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2022

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Full-Text Articles in Physical Sciences and Mathematics

Bank Error In Whose Favor? A Case Study Of Decentralized Finance Misgovernance, Ping Fan Ke, Ka Chung Boris Ng Dec 2022

Bank Error In Whose Favor? A Case Study Of Decentralized Finance Misgovernance, Ping Fan Ke, Ka Chung Boris Ng

Research Collection School Of Computing and Information Systems

Decentralized Finance (DeFi) emerged rapidly in recent years and provided open and transparent financial services to the public. Due to its popularity, it is not uncommon to see cybersecurity incidents in the DeFi landscape, yet the impact of such incidents is under-studied. In this paper, we examine two incidents in DeFi protocol that are mainly caused by misgovernance and mistake in the smart contract. By using the synthetic control method, we found that the incident in Alchemix did not have a significant effect on the total value locked (TVL) in the protocol, whereas the incident in Compound caused a 6.13% …


Mining Competitively-Priced Bundle Configurations, Ezekiel Ong Young, Hady W. Lauw Dec 2022

Mining Competitively-Priced Bundle Configurations, Ezekiel Ong Young, Hady W. Lauw

Research Collection School Of Computing and Information Systems

We examine the bundle configuration problem in the presence of competition. Given a competitor's bundle configuration and pricing, we determine what to bundle together, and at what prices, to maximize the target firm's revenue. We highlight the difficulty in pricing bundles and propose a scalable alternative and an efficient search heuristic to refine the approximate prices. Furthermore, we extend the heuristics proposed by previous work to accommodate the presence of a competitor. We analyze the effectiveness of our proposed models through experimentation on real-life ratings-based preference data.


Quote: Quality-Oriented Testing For Deep Learning Systems, Jialuo Chen, Jingyi Wang, Xingjun Ma, Youcheng Sun, Jun Sun, Peixin Zhang, Peng Cheng Dec 2022

Quote: Quality-Oriented Testing For Deep Learning Systems, Jialuo Chen, Jingyi Wang, Xingjun Ma, Youcheng Sun, Jun Sun, Peixin Zhang, Peng Cheng

Research Collection School Of Computing and Information Systems

Recently, there has been a significant growth of interest in applying software engineering techniques for the quality assurance of deep learning (DL) systems. One popular direction is deep learning testing, i.e., given a property of test, defects of DL systems are found either by fuzzing or guided search with the help of certain testing metrics. However, recent studies have revealed that the neuron coverage metrics, commonly used by most existing DL testing approaches, are not necessarily correlated with model quality (e.g., robustness, the most studied model property), and are also not an effective measurement on the confidence of the model …


Appearance-Preserved Portrait-To-Anime Translation Via Proxy-Guided Domain Adaptation, Wenpeng Xiao, Cheng Xu, Jiajie Mai, Xuemiao Xu, Yue Li, Chengze Li, Xueting Liu, Shengfeng He Dec 2022

Appearance-Preserved Portrait-To-Anime Translation Via Proxy-Guided Domain Adaptation, Wenpeng Xiao, Cheng Xu, Jiajie Mai, Xuemiao Xu, Yue Li, Chengze Li, Xueting Liu, Shengfeng He

Research Collection School Of Computing and Information Systems

Converting a human portrait to anime style is a desirable but challenging problem. Existing methods fail to resolve this problem due to the large inherent gap between two domains that cannot be overcome by a simple direct mapping. For this reason, these methods struggle to preserve the appearance features in the original photo. In this paper, we discover an intermediate domain, the coser portrait (portraits of humans costuming as anime characters), that helps bridge this gap. It alleviates the learning ambiguity and loosens the mapping difficulty in a progressive manner. Specifically, we start from learning the mapping between coser and …


Scalable Distributional Robustness In A Class Of Non Convex Optimization With Guarantees, Avinandan Bose, Arunesh Sinha, Tien Mai Dec 2022

Scalable Distributional Robustness In A Class Of Non Convex Optimization With Guarantees, Avinandan Bose, Arunesh Sinha, Tien Mai

Research Collection School Of Computing and Information Systems

Distributionally robust optimization (DRO) has shown lot of promise in providing robustness in learning as well as sample based optimization problems. We endeavor to provide DRO solutions for a class of sum of fractionals, non-convex optimization which is used for decision making in prominent areas such as facility location and security games. In contrast to previous work, we find it more tractable to optimize the equivalent variance regularized form of DRO rather than the minimax form. We transform the variance regularized form to a mixed-integer second order cone program (MISOCP), which, while guaranteeing near global optimality, does not scale enough …


