Other Computer Sciences Commons^™

Phase-Preserving Machine Learning Forecasting Of Nonlinear Predator–Prey Dynamics, Saira Batool, Muhammad Imran, Brett Mckinney

Biology and Medicine Through Mathematics Conference

No abstract provided.

Predicting And Decoding Allosteric Binding Sites Using Protein Language Models And Structure-Based Machine Learning: An Energy Landscape-Guided Explainable Ai Framework, Kamila Riedlová, Vít Skrhák, William G. Gatlin, Max Ludwick, Lucas Turano, Marian Novotný, David Hoksza, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Computational prediction of allosteric binding sites in protein structures remains a persistent challenge, as these regulatory pockets evade detection by both sequence-based and structure-based algorithms. Both computational and physical origins of this predictive asymmetry remain insufficiently understood. In this study, we systematically examine the determinants of binding site predictability using a dual framework that integrates a fine-tuned protein language model and the structure-based method P2Rank as complementary tools probing a diverse data set of 453 human kinases, together with a physics-based interpretability layer derived from energy landscape frustration analysis. Both predictors exhibit a sharp and reproducible dichotomy on protein kinases, …

A System And Method For Measuring Spatially Varying Surface Appearances With A Study Of Feathers, Jessica Baron-Lis

All Dissertations

Real-world materials, particularly biological structures such as feathers exhibit complex appearances that vary spatially across their surfaces. The field of computer graphics provides a means of understanding such surfaces through material modeling which uses both analytical models and data acquired from light-surface interactions. There are many efforts within the past decade in measuring materials for graphics, but common limitations in these works include not accounting for spatially varying properties and reliance on neural networks and synthetic datasets.

Feathers from modern birds present diverse appearances due to how light interacts with their unique hierarchical microstructures. Variations in those structures lead to …

Raising Awareness About Hydrographic Careers Through Sea-Going Opportunities, Juliet Kinney, Rochelle Wigley, Sara Cardigos, Fahima Bellabad, Larissa Marques Freguette

Center for Coastal and Ocean Mapping

There is a worldwide shortage of hydrographic personnel (van Wegen, 2021, Hydro International 2008).  Calls for action to address this issue include the IHO’s Hydrography at Sea opportunities, while intiatiative such as Seabed 2030 are bringing broader attention to the field and helping to catalyze new discussions and partnerships in hydrography (IHO, 2024).  The global sea floor mapping community needs to develop a broader workforce pipeline.  We would like to highlight the importance of providing time at sea and leadership opportunities in developing a robust workforce.  We start with an overview of a selection of current exchange and training programs …

Unmanned Aerial Systems (Uas) Image Preprocessing To Reduce Artifacts And Improve Geometric Registration When Generating Orthophoto Mosaics And 3d Models, Eddie Ironsmith

Electronic Theses and Dissertations

Drones can now be used to quickly collect imagery data in a highly automated way; however, individual images must be combined to form an orthomosaic or 3-Dimentional (3D) model using photogrammetry software. Currently, the existing software may generate erroneous output in the form of artifacts or positional errors caused by homogeneous areas, light reflections, object movement between photos, or sub-optimal algorithms. The goal of this research was to develop preprocessing algorithms that would filter movement (or other time or position-based differences) and areas of homogeneity. The hypothesis is that filtering these parts of the image would reduce artifacts and improve …

Time Series Decomposition Of Land Surface Temperature For Long-Term Trend Forecasting And Impact On Nesting Sea Turtle Habitats In The Arabian Gulf, Sachi Perera, Rommel H. Maneja, Mohamed Allali, Cyril Rakovski, Erik Linstead, Daniele Struppa, Ali Qasem, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

Improving land surface temperature (LST) modeling is vital for mitigating climate change effects on various ecosystems and marine habitats such as important sea turtle habitats. Over the past decade, extreme temperatures have likely significantly affected nesting sea turtle habitats in the Arabian Gulf, with predominantly female hatchlings creating an imbalance in the sex ratio. Such shifts have profound implications for these habitats’ long-term survival and conservation management. This study leverages statistical machine learning models to measure ongoing temporal variations in LST. We break down the LST time series into trend, seasonal, and noise components using classical decomposition methods like X11, …

Weed Seed Wizard Case Study - Don't Stop Harvest Weed Management Because It’S A Dry Year, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity research reports

The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.

The Weed Seed Wizard is a computer simulation tool that:

• applies to all Australian grain growing areas

• helps growers understand and manage weed seedbanks on their farms

• uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields

• uses farm-specific management and site-specific weather

• is multi-species

See www.dpird.wa.gov.au for further information on Weed Seed Wizard.

