood. Virtual reality (VR) training may be beneficial …

A Cluster Analysis Of Challenging Behaviors In Autism Spectrum Disorder, Elizabeth Stevens, Abigail Atchison, Laura Stevens, Esther Hong, Doreen Granpeesheh, Dennis Dixon, Erik J. Linstead

Mathematics, Physics, and Computer Science Faculty Articles and Research

We apply cluster analysis to a sample of 2,116 children with Autism Spectrum Disorder in order to identify patterns of challenging behaviors observed in home and centerbased clinical settings. The largest study of this type to date, and the first to employ machine learning, our results indicate that while the presence of multiple challenging behaviors is common, in most cases a dominant behavior emerges. Furthermore, the trend is also observed when we train our cluster models on the male and female samples separately. This work provides a basis for future studies to understand the relationship of challenging behavior profiles to …

Critical Digital Literacies Across Scales And Beneath The Screen, Noah Asher Golden

Education Faculty Articles and Research

Digital technologies and education scholarship tend to focus on either individual creative design or analysis of the political economy. To better understand how ideologies travel across networks, critical digital literacies must focus on enactments beneath the screen, as the linguistic constructs known as software can enact interests across scales of activity to “disembed” local actions and meaning. Investigations of these mobilities and disembedding effects challenge popular notions of digital technologies as neutral, rendering overt the ways that algorithms can naturalize manifestations of power and social arrangements. Such a framework allows for descriptive analyses of the ways hegemonic discourses are enacted …

Using Tablet Technologies To Engage And Motivate Urban High School Students, Nicol R. Howard, Keith Howard

Education Faculty Articles and Research

In this two-year study, researchers examined the impact of using tablet technologies across content areas in an urban high school setting. Class observations provided notable examples of how student motivation and learning appeared to be enhanced by use of the iPads in conjunction with opportunities to collaborate and be creative in the context of their learning. Interviews from a set of teachers with a range of classroom teaching experience provided multiple perspectives of the program’s impact. The opportunity for teachers and students to have the flexibility to select the apps they believe achieve curricular and/or learning goals supports the shift …

An Evaluation Of The Effects Of Intensity And Duration On Outcomes Across Treatment Domains For Children With Autism Spectrum Disorder, Erik J. Linstead, D. R. Dixon, E. Hong, C. O. Burns, Ryan French, M. N. Novack, D. Granpeesheh

Mathematics, Physics, and Computer Science Faculty Articles and Research

Applied behavior analysis (ABA) is considered an effective treatment for individuals with autism spectrum disorder (ASD), and many researchers have further investigated factors associated with treatment outcomes. However, few studies have focused on whether treatment intensity and duration have differential influences on separate skills. The aim of the current study was to investigate how treatment intensity and duration impact learning across different treatment domains, including academic, adaptive, cognitive, executive function, language, motor, play, and social. Separate multiple linear regression analyses were used to evaluate these relationships. Participants included 1468 children with ASD, ages 18 months to 12 years old, M= …

Optimized Forecasting Of Dominant U.S. Stock Market Equities Using Univariate And Multivariate Time Series Analysis Methods, Michael Schwartz

Computational and Data Sciences Theses

This dissertation documents an investigation into forecasting U.S. stock market equities via two very different time series analysis techniques: 1) autoregressive integrated moving average (ARIMA), and 2) singular spectrum analysis (SSA). Approximately 40% of the S&P 500 stocks are analyzed. Forecasts are generated for one and five days ahead using daily closing prices. Univariate and multivariate structures are applied and results are compared. One objective is to explore the hypothesis that a multivariate model produces superior performance over a univariate configuration. Another objective is to compare the forecasting performance of ARIMA to SSA, as SSA is a relatively recent development …

Relation Algebras, Idempotent Semirings And Generalized Bunched Implication Algebras, Peter Jipsen