Coresets For Vertical Federated Learning: Regularized Linear Regression And K-Means Clustering, Lingxiao Huang, Zhize Li, Jialin Sun, Haoyu Zhao Dec 2022

Coresets For Vertical Federated Learning: Regularized Linear Regression And K-Means Clustering, Lingxiao Huang, Zhize Li, Jialin Sun, Haoyu Zhao

Research Collection School Of Computing and Information Systems

Vertical federated learning (VFL), where data features are stored in multiple parties distributively, is an important area in machine learning. However, the communication complexity for VFL is typically very high. In this paper, we propose a unified framework by constructing coresets in a distributed fashion for communication-efficient VFL. We study two important learning tasks in the VFL setting: regularized linear regression and $k$-means clustering, and apply our coreset framework to both problems. We theoretically show that using coresets can drastically alleviate the communication complexity, while nearly maintain the solution quality. Numerical experiments are conducted to corroborate our theoretical findings.


Cover Cropping And Organic Amendments To Improve Sandy Soils Under Organic Vegetable Production, Charles Williamson Dec 2022

Cover Cropping And Organic Amendments To Improve Sandy Soils Under Organic Vegetable Production, Charles Williamson

All Theses

Coastal Plain soils in the Southeastern USA are typically sandy with poor soil structure, low soil organic carbon (SOC) content, and meager soil fertility that pose challenges to organic agriculture. Adding organic inputs is a strategy to improve these soils' physical, chemical, and biological characteristics. Here, we aim to investigate the impacts of Cover Cropping (CC) and manure inclusions on sandy soils under organic vegetable production. The experiment design was a randomized complete block with two treatments of manure application (with and without) and four CC treatments of cereal rye (Secale cereale), hairy vetch (Vicia villosa), …


Oam-Based Wavelets In A High Speed Optical Probing System For Measuring The Angular Decomposition Of The Environment, Justin Free Dec 2022

Oam-Based Wavelets In A High Speed Optical Probing System For Measuring The Angular Decomposition Of The Environment, Justin Free

All Theses

This thesis presents the theoretical development of orbital angular momentum (OAM) based wavelets for the analysis of localized OAM information in space. An optical probing system for generating and detecting these wavelets is demonstrated; individual wavelets can scan the environment in 10µs or less. The probing system was applied to a three-dimensional atmospheric turbulence distribution to obtain a continuous wavelet transform of the angular information of the turbulent propagation path about a fixed radius. An entire continuous wavelet transform was measured in 3.8ms; the measurements are much faster than the turbulence and give insight into the short time scale of …


Geology, Soils And Climate Of Western Australia's Wine Regions, Peter J. Tille, Angela Stuart-Street, Peter S. Gardiner Dec 2022

Geology, Soils And Climate Of Western Australia's Wine Regions, Peter J. Tille, Angela Stuart-Street, Peter S. Gardiner

Bulletins 4000 -

This bulletin details what is special and unique about the geology, soil and climate of the south-west of Western Australia (WA), an area that encompasses the state’s 9 wine regions.

We have arranged the information into 2 parts:

  • In Part 1, we broadly describe the special geological, soil and climate features of the south-west of WA to provide context for the wine regions.
  • In Part 2, we describe the geology, soil and climate of the regions and subregions of the Geographical Indications (GI) scheme (administered by Wine Australia) for WA.

Through this work we have found that the wine regions …


Representation Learning For Open Set Recognition And Novel Category Discovery, Jingyun Jia Dec 2022

Representation Learning For Open Set Recognition And Novel Category Discovery, Jingyun Jia

Theses and Dissertations

As machine learning models have achieved great success in various research and industry fields, the success of these models heavily relies on the massive amount of data collection and human annotations. While the real world is an open set, the daily emerged categories and the lacking of annotations have become new challenges for machine learning models. The absence of newly emerged categories in training samples can be captured by Open Set Recognition (OSR). Then, given the newly emerged samples, the process of automatically identifying the novel categories is called Novel Category Discovery (NCD). In this dissertation, we focused on learning …


