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AuthorBoggess, May (1)Brown, Donald L. (1)Cohen, Albert (1)Daubechies, Ingrid (1)Day, Sarah (1)View MoreJournalBMC Bioinformatics (1)Computing and Visualization in Science (1)Constructive Approximation (1)GEM - International Journal on Geomathematics (1)International Journal of Fracture (1)View MoreKAUST Grant Number

KUS-C1-016-04 (7)

Publisher
Springer Nature (7)

SubjectActive learning (1)Cholesky decomposition (1)Compressed sensing (1)Correlation modeling (1)Elasticity (1)View MoreType
Article (7)

Year (Issue Date)
2011 (7)

Item AvailabilityMetadata Only (5)Open Access (2)

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Capturing Ridge Functions in High Dimensions from Point Queries

Cohen, Albert; Daubechies, Ingrid; DeVore, Ronald; Kerkyacharian, Gerard; Picard, Dominique (Constructive Approximation, Springer Nature, 2011-12-21) [Article]

Constructing a good approximation to a function of many variables suffers from the "curse of dimensionality". Namely, functions on ℝ N with smoothness of order s can in general be captured with accuracy at most O(n -s/N) using linear spaces or nonlinear manifolds of dimension n. If N is large and s is not, then n has to be chosen inordinately large for good accuracy. The large value of N often precludes reasonable numerical procedures. On the other hand, there is the common belief that real world problems in high dimensions have as their solution, functions which are more amenable to numerical recovery. This has led to the introduction of models for these functions that do not depend on smoothness alone but also involve some form of variable reduction. In these models it is assumed that, although the function depends on N variables, only a small number of them are significant. Another variant of this principle is that the function lives on a low dimensional manifold. Since the dominant variables (respectively the manifold) are unknown, this leads to new problems of how to organize point queries to capture such functions. The present paper studies where to query the values of a ridge function f(x)=g(a · x) when both a∈ℝ N and g ∈ C[0,1] are unknown. We establish estimates on how well f can be approximated using these point queries under the assumptions that g ∈ C s[0,1]. We also study the role of sparsity or compressibility of a in such query problems. © 2011 Springer Science+Business Media, LLC.

An efficient and extensible approach for compressing phylogenetic trees

Matthews, Suzanne J; Williams, Tiffani L (BMC Bioinformatics, Springer Nature, 2011) [Article]

Background: Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference.Results: On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings.Conclusions: TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. © 2011 Matthews and Williams; licensee BioMed Central Ltd.

Higher-order schemes for the Laplace transformation method for parabolic problems

Douglas, C.; Kim, I.; Lee, H.; Sheen, D. (Computing and Visualization in Science, Springer Nature, 2011-01) [Article]

In this paper we solve linear parabolic problems using the three stage noble algorithms. First, the time discretization is approximated using the Laplace transformation method, which is both parallel in time (and can be in space, too) and extremely high order convergent. Second, higher-order compact schemes of order four and six are used for the the spatial discretization. Finally, the discretized linear algebraic systems are solved using multigrid to show the actual convergence rate for numerical examples, which are compared to other numerical solution methods. © 2011 Springer-Verlag.

On homogenization of stokes flow in slowly varying media with applications to fluid–structure interaction

Brown, Donald L.; Popov, Peter; Efendiev, Yalchin R. (GEM - International Journal on Geomathematics, Springer Nature, 2011-09-11) [Article]

In this paper we establish corrector estimates for Stokes flow in slowly varying perforated media via two scale asymptotic analysis. Current methods and techniques are often not able to deal with changing geometries prevalent in applied problems. For example, in a deformable porous medium environment, the geometry does not remain periodic under mechanical deformation and if slow variation in the geometry occurs. For such problems, one cannot use classical homogenization results directly and new homogenization results and estimates are needed. Our work uses asymptotic techniques of Marusic-Paloka and Mikelic (Bollettino U. M. I 7:661-671, 1996) where the authors constructed a downscaled velocity which converges to the fine-scale velocity at a rate of ε1/6 where ε is the characteristic length scale. We assume a slowly varying porous medium and study homogenization and corrector estimates for the Stokes equations. Slowly varying media arise, e. g., in fluid-structure interaction (FSI) problems (Popov et al. in Iterative upscaling of flows in deformable porous media, 2008), carbonation of porous concrete (Peter in C. R. Mecanique 335:357-362, 2007a; C. R. Mecanique 335:679-684, 2007b), and various other multiphysics processes. To homogenize Stokes flows in such media we restate the cell problems of Marusic-Paloka and Mikelic (Bollettino U. M. I 7:661-671, 1996) in a moving RVE framework. Further, to recover the same convergence properties it is necessary to solve an additional cell problem and add one more corrector term to the downscaled velocity. We further extend the framework of Marusic-Paloka and Mikelic (Bollettino U. M. I 7:661-671, 1996) to three spatial dimensions in both periodic and variable pore-space cases. Next, we also propose an efficient algorithm for computing the correctors by solving a limited number of cell problems at selected spatial locations. We present two computational examples: one for a constructed medium of elliptical perforations, and another for a fractured medium with FSI driven deformation. We obtain numerical estimates that confirm the theory in these two examples. © 2011 Springer-Verlag.

