diff --git a/tex/bibliography.bib b/tex/bibliography.bib index 88bc660..e40ad7a 100644 --- a/tex/bibliography.bib +++ b/tex/bibliography.bib @@ -74,29 +74,26 @@ @article{Bezanson_Karpinski_Shah_Edelman_2012 title = "Julia: A Fast Dynamic Language for Technical Computing", DOI = "10.48550/arxiv.1209.5145", journal = "arXiv", - year = "2018" + year = "2012" } -@article{christianson1994reverse, - author = "Christianson, Bruce", - title = "Reverse accumulation and attractive fixed points", - journal = "Optimization Methods and Software", - volume = "3", - number = "4", - pages = "311--326", - year = "1994", - publisher = "Taylor \& Francis" +@article{Julialang_2017, + author = "Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B.", + title = "Julia: A Fresh Approach to Numerical Computing", + volume = "59", + ISSN = "0036-1445", + DOI = "10.1137/141000671", + number = "1", + journal = "SIAM Review", + year = "2017", + pages = "65–98" } -@article{christianson1998reverse, - author = "Christianson, Bruce", - title = "Reverse aumulation and imploicit functions", - journal = "Optimization Methods and Software", - volume = "9", - number = "4", - pages = "307--322", - year = "1998", - publisher = "Taylor \& Francis" +@article{rackauckas2020universal, + author = "Rackauckas, Christopher and Ma, Yingbo and Martensen, Julius and Warner, Collin and Zubov, Kirill and Supekar, Rohit and Skinner, Dominic and Ramadhan, Ali and Edelman, Alan", + title = "Universal differential equations for scientific machine learning", + journal = "arXiv preprint arXiv:2001.04385", + year = "2020" } @article{Symbolics_jl_2022, @@ -176,42 +173,57 @@ @article{Lyness_1967 pages = "125–133" } -@article{PINNs_2019, - author = "Raissi, M. and Perdikaris, P. and Karniadakis, G.E.", - title = "Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations", - volume = "378", - ISSN = "0021-9991", - DOI = "10.1016/j.jcp.2018.10.045", - journal = "Journal of Computational Physics", - year = "2019", - pages = "686–707" +@article{Lyness_Moler_1967, + author = "Lyness, J N and Moler, C B", + title = "Numerical Differentiation of Analytic Functions", + volume = "4", + ISSN = "0036-1429", + DOI = "10.1137/0704019", + number = "2", + journal = "SIAM Journal on Numerical Analysis", + year = "1967", + pages = "202–210" } -@article{rackauckas2020universal, - author = "Rackauckas, Christopher and Ma, Yingbo and Martensen, Julius and Warner, Collin and Zubov, Kirill and Supekar, Rohit and Skinner, Dominic and Ramadhan, Ali and Edelman, Alan", - title = "Universal differential equations for scientific machine learning", - journal = "arXiv preprint arXiv:2001.04385", - year = "2020" +@article{Squire_Trapp_1998_complex_diff, + author = "Squire, William and Trapp, George", + title = "Using Complex Variables to Estimate Derivatives of Real Functions", + volume = "40", + ISSN = "0036-1445", + DOI = "10.1137/s003614459631241x", + year = "1998", + pages = "110–112" } -@article{Dandekar_2020, - author = "Dandekar, Raj and Rackauckas, Chris and Barbastathis, George", - title = "A Machine Learning-Aided Global Diagnostic and Comparative Tool to Assess Effect of Quarantine Control in COVID-19 Spread", - volume = "1", - ISSN = "2666-3899", - DOI = "10.1016/j.patter.2020.100145", - number = "9", - journal = "Patterns", - year = "2020", - pages = "100145" +@article{Martins_Sturdza_Alonso_2003_complex_differentiation, + author = "Martins, Joaquim R. R. A. and Sturdza, Peter and Alonso, Juan J.", + title = "The complex-step derivative approximation", + volume = "29", + ISSN = "0098-3500", + DOI = "10.1145/838250.838251", + journal = "ACM Transactions on Mathematical Software (TOMS)", + year = "2003", + pages = "245–262" } -@article{chen_neural_2019, - author = "Chen, Ricky TQ and Rubanova, Yulia and Bettencourt, Jesse and Duvenaud, David K", - title = "Neural ordinary differential equations", - journal = "Advances in neural information processing systems", - volume = "31", - year = "2018" +@book{stein2010complex, + author = "Stein, Elias M and Shakarchi, Rami", + title = "Complex analysis", + volume = "2", + year = "2010", + publisher = "Princeton University Press" +} + +@article{Lantoine_Russell_Dargent_2012, + author = "Lantoine, Gregory and Russell, Ryan P. and Dargent, Thierry", + title = "Using Multicomplex Variables for Automatic Computation of High-Order Derivatives", + volume = "38", + ISSN = "0098-3500", + DOI = "10.1145/2168773.2168774", + number = "3", + journal = "ACM Transactions on Mathematical Software (TOMS)", + year = "2012", + pages = "16" } @article{Giering_Kaminski_1998, @@ -341,7 +353,8 @@ @article{Razavi.2021 @article{ruder2016overview-gradient-descent, author = "Ruder, Sebastian", title = "An overview of gradient descent optimization algorithms", - journal = "arXiv preprint arXiv:1609.04747", + journal = "arXiv", + doi = "10.48550/arXiv.1609.04747", year = "2016" } @@ -848,16 +861,12 @@ @article{Zubov_McCarthy_Ma_Calisto_Pagliarino_Azeglio_Bottero_Luján_Sulzer_Bhar year = "2021" } -@article{ruelle1997differentiation, - author = "Ruelle, David", - title = "{Differentiation of SRB states}", - journal = "Communications in Mathematical Physics", - volume = "187", - number = "1", - pages = "227--241", - year = "1997", - publisher = "Springer", - doi = "https://doi.org/10.1007/s002200050134" +@book{lions1971optimal, + author = "Lions, Jacques Louis", + title = "Optimal control of systems governed by partial differential equations", + volume = "170", + year = "1971", + publisher = "Springer" } @book{nocedal1999numerical, @@ -910,16 +919,11 @@ @article{Pironneau_1974 pages = "97–110" } -@article{thuburn2005climate, - author = "Thuburn, John", - title = "{Climate sensitivities via a Fokker--Planck adjoint approach}", - journal = "Quarterly Journal of the Royal Meteorological Society: A journal of the atmospheric sciences, applied meteorology and physical oceanography", - volume = "131", - number = "605", - pages = "73--92", - year = "2005", - publisher = "Wiley Online Library", - doi = "https://doi.org/10.1256/qj.04.46" +@book{mohammadi2009applied, + author = "Mohammadi, Bijan and Pironneau, Olivier", + title = "Applied shape optimization for fluids", + year = "2009", + publisher = "OUP Oxford" } @article{allaire2014shape, @@ -939,15 +943,11 @@ @phdthesis{hu2010supersonic publisher = "Stanford University" } -@article{leith1975climate, - author = "Leith, Cecil E", - title = "Climate response and fluctuation dissipation", - journal = "Journal of Atmospheric Sciences", - volume = "32", - number = "10", - pages = "2022--2026", - year = "1975", - doi = "https://doi.org/10.1175/1520-0469(1975)032<2022:CRAFD>2.0.CO;2" +@phdthesis{fike2013multi, + author = "Fike, Jeffrey Alan", + title = "Multi-objective optimization using hyper-dual numbers", + year = "2013", + publisher = "Stanford university" } @article{chen2016aerodynamic, @@ -1021,63 +1021,71 @@ @article{jirari:2009 pages = "40003", year = "2009", publisher = "IOP Publishing", - doi = "https://iopscience.iop.org/article/10.1088/0951-7715/20/12/004" + doi = "10.1209/0295-5075/87/40003" } -@article{abramov2008new, - author = "Abramov, Rafail V and Majda, Andrew J", - title = "New approximations and tests of linear fluctuation-response for chaotic nonlinear forced-dissipative dynamical systems", - journal = "Journal of Nonlinear Science", - volume = "18", - pages = "303--341", - year = "2008", - publisher = "Springer", - doi = "https://doi.org/10.1007/s00332-007-9011-9" +@article{leung:2017, + author = "Leung, Nelson and Abdelhafez, Mohamed and Koch, Jens and Schuster, David", + title = "Speedup for quantum optimal control from automatic differentiation based on graphics processing units", + journal = "Physical Review A", + volume = "95", + number = "4", + pages = "042318", + year = "2017", + publisher = "APS", + doi = "10.1103/PhysRevA.95.042318", + url = "https://doi.org/10.1103/PhysRevA.95.042318" } -@article{wang2013forward, - author = "Wang, Qiqi", - title = "Forward and adjoint sensitivity computation of chaotic dynamical systems", - journal = "Journal of Computational Physics", - volume = "235", - pages = "1--13", - year = "2013", - publisher = "Elsevier", - doi = "https://doi.org/10.1016/j.jcp.2012.09.007" +@article{abdelhafez:2019, + author = "Abdelhafez, Mohamed and Schuster, David I and Koch, Jens", + title = "Gradient-based optimal control of open quantum systems using quantum trajectories and automatic differentiation", + journal = "Phys. Rev. A", + volume = "99", + number = "5", + pages = "052327", + year = "2019", + publisher = "APS", + url = "https://journals.aps.org/pra/abstract/10.1103/PhysRevA.99.052327", + doi = "10.1103/PhysRevA.99.052327" } -@article{wang2014least, - author = "Wang, Qiqi and Hu, Rui and Blonigan, Patrick", - title = "Least squares shadowing sensitivity analysis of chaotic limit cycle oscillations", - journal = "Journal of Computational Physics", - volume = "267", - pages = "210--224", - year = "2014", - publisher = "Elsevier", - doi = "https://doi.org/10.1016/j.jcp.2014.03.002" +@article{jirari2019quantum, + author = "Jirari, Hamza", + title = "From quantum optimal control theory to coherent destruction of tunneling", + journal = "The European Physical Journal B", + volume = "92", + pages = "1--8", + year = "2019", + publisher = "Springer", + url = "https://doi.org/10.1140/epjb/e2018-90231-5", + doi = "10.1140/epjb/e2018-90231-5" } -@article{wang2014convergence, - author = "Wang, Qiqi", - title = "Convergence of the least squares shadowing method for computing derivative of ergodic averages", - journal = "SIAM Journal on Numerical Analysis", - volume = "52", - number = "1", - pages = "156--170", - year = "2014", - publisher = "SIAM", - doi = "https://doi.org/10.1137/130917065" +@article{abdelhafez:2020, + author = "Abdelhafez, Mohamed and Baker, Brian and Gyenis, Andr{\'a}s and Mundada, Pranav and Houck, Andrew A and Schuster, David and Koch, Jens", + title = "Universal gates for protected superconducting qubits using optimal control", + journal = "Physical Review A", + volume = "101", + number = "2", + pages = "022321", + year = "2020", + publisher = "APS", + url = "https://doi.org/10.1103/PhysRevA.101.022321", + doi = "10.1103/PhysRevA.101.022321" } -@article{ni2017sensitivity, - author = "Ni, Angxiu and Wang, Qiqi", - title = "{Sensitivity analysis on chaotic dynamical systems by Non-Intrusive Least Squares Shadowing (NILSS)}", - journal = "Journal of Computational Physics", - volume = "347", - pages = "56--77", - year = "2017", - publisher = "Elsevier", - doi = "https://doi.org/10.1016/j.jcp.2017.06.033" +@article{schaefer:2020, + author = {Sch{\"a}fer, Frank and Kloc, Michal and Bruder, Christoph and L{\"o}rch, Niels}, + title = "A differentiable programming method for quantum control", + journal = "Machine Learning: Science and Technology", + volume = "1", + number = "3", + pages = "035009", + year = "2020", + publisher = "IOP Publishing", + doi = "10.1088/2632-2153/ab9802", + url = "https://doi.org/10.1088/2632-2153/ab9802" } @article{goerz:2022, @@ -1283,33 +1291,49 @@ @article{Rabier.1992 