%     <H2><center>Research and Publications that make use of TAO</center></H2>

@article {mazur2011dts,
author = {Mazur, G. and Makowski, M. and Włodarczyk, R. and Aoki, Y.},
title = {Dressed TDDFT study of low-lying electronic excited states in selected linear polyenes and diphenylopolyenes},
journal = {International Journal of Quantum Chemistry},
volume = {111},
number = {4},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
issn = {1097-461X},
url = {http://dx.doi.org/10.1002/qua.22876},
doi = {10.1002/qua.22876},
pages = {819--825},
year = {2011},
}

@inproceedings {bourdin2010stc,
  author = {Bourdin, B. and Knepley, M. and Maurini, C.},
  title = {Secondary thermal cracks in EGS: a variational approach},
  booktitle = {Proceedings of the 34th annual meeting of the Geothermal resources council},
  series = {GRC Transactions},
  volume={34},
  url = {https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}
  year = {2010},
  location = {Sacramento, CA},
}  

@article {fuentes2010arb,
  author = {Fuentes, D. and Feng, Y. and Elliott, A. and Shetty, A. and McNichols, R. J. and Oden, J. T. and Stafford, R. J.},
  title = {Adaptive Real-Time Bioheat Transfer Models for Computer Driven MR-guided Laser Induced Thermal Therapy},
  journal = {IEEE Trans. Biomed. Eng.},
  year = {2010},
  month = {May},
  Issue = {57},
  Number = {5},
  pages = {1024--1030},
  url = {http://dx.doi.org/10.1109/TBME.2009.2037733},
}


 

@Article{jaykka2010epb,
  title = {Easy plane baby skyrmions},
  author = {J\"aykk\"a, J.  and Speight, M. },
  journal = {Phys. Rev. D},
  volume = {82},
  number = {12},
  pages = {125030},
  numpages = {8},
  year = {2010},
  month = {Dec},
  doi = {10.1103/PhysRevD.82.125030},
  url = {http://link.aps.org/doi/10.1103/PhysRevD.82.125030}
  publisher = {American Physical Society}
}


@inproceedings{Meyerov2010CAE,
 author = {Meyerov, I. and Kamaev, A. and Kornyakov, K. and Zhivoderov, A.},
 title = {Comparative analysis of effectiveness of two timing-driven design approaches},
 booktitle = {Proceedings of the Second Russia-Taiwan conference on Methods and tools of parallel programming multicomputers},
 series = {MTPP'10},
 year = {2010},
 isbn = {3-642-14821-2, 978-3-642-14821-7},
 location = {Vladivostok, Russia},
 pages = {277--282},
 numpages = {6},
 url = {http://portal.acm.org/citation.cfm?id=1927517.1927555},
 acmid = {1927555},
 publisher = {Springer-Verlag},
 address = {Berlin, Heidelberg},
} 

@inproceedings{erkan2010ssr,
   author={Erkan, A.N. and Camps-Valls, G. and Altun, Y.},
   booktitle={Machine Learning for Signal Processing (MLSP), 2010 IEEE International Workshop on},
   title={Semi-supervised remote sensing image classification via maximum entropy },
  year={2010},
  month={September},
  volume={},
  number={},
  pages={313 -318},
  doi={10.1109/MLSP.2010.5589199},
  url = {http://dx.doi.org/10.1109/MLSP.2010.5589199},
}    

@inproceedings{Chao2010SGM,
 author = {Chao, Isaac and Pinkall, Ulrich and Sanan, Patrick and Schr\"{o}der, Peter},
 title = {A simple geometric model for elastic deformations},
 booktitle = {ACM SIGGRAPH 2010 papers},
 series = {SIGGRAPH '10},
 year = {2010},
 isbn = {978-1-4503-0210-4},
 location = {Los Angeles, California},
 pages = {38:1--38:6},
 articleno = {38},
 numpages = {6},
 url = {http://doi.acm.org/10.1145/1833349.1778775},
 doi = {http://doi.acm.org/10.1145/1833349.1778775},
 acmid = {1778775},
 publisher = {ACM},
 address = {New York, NY, USA},
} 

@phdthesis{erkan2010thesis,
        title = {{Semi-supervised Learning via Generalized Maximum Entropy}},
        author = {Erkan, A. N.},
        school = {New York University},
        year = {2010},
        month = {September}
}

@ARTICLE{david2009unl,
  AUTHOR = {C\'edric H. David and David J. Gochis and David R. Maidment and Wei Yu and David N. Yates and Zong-Liang Yang},
  TITLE = {Using NHDPlus as the Land Base for the Noah-distributed Model}
  JOURNAL = {T. GIS}
  PAGES = {363-377},
  YEAR = {2009}
}

