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refs.bib
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refs.bib
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@manual{pbd,
author = {Ostrouchov, G. and Chen, W.-C. and Schmidt, D. and Patel, P.},
title = {Programming with Big Data in \proglang{R}},
year = {2012},
url = {http://r-pbd.org/}
}
@article{Danc:etal:2011,
title={\pkg{Mlegp}: Maximum Likelihood Estimates of Gaussian Processes},
author={Dancik, Garrett M},
journal={R package version},
volume={3},
number={2},
pages={52},
year={2011}
}
@article{Danc:etal:2008,
title={\pkg{mlegp}: Statistical Analysis for Computer Models of Biological Systems Using \proglang{R}},
author={Dancik, Garrett M and Dorman, Karin S},
journal={Bioinformatics},
volume={24},
number={17},
pages={1966--1967},
year={2008},
publisher={Oxford Univ Press}
}
@article{Anit:etal:2012,
title={A Matrix-free Approach for Solving the Parametric Gaussian Process Maximum Likelihood Problem},
author={Anitescu, Mihai and Chen, Jie and Wang, Lei},
journal={SIAM Journal on Scientific Computing},
volume={34},
number={1},
pages={A240--A262},
year={2012},
publisher={SIAM}
}
@book{Rasm:Will:2006,
title={Gaussian Processes for Machine Learning},
author={Rasmussen, C.E. and Williams, C.K.I.},
volume={1},
year={2006},
publisher={{T}he {MIT} Press},
address={Cambridge, Massachusetts}
}
@Article{Rmpi,
title = {\pkg{Rmpi}: Parallel Statistical Computing in \proglang{R}},
author = {Yu, H.},
journal = {R News},
year = {2002},
volume = {2},
number = {2},
pages = {10--14},
url = {http://cran.r-project.org/doc/Rnews/Rnews\_2002-2.pdf},
}
@manual{MKL,
author={Intel},
title={Intel {M}ath {K}ernel {Library} - Documentation},
year={2013},
url={http://software.intel.com/en-us/articles/intel-math-kernel-library-documentation}
}
@article{gpfit,
title={\pkg{GPfit}: an \proglang{R} Package for Gaussian Process Model Fitting Using a New Optimization Algorithm},
author={MacDonald, Blake and Ranjan, Pritam and Chipman, Hugh},
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {arXiv:1305.0759},
year={2013}
}
@manual{lagp,
author={Gramacy, Robert B.},
title={\pkg{laGP}: Local Approximate Gaussian Process Regression. \proglang{R} package version 1.1-1},
year={2014},
url={http://CRAN.R-project.org/package=laGP}
}
@manual{gptk,
author={Kalaitzis, Alfredo and Honkela, Anttiand Gao, Pei and Lawrence, Neil D.},
title={\pkg{gptk}: Gaussian Processes Tool-Kit. \proglang{R} package version 1.08},
year={2014},
url={http://CRAN.R-project.org/package=gptk}
}
@manual{ACML,
author={AMD},
title={Core Math Library (\pkg{ACML})},
year={2013},
url={http://developer.amd.com/tools-and-sdks/cpu-development/amd-core-math-library-acml/}
}
@article{openCL,
title={\pkg{OpenCL}: A parallel Programming Standard for Heterogeneous Computing Systems},
author={Stone, John E and Gohara, David and Shi, Guochun},
journal={Computing in Science \& Engineering},
volume={12},
number={3},
pages={66},
year={2010},
publisher={NIH Public Access}
}
@techreport{scalaGauss,
title={An Inversion-Free Estimating Equation Approach for Gaussian Process Models},
author={Anitescu, Mihai and Chen, Jie and Stein, Michael},
year={2014},
institution={Argonne National Laboratory},
department={Mathematics and Computer Science Division},
number={ANL/MCS-P5078-0214}
}
@inproceedings{RScaLAPACK,
title={\pkg{RScaLAPACK}: High-Performance Parallel Statistical Computing with \proglang{R} and \pkg{ScaLAPACK}},
author={Yoginath, Srikanth B and Samatova, Nagiza F and Bauer, David and Kora, Guruprasad and Fann, George and Geist, Al},