local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/1992/1992-Rabier-Quarterly\%20Journal\%20of\%20the\%20Royal\%20Meteorological\%20Society.pdf" } -@article{ni2019adjoint, - author = "Ni, Angxiu and Talnikar, Chaitanya", - title = "{Adjoint sensitivity analysis on chaotic dynamical systems by Non-Intrusive Least Squares Adjoint Shadowing (NILSAS)}", - journal = "Journal of Computational Physics", - volume = "395", - pages = "690--709", - year = "2019", - publisher = "Elsevier", - doi = "https://doi.org/10.1016/j.jcp.2019.06.035" +@article{Rabier:2000uu, + author = "Rabier, F and Järvinen, H and Klinker, E and Mahfouf, J F and Simmons, A", + year = "2000", + rating = "0", + title = "{The ECMWF operational implementation of four‐dimensional variational assimilation. I: Experimental results with simplified physics}", + journal = "Quarterly Journal of the Royal Meteorological Society", + doi = "10.1002/qj.49712656415", + url = "https://doi.org/10.1002/qj.49712656415", + abstract = "{This paper presents results of a comparison between four‐dimensional variational assimilation (4D‐Var). using a 6‐hour assimilation window and simplified physics during the minimization, and three‐di...}", + pages = "1143 -- 1170", + number = "564", + volume = "126", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2000/2000-Rabier-Quarterly\%20Journal\%20of\%20the\%20Royal\%20Meteorological\%20Society.pdf" } -@article{ni2019sensitivity, - author = "Ni, Angxiu and Wang, Qiqi and Fernandez, Pablo and Talnikar, Chaitanya", - title = "{Sensitivity analysis on chaotic dynamical systems by finite difference non-intrusive least squares shadowing (FD-NILSS)}", - journal = "Journal of Computational Physics", - volume = "394", - pages = "615--631", - year = "2019", - publisher = "Elsevier", - doi = "https://doi.org/10.1016/j.jcp.2019.06.004" +@article{Bauer.2015, + author = "Bauer, Peter and Thorpe, Alan and Brunet, Gilbert", + year = "2015", + rating = "0", + title = "{The quiet revolution of numerical weather prediction}", + journal = "Nature", + issn = "0028-0836", + doi = "10.1038/nature14956", + pmid = "26333465", + url = "http://www.nature.com/doifinder/10.1038/nature14956", + abstract = "{Advances in numerical weather prediction represent a quiet revolution because they have resulted from a steady accumulation of scientific knowledge and technological advances over many years that, with only a few exceptions, have not been associated with the aura of fundamental physics breakthroughs. Nonetheless, the impact of numerical weather prediction is among the greatest of any area of physical science. As a computational problem, global weather prediction is comparable to the simulation of the human brain and of the evolution of the early Universe, and it is performed every day at major operational centres across the world. The cumulative progress of numerical weather prediction represents one of the most remarkable successes of modern science; here the many technological and scientific advances that have brought NWP to its present level are reviewed, as are the considerable challenges for the future. The outputs from numerical weather prediction (NWP) models are pervasive throughout society, and now provide skillful forecasts a week into the future. Looking back several decades, the increase in forecasting accuracy has been remarkable, but it was gradual, amounting to about an extra day of skillful forecast lead time per decade. Peter Bauer and colleagues review the many technological and scientific advances that have brought NWP to its present level, and reveal the considerable challenges in the future, if the historical rate of improvement is to continue.