Physical Sciences and Mathematics Commons^™

Computational Approaches To Facilitate Automated Interchange Between Music And Art, Rao Hamza Ali

Computational and Data Sciences (PhD) Dissertations

Recently, there has been a tremendous increase in generating and synthesizing music and art using various computational techniques. An area that is still under-researched, however, is how one medium can be converted into the other, while maintaining the overall aesthetics. Over the last few centuries, artists, composers, and scholars, have attempted to use substitute one form of art for the other: by proposing techniques where music notes are synonymous to colors, by inventing instruments that combine the aesthetics of music and visual art, and by incorporating the two media in live performances. A widely accepted computational approach, for the conversion, …

Computer Simulations And Network-Based Profiling Of Binding And Allosteric Interactions Of Sars-Cov-2 Spike Variant Complexes And The Host Receptor: Dissecting The Mechanistic Effects Of The Delta And Omicron Mutations, Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we combine all-atom MD simulations and comprehensive mutational scanning of S-RBD complexes with the angiotensin-converting enzyme 2 (ACE2) host receptor in the native form as well as the S-RBD Delta and Omicron variants to (a) examine the differences in the dynamic signatures of the S-RBD complexes and (b) identify the critical binding hotspots and sensitivity of the mutational positions. We also examined the differences in allosteric interactions and communications in the S-RBD complexes for the Delta and Omicron variants. Through the perturbation-based scanning of the allosteric propensities of the SARS-CoV-2 S-RBD residues and dynamics-based network centrality and …

Machine Learning Based Medical Image Deepfake Detection: A Comparative Study, Siddharth Solaiyappan, Yuxin Wen

Engineering Faculty Articles and Research

Deep generative networks in recent years have reinforced the need for caution while consuming various modalities of digital information. One avenue of deepfake creation is aligned with injection and removal of tumors from medical scans. Failure to detect medical deepfakes can lead to large setbacks on hospital resources or even loss of life. This paper attempts to address the detection of such attacks with a structured case study. Specifically, we evaluate eight different machine learning algorithms, which include three conventional machine learning methods (Support Vector Machine, Random Forest, Decision Tree) and five deep learning models (DenseNet121, DenseNet201, ResNet50, ResNet101, VGG19) …

How Apis Create Growth By Inverting The Firm, Seth G. Benzell, Jonathan Hersh, Marshall Van Alstyne

Economics Faculty Articles and Research

Traditional asset management strategy has emphasized building barriers to entry or closely guarding unique assets to maintain a firm’s comparative advantage. A new “Inverted Firm” paradigm, however, has emerged. Under this strategy, firms share data seeking to become platforms by opening digital services to third-parties and capturing part of their external surplus. This contrasts with a “pipeline” strategy where the firm itself creates value. This paper quantitatively estimates the effect of adopting an inverted firm strategy through the lens of Application Programming Interfaces (APIs), a key enabling technology. Using both public data and that of a private API development firm, …

Dissecting Mutational Allosteric Effects In Alkaline Phosphatases Associated With Different Hypophosphatasia Phenotypes: An Integrative Computational Investigation, Fei Xiao, Ziyun Zhou, Xingyu Song, Mi Gan, Jie Long, Gennady M. Verkhivker, Guang Hu

Mathematics, Physics, and Computer Science Faculty Articles and Research

Hypophosphatasia (HPP) is a rare inherited disorder characterized by defective bone mineralization and is highly variable in its clinical phenotype. The disease occurs due to various loss-of-function mutations in ALPL, the gene encoding tissue-nonspecific alkaline phosphatase (TNSALP). In this work, a data-driven and biophysics-based approach is proposed for the large-scale analysis of ALPL mutations-from nonpathogenic to severe HPPs. By using a pipeline of synergistic approaches including sequence-structure analysis, network modeling, elastic network models and atomistic simulations, we characterized allosteric signatures and effects of the ALPL mutations on protein dynamics and function. Statistical analysis of molecular features computed for the …

A Deep Learning-Based Approach To Extraction Of Filler Morphology In Sem Images With The Application Of Automated Quality Inspection, Md. Fashiar Rahman, Tzu-Liang Bill Tseng, Jianguo Wu, Yuxin Wen, Yirong Lin