The Use Of Flexible Organic And Inorganic Building Blocks In Complex Metal- Organic Frameworks, Sahar Yahia Rajeh Dec 2022

The Use Of Flexible Organic And Inorganic Building Blocks In Complex Metal- Organic Frameworks, Sahar Yahia Rajeh

Theses and Dissertations

Metal organic frameworks (MOFs) are new class of hybrid materials that draw the attention of scientists to discover new properties that help in many fields. The structural diversity of MOFs is accessible by incorporating different organic linkers to the same metal cluster. In this work, we reacted seven flexible organic linkers with different lengths varying from 4-carbons to 10-carbons to a copper-paddlewheel metal cluster. The flexibility of the linkers make the confirmation of MOFs a challenge, although we were able to prepare a new crystalline MOF from a 5-carbon organic linker with two different copper-clusters. Another MOF in powder form …


Characterization Of Water Quality And Periphyton Assemblages In An Urban Stream, Knoxville, Tennessee, Allison Rogers Dec 2022

Characterization Of Water Quality And Periphyton Assemblages In An Urban Stream, Knoxville, Tennessee, Allison Rogers

Masters Theses

Periphyton consists of assemblages of algae, diatoms, organic matter, and other microorganisms that grow on rock, sediment, and plant surfaces in aquatic systems. Periphyton growth and diversity can be affected by a range of environmental factors, but there have been few studies to understand periphyton diversity in nutrient-impaired waterways, such as in Tennessee. This study investigated whether stream periphyton communities could be used to indicate different levels of potential impairment. The study took place along a 4.8-kilometer-long segment of Third Creek in Knoxville, Tennessee. Twelve sites were selected and samples were collected at base-flow conditions in July, September, and October …


Case Study Of A District-University Partnership: Developing Culturally Responsive Educators In A Rural Setting, Trenice Shauntel Durio Dec 2022

Case Study Of A District-University Partnership: Developing Culturally Responsive Educators In A Rural Setting, Trenice Shauntel Durio

Educational Leadership & Workforce Development Theses & Dissertations

Using a theoretical framework of critical race theory and conceptual frameworks of cultural education, this study explores the intersection of district-university partnerships and culturally responsive education. The purpose of this mixed methods case study was to examine the formulation and outcomes of a district-university partnership established to offer a college level course focused on anti-discrimination, equity and inclusion, and social justice in schools. Using survey data, I explored the relationship between participation in the course and the participants’ self-reflection in the areas of empathic concern and perspective taking, preparation for culturally responsive teaching and equitable practices, and comfortability with discussions …


Statistical Methods For Meta-Analysis In Large-Scale Genomic Experiments, Wimarsha Thathsarani Jayanetti Dec 2022

Statistical Methods For Meta-Analysis In Large-Scale Genomic Experiments, Wimarsha Thathsarani Jayanetti

Mathematics & Statistics Theses & Dissertations

Recent developments in high throughput genomic assays have opened up the possibility of testing hundreds and thousands of genes simultaneously. With the availability of vast amounts of public databases, researchers tend to combine genomic analysis results from multiple studies in the form of a meta-analysis. Meta-analysis methods can be broadly classified into two main categories. The first approach is to combine the statistical significance (pvalues) of the genes from each individual study, and the second approach is to combine the statistical estimates (effect sizes) from the individual studies. In this dissertation, we will discuss how adherence to the standard null …


Kinetic Simulations Of Active Nematic Polymers In Channel Flow, Lacey Savoie Schenk Dec 2022

Kinetic Simulations Of Active Nematic Polymers In Channel Flow, Lacey Savoie Schenk

Mathematics & Statistics Theses & Dissertations

Suspensions of active nematic liquid crystalline polymers exhibit complex phenomena such as spontaneous flows, pattern formations, and defects. They have many applications in industry, commercial settings, and our daily lives. We employ the Kinetic Model for our research, an extensive model that couples the Smoluchowski Equation and the incompressible Navier-Stokes Equations to solve for the active nanorod number density function–a function dependent on the polymer’s physical orientation and space at a given time. Using this function, we can derive the polymer’s polarity and nematic orientations as well as other rheological properties. In this research, we conduct numerical simulations of active, …


Forks Over Knives: Predictive Inconsistency In Criminal Justice Algorithmic Risk Assessment Tools, Travis Greene, Galit Shmueli, Jan Fell, Ching-Fu Lin, Han-Wei Liu Dec 2022

