Now showing items 1-20 of 70

    • A Branch Decomposition Algorithm for the p-Median Problem 

      Fast, Caleb C.; Hicks, Illya V. (2017)
      In this paper, we use a branch decomposition technique to improve approximations to the p-median problem. Starting from a support graph produced either by a combination of heuristics or by linear programming, we use dynamic programming guided by a branch decomposition of that support graph to find the best p-median solution on the support graph. Our ...
    • A discrepancy-based penalty method for extended waveform inversion 

      Fu, Lei; Symes, William W.; The Rice Inversion Project (2017)
      Extended waveform inversion globalizes the convergence of seismic waveform inversion by adding nonphysical degrees of freedom to the model, thus permitting it to fit the data well throughout the inversion process. These extra degrees of freedom must be curtailed at the solution, for example, by penalizing them as part of an optimization formulation. ...
    • A Distributed-Memory Randomized Structured Multifrontal Method for Sparse Direct Solutions 

      Xin, Zixing; Xia, Jianlin; de Hoop, Maarten V.; Cauley, Stephen; Balakrishnan, Venkataramanan (2017)
      We design a distributed-memory randomized structured multifrontal solver for large sparse matrices. Two layers of hierarchical tree parallelism are used. A sequence of innovative parallel methods are developed for randomized structured frontal matrix operations, structured update matrix computation, skinny extend-add operation, selected entry extraction ...
    • A Topological Model of the Hippocampal Cell Assembly Network 

      Babichev, Andrey; Ji, Daoyun; Mémoli, Facundo; Dabaghian, Yuri A. (2016)
      It is widely accepted that the hippocampal place cells' spiking activity produces a cognitive map of space. However, many details of this representation's physiological mechanism remain unknown. For example, it is believed that the place cells exhibiting frequent coactivity form functionally interconnected groups—place cell assemblies—that drive ...
    • An adaptive multiscale algorithm for efficient extended waveform inversion 

      Fu, Lei; Symes, William W.; The Rice Inversion Project (2017)
      Subsurface-offset extended full-waveform inversion (FWI) may converge to kinematically accurate velocity models without the low-frequency data accuracy required for standard data-domain FWI. However, this robust alternative approach to waveform inversion suffers from a very high computational cost resulting from its use of nonlocal wave physics: The ...
    • An Algebraic Exploration of Dominating Sets and Vizing's Conjecture 

      (2012)
      Systems of polynomial equations are commonly used to model combinatorial problems such as independent set, graph coloring, Hamiltonian path, and others. We formulate the dominating set problem as a system of polynomial equations in two di erent ways: rst, as a single, high-degree polynomial, and second as a collection of polynomials based on the ...
    • An accelerated Poisson solver based on multidomain spectral discretization 

      Babb, Tracy; Gillman, Adrianna; Hao, Sijia; Martinsson, Per-Gunnar (2018)
      This paper presents a numerical method for variable coefficient elliptic PDEs with mostly smooth solutions on two dimensional domains. The method works best for domains that can readily be mapped onto a rectangle, or a collection of nonoverlapping rectangles. The PDE is discretized via a multi-domain spectral collocation method of high local order ...
    • An alternating direction and projection algorithm for structure-enforced matrix factorization 

      Xu, Lijun; Yu, Bo; Zhang, Yin (2017)
      Structure-enforced matrix factorization (SeMF) represents a large class of mathematical models appearing in various forms of principal component analysis, sparse coding, dictionary learning and other machine learning techniques useful in many applications including neuroscience and signal processing. In this paper, we present a unified algorithm ...
    • An exact redatuming procedure for the inverse boundary value problem for the wave equation 

      de Hoop, Maarten V.; Kepley, Paul; Oksanen, Lauri (2018)
      Redatuming is a data processing technique to transform measurements recorded in one acquisition geometry to an analogous data set corresponding to another acquisition geometry, for which there are no recorded measurements. We consider a redatuming problem for a wave equation on a bounded domain, or on a manifold with boundary, and model data acquisition ...
    • Angola Cameia Development Casing-Settlement Calculations 

      Akin, J. Ed; Dove, N. Roland; Ruddy, Ken (2017)
      The amount of axial settlement of casings supported by regions of axial elastic foundations is computed. The differential equation of axial equilibrium, including the foundation stiffnesses, is solved by use of cubic axial finite elements. The analysis is applied to 101 m of a vertical 914-mm (36-in.) casing supporting a 559-mm (22-in.) casing running ...
    • An approximate inverse to the extended Born modeling operator 