This case …

Mixed Uncertainty Analysis On Pumping By Peristaltic Hearts Using Dempster-Shafer Theory, Yanyan He, Nicholas A. Battista, Lindsay D. Waldrop

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this paper, we introduce the numerical strategy for mixed uncertainty propagation based on probability and Dempster–Shafer theories, and apply it to the computational model of peristalsis in a heart-pumping system. Specifically, the stochastic uncertainty in the system is represented with random variables while epistemic uncertainty is represented using non-probabilistic uncertain variables with belief functions. The mixed uncertainty is propagated through the system, resulting in the uncertainty in the chosen quantities of interest (QoI, such as flow volume, cost of transport and work). With the introduced numerical method, the uncertainty in the statistics of QoIs will be represented using belief …

Weed Seed Wizard Case Study - An Early Harvest Versus A Late Harvest, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity research reports

The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.

The Weed Seed Wizard is a computer simulation tool that:

• applies to all Australian grain growing areas

• helps growers understand and manage weed seedbanks on their farms

• uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields

• uses farm-specific management and site-specific weather

• is multi-species

See www.dpird.wa.gov.au for further information on Weed Seed Wizard.

This case …

Weed Seed Wizard Scenario - Herbicide Resistance In Wild Radish In Moora, Western Australia, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity research reports

The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.

The Weed Seed Wizard is a computer simulation tool that:

• applies to all Australian grain growing areas

• helps growers understand and manage weed seedbanks on their farms

• uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields

• uses farm-specific management and site-specific weather

• is multi-species

See www.dpird.wa.gov.au for further information on Weed Seed Wizard.

This Western …

Weed Seed Wizard Scenario - Glyphosate Resistance In Barnyard Grass In Goondiwindi, Queensland, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity research reports

The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.

The Weed Seed Wizard is a computer simulation tool that:

• applies to all Australian grain growing areas

• helps growers understand and manage weed seedbanks on their farms

• uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields

• uses farm-specific management and site-specific weather

• is multi-species

See www.dpird.wa.gov.au for further information on Weed Seed Wizard.

This Queensland …

Weed Seed Wizard Scenario - Dormancy Shift In Barley Grass In Balaklava, South Australia, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity research reports

The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.

The Weed Seed Wizard is a computer simulation tool that:

• applies to all Australian grain growing areas

• helps growers understand and manage weed seedbanks on their farms

• uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields

• uses farm-specific management and site-specific weather

• is multi-species

See www.dpird.wa.gov.au for further information on Weed Seed Wizard.

This South …

Weed Seed Wizard Case Study - Grower From Western Australia’S Central Wheatbelt, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity research reports

The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.

The Weed Seed Wizard is a computer simulation tool that:

• applies to all Australian grain growing areas

• helps growers understand and manage weed seedbanks on their farms

• uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields

• uses farm-specific management and site-specific weather

• is multi-species

See www.dpird.wa.gov.au for further information on Weed Seed Wizard.

This case …

Weed Seed Wizard Scenario - Herbicide Resistance In Wild Oats In Wagga Wagga, New South Wales, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity research reports

The Weed Seed Wizard is a national collaborative project that uses paddock management information to predict weed emergence and crop losses now and in the future.

The Weed Seed Wizard is a computer simulation tool that:

• applies to all Australian grain growing areas

• helps growers understand and manage weed seedbanks on their farms

• uses farm management records to simulate how different crop rotations, weed control techniques, irrigation, grazing and harvest management tactics can affect weed numbers, the weed seedbank and yields

• uses farm-specific management and site-specific weather

• is multi-species

See www.dpird.wa.gov.au for further information on Weed Seed Wizard.

This New …

Ascot App, Milla Penelope Markovic

Honors Thesis

The Ascot App is a research tool for acquiring and analyzing data. The app comprises of both mobile and web platforms, each serving a unique purpose. The mobile side allows users to input data through the app’s form, which is uploaded to a database for further processing and analysis. The web app, which is still under development as of April of 2024, allows users to manage their research project and download data in the form of a parsed CSV. These components ensure a seamless process for research teams to record data with persistence and security while allowing for analysis.