booktitle={ISCA PDCS},
pages={61--67},
year={2005}
}
@manual{openBLAS,
author={Zhang, X.},
title={\pkg{open{BLAS}}},
year={2013},
url={https://github.com/xianyi/OpenBLAS}
}
@article{MAGMA,
title={\pkg{MAGMA} Users' Guide},
author={Tomov, S. and Nath, R. and Du, P. and Dongarra, J.},
journal={ICL, UTK (November 2009)},
year={2011}
}
@manual{CUBLAS,
author = {nVidia},
edition = {v5.0},
howpublished = {http://docs.nvidia.com/cublas/index.html},
keywords = {cuda, gpgpu, linear\_algebra, nvidia},
month = oct,
organization = {nVidia},
posted-at = {2011-01-27 02:17:11},
priority = {0},
title = {\pkg{CUBLAS} Library User Guide},
url = {http://docs.nvidia.com/cublas/index.html},
year = {2012}
}
@book{openMP,
title={Using \pkg{OpenMP}: Portable Shared Memory Parallel Programming},
author={Chapman, B. and Jost, G. and Van Der Pas, R.},
volume={10},
year={2008},
publisher={{T}he {MIT} Press}
}
@ONLINE{pbdR2012,
author = {Ostrouchov, G. and Chen, W.-C. and Schmidt, D. and Patel, P.},
title = {Programming with Big Data in \proglang{R}},
year = {2012},
url = {http://r-pbd.org/}
}
@book{MPI,
title={Using \pkg{MPI}: Portable Parallel Programming with the Message-Passing Interface},
author={Gropp, W.D. and Lusk, E.L. and Skjellum, A.},
volume={1},
year={1999},
publisher={{T}he {MIT} Press}
}
@incollection{openMPI,
title={Open \pkg{MPI}: Goals, Concept, and Design of a Next Generation \pkg{MPI} Implementation},
author={Gabriel, E. and Fagg, G.E. and Bosilca, G. and Angskun, T. and Dongarra, J.J. and Squyres, J.M. and Sahay, V. and Kambadur, P. and Barrett, B. and Lumsdaine, A. and others},
booktitle={Recent Advances in Parallel Virtual Machine and Message Passing Interface},
pages={97--104},
year={2004},
publisher={Springer}
}
@Manual{R,
title = {\proglang{R}: A Language and Environment for Statistical Computing},
author = {{\proglang{R} Core Team}},
organization = {\proglang{R} Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2013},
url = {http://www.R-project.org/},
}
@article{hsiao2007,
title={K-corrections and Spectral Templates of {T}ype {I}a Supernovae},
author={Hsiao, E.Y. and Conley, A. and Howell, D.A. and Sullivan, M. and Pritchet, C.J. and Carlberg, R.G. and Nugent, P.E. and Phillips, M.M.},
journal={The Astrophysical Journal},
volume={663},
number={2},
pages={1187},
year={2007},
publisher={IOP Publishing}
}
@inproceedings{Henon:2000:PPS:645612.662662,
author = {H{\'e}non, P. and Ramet, P. and Roman, J.},
title = {\pkg{PaStiX}: A Parallel Sparse Direct Solver Based on a Static Scheduling for Mixed 1D/2D Block Distributions},
booktitle = {Proceedings of the 15 IPDPS 2000 Workshops on Parallel and Distributed Processing},
series = {IPDPS '00},
year = {2000},
isbn = {3-540-67442-X},
pages = {519--527},
numpages = {9},
url = {http://dl.acm.org/citation.cfm?id=645612.662662},
acmid = {662662},
publisher = {Springer-Verlag},
address = {London, UK, UK},
}
@ARTICLE{pere:etal:2013,
author = {{Pereira}, R. and {Thomas}, R.~C. and {Aldering}, G. and {Antilogus}, P. and
{Baltay}, C. and {Benitez-Herrera}, S. and {Bongard}, S. and
{Buton}, C. and {Canto}, A. and {Cellier-Holzem}, F. and {Chen}, J. and
{Childress}, M. and {Chotard}, N. and {Copin}, Y. and {Fakhouri}, H.~K. and
{Fink}, M. and {Fouchez}, D. and {Gangler}, E. and {Guy}, J. and
{Hillebrandt}, W. and {Hsiao}, E.~Y. and {Kerschhaggl}, M. and
{Kowalski}, M. and {Kromer}, M. and {Nordin}, J. and {Nugent}, P. and
{Paech}, K. and {Pain}, R. and {P{\'e}contal}, E. and {Perlmutter}, S. and