Mathematics, Physics, and Computer Science Faculty Articles and Research

This paper investigates connections between algebraic structures that are common in theoretical computer science and algebraic logic. Idempotent semirings are the basis of Kleene algebras, relation algebras, residuated lattices and bunched implication algebras. Extending a result of Chajda and Länger, we show that involutive residuated lattices are determined by a pair of dually isomorphic idempotent semirings on the same set, and this result also applies to relation algebras. Generalized bunched implication algebras (GBI-algebras for short) are residuated lattices expanded with a Heyting implication. We construct bounded cyclic involutive GBI-algebras from so-called weakening relations, and prove that the class of weakening …

Computational Analysis Of Residue Interaction Networks And Coevolutionary Relationships In The Hsp70 Chaperones: A Community- Hopping Model Of Allosteric Regulation And Communication, Gabrielle Stetz, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks …

Foreword: Special Issue On Coalgebraic Logic, Alexander Kurz

Engineering Faculty Articles and Research

The second Dagstuhl seminar on coalgebraic logics took place from October 7-12, 2012, in the Leibniz Forschungszentrum Schloss Dagstuhl, following a successful earlier one in December 2009. From the 44 researchers who attended and the 30 talks presented, this collection highlights some of the progress that has been made in the field. We are grateful to Giuseppe Longo and his interest in a special issue in Mathematical Structures in Computer Science.

The Positivication Of Coalgebraic Logics, Fredrik Dahlqvist, Alexander Kurz

Engineering Faculty Articles and Research

We present positive coalgebraic logic in full generality, and show how to obtain a positive coalgebraic logic from a boolean one. On the model side this involves canonically computing a endofunctor T': Pos->Pos from an endofunctor T: Set->Set, in a procedure previously defined by the second author et alii called posetification. On the syntax side, it involves canonically computing a syntax-building functor L': DL->DL from a syntax-building functor L: BA->BA, in a dual procedure which we call positivication. These operations are interesting in their own right and we explicitly compute posetifications and positivications in the case …

Features Of Agent-Based Models, Reiko Heckel, Alexander Kurz, Edmund Chattoe-Brown

Engineering Faculty Articles and Research

The design of agent-based models (ABMs) is often ad-hoc when it comes to defining their scope. In order for the inclusion of features such as network structure, location, or dynamic change to be justified, their role in a model should be systematically analysed. We propose a mechanism to compare and assess the impact of such features. In particular we are using techniques from software engineering and semantics to support the development and assessment of ABMs, such as graph transformations as semantic representations for agent-based models, feature diagrams to identify ingredients under consideration, and extension relations between graph transformation systems to …

Quasivarieties And Varieties Of Ordered Algebras: Regularity And Exactness, Alexander Kurz

Engineering Faculty Articles and Research

We characterise quasivarieties and varieties of ordered algebras categorically in terms of regularity, exactness and the existence of a suitable generator. The notions of regularity and exactness need to be understood in the sense of category theory enriched over posets.

We also prove that finitary varieties of ordered algebras are cocompletions of their theories under sifted colimits (again, in the enriched sense).

Multi-Type Display Calculus For Propositional Dynamic Logic, Sabine Frittella, Giuseppe Greco, Alexander Kurz, Alessandra Palmigiano

Engineering Faculty Articles and Research

We introduce a multi-type display calculus for Propositional Dynamic Logic (PDL). This calculus is complete w.r.t. PDL, and enjoys Belnap-style cut-elimination and subformula property.

Tool Support For Reasoning In Display Calculi, Samuel Balco, Sabine Frittella, Giuseppe Greco, Alexander Kurz, Alessandra Palmigiano

Engineering Faculty Articles and Research

We present a tool for reasoning in and about propositional sequent calculi. One aim is to support reasoning in calculi that contain a hundred rules or more, so that even relatively small pen and paper derivations become tedious and error prone. As an example, we implement the display calculus D.EAK of dynamic epistemic logic. Second, we provide embeddings of the calculus in the theorem prover Isabelle for formalising proofs about D.EAK. As a case study we show that the solution of the muddy children puzzle is derivable for any number of muddy children. Third, there is a set of meta-tools, …