@inproceedings{Gauthier2009PSE,
 author = {Gauthier, M. and Poulin, P.},
 title = {Preserving sharp edges in geometry images},
 booktitle = {Proceedings of Graphics Interface 2009},
 series = {GI '09},
 year = {2009},
 isbn = {978-1-56881-470-4},
 location = {Kelowna, British Columbia, Canada},
 pages = {1--6},
 numpages = {6},
 url = {http://portal.acm.org/citation.cfm?id=1555880.1555890},
 acmid = {1555890},
 publisher = {Canadian Information Processing Society},
 address = {Toronto, Ont., Canada, Canada},
} 
@inproceedings{Tylenda2009ttl}
 author = {Tylenda, Tomasz and Angelova, Ralitsa and Bedathur, Srikanta},
 title = {Towards time-aware link prediction in evolving social networks},
 booktitle = {Proceedings of the 3rd Workshop on Social Network Mining and Analysis},
 series = {SNA-KDD '09},
 year = {2009},
 isbn = {978-1-60558-676-2},
 location = {Paris, France},
 pages = {9:1--9:10},
 articleno = {9},
 numpages = {10},
 url = {http://doi.acm.org/10.1145/1731011.1731020},
 doi = {http://doi.acm.org/10.1145/1731011.1731020},
 acmid = {1731020},
 publisher = {ACM},
 address = {New York, NY, USA},

} 


@inproceedings{Gulati2009FPC,
 author = {Gulati, Shilpa and Jhurani, Chetan and Kuipers, Benjamin and Longoria, Raul},
 title = {A framework for planning comfortable and customizable motion of an assistive mobile robot},
 booktitle = {Proceedings of the 2009 IEEE/RSJ international conference on Intelligent robots and systems},
 series = {IROS'09},
 year = {2009},
 isbn = {978-1-4244-3803-7},
 location = {St. Louis, MO, USA},
 pages = {4253--4260},
 numpages = {8},
 url = {http://portal.acm.org/citation.cfm?id=1732643.1732744},
 acmid = {1732744},
 publisher = {IEEE Press},
 address = {Piscataway, NJ, USA},
} 


@inproceedings{davies2009taa,
 author = {Davies, M. and Lew, A.},
 title = {Tests of the affinity assumption in phantomlike elastomer networks},
 booktitle = {Mater. Res. Soc. Symp. Proc.},
 year = {2009},
 volume = {1190},
 url = {http://www.stanford.edu/group/lavxm/publications/other-articles/DaLe09.pdf}
 publisher = {Materials Research Society},
} 

@phdthesis{jhurani2009mmu,
  title = {{Multiscale modeling using goal-oriented adaptivity and numerical homogenization}},
  year = {2009},
  month = {August},
  school = {University of Texas},
  url={http://hdl.handle.net/2152/6545},
}

@article{feng2009nml,
	title 	= 	{{Nanoshell-mediated laser surgery simulation for prostate cancer treatment}},
	author 	= 	{Feng, Y. and Fuentes, D. and Hawkins, A. and Bass, J. and Rylander, N.R. and Elliott, A. and Shetty, A. and Stafford, R.J. and Oden, J.T.},
	journal 	= 	{Engineering with Computers},
	year 	= 	{2009},
	publisher 	= 	{Springer},
	volume 	= 	{25},
	pages 	= 	{3--13},
	url	= 	{http://www.springerlink.com/content/0v05659046803634},
}

@article{feng2009oar,
	title	= 	{{Optimization and real-time control for laser treatment of heterogeneous soft tissues}},
	author	= 	{Feng, Y. and Fuentes, D. and Hawkins, A. and Bass, J.M. andRylander, M.N.},
	journal	= 	{Computer Methods in Applied Mechanics and Engineering},
	year	= 	{2009},
	publisher	= 	{Elsevier},
	url	= 	{http://dx.doi.org/10.1016/j.cma.2008.12.027}
}



@phdthesis{sears2008gme,
       title = {{Generalized Maximum Entropy, Convexity, and Machine Learning}},
       author = {Sears, T. D.},
       school = {The Australian National University},
       year = {2008},
       month = {May},
}



@InProceedings{kazama2008ign,
  author    = {Kazama, J.  and  Torisawa, K.},
  title     = {Inducing Gazetteers for Named Entity Recognition by Large-Scale Clustering of Dependency Relations},
  booktitle = {Proceedings of ACL-08: HLT},
  month     = {June},
  year      = {2008},
  address   = {Columbus, Ohio},
  publisher = {Association for Computational Linguistics},
  pages     = {407--415},
  url       = {http://www.aclweb.org/anthology/P/P08/P08-1047.pdf}
}