      Hou, Jie; Symes, William W.; The Rice Inversion Project (2015)
      Given a correct (data-consistent) velocity model, reverse time migration (RTM) correctly positions reflectors but generally with incorrect amplitudes and wavelets. Iterative least-squares migration (LSM) corrects the amplitude and wavelet by fitting data in the sense of Born modeling, that is, replacing migration by Born inversion. However, LSM also ...
    • Chromatin architecture transitions from zebrafish sperm through early embryogenesis 

      Wike, Candice L.; Guo, Yixuan; Tan, Mengyao; Nakamura, Ryohei; Shaw, Dana Klatt; (2021)
      Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a genome. The 3D chromatin genome shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic genome activation ...
    • Chromosome size affects sequence divergence between species through the interplay of recombination and selection 

      Tigano, Anna; Khan, Ruqayya; Omer, Arina D.; Weisz, David; Dudchenko, Olga; (2022)
      The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from ...
    • Clustering earthquake signals and background noises in continuous seismic data with unsupervised deep learning 

      Seydoux, Léonard; Balestriero, Randall; Poli, Piero; de Hoop, Maarten; Campillo, Michel; (2020)
      The continuously growing amount of seismic data collected worldwide is outpacing our abilities for analysis, since to date, such datasets have been analyzed in a human-expert-intensive, supervised fashion. Moreover, analyses that are conducted can be strongly biased by the standard models employed by seismologists. In response to both of these ...
    • A Comparison of High Order Interpolation Nodes for the Pyramid 

      Chan, Jesse; Warburton, T. (2015)
      The use of pyramid elements is crucial to the construction of efficient hex-dominant meshes [M. Bergot, G. Cohen, and M. Duruflé, J. Sci. Comput., 42 (2010), pp. 345--381]. For conforming nodal finite element methods with mixed element types, it is advantageous for nodal distributions on the faces of the pyramid to match those on the faces and edges ...
    • Compositional heterogeneity near the base of the mantle transition zone beneath Hawaii 

      Yu, Chunquan; Day, Elizabeth A.; de Hoop, Maarten V.; Campillo, Michel; Goes, Saskia; (2018)
      Global seismic discontinuities near 410 and 660 km depth in Earth’s mantle are expressions of solid-state phase transitions. These transitions modulate thermal and material fluxes across the mantle and variations in their depth are often attributed to temperature anomalies. Here we use novel seismic array analysis of SSwaves reflecting off ...
    • Convergence of a Class of Stationary Iterative Methods for Saddle Point Problems 

      Zhang, Yin (2019)
      A unified convergence theory is derived for a class of stationary iterative methods for solving linear equality constrained quadratic programs or saddle point problems. This class is constructed from essentially all possible splittings of the submatrix residing in the (1,1)-block of the augmented saddle point matrix that would produce non-expansive ...
    • Convergence of a high order method in time and space for the miscible displacement equations 

      (2015)
      A numerical method is formulated and analyzed for solving the miscible displacement problem under low regularity assumptions. The scheme employs discontinuous Galerkin time stepping with mixed and interior penalty discontinuous Galerkin finite elements in space. The numerical approximations of the pressure, velocity, and concentration converge to the ...
    • Cytoplasmic sphingosine-1-phosphate pathway modulates neuronal autophagy 

      (2015)
      Autophagy is an important homeostatic mechanism that eliminates long-lived proteins, protein aggregates and damaged organelles. Its dysregulation is involved in many neurodegenerative disorders. Autophagy is therefore a promising target for blunting neurodegeneration. We searched for novel autophagic pathways in primary neurons and identified the ...
    • A DEIM Induced CUR Factorization 

      Sorensen, D.C.; Embree, Mark (2016)
      We derive a CUR approximate matrix factorization based on the discrete empirical interpolation method (DEIM). For a given matrix ${\bf A}$, such a factorization provides a low-rank approximate decomposition of the form ${\bf A} \approx \bf C \bf U \bf R$, where ${\bf C}$ and ${\bf R}$ are subsets of the columns and rows of ${\bf A}$, and ${\bf U}$ ...