Forks Over Knives: Predictive Inconsistency In Criminal Justice Algorithmic Risk Assessment Tools, Travis Greene, Galit Shmueli, Jan Fell, Ching-Fu Lin, Han-Wei Liu

Research Collection Yong Pung How School Of Law

Big data and algorithmic risk prediction tools promise to improve criminal justice systems by reducing human biases and inconsistencies in decision-making. Yet different, equally justifiable choices when developing, testing and deploying these socio-technical tools can lead to disparate predicted risk scores for the same individual. Synthesising diverse perspectives from machine learning, statistics, sociology, criminology, law, philosophy and economics, we conceptualise this phenomenon as predictive inconsistency. We describe sources of predictive inconsistency at different stages of algorithmic risk assessment tool development and deployment and consider how future technological developments may amplify predictive inconsistency. We argue, however, that in a diverse and …


Raman Scattering Measurements And Analyses Of Gan Thin Films Grown On Zno Substrates By Metalorganic Chemical Vapor Deposition, Zane Mcdaniel, Zhe Chuan Feng, Kevin Stokes Nov 2022

Raman Scattering Measurements And Analyses Of Gan Thin Films Grown On Zno Substrates By Metalorganic Chemical Vapor Deposition, Zane Mcdaniel, Zhe Chuan Feng, Kevin Stokes

Symposium of Student Scholars

Metalorganic chemical vapor deposition (MOCVD) is a popularly used method of growing thin films of GaN on ZnO (GZ) substrates, which pair well due to their structural and characteristic similarities. In this research, optical characterization of the surface quality of GZ sample films is measured by analyzing Raman scattering (RS) using a Renishaw inVia spectrometer fitted with a 532nm laser. Samples were grown in an improved double injection block rotating disc reactor. Multiple samples' spectra show broad peaks that correspond with the E2 (high) and A1 (LO) branches of GaN, and nicely fitted curves are observed for the characteristic E2 …


Secure Decentralized Blockchain Based Web Application For Medical Records, Sri Harshini Popuri, Liang Zhao Nov 2022

Secure Decentralized Blockchain Based Web Application For Medical Records, Sri Harshini Popuri, Liang Zhao

Symposium of Student Scholars

The online storage and sharing of electronic health records has undergone a paradigm shift in recent years. The introduction of a centralized cloud computing concept to streamline records transfer between patients and healthcare providers has been an easy task. As a result, the availability of electronically stored health records with minimal operational costs is made possible, but the primary concern is related to the privacy and security of records. How can we securely exchange medical documents online while maintaining strong security standards? This research suggests a framework that fuses online federated learning with blockchain technology. In particular, we develop a …


Learning From Public Spaces In Historic Cities, Cody Josh Kucharski Nov 2022

Learning From Public Spaces In Historic Cities, Cody Josh Kucharski

Symposium of Student Scholars

Successful public spaces in cities are key for enhancing social cohesion and improving health and safety. Learning from historic cities involves the development of representational and analytical tools aimed at capturing their essence as places of human interaction. The research reports findings of the spatial analysis of twenty Adriatic and Ionian coastal cities, which addresses the question of how the network of public spaces calibrates different degrees of spatial enclosure necessary for creating successful social interactions. Cities in the littoral region include well-preserved historic centers that are renowned for the successful integration of urban squares into the urban fabric. For …


Panarchy Suggests Why Management Mitigates Rather Than Restores Ecosystems From Anthropogenic Impact, David G. Angeler, Ran Hur Nov 2022

Panarchy Suggests Why Management Mitigates Rather Than Restores Ecosystems From Anthropogenic Impact, David G. Angeler, Ran Hur

School of Natural Resources: Faculty Publications

Panarchy, a model of dynamic systems change at multiple, interconnected spatiotemporal scales, allows assessing whether management influences ecological processes and resilience. We assessed whether liming, a management action to counteract anthropogenic acidification, influenced scale-specific temporal fluctuation frequencies of benthic invertebrates and phytoplankton assemblages in lakes. We also tested whether these fluctuations correlated with proxies of liming (Ca:Mg ratios) to quantify scale-specific management effects. Using an ecosystem experiment and monitoring data, time series analyses (1998–2019) revealed significant multiscale temporal (and thus panarchy) structure for littoral invertebrates across limed and reference lakes. Such patterns were inconsistent for sublittoral invertebrates and phytoplankton. When …


Assessing Changes In Tornado Vulnerablitiy In North Alabama, Mckenna Danielle Brahler Nov 2022

Assessing Changes In Tornado Vulnerablitiy In North Alabama, Mckenna Danielle Brahler

Honors Capstone Projects and Theses

No abstract provided.