Engineering Faculty Articles and Research

Automatic extraction of filler morphology (size, orientation, and spatial distribution) in Scanning Electron Microscopic (SEM) images is essential in many applications such as automatic quality inspection in composite manufacturing. Extraction of filler morphology greatly depends on accurate segmentation of fillers (fibers and particles), which is a challenging task due to the overlap of fibers and particles and their obscure presence in SEM images. Convolution Neural Networks (CNNs) have been shown to be very effective at object recognition in digital images. This paper proposes an automatic filler detection system in SEM images, utilizing a Mask Region-based CNN architecture. The proposed system …

A High Precision Machine Learning-Enabled System For Predicting Idiopathic Ventricular Arrhythmia Origins, Jianwei Zheng, Guohua Fu, Daniele Struppa, Islam Abudayyeh, Tahmeed Contractor, Kyle Anderson, Huimin Chu, Cyril Rakovski

Mathematics, Physics, and Computer Science Faculty Articles and Research

Background: Radiofrequency catheter ablation (CA) is an efficient antiarrhythmic treatment with a class I indication for idiopathic ventricular arrhythmia (IVA), only when drugs are ineffective or have unacceptable side effects. The accurate prediction of the origins of IVA can significantly increase the operation success rate, reduce operation duration and decrease the risk of complications. The present work proposes an artificial intelligence-enabled ECG analysis algorithm to estimate possible origins of idiopathic ventricular arrhythmia at a clinical-grade level accuracy.

Method: A total of 18,612 ECG recordings extracted from 545 patients who underwent successful CA to treat IVA were proportionally sampled into training, …

Three Wave Mixing In Epsilon-Near-Zero Plasmonic Waveguides For Signal Regeneration, Nicholas Mirchandani, Mark C. Harrison

Engineering Faculty Articles and Research

Vast improvements in communications technology are possible if the conversion of digital information from optical to electric and back can be removed. Plasmonic devices offer one solution due to optical computing’s potential for increased bandwidth, which would enable increased throughput and enhanced security. Plasmonic devices have small footprints and interface with electronics easily, but these potential improvements are offset by the large device footprints of conventional signal regeneration schemes, since surface plasmon polaritons (SPPs) are incredibly lossy. As such, there is a need for novel regeneration schemes. The continuous, uniform, and unambiguous digital information encoding method is phase-shift-keying (PSK), so …

Applications Of Unsupervised Machine Learning In Autism Spectrum Disorder Research: A Review, Chelsea Parlett-Pelleriti, Elizabeth Stevens, Dennis R. Dixon, Erik J. Linstead

Engineering Faculty Articles and Research

Large amounts of autism spectrum disorder (ASD) data is created through hospitals, therapy centers, and mobile applications; however, much of this rich data does not have pre-existing classes or labels. Large amounts of data—both genetic and behavioral—that are collected as part of scientific studies or a part of treatment can provide a deeper, more nuanced insight into both diagnosis and treatment of ASD. This paper reviews 43 papers using unsupervised machine learning in ASD, including k-means clustering, hierarchical clustering, model-based clustering, and self-organizing maps. The aim of this review is to provide a survey of the current uses of …

Feel And Touch: A Haptic Mobile Game To Assess Tactile Processing, Ivonne Monarca, Monica Tentori, Franceli L. Cibrian

Engineering Faculty Articles and Research

Haptic interfaces have great potential for assessing the tactile processing of children with Autism Spectrum Disorder (ASD), an area that has been under-explored due to the lack of tools to assess it. Until now, haptic interfaces for children have mostly been used as a teaching or therapeutic tool, so there are still open questions about how they could be used to assess tactile processing of children with ASD. This article presents the design process that led to the development of Feel and Touch, a mobile game augmented with vibrotactile stimuli to assess tactile processing. Our feasibility evaluation, with 5 children …

Let's Read: Designing A Smart Display Application To Support Codas When Learning Spoken Language, Katie Rodeghiero, Yingying Yuki Chen, Annika M. Hettmann, Franceli L. Cibrian

Engineering Faculty Articles and Research

Hearing children of Deaf adults (CODAs) face many challenges including having difficulty learning spoken languages, experiencing social judgment, and encountering greater responsibilities at home. In this paper, we present a proposal for a smart display application called Let's Read that aims to support CODAs when learning spoken language. We conducted a qualitative analysis using online community content in English to develop the first version of the prototype. Then, we conducted a heuristic evaluation to improve the proposed prototype. As future work, we plan to use this prototype to conduct participatory design sessions with Deaf adults and CODAs to evaluate the …