Ascot …

Deficiency Of Acute-Phase Serum Amyloid A Exacerbates Sepsis-Induced Mortality And Lung Injury In Mice, Ailing Ji, Andrea C. Trumbauer, Victoria P. Noffsinger, Luke W. Meredith, Brittany Dong, Qian Wang, Ling Guo, Xiangan Li, Frederick C. De Beer, Nancy R. Webb, Lisa R. Tannock, Marlene E. Starr, Christopher M. Waters, Preetha Shridas

Saha Cardiovascular Research Center Faculty Publications

Serum amyloid A (SAA) is a family of proteins, the plasma levels of which may increase >1000-fold in acute inflammatory states. We investigated the role of SAA in sepsis using mice deficient in all three acute-phase SAA isoforms (SAA-TKO). SAA deficiency significantly increased mortality rates in the three experimental sepsis mouse models: cecal ligation and puncture (CLP), cecal slurry (CS) injection, and lipopolysaccharide (LPS) treatments. SAA-TKO mice had exacerbated lung pathology compared to wild-type (WT) mice after CLP. A bulk RNA sequencing performed on lung tissues excised 24 h after CLP indicated significant enrichment in the expression of genes associated …

Emerging Sensing, Imaging, And Computational Technologies To Scale Nano-To Macroscale Rhizosphere Dynamics – Review And Research Perspectives, Amir H. Ahkami, Odeta Qafoku, Tiina Roose, Quanbing Mou, Yi Lu, Zoe G. Cardon, Yuxin Wu, Chunwei Chou, Joshua B. Fisher, Tamas Varga, Pubudu Handakumbura, Jayde A. Aufrecht, Arunima Bhattacharjee, James J. Moran

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The soil region influenced by plant roots, i.e., the rhizosphere, is one of the most complex biological habitats on Earth and significantly impacts global carbon flow and transformation. Understanding the structure and function of the rhizosphere is critically important for maintaining sustainable plant ecosystem services, designing engineered ecosystems for long-term soil carbon storage, and mitigating the effects of climate change. However, studying the biological and ecological processes and interactions in the rhizosphere requires advanced integrated technologies capable of decoding such a complex system at different scales. Here, we review how emerging approaches in sensing, imaging, and computational modeling …

Self-Supervised Pretraining And Transfer Learning On Fmri Data With Transformers, Sean Paulsen

Dartmouth College Ph.D Dissertations

Transfer learning is a machine learning technique founded on the idea that knowledge acquired by a model during “pretraining” on a source task can be transferred to the learning of a target task. Successful transfer learning can result in improved performance, faster convergence, and reduced demand for data. This technique is particularly desirable for the task of brain decoding in the domain of functional magnetic resonance imaging (fMRI), wherein even the most modern machine learning methods can struggle to decode labelled features of brain images. This challenge is due to the highly complex underlying signal, physical and neurological differences between …

Novel Approach For Non-Invasive Prediction Of Body Shape And Habitus, Emma Young

Electronic Theses and Dissertations

While marker-based motion capture remains the gold standard in measuring human movement, accuracy is influenced by soft-tissue artifacts, particularly for subjects with high body mass index (BMI) where markers are not placed close to the underlying bone. Obesity influences joint loads and motion patterns, and BMI may not be sufficient to capture the distribution of a subject’s weight or to differentiate differences between subjects. Subjects in need of a joint replacement are more likely to have mobility issues or pain, which prevents exercise. Obesity also increases the likelihood of needing a total joint replacement. Accurate movement data for subjects with …

Creating Project Contrast: A Video Game Exploring Consciousness And Qualia, Pierce Papke

Honors Projects

Project Contrast is a video game that explores how the unique traits inherent to video games might engage reflective player responses to qualitative experience. Project Contrast does this through suspension of disbelief, avatar projection, presence, player agency in storytelling, visual perception, functional gameplay, and art. Considering the difficulty in researching qualitative experience due to its subjectivity and circular explanations, I created Project Contrast not to analyze qualia, though that was my original hope. I instead created Project Contrast as an avenue for player self-reflection and learning about qualitative experience. While video games might be just code and art on a …

Du Undergraduate Showcase: Research, Scholarship, And Creative Works, Caitlyn Aldersea, Justin Bravo, Sam Allen, Anna Block, Connor Block, Emma Buechler, Maria De Los Angeles Bustillos, Arianna Carlson, William Christensen, Olivia Kachulis, Noah Craver, Kate Dillon, Muskan Fatima, Angel Fernandes, Emma Finch, Colleen Cassidy, Amy Fishman, Andrea Francis, Stacia Fritz, Simran Gill, Emma Gries, Rylie Hansen, Shannon Powers, Jacqueline Martinez, Zachary Harker, Ashley Hasty, Mykaela Tanino-Springsteen, Kathleen Hopps, Adelaide Kerenick, Colin Kleckner, Ci Koehring, Elijah Kruger, Braden Krumholz, Maddie Leake, Lyneé Alves, Seraphina Loukas, Yatzari Lozano Vazquez, Haley Maki, Emily Martinez, Sierra Mckinney, Audrey Mitchell, Kipling Newman, Audrey Ng, Megan Lucyshyn, Andrew Nguyen, Stevie Ostman, Casandra Pearson, Alexandra Penney, Julia Gielczynski, Tyler Ball, Anna Rini, Christina Rorres, Simon Ruland, Helayna Schafer, Emma Sellers, Sarah Schuller, Claire Shaver, Kevin Summers, Isabella Shaw, Madison Sinar, Claudia Pena, Apshara Siwakoti, Carter Sorensen, Madi Sousa, Anna Sparling, Alexandra Revier, Brandon Thierry, Dylan Tyree, Maggie Williams, Lauren Wols

