Physical Sciences and Mathematics Commons^™

Sensor Emulation With Physiolocal Data In Immersive Virtual Reality Driving Simulator, Jungsu Pak, Oliver Mathias, Ariane Guirguis, Uri Maoz

Student Scholar Symposium Abstracts and Posters

Can we enhance the safety and comfort of AVs by training AVs with physiological data of human drivers? We will train and compare AV algorithm with/without physiological data.

The Trolley Problem In Virtual Reality, Jungsu Pak, Ariane Guirguis, Nicholas Mirchandani, Scott Cummings, Uri Maoz

Student Scholar Symposium Abstracts and Posters

Would people react to the Trolley problem differently based on the medium? Immersive Virtual Reality Driving Simulator was used to examine participants respond to the trolley problem in a realistic and controlled simulated environment.

Food Scan: A Yelp For Dietary Restrictions, Andrew M. Bauer, Charlie Story, Curren Taber

Student Scholar Symposium Abstracts and Posters

Food restrictions pose a serious issue for Chapman students, with consequences as extreme as anaphylactic shock and death. Our team started the Food Scan project with a simple goal of streamlining how individuals with dietary restrictions find safe places to eat or buy food. The project name highlights our intention to clarify restaurant menu items for users by displaying important allergen and dietary information. Using Human-Computer Interaction methods, our team chose to develop a technology that is usable, effective, enjoyable, and inclusive by involving users during the entire design process. By integrating multimodal interfaces (including speech to text inputs), we …

Improving Medication Information Presentation Through Interactive Visualization In Mobile Apps: Human Factors Design, Don Roosan, Yan Li, Anandi Law, Huy Truong, Mazharul Karim, Jay Chok, Moom Roosan

Pharmacy Faculty Articles and Research

Background: Despite the detailed patient package inserts (PPIs) with prescription drugs that communicate crucial information about safety, there is a critical gap between patient understanding and the knowledge presented. As a result, patients may suffer from adverse events. We propose using human factors design methodologies such as hierarchical task analysis (HTA) and interactive visualization to bridge this gap. We hypothesize that an innovative mobile app employing human factors design with an interactive visualization can deliver PPI information aligned with patients’ information processing heuristics. Such an app may help patients gain an improved overall knowledge of medications.

Objective: The …

Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study Of Plasmodium Falciparum Hsp70s, Arnold Amusengeri, Lindy Astl, Kevin Lobb, Gennady M. Verkhivker, Özlem Tastan Bishop

Mathematics, Physics, and Computer Science Faculty Articles and Research

Combating malaria is almost a never-ending battle, as Plasmodium parasites develop resistance to the drugs used against them, as observed recently in artemisinin-based combination therapies. The main concern now is if the resistant parasite strains spread from Southeast Asia to Africa, the continent hosting most malaria cases. To prevent catastrophic results, we need to find non-conventional approaches. Allosteric drug targeting sites and modulators might be a new hope for malarial treatments. Heat shock proteins (HSPs) are potential malarial drug targets and have complex allosteric control mechanisms. Yet, studies on designing allosteric modulators against them are limited. Here, we identified allosteric …

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 …

Paper Prototyping Comfortable Vr Play For Diverse Sensory Needs, Louanne E. Boyd, Kendra Day, Ben Wasserman, Kaitlyn Abdo, Gillian Hayes, Erik J. Linstead

Engineering Faculty Articles and Research

We co-designed paper prototype dashboards for virtual environments for three children with diverse sensory needs. Our goal was to determine individual interaction styles in order to enable comfortable and inclusive play. As a first step towards an inclusive virtual world, we began with designing for three sensory-diverse children who have labels of neurotypical, ADHD, and autism respectively. We focused on their leisure interests and their individual sensory profiles. We present the results of co-design with family members and paper prototyping sessions conducted by family members with the children. The results contribute preliminary empirical findings for accommodating different levels of engagement …

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 …

Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an …

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 …