Pre-Earthquake Ionospheric Perturbation Identification Using Cses Data Via Transfer Learning, Pan Xiong, Cheng Long, Huiyu Zhou, Roberto Battiston, Angelo De Santis, Dimitar Ouzounov, Xuemin Zhang, Xuhui Shen

Mathematics, Physics, and Computer Science Faculty Articles and Research

During the lithospheric buildup to an earthquake, complex physical changes occur within the earthquake hypocenter. Data pertaining to the changes in the ionosphere may be obtained by satellites, and the analysis of data anomalies can help identify earthquake precursors. In this paper, we present a deep-learning model, SeqNetQuake, that uses data from the first China Seismo-Electromagnetic Satellite (CSES) to identify ionospheric perturbations prior to earthquakes. SeqNetQuake achieves the best performance [F-measure (F1) = 0.6792 and Matthews correlation coefficient (MCC) = 0.427] when directly trained on the CSES dataset with a spatial window centered on the earthquake epicenter with the Dobrovolsky …

Multi-Modal Data Fusion, Image Segmentation, And Object Identification Using Unsupervised Machine Learning: Conception, Validation, Applications, And A Basis For Multi-Modal Object Detection And Tracking, Nicholas Lahaye

Computational and Data Sciences (PhD) Dissertations

Remote sensing and instrumentation is constantly improving and increasing in capability. Included within this, is the increase in amount of different instrument types, with various combinations of spatial and spectral resolutions, pointing angles, and various other instrument-specific qualities. While the increase in instruments, and therefore datasets, is a boon for those aiming to study the complexities of the various Earth systems, it can also present a large number of new challenges. With this information in mind, our group has set our aims on combining datasets with different spatial and spectral resolutions in an effective and as-general-as-possible way, with as little …

Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem

Computational and Data Sciences (MS) Theses

Computational investigation of molecular structures and reactions of biological and pharmaceutical interests remains a grand scientific challenge due to the size and conformational flexibility of these systems. The work requires parsing and analyzing thousands of conformations in each molecular state for meaningful chemical information and subjecting the ensemble to costly quantum chemical calculations. The current status quo typically involves a manual process where the investigator must look at each conformation, separating each into structural families. This process is time-intensive and tedious, making this process infeasible in some cases, and limiting the ability of theoreticians to study these systems. However, the …

Enhancing Microbiome Host Disease Prediction With Variational Autoencoders, Celeste Manughian-Peter

Computational and Data Sciences (MS) Theses

Advancements in genetic sequencing methods for microbiomes in recent decades have permitted the collection of taxonomic and functional profiles of microbial communities, accelerating the discovery of the functional aspects of the microbiome and generating an increased interest among clinicians in applying these techniques with patients. This advancement has coincided with software and hardware improvements in the field of machine learning and deep learning. Combined, these advancements implicate further potential for progress in disease diagnosis and treatment in humans. The ability to classify a human microbiome profile into a disease category, and additionally identify the differentiating factors within the profile between …

A Quantitative Validation Of Multi-Modal Image Fusion And Segmentation For Object Detection And Tracking, Nicholas Lahaye, Michael J. Garay, Brian D. Bue, Hesham El-Askary, Erik Linstead

Mathematics, Physics, and Computer Science Faculty Articles and Research

In previous works, we have shown the efficacy of using Deep Belief Networks, paired with clustering, to identify distinct classes of objects within remotely sensed data via cluster analysis and qualitative analysis of the output data in comparison with reference data. In this paper, we quantitatively validate the methodology against datasets currently being generated and used within the remote sensing community, as well as show the capabilities and benefits of the data fusion methodologies used. The experiments run take the output of our unsupervised fusion and segmentation methodology and map them to various labeled datasets at different levels of global …

Landscape-Based Mutational Sensitivity Cartography And Network Community Analysis Of The Sars-Cov-2 Spike Protein Structures: Quantifying Functional Effects Of The Circulating D614g Variant, Gennady M. Verkhivker, Steve Agajanian, Deniz Yasar Oztas, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

We developed and applied a computational approach to simulate functional effects of the global circulating mutation D614G of the SARS-CoV-2 spike protein. All-atom molecular dynamics simulations are combined with deep mutational scanning and analysis of the residue interaction networks to investigate conformational landscapes and energetics of the SARS-CoV-2 spike proteins in different functional states of the D614G mutant. The results of conformational dynamics and analysis of collective motions demonstrated that the D614 site plays a key regulatory role in governing functional transitions between open and closed states. Using mutational scanning and sensitivity analysis of protein residues, we identified the stability …