2022 Wics Conference: Driving Research, Teaching, And Extension Impact, Daren Redfearn, Daran Rudnick Nov 2022

2022 Wics Conference: Driving Research, Teaching, And Extension Impact, Daren Redfearn, Daran Rudnick

WICS Conferences

The Water and Integrated Cropping Systems (WICS) Hub was established to facilitate and provide collaborative opportunities for IANR faculty to leverage their individual and collective knowledge, talents, and interests to drive impact in Research and Discovery, Teaching and Learning, Extension and Outreach. This past year we focused on building connections as well as identifying and prioritizing big challenges and opportunities facing Nebraskans. The faculty identified and organized around the following themes, Digital/Precision Agriculture, Soil Health, Integrated Cropping Systems, Water Quality, and Water Quantity. The Theme Groups are faculty led and multi-disciplinary with representation across IANR Departments and Faculty appointments. We …


Spinosaurus Is Not An Aquatic Dinosaur, Paul C. Sereno, Nathan Myhrvold, Donald M. Henderson, Frank E. Fish, Stephanie L. Baumgart, Tyler M. Keillor, Kiersten K. Formoso, Lauren L. Conroy Nov 2022

Spinosaurus Is Not An Aquatic Dinosaur, Paul C. Sereno, Nathan Myhrvold, Donald M. Henderson, Frank E. Fish, Stephanie L. Baumgart, Tyler M. Keillor, Kiersten K. Formoso, Lauren L. Conroy

Biology Faculty Publications

A predominantly fish-eating diet was envisioned for the sail-backed theropod dinosaur Spinosaurus aegyptiacus when its elongate jaws with subconical teeth were unearthed a century ago in Egypt. Recent discovery of the high-spined tail of that skeleton, however, led to a bolder conjecture that S. aegyptiacus was the first fully aquatic dinosaur. The "aquatic hypothesis' posits that S. aegyptiacus was a slow quadruped on land but a capable pursuit predator in coastal waters, powered by an expanded tail. We test these functional claims with skeletal and flesh models of S. aegyptiacus. We assembled a CT- based skeletal reconstruction based on the …


Realizing The Vision Of Wcu’S Landscape Master Plan: A Panel Discussion, Josh Braid, Rodney Mader, Bradley Flamm Nov 2022

Realizing The Vision Of Wcu’S Landscape Master Plan: A Panel Discussion, Josh Braid, Rodney Mader, Bradley Flamm

Sustainability Research & Practice Seminar Presentations

Bradley Flamm, WCU Office of Sustainability (Moderator), with Josh Braid, WCU Grounds Department, and Rodney Mader, WCU Campus Tree Committee Chair - Panel discussion: Realizing the Vision of WCU’s Landscape Master Plan


The Potential Of Private Health Insurance Ownership Based On The 2018-2020 National Socioeconomic Survey Data, Arief Rosyid Hasan, Adang Bachtiar, Cicilya Candi Nov 2022

The Potential Of Private Health Insurance Ownership Based On The 2018-2020 National Socioeconomic Survey Data, Arief Rosyid Hasan, Adang Bachtiar, Cicilya Candi

Kesmas

In 2014, the Indonesian Government introduced a social security program in the health sector. However, Indonesia’s out-of-pocket expenses remain high due to a lack of public interest in National Health Insurance services. Financing expensive health services with high out-of-pocket expenses has the potential to cause poverty. Private health insurance is considered a solution to this problem. This study aimed to determine the socioeconomic factors of private health insurance ownership and its potential in Indonesia. This study used secondary data from the 2018, 2019, and 2020 National Socioeconomic Surveys. Logistic regression analysis showed that the variables related to private health insurance …


Increased Aerosols Can Reverse Twomey Effect In Water Clouds Through Radiative Pathway, Pradeep Khatri, Tadahiro Hayasaka, Brent N. Holben, Ramesh P. Singh, Husi Letu, Sachchida N. Tripathi Nov 2022

