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  • Protein secondary structure prediction using conditional random fields and profiles

    Creator:
    Shen, Rongkun
    Abstract:
    Protein secondary structure prediction plays a pivotal role in predicting protein folding in three-dimensions. Its task is to assign each residue one of the three secondary structure classes helix, strand, or random coil. This is an instance of the problem of sequential supervised learning in machine learning. This thesis describes...
    Resource Type:
    Masters Thesis
    Full Text:
    window size of 15 residues, and 3 rounds of PSI-BLAST searching. The mean three-state prediction

  • The density signature

    Creator:
    Migler-VonDollen, Theresa
    Abstract:
    In real networks, identifying dense regions is of great importance. For example, in a network that represents academic collaboration, authors within the densest component of the graph tend to be the most prolific. Dense subgraphs often identify communities in social networks. And dense subgraphs can be used to discover regulatory...
    Resource Type:
    Dissertation
    Full Text:
    the case in existing random graph models. No existing random graph model generates graphs that

  • Parsing with Recurrent Neural Networks

    Creator:
    Cross, James Henry, III
    Abstract:
    Machine learning models for natural language processing have traditionally relied on large numbers of discrete features, built up from atomic categories such as word forms and part-of-speech labels, which are considered completely distinct from each other. Recently however, the advent of dense feature representations coupled with deep learning techniques has...
    Resource Type:
    Dissertation
    Full Text:
    languages de- spite no language-specific architectural or hyper-parameter tuning, including achieving the

  • Efficient Incremental Panorama Reconstruction from Multiple Videos

    Creator:
    Feng, Zhongyuan
    Abstract:
    Constructing a panorama from a set of videos is a long-standing problem in computer vision. A panorama represents an enhanced still-image representation of an entire scene captured in a set of videos, where each video shows only a part of the scene. Importantly, a panorama shows only the scene background,...
    Resource Type:
    Capstone Project
    Full Text:
    with different parts of the panorama stop changing, or when there are no new video frames that would

  • Improving automated email tagging with implicit feedback

    Creator:
    Sorower, Mohammad Shahed
    Abstract:
    Machine learning systems are generally trained offline using ground truth data that has been labeled by experts. However, these batch training methods are not a good fit for many applications, especially in the cases where complete ground truth data is not available for offline training. In addition, batch methods do...
    Resource Type:
    Dissertation
    Full Text:
    Baseline Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 3.3.1 No Implicit

  • 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:
    . Focus- ing on the cases where little to no homologous sequences can be found for a given input protein

  • Bayesian optimization with empirical constraints

    Creator:
    Azimi, Javad
    Abstract:
    Bayesian Optimization (BO) methods are often used to optimize an unknown function f(•) that is costly to evaluate. They typically work in an iterative manner. In each iteration, given a set of observation points, BO algorithms select k ≥ 1 points to be evaluated. The results of those points are...
    Resource Type:
    Dissertation
    Full Text:
    unobserved point, ([54, 49, 73, 57]) and the selection criterion, [40, 34, 65, 42, 15] which selects the next

  • Learning multiple non-redundant codebooks with word clustering for document classification

    Creator:
    Surve, Akshat Sudhakar
    Abstract:
    The problem of document classification has been widely studied in machine learning and data mining. In document classification, most of the popular algorithms are based on the bag-of-words representation. Due to the high dimensionality of the bag-of-words representation, significant research has been conducted to reduce the dimensionality via different approaches....
    Resource Type:
    Masters Thesis
    Full Text:
    .............................................................11 2.2 Information Bottleneck with Side Information ..........................................15

  • Semantic embodied navigation : developing agents that navigate from language and vision

    Creator:
    Krantz, Jacob
    Abstract:
    Autonomous robotic agents are on their way to becoming in-home personal assistants, construction assistants, and warehouse workers. The degree of autonomy of such systems is reflected by the manner in which we specify goals to them; the abstraction of low-level commands to high-level goals goes hand-in-hand with increased autonomy. In...
    Resource Type:
    Dissertation
    Full Text:
    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2.2 We successfully transfer 77% of the R2R trajectories. (a) Most panorama nodes transfer

  • Learning MDP action models via discrete mixture trees

    Creator:
    Wynkoop, Michael S.
    Abstract:
    This thesis addresses the problem of learning dynamic Bayesian network (DBN) models to support reinforcement learning. It focuses on learning regression tree models of the conditional probability distributions of the DBNs. Existing algorithms presume that the stochasticity in the domain can be modeled as a deterministic function with additive noise....
    Resource Type:
    Masters Thesis
    Full Text:
    pre-pruning in our tree growth algorithm. First, 15 no split can be made from a node that contains