{Rabinowitz}, D. and {Rigault}, M. and {Runge}, K. and {Saunders}, C. and
{Smadja}, G. and {Tao}, C. and {Taubenberger}, S. and {Tilquin}, A. and
{Wu}, C.},
title = "{Spectrophotometric Time Series of {SN} 2011fe from the {N}earby {S}upernova {F}actory}",
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {arXiv:1302.1292},
primaryClass = "astro-ph.CO",
keywords = {Astrophysics - Cosmology and Extragalactic Astrophysics},
year = 2013,
month = feb,
adsurl = {http://adsabs.harvard.edu/abs/2013arXiv1302.1292P},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@article{Fran:etal:2012,
author = {Franey, M. and Ranjan, P. and Chipman, H.},
title = {A Short Note on {G}aussian Process Modeling for Large Datasets Using Graphics Processing Units},
journal = {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {arXiv:1203.1269},
primaryClass = "stat.CO",
year = 2012}
@INPROCEEDINGS{spie,
author = {{Aldering}, G. and {Adam}, G. and {Antilogus}, P. and {Astier}, P. and
{Bacon}, R. and {Bongard}, S. and {Bonnaud}, C. and {Copin}, Y. and
{Hardin}, D. and {Henault}, F. and {Howell}, D.~A. and {Lemonnier}, J.-P. and
{Levy}, J.-M. and {Loken}, S.~C. and {Nugent}, P.~E. and {Pain}, R. and
{Pecontal}, A. and {Pecontal}, E. and {Perlmutter}, S. and {Quimby}, R.~M. and
{Schahmaneche}, K. and {Smadja}, G. and {Wood-Vasey}, W.~M.},
title = {Overview of the Nearby Supernova Factory},
booktitle = {Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series},
year = 2002,
series = {Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series},
volume = 4836,
editor = {{Tyson}, J.~A. and {Wolff}, S.},
month = dec,
pages = {61-72},
doi = {10.1117/12.458107},
adsurl = {http://adsabs.harvard.edu/abs/2002SPIE.4836...61A},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@article{blas,
title={A Set of Level 3 Basic Linear Algebra Subprograms},
author={Dongarra, J.J. and Du Croz, J. and Hammarling, S. and Duff, I.S.},
journal={ACM Transactions on Mathematical Software (TOMS)},
volume={16},
number={1},
pages={1--17},
year={1990},
publisher={ACM}
}
@book{scalapack,
title={\pkg{ScaLAPACK} Users' Guide},
author={Blackford, L.S. and Choi, J. and Cleary, A. and D'Azevedo, E. and Demmel, J. and Dhillon, I. and Dongarra, J. and Hammarling, S. and Henry, G. and Petitet, A. and others},
volume={4},
year={1987},
publisher={Society for Industrial and Applied Mathematics}
}
@book{lapack,
title={\pkg{LAPACK} Users' Guide},
author={Anderson, E.},
Volume={9},
year={1999},
publisher={Society for Industrial and Applied Mathematics}
}
@article{Bane:etal:2003,
author = {Banerjee, S. and Gelfand, A.E. and Sirmans, C.F.},
title = {Directional Rates of Change Under Spatial Process Models},
year = {2003},
journal = {Journal of the American Statistical Association},
volume = {98},
number = {464},
pages = {946--954},
keywords = {Gradient; MATERN CORRELATION FUNCTION; ORTHONORMAL BASIS; SCALE OF RESOLUTION; SLICE GIBBS SAMPLER; STATIONARY GAUSSIAN ROCESS}
}
@article{Bane:etal:2008,
title={Gaussian Predictive Process Models for Large Spatial Data Sets},
author={Banerjee, S. and Gelfand, A.E. and Finley, A.O. and Sang, H.},
journal={Journal of the Royal Statistical Society B},
volume={70},
number={4},
pages={825--848},
year={2008},
publisher={Blackwell Publishing}
}
@article{Cres:Joha:2008,
title={Fixed Rank Kriging for Very Large Spatial Data Sets},
author={Cressie, N. and Johannesson, G.},
journal={Journal of the Royal Statistical Society B},
volume={70},
number={1},
pages={209--226},
year={2008},
publisher={Blackwell Synergy}