Increased Aerosols Can Reverse Twomey Effect In Water Clouds Through Radiative Pathway, Pradeep Khatri, Tadahiro Hayasaka, Brent N. Holben, Ramesh P. Singh, Husi Letu, Sachchida N. Tripathi

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aerosols play important roles in modulations of cloud properties and hydrological cycle by decreasing the size of cloud droplets with the increase of aerosols under the condition of fixed liquid water path, which is known as the first aerosol indirect effect or Twomey-effect or microphysical effect. Using high-quality aerosol data from surface observations and statistically decoupling the influence of meteorological factors, we show that highly loaded aerosols can counter this microphysical effect through the radiative effect to result both the decrease and increase of cloud droplet size depending on liquid water path in water clouds. The radiative effect due to …


Room-Temperature Polariton Quantum Fluids In Halide Perovskites, Kai Peng, Renjie Tao, Louis Haeberlé, Quanwei Li, Dafei Jin, Graham R. Fleming, Stéphane Kéna-Cohen, Xiang Zhang, Wei Bao Nov 2022

Room-Temperature Polariton Quantum Fluids In Halide Perovskites, Kai Peng, Renjie Tao, Louis Haeberlé, Quanwei Li, Dafei Jin, Graham R. Fleming, Stéphane Kéna-Cohen, Xiang Zhang, Wei Bao

School of Computing: Faculty Publications

Quantum fluids exhibit quantum mechanical effects at the macroscopic level, which contrast strongly with classical fluids. Gain-dissipative solid-state exciton-polaritons systems are promising emulation platforms for complex quantum fluid studies at elevated temperatures. Recently, halide perovskite polariton systems have emerged as materials with distinctive advantages over other room-temperature systems for future studies of topological physics, non-Abelian gauge fields, and spin-orbit interactions. However, the demonstration of nonlinear quantum hydrodynamics, such as superfluidity and Čerenkov flow, which is a consequence of the renormalized elementary excitation spectrum, remains elusive in halide perovskites. Here, using homogenous halide perovskites single crystals, we report, in both one- …


2022 Fall Engr333 Seminar Presentation, Jordan Tuter, Aidan Bakker, Samuel Hoover, Jessica Camp Nov 2022

2022 Fall Engr333 Seminar Presentation, Jordan Tuter, Aidan Bakker, Samuel Hoover, Jessica Camp

ENGR 333

File for student presentation on Carbon Neutrality for Calvin University, given by students in the Fall 2022 class of ENGR333.


Substrate Availability And Not Thermal Acclimation Controls Microbial Temperature Sensitivity Response To Long-Term Warming, Luiz A. Domeignoz-Horta, Grace Pold, Hailey Erb, David Sebag, Eric Verrecchia, Trent Northen, Katherine Louie, Emiley Eloe-Fadrosh, Christa Pennacchio, Melissa A. Knorr, Serita D. Frey, Jerry M. Melillo, Kristen M. Deangelis Nov 2022

Substrate Availability And Not Thermal Acclimation Controls Microbial Temperature Sensitivity Response To Long-Term Warming, Luiz A. Domeignoz-Horta, Grace Pold, Hailey Erb, David Sebag, Eric Verrecchia, Trent Northen, Katherine Louie, Emiley Eloe-Fadrosh, Christa Pennacchio, Melissa A. Knorr, Serita D. Frey, Jerry M. Melillo, Kristen M. Deangelis

Faculty Publications

Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mechanisms have been suggested to explain the long-term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year-old soil warming experiments in different …


A Pipeline To Generate Deep Learning Surrogates Of Genome-Scale Metabolic Models, Achilles Rasquinha Nov 2022

A Pipeline To Generate Deep Learning Surrogates Of Genome-Scale Metabolic Models, Achilles Rasquinha

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Genome-Scale Metabolic Models (GEMMs) are powerful reconstructions of biological systems that help metabolic engineers understand and predict growth conditions subjected to various environmental factors around the cellular metabolism of an organism in observation, purely in silico. Applications of metabolic engineering range from perturbation analysis and drug-target discovery to predicting growth rates of biotechnologically important metabolites and reaction objectives within dierent single-cell and multi-cellular organism types. GEMMs use mathematical frameworks for quantitative estimations of flux distributions within metabolic networks. The reasons behind why an organism activates, stuns, or fluctuates between alternative pathways for growth and survival, however, remain relatively unknown. GEMMs …