@inproceedings{Ayupov2008AAP,
 author = {Ayupov, A. and Marchenko, A. and Tiourin, V.},
 title = {An analytical approach to placement legalization},
 booktitle = {Proceedings of the 18th ACM Great Lakes symposium on VLSI},
 series = {GLSVLSI '08},
 year = {2008},
 isbn = {978-1-59593-999-9},
 location = {Orlando, Florida, USA},
 pages = {167--170},
 numpages = {4},
 url = {http://doi.acm.org/10.1145/1366110.1366152},
 doi = {http://doi.acm.org/10.1145/1366110.1366152},
 acmid = {1366152},
 publisher = {ACM},
 address = {New York, NY, USA},
} 



@INPROCEEDINGS{aypov2008ntp,
author={Ayupov, A. and Kraginskiy, L.},
booktitle={Design Test Symposium (EWDTS), 2008 East-West}, 
title={A novel timing-driven placement algorithm using smooth timing analysis},
year={2008},
month={October},
volume={},
number={},
pages={137--140},
doi={10.1109/EWDTS.2008.5580152},
url = {http://dx.doi.org/10.1109/EWDTS.2008.5580152},
}

@conference{feng2008mbo,
	title	= 	{{MRTI-Based Optimization and Real-Time Laser Surgical Control for Cancer Treatment Using Fast Inverse Analysis Techniques}},
	author	= 	{Feng, Y. and Fuentes, D. and Hawkins, A. and Oden, J.T.},
	booktitle	= 	{BioMedical Engineering and Informatics, 2008. BMEI 2008.International Conference on},
	volume	= 	{2},
	year	= 	{2008},
	url	= 	{http://doi.ieeecomputersociety.org/10.1109/BMEI.2008.282}
}

@article{sosonkina2008iai,
	title	= 	{{Integration of Ab Initio Nuclear Physics Calculations with Optimization Techniques}},
	author	= 	{Sosonkina, M. and Sharda, A. and Negoita, A. and Vary, J.P.},
	journal	= 	{Lecture Notes in Computer Science},
	volume	= 	{5101},
	pages	= 	{833--842},
	year	= 	{2008},
	publisher	= 	{Springer}
}


@article{chang2008pph,
	title 	= 	{{Photons, photosynthesis, and high-performance computing: challenges, progress, and promise of modeling metabolism in green algae}},
	author 	= 	{Chang, C. and Graf, P, and Alber, D. and Kim, K., and Murray, G. and Posewitz, M. and Seibert, M.},
	booktitle	= 	{Journal of Physics: Conference Series},
	year 	= 	{2008},
	volume	= 	{125},
	pages	= 	{012048},
	organization	= 	{Institute of Physics Publishing},
	url	= 	{http://dx.doi.org/10.1088/1742-6596/125/1/012048}
}
@conference{cheng2008crf,
	title 	= 	{{CRF-OPT: An efficient high-quality conditional random field solver}},
	author 	= 	{Chen, M. and Chen, Y. and Brent, M.R.},
	booktitle	= 	{Proceedings of the Twenty-Third AAAI Conference on Artificial Intelligence},
	year 	= 	{2008},
	organization	= 	{Association for the Advancement of Artificial Intelligence},
	url	= 	{http://www.aaai.org/Papers/AAAI/2008/AAAI08-161.pdf}
}
@article{gokhale2008sne,
	title	= 	{{Solution of the nonlinear elasticity imaging inverse problem: the compressible case}},
	author	= 	{Gokhale, N.H. and Barbone, P.E. and Oberai, A.A},
	journal	= 	{Inverse Problems},
	Volume	= 	{24},
	year	= 	{2008},
	pages	= 	{045010}, 
        url     =       {http://dx.doi.org/10.1088/0266-5611/24/4/045010}
	publisher	= 	{IOP Publishing}
}

@article{diller2008cir,
	title	= 	{{Computational infrastructure for the real-time patient-specific treatment of cancer}},
	author	= 	{Diller, K.R and Oden, J.T and Bajaj, C. and Browne, J.C and Hazle, J. and Babuska, I. and Bass, J. and Bidaut, L. and Demkowicz, L. and Elliott, A. and Feng, Y. and Fuentes, D. and Goswami, S. and Hawkins, A. and Khoshnevis, S. and Kwon, B. and Prodhomme, S. and Stafford, R.J.},
	booktitle	= 	{Advances in Numerical Heat Transfer, vol. 3},
	publisher	= 	{Taylor \& Francis Group},
	year	= 	{2008},
	chapter	= 	{9},
}

