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Filtering by: Creator Groman, David B. Remove constraint Creator: Groman, David B. Degree Field Computer Science Remove constraint Degree Field: Computer Science

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  • Computational Approaches for RNA Structure Prediction with Dynamic Programming and Deep Neural Networks

    Creator:
    Deng, Dezhong
    Abstract:
    Our goal is to build a system to model the RNA sequences that reveals their structural information by using efficient dynamic programming algorithms and deep learning approaches. We aim to 1) achieve linear-time for RNA secondary structure prediction based on existing minimum free energy models; 2) utilize deep neural networks...
    Resource Type:
    Dissertation
    Full Text:
    Abstract approved: David A. Hendrix Our goal is to build a system to model the RNA sequences that reveals

  • Position-Dependent Codon Usage Bias in the Human Transcriptome

    Creator:
    Subramanian, Kaavya
    Abstract:
    All life depends on the reliable translation of RNA to protein according to complex interactions between translation machinery and RNA sequence features. While ribosomal occupancy and codon frequencies vary across coding regions, well-established metrics for computing coding potential of RNA do not capture such positional dependence. Here, we investigate position-dependent...
    Resource Type:
    Honors College Thesis
    Full Text:
    :_____________________________________________________ David Hendrix All life depends on the reliable translation of RNA to protein according

  • Determining free energies of hard sphere fluids via Monte Carlo simulation

    Creator:
    Valeskea, Austin
    Abstract:
    Free energy is a fundamental property of a thermodynamic system, from which pressure, entropy, and other interesting properties can be derived. It is useful, then, to be able to accurately compute the free energy at various densities and temperatures in a way that can serve as the basis for further...
    Resource Type:
    Honors College Thesis
    Full Text:
    . Abstract approved: David Roundy Free energy is a fundamental property of a thermodynamic system, from

  • An enhanced version of Caesar supporting 45° geometries

    Creator:
    Lanfri, Ann R.
    Abstract:
    Caesar is an interactive graphic editor that is used to generate layouts for VLSI circuits. It runs on a VAX-11 /780 under the UNIX operating system with Berkeley extensions. Caesar has a unique and simple user interface. Phled is an enhanced version of Caesar that runs on a M68000-based engineering...
    Resource Type:
    Capstone Project
    Full Text:
    -Manhattan Clipping B against A creates 4 shapes: the top and bottom are from horizontal clipping; the

  • New Strategies to Develop Hidden Markov Models Combining KEGG and Pfam

    Creator:
    Gupta, Sonica
    Abstract:
    Profile Hidden Markov Models utilize the information stored in a multiple sequence alignment such as its residues and conserved regions to assign probabilities at each column. This indicates areas in the sequences where similar functionality is observed. These probability weights are then combined to assign a sequence score, which is...
    Resource Type:
    Honors College Thesis
    Full Text:
    . Abstract approved:_____________________________________________________ Maude David Profile

  • Tracing the Pacific Islander Diaspora in the Pacific Northwest

    Creator:
    Yarbrough, Nicole
    Abstract:
    The Pacific Islander diaspora in the Pacific Northwest United States is a unique community characterized by diverse cultures, experiences, and motivations for migration. This study aimed to explore the narratives of individuals from different Pacific Islander backgrounds residing in Oregon, shedding light on their reasons for migration and the impact...
    Resource Type:
    Honors College Thesis
    Full Text:
    Abstract approved: _____________________________________________________ David G. Lewis The

  • Two Sides of a Coin: Adversarial-Based Image Privacy and Defending Against Adversarial Perturbations for Robust CNNs

    Creator:
    Rajabi, Arezoo
    Abstract:
    Emergence of highly accurate Convolutional Neural Networks (CNNs) with the capability to process large datasets, has led to their popularity in many applications, including safety/security-sensitive (e.g. disease recognition, self-driving cars). Despite the high accuracy of convolutional neural networks, they have been found to be susceptible to adversarial noise added to...
    Resource Type:
    Dissertation
    Full Text:
    CNNs Abstract approved: Rakesh B. Bobba Emergence of highly accurate Convolutional Neural Networks

  • Deep Learning for Human and Biological Languages

    Creator:
    Hong, Junki
    Abstract:
    We explore the application of deep learning to the disparate fields of natural language processing and computational biology. Both the sentences uttered by humans as well as the RNA and protein sequences found within the cells of their bodies can be considered formal languages in computer science, as sets of...
    Resource Type:
    Dissertation
    Full Text:
    Human and Biological Languages Abstract approved: David Hendrix and Liang Huang We explore the

  • Machine Learning Methods for the Discovery and Analysis of MicroRNAs

    Creator:
    Bell, Jimmy D.
    Abstract:
    MicroRNAs are a highly conserved class of small endogenous RNA, about ~22nt in length, involved in post-transcriptional gene silencing and have prominent roles in disease and development. Though the process of microRNA discovery was once an arduous task, the advent of high throughput sequencing technology has resulted in novel microRNAs...
    Resource Type:
    Masters Thesis
    Full Text:
    : ______________________________________________________ David A. Hendrix MicroRNAs are a highly conserved class of small endogenous RNA, about

  • Type-correct changes — a safe approach to version control implementation

    Creator:
    Dagit, Jason
    Abstract:
    Ensuring correctness of real-world software applications is a challenging task. Testing can be used to find many bugs, but is typically not sufficient for proving correctness or even eliminating entire classes of bugs. However, formal proof and verification techniques tend to be very heavy weight and are simply not available...
    Resource Type:
    Masters Thesis
    Full Text:
    Implementation Abstract approved: David Roundy Martin Erwig Ensuring correctness of real-world software