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Filtering by: Creator Jager, Matthew J. Remove constraint Creator: Jager, Matthew J. Committee Member Fern, Xiaoli Remove constraint Committee Member: Fern, Xiaoli Peer Reviewed No Remove constraint Peer Reviewed: No

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  • Creating, Understanding and Applying Machine Learning Models of Multiple Species

    Creator:
    Griffioen, Arwen Twinkle E.
    Abstract:
    Many problems in ecology and conservation biology can be formulated and solved using machine learning algorithms for multi-label classification. This dissertation addresses three topics related to predicting the distributions of multiple species. It improves existing methods and proposes a new modeling paradigm to address the multi-species, multi-label problem. The first...
    Resource Type:
    Dissertation
    Full Text:
    term contains two penalty terms. The first is an L2 (ridge) penalty ‖𝛽‖2 2 = ∑ 𝛽𝑗 2𝐽 𝑗=1

  • Novel Approaches to Porous Material Discovery

    Creator:
    Sturluson, Arni
    Abstract:
    Uses for materials with a large surface area and high porosity have grown sig-nificantly in recent years. Porous materials have found usage in applications such as separation, gas storage, sensing, purification and more, prompting researchers to find and discover numerous new porous materials to suit a specific purpose. Hundreds of...
    Resource Type:
    Dissertation
    Full Text:
    . The 3D cage cavity image is then a 3D array; element (i, j, k) is 0 if grid 9 1 nm Figure 2: The

  • Towards Narrative Understanding with Deep Neural Networks and Hidden Markov Models

    Creator:
    Orr, J. Walker
    Abstract:
    Narratives are central to communication and the human experience. For a computer system to understand a narrative, it must be able to identify the key facts or plot elements that describe what happened or how the world has changed. These element are called events;establishing a document’s events and the relationships...
    Resource Type:
    Dissertation
    Full Text:
    AN ABSTRACT OF THE DISSERTATION OF J. Walker Orr for the

  • A statistical inference framework for finding recurring patterns in large data with applications to energy management

    Creator:
    You, Zeyu
    Abstract:
    We consider the problem of finding unknown patterns that are recurring across multiple sets. For example, finding multiple objects that are present in multiple images or a short DNA code that is repeated across multiple DNA sequences. We first consider a simple problem of finding a single unknown pattern in...
    Resource Type:
    Masters Thesis
    Full Text:
    only with respect to τ min τ N∑ i=1 ‖Yieτi − 1 N N∑ j=1 Yjeτj‖2 + N∑ i=1 φi(τi). (2.6) While

  • Computational Elucidation of the Regulatory SNPs in the Non-Coding Regions of the Human Genome

    Creator:
    Yao, Yao
    Abstract:
    We describe a series of novel computational models, CERENKOV (Computational Elucidation of the REgulatory NonKOding Variome) and its successors CERENKOV2, CERENKOV3, and Convolutional CERENKOV3, for discriminating regulatory single nucleotide polymorphisms (rSNPs) from non-regulatory SNPs within non-coding genetic loci. The CERENKOV models are designed for recognizing rSNPs in the context of...
    Resource Type:
    Dissertation

  • Interpretable Machine Learning: Applications in Biology and Genomics

    Creator:
    Danaee, Padideh
    Abstract:
    Machine learning (ML) and deep learning (DL) models impact our daily lives with applications in natural language modeling, image analysis, healthcare, genomics, and bioinformatics. The exponential growth of biological sequence data necessitates accompanying advances in computational methods. Although deep learning is highly effective for detecting and classifying biological sequences, challenges...
    Resource Type:
    Dissertation
    Full Text:
    that has base pair (i, j) with all other base pairs such that i < i0 < j0 < j as with (i0, j0), or i

  • Semantic image segmentation using domain constraints

    Creator:
    Roy, Anirban
    Abstract:
    This dissertation addresses the problem of semantic labeling of image pixels. In the course of our work, we considered different types of semantic labels, including object classes (e.g., car, person), 3D depth values (in the range 0 to 80 meters), and affordance classes (e.g., walkable, sittable). Semantic pixel labeling is...
    Resource Type:
    Dissertation
    Full Text:
    pixel i and a window at neighboring pixel j have simi- lar depths, but are different in appearance

  • Exploration of regression models for cancer noncoding mutation recurrence

    Creator:
    Xu, Tanjin
    Abstract:
    An important impact of the genome technology revolution will be the elucidation of mechanisms of cancer pathogenesis, leading to improvements in the diagnosis of cancer and the selection of cancer treatment. Integrated with current well-studied massive knowledge and findings about the role of protein-coding mutations in cancer, demystifying the functional...
    Resource Type:
    Masters Thesis
    Full Text:
    ) to pseudo-residuals. Let J be the number of the 20 tree’s leaves. The tree partitions the feature

  • A study of methods for fine-grained object classification of arthropod specimens

    Creator:
    Lin, Junyuan
    Abstract:
    Object categorization is one of the fundamental topics in computer vision research. Most current work in object categorization aims to discriminate among generic object classes with gross differences. However, many applications require much finer distinctions. This thesis focuses on the design, evaluation and analysis of learning algorithms for fine- grained...
    Resource Type:
    Masters Thesis
    Full Text:
    the within-cluster scatter is defined as min µk,cj J = M∑ j=1 K∑ k=1 cjk‖xj − µk‖22. The

  • Information-theoretic Approach to Design and Evaluate Privacy-preserving and Fair Frameworks for Continuous High-dimensional Data

    Creator:
    Alsulaimawi, Zahir Ahmed Hussein
    Abstract:
    Deep learning is becoming the latest trend in sensitive applications, such as healthcare, criminal justice, and finance. As these new applications emerge, adversaries are circumventing them. Further, there have been concerns about the possibility of bias and discrimination in predictive applications. In order to address these issues, we propose an...
    Resource Type:
    Dissertation