@InProceedings{li2008mmr,
	author 	= 	{Li, Zhifei and Yarowsky, David},
	title 	= 	{Mining and Modeling Relations between Formal and Informal {C}hinese Phrases from Web Corpora},
	booktitle 	= 	{Proceedings of the 2008 Conference on Empirical Methods in Natural Language Processing},
	month 	= 	{October},
	year 	= 	{2008},
	address 	= 	{Honolulu, Hawaii},
	publisher 	= 	{Association for Computational Linguistics},
	pages 	= 	{1031--1040},
	url 	= 	{http://www.aclweb.org/anthology/D08-1108}
}


@article{springborn2008cet,
	title	= 	{{Conformal equivalence of triangle meshes}},
	author	= 	{Springborn, B. and Schroder, P. and Pinkall, U.},
	publisher	= 	{ACM New York, NY},
	year	= 	{2008},
	volume	= 	{27},
	number	= 	{3},
	journal	= 	{ACM Transactions on Graphics},
	url	= 	{http://doi.acm.org/10.1145/1360612.1360676}
}

@article{bauman2008amm,
	title	= 	{{Adaptive multiscale modeling of polymeric materials with Arlequin coupling and Goals algorithms}},
	author	= 	{Bauman, P.T. and Oden, J.T. and Prudhomme, S.},
	journal	= 	{Computer Methods in Applied Mechanics and Engineering},
	year	= 	{2008},
	publisher	= 	{Elsevier},
	url	= 	{http://dx.doi.org/10.1016/j.cma.2008.10.014}
}
@article{tber2008pis,
	title	= 	{{Parameters identification in a seawater intrusion model using adjoint sensitive method}},
	author	= 	{Tber, M.H. and El Alaoui Talibi, M. and Ouazar, D.},
	journal	= 	{Mathematics and Computers in Simulation},
	volume	= 	{77},
	number	= 	{2-3},
	pages	= 	{301--312},
	year	= 	{2008},
	publisher	= 	{Elsevier},
	url	= 	{http://dx.doi.org/10.1016/j.matcom.2007.08.015}
}

@conference{seelam2008eea,
	title	= 	{{Early experiences in application level I/O tracing on blue gene systems}},
	author	= 	{Seelam, S. and Chung, I.H. and Hong, D.Y. and Wen, H.F. and Yu,H.},
	booktitle	= 	{IEEE International Symposium on Parallel and DistributedProcessing, 2008. IPDPS 2008},
	pages	= 	{1--8},
	year	= 	{2008},
	url	= 	{http://dx.doi.org/10.1109/IPDPS.2008.4536550}
}


@ARTICLE{broderick2007fsi,
  author = {Broderick, T. and Dudik, M. and Tkacik, R. and Schapire, R. and Bialek, W.},
  title = {Faster solutions of the inverse pairwise Ising problem},
  year = {2007},
  url = {http://arxiv.org/abs/0712.2437v2},
}


@article{joshi2007emc,
	title	= 	{{Energy minimizers for curvature-based surface functionals}},
	author	= 	{Joshi, P. and S{\'e}quin, C.},
	journal	= 	{Comput. Aided Design Appl},
	volume	= 	{4},
	number	= 	{5},
	pages	= 	{607--617},
	year	= 	{2007},
	url	= 	{http://www.cadanda.com/cad_4_5__04.pdf}
}

@article{friedel2007usp,
	title	= 	{{Unconstrained spherical parameterization}},
	author	= 	{Friedel, I. and Schr{\"o}der, P. and Desbrun, M.},
	journal	= 	{Journal of Graphics Tools},
	volume	= 	{12},
	number	= 	{1},
	pages	= 	{17--26},
	year	= 	{2007},
	publisher	= 	{AK Peters},
	url	= 	{http://doi.acm.org/10.1145/1187112.1187274}
}

@incollection{zhang2007hlg,
	title 	= 	{{Hyperparameter Learning for Graph Based Semi-supervised Learning Algorithms}},
	author 	= 	{Xinhua Zhang and Wee Sun Lee},
	booktitle 	= 	{Advances in Neural Information Processing Systems 19},
	editor 	= 	{B. Sch\"{o}lkopf and J. Platt and T. Hoffman},
	publisher 	= 	{MIT Press},
	address 	= 	{Cambridge, MA},
	pages 	= 	{1585--1592},
	year 	= 	{2007}
}

@article{roark2007dng,
	title	= 	{{Discriminative n-gram language modeling}},
	author	= 	{Roark, B. and Saraclar, M. and Collins, M.},
	journal	= 	{Computer Speech \& Language},
	volume	= 	{21},
	number	= 	{2},
	pages	= 	{373--392},
	year	= 	{2007},
	publisher	= 	{Academic Press Ltd.},
	url	= 	{http://dx.doi.org/10.1016/j.csl.2006.06.006}
}