DU Undergraduate Research Journal Archive

DU Undergraduate Showcase: Research, Scholarship, and Creative Works

A Programmatic Geographic Information Systems Analysis Of Plant Hardiness Zones, Andrew Bowen

Electronic Theses and Dissertations

The Plant Hardiness Zone Map consists of thirteen geographical zones that describe whether a plant can survive based on average annual minimal temperatures. As climate change progresses, minimum temperatures in all regions are expected to change. This work programmatically evaluates predicted future climate projection data and converts it to United States Department of Agriculture-defined hardiness zones. Through the next 80 years, hardiness zones are projected to move poleward; in effect, colder zones will lose area and warmer zones will gain area globally. Some implications include changes in crop growing degree days, which could alter crop productivity, migration and settlement of …

From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric …

Invasive Buckthorn Mapping: A Uav-Based Approach Utilizing Machine Learning, Gis, And Remote Sensing Techniques In The Upper Peninsula Of Michigan, Vikranth Madeppa

Dissertations, Master's Theses and Master's Reports

An Invasive species is a species that is alien or non-native to the ecosystem which causes harm to economic, environmental, or human health (E.O. 13112 of Feb 3, 1999). Invasive species have posed a serious threat to ecosystems across the globe. These invasive species have impacts on the biodiversity and productivity of invaded forests. Remotely sensed data is a valuable resource for understanding and addressing issues related to invasive species. This study presents a novel approach for mapping the distribution of two invasive plant species, Common and Glossy Buckthorn, using unmanned aerial vehicles (UAVs), machine learning algorithms, geographic information systems …

Machine Learning And Protein Allostery, Sian Xiao, Gennady M. Verkhivker, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The fundamental biological importance and complexity of allosterically regulated proteins stem from their central role in signal transduction and cellular processes. Recently, machine-learning approaches have been developed and actively deployed to facilitate theoretical and experimental studies of protein dynamics and allosteric mechanisms. In this review, we survey recent developments in applications of machine-learning methods for studies of allosteric mechanisms, prediction of allosteric effects and allostery-related physicochemical properties, and allosteric protein engineering. We also review the applications of machine-learning strategies for characterization of allosteric mechanisms and drug design targeting SARS-CoV-2. Continuous development and task-specific adaptation of machine-learning methods for protein allosteric …

The Significance Of Sonic Branding To Strategically Stimulate Consumer Behavior: Content Analysis Of Four Interviews From Jeanna Isham’S “Sound In Marketing” Podcast, Ina Beilina

Student Theses and Dissertations

Purpose:
Sonic branding is not just about composing jingles like McDonald’s “I’m Lovin’ It.” Sonic branding is an industry that strategically designs a cohesive auditory component of a brand’s corporate identity. This paper examines the psychological impact of music and sound on consumer behavior reviewing studies from the past 40 years and investigates the significance of stimulating auditory perception by infusing sound in consumer experience in the modern 2020s.

Design/methodology/approach:
Qualitative content analysis of audio media was used to test two hypotheses. Four archival oral interview recordings from Jeanna Isham’s podcast “Sound in Marketing” featuring the sonic branding experts …

Ubjective Information And Survival In A Simulated Biological System, Tyler S. Barker, Massimiliano Pierobon, Peter J. Thomas

School of Computing: Faculty Publications

Information transmission and storage have gained traction as unifying concepts to characterize biological systems and their chances of survival and evolution at multiple scales. Despite the potential for an information-based mathematical framework to offer new insights into life processes and ways to interact with and control them, the main legacy is that of Shannon’s, where a purely syntactic characterization of information scores systems on the basis of their maximum information efficiency. The latter metrics seem not entirely suitable for biological systems, where transmission and storage of different pieces of information (carrying different semantics) can result in different chances of survival. …

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 …

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 …

Analysis Of The Slo Bay Microbiome From A Network Perspective, Lien Viet Nguyen

Master's Theses

Microorganisms are key players in the ecosystem functioning. In this thesis, we developed a framework to preprocess raw microbiome data, build a correlation network, and analyze co-occurrence patterns between microbes. We then applied this framework to a marine microbiome dataset. The dataset used in this study comes from a year-long time-series to characterize the microbial communities in our coastal waters off the Cal Poly Pier. In analyzing this dataset, we were able to observe and confirm previously discovered patterns of interactions and generate hypotheses about new patterns. The analysis of co-occurrences between prokaryotic and eukaryotic taxa is relatively novel and …