Modeling fracture in the context of a strain-limiting theory of elasticity: a single anti-plane shear crack

Rajagopal, K. R.; Walton, J. R. (International Journal of Fracture, Springer Nature, 2011-01-06) [Article]

This paper is the first part of an extended program to develop a theory of fracture in the context of strain-limiting theories of elasticity. This program exploits a novel approach to modeling the mechanical response of elastic, that is non-dissipative, materials through implicit constitutive relations. The particular class of models studied here can also be viewed as arising from an explicit theory in which the displacement gradient is specified to be a nonlinear function of stress. This modeling construct generalizes the classical Cauchy and Green theories of elasticity which are included as special cases. It was conjectured that special forms of these implicit theories that limit strains to physically realistic maximum levels even for arbitrarily large stresses would be ideal for modeling fracture by offering a modeling paradigm that avoids the crack-tip strain singularities characteristic of classical fracture theories. The simplest fracture setting in which to explore this conjecture is anti-plane shear. It is demonstrated herein that for a specific choice of strain-limiting elasticity theory, crack-tip strains do indeed remain bounded. Moreover, the theory predicts a bounded stress field in the neighborhood of a crack-tip and a cusp-shaped opening displacement. The results confirm the conjecture that use of a strain limiting explicit theory in which the displacement gradient is given as a function of stress for modeling the bulk constitutive behavior obviates the necessity of introducing ad hoc modeling constructs such as crack-tip cohesive or process zones in order to correct the unphysical stress and strain singularities predicted by classical linear elastic fracture mechanics. © 2011 Springer Science+Business Media B.V.

Robust estimation of the correlation matrix of longitudinal data

Maadooliat, Mehdi; Pourahmadi, Mohsen; Huang, Jianhua Z. (Statistics and Computing, Springer Nature, 2011-09-23) [Article]

We propose a double-robust procedure for modeling the correlation matrix of a longitudinal dataset. It is based on an alternative Cholesky decomposition of the form Σ=DLL⊤D where D is a diagonal matrix proportional to the square roots of the diagonal entries of Σ and L is a unit lower-triangular matrix determining solely the correlation matrix. The first robustness is with respect to model misspecification for the innovation variances in D, and the second is robustness to outliers in the data. The latter is handled using heavy-tailed multivariate t-distributions with unknown degrees of freedom. We develop a Fisher scoring algorithm for computing the maximum likelihood estimator of the parameters when the nonredundant and unconstrained entries of (L,D) are modeled parsimoniously using covariates. We compare our results with those based on the modified Cholesky decomposition of the form LD2L⊤ using simulations and a real dataset. © 2011 Springer Science+Business Media, LLC.

Coexistence of competing stage-structured populations.

Fujiwara, Masami; Pfeiffer, Georgia; Boggess, May; Day, Sarah; Walton, Jay (Scientific Reports, Springer Nature, 2011-10-05) [Article]

This paper analyzes the stability of a coexistence equilibrium point of a model for competition between two stage-structured populations. In this model, for each population, competition for resources may affect any one of the following population parameters: reproduction, juvenile survival, maturation rate, or adult survival. The results show that the competitive strength of a population is affected by (1) the ratio of the population parameter influenced by competition under no resource limitation (maximum compensatory capacity) over the same parameter under a resource limitation due to competition (equilibrium rate) and (2) the ratio of interspecific competition over intraspecific competition; this ratio was previously shown to depend on resource-use overlap. The former ratio, which we define as fitness, can be equalized by adjusting organisms' life history strategies, thereby promoting coexistence. We conclude that in addition to niche differentiation among populations, the life history strategies of organisms play an important role in coexistence.

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