@conference{chang2007auc,
	title	= 	{{Addressing unknown constants and metabolic network behaviors through petascale computing: understanding H2 production in green algae}},
	author	= 	{Chang, C. and Alber, D. and Graf, P. and Kim, K. and Seibert, M.},
	booktitle	= 	{Journal of Physics: Conference Series},
	volume	= 	{78},
	number	= 	{1},
	pages	= 	{012011},
	year	= 	{2007},
	organization	= 	{Institute of Physics Publishing},
	url	= 	{http://dx.doi.org/10.1088/1742-6596/78/1/012011}
}

@article{negrut2007qlr,
	title	= 	{{Quasicontinuum-like reduction of DFT calculations of nanostructures}},
	author	= 	{Negrut, D. and Anitescu, M. and El-Azab, A. and Zapol, P.},
	journal	= 	{J. Nanosci. Nanotechnol},
	year	= 	{2007}
}

@conference{hall2007llm,
	title	= 	{{Log-linear models of non-projective trees, k-best MST parsing and tree-ranking}},
	author	= 	{Hall, K. and Havelka, J. and Smith, D.A.},
	booktitle	= 	{Proceedings of the CoNLL Shared Task Session of EMNLP-CoNLL},
	pages	= 	{962--966},
	year	= 	{2007},
	url	= 	{http://www.aclweb.org/anthology/D/D07/D07-1102.pdf}
}


@article{talibi2007ihc,
	title	= 	{{Identification of the hydraulic conductivities in a saltwater intrusion problem}},
	author	= 	{Talibi, M.E.A and Ouazar, D. and Tber, M.H.},
	year	= 	{2007},
	journal	= 	{Journal of Inverse and Ill-posed Problems},
	volume	= 	{15},
	issue	= 	{9},
	pages	= 	{935--954}
	publisher	= 	{Mouton de Gruyter},
	url	= 	{http://dx.doi.org/10.1016/j.cageo.2006.10.012}
}

@article{mohan2007tcl,
	title 	= 	{{Tabletop computed lighting for practical digital photography}},
	author 	= 	{Mohan, A. and Bailey, R. and Waite, J. and Tumblin, J. and Grimm, C. and Bodenheimer, B.},
	year	= 	{2007},
	journal	= 	{IEEE Transactions on Visualization and Computer Graphics},
	volume	= 	{13},
	number	= 	{4},
	pages	= 	{652--662},
	organization	= 	{IEEE},
	url	= 	{http://doi.acm.org/10.1145/1185657.1185742}
}


@conference{teo2007smc,
	title 	= 	{{A scalable modular convex solver for regularized risk minimization}},
	author	= 	{Teo, C.H. and Le, Q. and Smola, A. and Vishwanathan, S.V.N.},
	booktitle	= 	{Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data minings},
	organization	= 	{ACM},
	year	= 	{2007},
	pages	= 	{727--736},
	url	= 	{http://doi.acm.org/10.1145/1281192.1281270}
}

@conference{kharevych2006gvi,
	title	= 	{{Geometric, variational integrators for computer animation}}
	author	= 	{Kharevych, L. and Yong, W. and Tong, Y. and Kanso, E. and Marsden, J.E. and Schroder, P. and Desbrun, M.},
	booktitle	= 	{Eurographics/ACM SIGGRAPH Symposium on Computer Animation},
	year	= 	{2006},
	publisher	= 	{Eurographics Association}
}


@article{rajan2006gim,
        title = {{General implementation of multilevel parallelization in a 
                  gradient-based design optimization algorithm}},
        author = {Rajan, S. D. and  Belegundu, A. D. and  Damle, A. S. and Lau, D. and St. Villek, J.},
        journal = {AIAA J},
        year = {2006},
        volume = {44},
        number = {9},
        pages = {1993--2008},
        url = {http://dx.doi.org/10.2514/1.17470},
}


@conference{chieu2006arp,
	title	= 	{{Activity recognition from physiological data using conditional random fields}},
	author	= 	{Chieu, H.L and Lee, W.S. and Kaelbling, L.P},
	year	= 	{2006},
	booktitle	= 	{SMA Symposium},
	organization	= 	{Singapore-MIT Alliance},
	url	= 	{http://hdl.handle.net/1721.1/30197}
}

@article{saraclar2006ucw,
	title 	= 	{{Utterance classification with discriminative language modeling}},
	author 	= 	{Saraclar, M. and Roark, B},
	journal 	= 	{Speech Communication},
	year 	= 	{2006},
	volume	= 	{48},
	number	= 	{3--4},
	pages	= 	{276--287},
	publisher	= 	{Elsevier},
	url	= 	{http://dx.doi.org/10.1016/j.specom.2005.06.010}
}


@article{kazama05maximum,
    author = {J. Kazama and J. Tsujii},
    title = "Maximum Entropy Models with Inequality Constraints: A Case Study on Text Categorization",
    journal = "Machine Learning",
    year={2005}
    volume = "60",
    number = "1-3",
    pages = "159--194",
}

