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      • Tensor Decomposition for Concept Recognition

        Wahba, Ahmed University of California, Santa Barbara ProQuest D 2019 해외박사(DDOD)

        RANK : 247343

        The yield optimization data analytic process is an iterative search process. Each iterationcomprises of two main steps: data preparation, and result evaluation. In this thesis, wefocus on the result evaluation step, where the analyst evaluates the result from runninga certain analytic task looking for some specic concept. For example this concept canbe in the form a pattern formed by the failing dies on a wafer.A wafer pattern may hint a particular issue in the production by itself or guide theanalysis into a certain direction. In this thesis, we show how Generative AdversarialNetworks (GANs) can be used to build concept recognizers, we present the architecturechosen for the convolutional neural networks, we show how the network is trained, andwe show how the discriminator network can be used for concept recognition.However, the main focus of this work is on rules of Tensor decomposition in theautomated concept recognition ow. We introduce a novel concept recognition approachbased on Tucker decomposition. Tensor-based concept recognizers are combined withGANs-based recognizers to prevent escapes, also known as adversarial examples.In this work, we are concerned with two main aspects: (1) automation of the conceptrecognition process, and (2) ensuring robustness. Two tensor methods are introduced toaddress both aspects.The rst tensor method is based on clustering and is used to automatically extractconcepts that might be of interest to the analyst as well as choose the set of wafers to beused in training for each concept.Our second tensor method is to ensure robustness of the GANs-based recognizersby introducing the containment check to continuously check for GANs performance andreport to the expert if a problem occurs.We also address other challenges, such as automating the training process for GANs.We also introduce a collaboration view where the machine learning expert is assumedto be a separate entity. Hence he is not allowed to have access to protected informationsuch as yield. we present a tensor-based transformation for training wafers such that theprotected information is hidden.Our automated and robust software is applied to two high reliability automotiveproducts, with 8300 and 7052 wafers respectively.

      • Roles for transcription and DNA repair in generating genome instability

        Wahba, Lamia The Johns Hopkins University 2013 해외박사(DDOD)

        RANK : 247343

        The occurrence of genome instability has been implicated in many detrimental outcomes, from cell death to cancer progression, as well as many other human diseases. Studies in yeast and mammalian cells have revealed that one cause of instability is the occurrence of RNA-DNA hybrids. Previously thought to be a rare consequence of transcription, in this study, I expand both the number of processes, as well as the number of mutants susceptible to RNA-DNA hybrid formation. I find that mutants defective in transcriptional repression, elongation, RNA export and RNA degradation exhibit increased hybrids and associated genome instability. I propose that even under wild-type conditions, hybrids readily form at many loci, likely due to transcriptional errors, but their accumulation is kept in check by two evolutionarily conserved RNase H enzymes. In this study, I also discuss one mechanism by which RNA-DNA hybrid formation can be mediated, via the strand-exchange protein Rad51p. In vivo and in vitro data indicate that Rad5lp facilitates the invasion of RNA into duplex DNA through an inverse strand exchange process; this Rad51-mediated hybrid formation may be a byproduct of the ability of Rad51 to form filaments on duplex DNA. This leads to a model in which RNA-DNA hybrids are kept under check by limiting Rad51 binding to undamaged chromatin, as well as free RNA in the nucleus. In summary, my work has established RNA-DNA hybrids as a potent source for changing genome structure and expanded the processes and mechanisms by which hybrids form, and can be removed.

      • Hierarchical formulations for numerical flow simulations

        Wahba, Essam Moustafa University of California, Davis 2004 해외박사(DDOD)

        RANK : 247343

        A new hierarchical formulation for the equations of fluid motion is developed. The hierarchical nature of the new formulation is due to its ability to simulate all levels of fluid flow approximations, namely, inviscid irrotational isentropic flows (potential flow formulation), inviscid rotational non-isentropic flows (Euler formulation) and viscous heat conducting flows (Navier-Stokes formulation). The new formulation uses a potential flow solver as a base solver which is evaluated everywhere in the flow field, while convection/diffusion equations for entropy, vorticity and total enthalpy are only evaluated within limited domains of the flow field where rotational effects are present such as in regions containing shocks, boundary layers and/or wakes. This is accomplished by using a Helmholtz decomposition of the velocity vector into the gradient of a potential function plus a rotational component. The density and pressure are reformulated in terms of the speed and entropy. The new formulation identifies an acoustic mode, governed by the potential equation, from the convection/diffusion mode governing the entropy, vorticity and total enthalpy. This identification of modes together with the ability to restrict the evaluation of entropy, vorticity and total enthalpy to relatively small domains within the flow field offers several advantages over the traditional Euler and Navier-Stokes formulations from the point of view of upwinding, multigrid and the incompressible flow limit. To test the robustness, efficiency and accuracy of this new approach, several flow problems are simulated. These problems include 2-D shock wave/boundary layer interaction, 2-D inviscid and viscous flows over cylinders, 2-D inviscid and viscous flows over airfoils and 3-D inviscid and viscous flows over wings. The results obtained using the new formulation agree well with both experimental results and numerical results obtained from traditional Euler and Navier-Stokes formulations. Fast convergence rates are also achieved through the implementation of multigrid to the augmented potential equation which results in an order of magnitude reduction in work units as compared to single grid computations.

      • Statistical mechanics of membrane proteins

        Wahba, Karim A University of California, Los Angeles 2009 해외박사(DDOD)

        RANK : 247343

        We examine the properties of transmembrane (TM) proteins from a thermodynamic equilibrium point of view. Motivated by recent experiments that describe the Boltzmann nature of the insertion of TM segments, we construct statistical mechanical models of membrane proteins to capitalize on this finding. This is achieved using a course-grained model that treats the TM protein as a homopolymer chain. The TM segments are allowed to interact with the membrane as well as with each other once inserted. A phase diagram is constructed describing the various equilibrium phases and the transitions separating them. Next we use an approach that utilizes the full amino acid sequence of bacteriorhodopsin . We are able to do away with the coarse graining over the individual amino acid hydrophobicities by treating the TM segments as a confined fluid of rods in an external potential. Information is extracted from the sequence that supports the robustness of the TM structure against changes in temperature, chemical potential, mutations and various assembly scenarios. In the last Chapter we examine the role of the newly discovered RNA interference (RNAi) mechanism in suppressing viral growth. We analyze the competing dynamics of viral and RNAi populations and describe the conditions for which suppression can be successful at the intercellular and intracellular levels.

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