}
@article{Furr:etal:2006,
author = {Furrer, R. and Genton, M. G. and Nychka, D.},
title = {Covariance Tapering for Interpolation of Large Spatial Datasets},
year = {2006},
journal = JCGS,
volume = 15,
pages={502--523}
}
@article{Gram:etal:2008,
title={Bayesian Treed {G}aussian Process Models with an Application to Computer Modeling},
author={Gramacy, R.B. and Lee, H.K.H.},
journal={Journal of the American Statistical Association},
volume={103},
number={483},
pages={1119--1130},
year={2008}
}
@article{Kamm:Wand:2003,
author={Kammann, E.E. and M.P. Wand},
Title={Geoadditive Models},
year=2003,
journal={Journal of the Royal Statistical Society C},
volume=52,
pages={1--18}
}
@article{Kauf:etal:2008,
author={Kaufman, C. and M. Schervish and D. Nychka},
Title={Covariance Tapering for Likelihood-based Estimation in Large Spatial Datasets},
year=2008,
journal={Journal of the American Statistical Association},
volume=103,
pages={1556--1569}
}
@article{Kenn:OHag:2001,
author = {Kennedy, M.C. and O'Hagan, A.},
title = {Bayesian Calibration of Computer Models},
year = {2001},
journal = {JRSSB},
volume = {63},
pages = {425--464},
keywords = {computer experiments; deterministic models; {G}aussian process; Interpolation; model inadequacy; Sensitivity analysis; Uncertainty analysis}
}
@article{Lind:etal:2011,
title={An Explicit Link between {G}aussian fields and {G}aussian {M}arkov Random Fields: the Stochastic Partial Differential Equation Approach},
author={Lindgren, F. and Rue, H. and Lindstr{\"o}m, J.},
journal={Journal of the Royal Statistical Society B},
volume={73},
issue={4},
pages={423--498},
year={2011}
}
@article{Rue:etal:2009,
title={Approximate {B}ayesian Inference for Latent {G}aussian models by Using Integrated Nested {L}aplace Approximations},
author={Rue, H. and Martino, S. and Chopin, N.},
journal={Journal of the Royal Statistical Society B},
volume={71},
number={2},
pages={319--392},
year={2009},
publisher={Wiley Online Library}
}
@article{Sang:Huan:2012,
title={A Full Scale Approximation of Covariance Functions for Large Spatial Data Sets},
author={Sang, H. and Huang, J.Z.},
journal={Journal of the Royal Statistical Society B},
year={2012},
volume = 74,
pages = {111--132},
publisher={Wiley Online Library}
}
@article{Stei:etal:2004,
author = {Stein, M.L. and Chi, Z. and Welty, L.J.},
title = {Approximating Likelihoods for Large Spatial Data Sets},
year = {2004},
journal = {Journal of the Royal Statistical Society B},
volume = {66},
number = {2},
pages = {275--296},
keywords = {Chlorophyll fluorescence; estimating equations; Restricted maximum likelihood; Variogram estimation}
}
@InProceedings{GGSYTY12,
author = {Georganas, E. and Gonz\'{a}lez-Dom\'{\i}nguez, J. and Solomonik, E. and Zheng, Y. and Touri\~{n}o, J. and Yelick, K.},
title = {Communication Avoiding and Overlapping for Numerical Linear Algebra},
booktitle = {Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis},
series = {SC '12},
year = {2012},
isbn = {978-1-4673-0804-5},
location = {Salt Lake City, Utah},
pages = {100:1--100:11},
articleno = {100},
numpages = {11},
url = {http://dl.acm.org/citation.cfm?id=2388996.2389132},
acmid = {2389132},
publisher = {IEEE Computer Society Press},
address = {Los Alamitos, CA, USA},
}
@article{BDHS11,
title={Minimizing Communication in Numerical Linear Algebra},
author={Ballard, Grey and Demmel, James and Holtz, Olga and Schwartz, Oded},
journal={SIAM Journal on Matrix Analysis and Applications},
volume={32},
number={3},
pages={866--901},
year={2011},
publisher={SIAM}
}