@article{naumann2005differentiation,
    author = {U. Naumann and J. Riehme},
    title = "A Differentiation-Enabled Fortran 95 Compiler",
    journal = "ACM Tr. on Mat. Soft.",
    volume = "31",
    number = "4",
    month = {Dec},
    year = "2005",
    url={http://www.stce.rwth-aachen.de/classes/AMSNP/papers/compad_tl.pdf},
}

@InProceedings{smith2005guiding,
  author = {Noah A. Smith and Jason Eisner},
  title = "Guiding Unsupervised Grammar Induction Using Contrastive Estimation",
  booktitle = {In Working Notes of the International Joint Conference on Artificial Intelligence},
  year = {2005},
  note = {Workshop on Grammatical Inference Applications},
  url={http://nlp.cs.jhu.edu/%7Enasmith/ijcai_gia_2005.pdf},
}

@InProceedings{smith2005contrastive,
  author = {Noah A. Smith and Jason Eisner},
  title = "Contrastive Estimation: Training Log-Linear Models on Unlabeled Data",
  booktitle = {Proceedings of the Association for Computational Linguistics},
  year = {2005},
  url={http://nlp.cs.jhu.edu/%7Enasmith/ce_acl05.pdf},
}

@InProceedings{smith2005context,
  author = {Noah A. Smith, David A. Smith, and Roy W. Tromble},
  title = "Context-Based Morphological Disambiguation with Random Fields",
  booktitle={Proceedings of the Conference on Human Language Technology
and Empirical Methods in Natural Language Processing},
  year={2005},
  url={http://nlp.cs.jhu.edu/%7Enasmith/sst_emnlp_2005.pdf},
}

@misc{negrutFEopt2005,
  author = {Dan Negrut and Mihai Anitescu},
  title = "DFT-Based Nanostructure Investigation",
  address = "Argonne, Illinois, USA",
  institution = "Argonne National Laboratory",
  url={http://www-unix.mcs.anl.gov/%7Enano/htm/simulations.htm}
}

@InProceedings{bobenko05willmore,
   author = {A.I. Bobenko and P. Schr\"oder},
   title = "Discrete Willmore Flow",
   booktitle =  {Eurographics Symposium on Geometry Processing},
   year = {2005}
   editor = {M. Desbrun and  H. Pottmann},
   url = {http://multires.caltech.edu/pubs/Willmore.pdf}
}

@InProceedings{friedel05unconstrained,
  author = {I. friedel and P. Schr\"oder and M. Desbrun},
  title = "Unconstrained Spherical Parameterizations",
  booktitle = {ACM/SIGGRAPH},
  year = {2005},
  url = {http://multires.caltech.edu/pubs/SParam_JGT.pdf},
}

@InProceedings{charniak-johnson:2005:ACL,
  author    = {E. Charniak and  M. Johnson},
  title     = {Coarse-to-Fine n-Best Parsing and MaxEnt Discriminative Reranking},
  booktitle = {Proc. of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05)},
  month     = {June},
  year      = {2005},
  publisher = {Association for Computational Linguistics},
  pages     = {173--180},
  url       = {http://www.aclweb.org/anthology/P/P05/P05-1022},
  note={<a href="http://www.cog.brown.edu/%7Emj">Software for Maximum Entropy Discriminative reranking for computational linguistics</a>},

}


@misc{deo2005oos,
  title = {{  On-line Optimization-Based Simulators for Fractured and Non-fractured Reservoirs}},
  author = {Deo, M. D.},
  year = {2005},
  note = {Final Report, Department of Chemical and Fuels Engineering, University of Utah, DOE contract FC26-01BC15313},
  url={http://www.osti.gov/bridge/product.biblio.jsp?osti_id=918646}
}

@phdthesis{altun2005dml,
  title={Discriminative Methods for Label Sequence Learning}
  author = {Altun, Y.}
  year = {2005},
  month = {May},
  school = {Brown University},
}

@ARTICLE{sande2004stt,
author={Sande, H.V. and Boonen, T. and Podoleanu, I. and Henrotte, F. and Hameyer, K.},
journal={Magnetics, IEEE Transactions on}, 
title={Simulation of a three-phase transformer using an improved anisotropy model},
year={2004},
month=march,
volume={40},
number={2},
pages={ 850 - 855},
doi={10.1109/TMAG.2004.825004},
url = {http://dx.doi.org/10.1109/TMAG.2004.825004},
ISSN={0018-9464}
}