Hierarchical Scheduling For Real-Time Periodic Tasks In Symmetric Multiprocessing, Tom Springer, Peiyi Zhao

Engineering Faculty Articles and Research

In this paper, we present a new hierarchical scheduling framework for periodic tasks in symmetric multiprocessor (SMP) platforms. Partitioned and global scheduling are the two main approaches used by SMP based systems where global scheduling is recommended for overall performance and partitioned scheduling is recommended for hard real-time performance. Our approach combines both the global and partitioned approaches of traditional SMP-based schedulers to provide hard real-time performance guarantees for critical tasks and improved response times for soft real-time tasks. Implemented as part of VxWorks, the results are confirmed using a real-time benchmark application, where response times were improved for soft …

Computational Analysis Of Protein Stability And Allosteric Interaction Networks In Distinct Conformational Forms Of The Sars Cov 2 Spike D614g Mutant: Reconciling Functional Mechanisms Through Allosteric Model Of Spike Regulation, Gennady M. Verkhivker, Steve Agajanian, Deniz Oztas, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we used an integrative computational approach to examine molecular mechanisms underlying functional effects of the D614G mutation by exploring atomistic modeling of the SARS-CoV-2 spike proteins as allosteric regulatory machines. We combined coarse-grained simulations, protein stability and dynamic fluctuation communication analysis with network-based community analysis to examine structures of the native and mutant SARS-CoV-2 spike proteins in different functional states. Through distance fluctuations communication analysis, we probed stability and allosteric communication propensities of protein residues in the native and mutant SARS-CoV-2 spike proteins, providing evidence that the D614G mutation can enhance long-range signaling of the allosteric spike …

Pitcher Effectiveness: A Step Forward For In Game Analytics And Pitcher Evaluation, Christopher Watkins, Vincent Berardi, Cyril Rakovski

Mathematics, Physics, and Computer Science Faculty Articles and Research

With the introduction of Statcast in 2015, baseball analytics have become more precise. Statcast allows every play to be accurately tracked and the data it generates is easily accessible through Baseball Savant, which opens the opportunity for improved performance statistics to be developed. In this paper we propose a new tool, Pitcher Effectiveness, that uses Statcast data to evaluate starting pitchers dynamically, based on the results of in-game outcomes after each pitch. Pitcher Effectiveness successfully predicts instances where starting pitchers give up several runs, which we believe make it a new and important tool for the in-game and post-game evaluation …

Gender Gap In Computer Science: An Invitational Rhetoric Study, Cindy Ramirez

Student Scholar Symposium Abstracts and Posters

This project will address the gender gap in computer science through a discourse analysis of materials used to attract young girls to the field. Applying Invitational Rhetoric, Foss and Griffin’s feminist rhetorical theory, I will determine how rhetoric is being used to attract or possibly dissuade young females from entering computer science. Women have contributed to the field of computer science beginning in the 19th century even though computers were not yet invented. Considered the world’s first programmer, Ada Lovelace helped pioneer the first modern computer science concepts, and many of the same ideas we use today, like variables and …

On-Device Deep Learning Inference For System-On-Chip (Soc) Architectures, Tom Springer, Elia Eiroa-Lledo, Elizabeth Stevens, Erik Linstead

Engineering Faculty Articles and Research

As machine learning becomes ubiquitous, the need to deploy models on real-time, embedded systems will become increasingly critical. This is especially true for deep learning solutions, whose large models pose interesting challenges for target architectures at the “edge” that are resource-constrained. The realization of machine learning, and deep learning, is being driven by the availability of specialized hardware, such as system-on-chip solutions, which provide some alleviation of constraints. Equally important, however, are the operating systems that run on this hardware, and specifically the ability to leverage commercial real-time operating systems which, unlike general purpose operating systems such as Linux, can …

A High-Precision Machine Learning Algorithm To Classify Left And Right Outflow Tract Ventricular Tachycardia, Jianwei Zhang, Guohua Fu, Islam Abudayyeh, Magdi Yacoub, Anthony Chang, William Feaster, Louis Ehwerhemuepha, Hesham El-Askary, Xianfeng Du, Bin He, Mingjun Feng, Yibo Yu, Binhao Wang, Jing Liu, Hai Yao, Hulmin Chu, Cyril Rakovski

Mathematics, Physics, and Computer Science Faculty Articles and Research

Introduction: Multiple algorithms based on 12-lead ECG measurements have been proposed to identify the right ventricular outflow tract (RVOT) and left ventricular outflow tract (LVOT) locations from which ventricular tachycardia (VT) and frequent premature ventricular complex (PVC) originate. However, a clinical-grade machine learning algorithm that automatically analyzes characteristics of 12-lead ECGs and predicts RVOT or LVOT origins of VT and PVC is not currently available. The effective ablation sites of RVOT and LVOT, confirmed by a successful ablation procedure, provide evidence to create RVOT and LVOT labels for the machine learning model.