@InProceedings{roark2004acl,
  author    = {B. Roark and M. Saraclar and M. Collins and M. Johnson}
  title     = {Discriminative language modeling with conditional random fields and the perceptron algorithm},
  booktitle = {Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics (ACL'04)},
  month     = {July},
  year      = {2004},
  publisher = {Association for Computational Linguistics},
  url       = {http://acl.ldc.upenn.edu/acl2004/main/pdf/320_pdf_2-col.pdf}
}

@InProceedings{bernholdt2004raising,
  author = {D. Bernholdt and J. Nieplocha and P. Sadayappan},
  title = {Raising the Level of Programming Abstraction in Scalable 
           Programming Models}, 
  booktitle = {Proceedings of the HPCA Workshop on Productivity 
           and Performance in High-End Computing},
  year = {2004},
  publisher = {IEEE Computer Society},
  url = {http://www.emsl.pnl.gov/docs/global/papers/pphec-tce-xga-final.pdf}
}

@article{bodoff04relevance,
     author = {D. Bodoff},
     title = "Relevance Models to Help Estimate Document and Query Models", 
     journal = "ACM Transactions on Information Systems",
     volume = {22},
     issue = {3},
     month = {July},
     year= {2004},
     pages = {357 - 380},  
}

@conference{rajan2004fea,
	title	= 	{{Finite Element Analysis & Design Optimization in a Distributed Computing Environment}},
	author	= 	{Rajan, S.D. and Belegundu, A.D. and Lee, D. and Damle, A.S. and St. Ville, J},
	booktitle	= 	{10th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conference},
	year	= 	{2004},
	organization	= 	{American Institute of Aeronautics and Astronautics}
}

@InProceedings{smith2004bilingual,
  author = {David A. Smith and Noah A. Smith},
  title = {Bilingual Parsing with Factored Estimation: Using English to Parse Korean},
  booktitle={Proceedings of the Conference on Empirical Methods in Natural Language Processing},
  year={2004},
  pages = {49--54},
  url={http://nlp.cs.jhu.edu/%7Enasmith/biparse.pdf},
}

@InProceedings{malouf2004wide,
  author    = {R. Malouf and G. van Noord},
  title     = {Wide Coverage Parsing with Stochastic Attribute Value Grammars},
  booktitle = {IJCNLP-04 Workshop: Beyond shallow analyses - Formalisms and statistical modeling for deep analyses.},
  month     = {March},
  year      = {2004},
  publisher = {JST CREST},
  url       = {http://www-tsujii.is.s.u-tokyo.ac.jp/bsa/papers/malouf.pdf},
}

@article{kazama03evaluation,
    author = {J. Kazama and J. Tsujii},
    title = "Evaluation and extension of maximum entropy 
             models with inequality constraints",
    journal = "Proceedings of the 2002 Empirical Methods in
               Natural Language Processing",
    pages = "137--144",
    year = "2003",
    url= {http://www-tsujii.is.s.u-tokyo.ac.jp/%7Ekazama/papers/kazama_emnlp03r.pdf}
}

@mastersthesis{dajani2003,
   author = {Hala Dajani},
   title = "Client-Server Component Architecture for Scientific 
            Computing",
   school = "Rice University",
   year = {2003},
   url={http://www.caam.rice.edu/caam/trs/2003/TR03-07.pdf}
}
@article{scholz03scalable,
    author = {W. Scholz and J. Fidler and T. Schrefl and
              D. Suess and R. Dittrich and H. Forster and V. Tsiantos},
    title = "Scalable parallel micromagnetic solvers for magnetic
             nanostructures",
    journal = "Comp. Mat. Sci.",
    year = {2003},
    pages = "366--383",
    volume = 28,
    url={http://magnet.atp.tuwien.ac.at/scholz/projects/diss/diss.pdf},
    note={<a href="http://magnet.atp.tuwien.ac.at/scholz/magpar">Parallel Finite Element Micromagnetics Package (magpar)</a>},
} 

@article{scholz03implementation,
    author = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and
              V. Tsiantos and H. Forster and J. Fidler},
    title = "Implementation of a high performance parallel
             finite element micromagnetics package",
    journal 	= 	"J. Magn. Magn. Mater.",
    year 	= 	2004,
    url = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}
    
}

@article{liang03optimization,
    author = {J. Liang and Y.-Q. Chen},
    title="Optimization of A fed-batch fermentation process control 
           competition problem using the NEOS server",
    journal = "Proceedings - Institution of Mechanical Engineers Part I Journal of Systems and Control Engineering",
    year = 2003,
    volume = 217; Part 5,
    pages = "427--432",
    url = {http://www.csois.usu.edu/publications/pdf/pub104.pdf}
}


@article{liang03solving,
   author = {J. Liang and Y.-Q. Chen an M. Meng and R. Fullmer},
   title = "Solving tough optimal control problems by Network Enabled Optimization Server (NEOS)",
   journal = "Proc. of the 2003 IEEE Intelligent Automation Conference"
   year = 2003,
   url = {http://mechatronics.ece.usu.edu/yqchen/paper/03C15_IEEE_CIAC2003_IAC-M24.pdf}
}

@misc{wiang03cgmethods,
    author = {J. Wang and X. Chi and T. Gu},
    title = "Nonlinear Conjugate Gradient Methods and Their Implementations by TAO on Dawning 2000-II",
    note = "In Inter. Conf. on Parallel Algorithms and Computing Environments (ICPACE) 2003",
    url = {http://www.sccas.cn/ICPACE/papers/Jian%20Wang.pdf}
}  



@article{bischof2003interactive,
  author = {C. Bischof and H. Busker and B. Lang and A. Rasch},
  title = {An interactive environment for supporting the transition from simulation to optimization},
  journal = {Sci. Prog.},
  volume = {4},
  year = {2003},
  pages = {263--272},
  url={http://www.iospress.nl/html/10589244.php},
}


@article{sande2003snm,
	title 	= 	{{Solving nonlinear magnetic problems using Newton trust region methods}},
	author	= 	{Vande Sande, H. and De Gersem, H. and Henrotte, F. and Hameyer, K.},
	year	= 	{2003},
	journal	= 	{IEEE Transactions on Magnetics},
	volume	= 	{30},
	number	= 	{3},
	pages	= 	{1709-1712},
	url	= 	{http://dx.doi.org/10.1109/TMAG.2003.810212}
}

@conference{sande2002anl,
	title	= 	{{Accelerating non-linear time-harmonic problems by a Hybrid Picard-Newton approach}},
	author	= 	{Vande Sande, H. and Boonen, T. and De Gersem, H. and Henrotte, F. and Hameyer, K.},
	year	= 	{2002},
	booktitle	= 	{Proceedings of the 10th International Symposium on Numerical Field Calculations in Electrical Engineering},
	pages	= 	{85--90},
	url	= 	{http://www.iem.rwth-aachen.de/uploads/bibliotest/pub_988.pdf}
}


@mastersthesis{wallach2002,
  author = {Hanna Wallach},
  title = "Efficient Training of Conditional Random Fields",
  school = "University of Edinburgh",
  year = "2002",
  url={http://www.inference.phy.cam.ac.uk/hmw26/publications.html}
}


@misc{yabusaki02mechanistic,
     author = {S. Yabusaki and S. Bryant and S. Chen and G. Fann and G. Flach and W. Gray and J. Holland and K. Jordan and R. Maier and J. Malard and D. Rector and W. Soll and C. Steefel and A. Tompson and H. Trease and M. Wheeler and B. Wood},
     title = "Mechanistic Process Modeling for Subsurface Remediation",
     month="August",
     year="2002",
     note = "PNNL-14011, Published by Pacific Northwest National Laboratory for the Environmental Molecular Sciences Laboratory",
     url = {http://www.pnl.gov/main/publications/external/technical_reports/pnnl-14011.pdf},
}



@Book{sourcebook2002,
  editor ={J. Dongarra and I. Foster and G. Fox and W.
                  Gropp and K. Kennedy and L. Torczon and A. White},
  title="The Sourcebook of Parallel Computing",
  series="The Morgan Kaufmann Series in Computer Architecture and Design",
  publisher="Elsevier",
  month="November",
  year="2002",
  page="842",
  url={http://books.elsevier.com/computerscience/default.asp?isbn=1558608710},
}

@InProceedings{malouf02comparison,
  author = {Robert Malouf},
  title = "A comparison of algorithms for maximum entropy parameter 
         estimation",
  booktitle = "In Sixth Conf. on Natural Language Learning"
  pages = "49--55",
  year={2002},
  url={http://cnts.ua.ac.be/conll2002/abstracts/04955mal.html}
}

@article{malard02parallel,
    author = {J. Malard},
    title = "Parallel restricted maximum likelihood estimation for linear 
    models with a dense exogenous matrix",
    journal = "Parallel Computing",
    volume = "28",
    number = "2",
    pages = "343--353",
    year = "2002",
    url = {http://csm.pnl.gov/statistics/dll/pml.html}
    note="<a href="http://csm.pnl.gov/statistics/dll/pml.html">ACRE software package for maximum likelihood estimates of covariance matrices</a>",
}


@misc{Noord02algorithms,
    author = {L. v. d. Beek and G. Bouma and J. Daciuk and T. Gaustad and R. Malouf and G. v. Noord and R. Prins and B. Villada},
    title = "Algorithms for Linguistic Processing. NWO PIONIER Progress Report.",
    year = "2002",
    url = {http://odur.let.rug.nl/%7Evannoord/alp/midterm.ps}
}