Methods: We randomly sampled training, validation, and testing …

Applications Of Machine Learning To Facilitate Software Engineering And Scientific Computing, Natalie Best

Computational and Data Sciences (PhD) Dissertations

The use of machine learning has risen in recent years, though many areas remain unexplored due to lack of data or lack of computational tools. This dissertation explores machine learning approaches in case studies involving image classification and natural language processing. In addition, a software library in the form of two-way bridge connecting deep learning models in Keras with ones available in the Fortran programming language is also presented.

In Chapter 2, we explore the applicability of transfer learning utilizing models pre-trained on non-software engineering data applied to the problem of classifying software unified modeling language diagrams where data is …

Spatial Frequency Implications For Global And Local Processing In Autistic Children, Riya Mody, Ayra Tusneem, Louanne Boyd, Vincent Berardi

Student Scholar Symposium Abstracts and Posters

Visual processing in humans is done by integrating and updating multiple streams of global and local sensory input. Interaction between these two systems can be disrupted in individuals with ASD and other learning disabilities. When this integration is not done smoothly, it becomes difficult to see the “big picture”, which has been found to have implications on emotion recognition, social skills, and conversation skills. An example of this phenomenon is local interference, which is when local details are prioritized over the global features. Previous research in this field has aimed to decrease local interference by developing and evaluating a filter …

An Introduction To Seshat: Global History Databank, Peter Turchin, Harvey Whitehouse, Pieter François, Daniel Hoyer, Abel Alves, John Baines, David Baker, Marta Bartkowiak, Jennifer Bates, James Bennett, Julye Bidmead, Peter Bol, Alessandro Ceccarelli, Kostis Christakis, David Christian, Alan Covey, Franco De Angelis, Timothy K. Earle, Neil R. Edwards, Gary Feinman, Stephanie Grohmann, Philip B. Holden, Árni Júlíusson, Andrey Korotayev, Axel Kristinsson, Jennifer Larson, Oren Litwin, Victor Mair, Joseph G. Manning, Patrick Manning, Arkadiusz Marciniak, Gregory Mcmahon, John Miksic, Juan Carlos Moreno Garcia, Ian Morris, Ruth Mostern, Daniel Mullins, Oluwole Oyebamiji, Peter Peregrine, Cameron Petrie, Johannes Preiser-Kapeller, Peter Rudiak-Gould, Paula Sabloff, Patrick Savage, Charles Spencer, Miriam Stark, Barend Ter Haar, Stefan Thurner, Vesna Wallace, Nina Witoszek, Liye Xie

Religious Studies Faculty Articles and Research

This article introduces the Seshat: Global History Databank, its potential, and its methodology. Seshat is a databank containing vast amounts of quantitative data buttressed by qualitative nuance for a large sample of historical and archaeological polities. The sample is global in scope and covers the period from the Neolithic Revolution to the Industrial Revolution. Seshat allows scholars to capture dynamic processes and to test theories about the co-evolution (or not) of social scale and complexity, agriculture, warfare, religion, and any number of such Big Questions. Seshat is rapidly becoming a massive resource for innovative cross-cultural and cross-disciplinary research. Seshat is …

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 …

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 …

Developing Employment Environments Where Individuals With Asd Thrive: Using Machine Learning To Explore Employer Policies And Practices, Amy Jane Griffiths, Amy E. Hurley Hanson, Cristina M. Giannantonio, Sneha Kohli Mathur, Kayleigh Hyde, Erik Linstead

Education Faculty Articles and Research

An online survey instrument was developed to assess employers’ perspectives on hiring job candidates with Autism Spectrum Disorder (ASD). The investigators used K-means clustering to categorize companies in clusters based on their hiring practices related to individuals with ASD. This methodology allowed the investigators to assess and compare the various factors of businesses that successfully hire employees with ASD versus those that do not. The cluster analysis indicated that company structures, policies and practices, and perceptions, as well as the needs of employers and employees, were important in determining who would successfully hire individuals with ASD. Key areas that require …

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 …