}", + pages = "47--55", + number = "7567", + volume = "525", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2015/2015-Bauer-Nature.pdf" } -@article{chandramoorthy2022efficient, - author = "Chandramoorthy, Nisha and Wang, Qiqi", - title = "Efficient computation of linear response of chaotic attractors with one-dimensional unstable manifolds", - journal = "SIAM Journal on Applied Dynamical Systems", - volume = "21", +@article{Farrell.1988, + author = "Farrell, Brian", + year = "1988", + title = "{Optimal Excitation of Neutral Rossby Waves}", + journal = "Journal of the Atmospheric Sciences", + issn = "0022-4928", + doi = "10.1175/1520-0469(1988)045<0163:oeonrw>2.0.co;2", + abstract = "{Properly configured disturbances are known to be effective in transferring the kinetic energy of a mean shear flow to neutrally stable modal and nonmodal waves. Consideration of perturbation energetics requires that such disturbances produce down-gradient momentum fluxes which are associated with perturbation phase lines oriented against the mean shear. Initial conditions chosen arbitrarily, except that they satisfy this requirement, have been shown to result in robust excitation of neutral waves. A question naturally arising from such studies is whether there exists, in some well-defined sense, a best or most effective choice of initial conditions which optimally excites the waves. This question is addressed as a variational problem, and examples of optimal initial conditions are identified for the barotropic β-plane channel. These examples include the most effective excitation of a given neutral Rossby mode and the most rapidly growing perturbation for a given time period without restriction on spectra composition.}", + pages = "163--172", number = "2", volume = "45", local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/Farrell-Optimal\%20Excitation\%20of\%20Neutral\%20Rossby\%20Waves-1988-Journal\%20of\%20the\%20Atmospheric\%20Sciences.pdf" @@ -1431,12 +1455,20 @@ @article{Thacker:1988kp local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/1988/1988-Thacker-Journal\%20of\%20Geophysical\%20Research-\%20Oceans\%20(1978–2012).pdf" } -@article{ni2020fast, - author = "Ni, Angxiu", - title = "Fast linear response algorithm for differentiating chaos", - journal = "arXiv preprint arXiv:2009.00595", - year = "2020", - doi = "https://arxiv.org/abs/2009.00595v5" +@article{Thacker:1988ed, + author = "Thacker, William Carlisle", + year = "1988", + rating = "0", + title = "{Fitting models to inadequate data by enforcing spatial and temporal smoothness}", + journal = "Journal of Geophysical Research: Oceans (1978–2012)", + doi = "10.1029/jc093ic09p10655", + url = "http://doi.org/10.1029/JC093iC09p10655", + abstract = "{When observations are too sparse to determine the state of a dynamical model , it is necessary to make use of prior knowledge or prejudice. The approach discussed here is to require that the model state be the best smooth fit to the sparse data . The requirement of ...}", + pages = "10655 -- 10665", + number = "C9", + volume = "93", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/Thacker-Fitting\%20models\%20to\%20inadequate\%20data\%20by\%20enforcing\%20spatial\%20and\%20temporal\%20smoothness-1988-Journal\%20of\%20Geophysical\%20Research-\%20Oceans\%20(1978–2012).pdf" } @article{Thacker:1989jf, @@ -1472,36 +1504,36 @@ @article{Tziperman.1989 local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/1989/1989-Tziperman-Journal\%20of\%20Physical\%20Oceanography.pdf" } -@article{ODESSA, - author = "Leis, Jorge R. and Kramer, Mark A.", - title = "Algorithm 658: ODESSA–an Ordinary Differential Equation Solver with Explicit Simultaneous Sensitivity Analysis", - year = "1988", - issue_date = "March 1988", - publisher = "Association for Computing Machinery", - address = "New York, NY, USA", - volume = "14", - number = "1", - issn = "0098-3500", - url = "https://doi.org/10.1145/42288.214371", - doi = "10.1145/42288.214371", - journal = "ACM Trans. Math. Softw.", - month = "mar", - pages = "61–67", - numpages = "7", - keywords = "model error, sensitivity analysis, parameter variation, model prediction uncertainty" +@article{Tziperman:1992hg, + author = "Tziperman, E and Thacker, W C and Long, R B", + year = "1992", + rating = "0", + title = "{Oceanic data analysis using a general circulation model. Part I: Simulations}", + journal = "Journal of Physical Oceanography", + doi = "10.1175/1520-0485(1992)022<1434:odauag>2.0.co;2", + url = "http://journals.ametsoc.org/doi/abs/10.1175/1520-0485\\%281992\\%29022\\%3C1434\\%3AODAUAG\\%3E2.0.CO\\%3B2", + abstract = "{Abstract This paper deals with the solution of inverse problems involving complex numerical models of the oceanic general circulation and large datasets. The goal of these inverse problems is to find values for model inputs consistent with a steady circulation and, at the ...}", + pages = "1434 -- 1457", + number = "12", + volume = "22", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/Tziperman-Oceanic\%20data\%20analysis\%20using\%20a\%20general\%20circulation\%20model.\%20Part\%20I-\%20Simulations-1992-Journal\%20of\%20Physical\%20Oceanography.pdf" } -@article{dolfin2013, - author = "Farrell, P. E. and Ham, D. A. and Funke, S. W. and Rognes, M. E.", - title = "Automated Derivation of the Adjoint of High-Level Transient Finite Element Programs", - journal = "SIAM Journal on Scientific Computing", - volume = "35", - number = "4", - pages = "C369-C393", - year = "2013", - doi = "10.1137/120873558", - URL = "https://doi.org/10.1137/120873558", - eprint = "https://doi.org/10.1137/120873558" +@article{Tziperman:1992jw, + author = "Tziperman, E and Thacker, W C and Long, R B", + year = "1992", + rating = "0", + title = "{Oceanic data analysis using a general circulation model. Part II: A North Atlantic model}", + journal = "Journal of Physical Oceanography", + doi = "10.1175/1520-0485(1992)022<1458:odauag>2.0.co;2", + url = "http://journals.ametsoc.org/doi/abs/10.1175/1520-0485\\%281992\\%29022\\%3C1458\\%3AODAUAG\\%3E2.0.CO\\%3B2", + abstract = "{Abstract A general circulation model and North Atlantic climatological data of temperature salinity, wind stress, evaporation minus precipitation, and air-sea heat fluxes are used to examine the possibility of solving inverse problems using a full-scale numerical GCM and ...}", + pages = "1458 -- 1485", + number = "12", + volume = "22", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/1992/1992-Tziperman-Journal\%20of\%20Physical\%20Oceanography.pdf" } @article{Moore.1997ah, @@ -1537,46 +1569,52 @@ @article{Moore.1997 local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/1997/1997-Moore-Quarterly\%20Journal\%20of\%20the\%20Royal\%20Meteorological\%20Society.pdf" } -@inproceedings{moses_Enzyme, - author = "Moses, William and Churavy, Valentin", - editor = "Larochelle, H. and Ranzato, M. and Hadsell, R. and Balcan, M. F. and Lin, H.", - booktitle = "Advances in Neural Information Processing Systems", - pages = "12472--12485", - publisher = "Curran Associates, Inc.", - title = "Instead of Rewriting Foreign Code for Machine Learning, Automatically Synthesize Fast Gradients", - url = "https://proceedings.neurips.cc/paper/2020/file/9332c513ef44b682e9347822c2e457ac-Paper.pdf", - volume = "33", - year = "2020" -} - -@article{Zhuang_2020, - author = "Zhuang, Juntang and Dvornek, Nicha and Li, Xiaoxiao and Tatikonda, Sekhar and Papademetris, Xenophon and Duncan, James", - title = "Adaptive Checkpoint Adjoint Method for Gradient Estimation in Neural ODE.", - volume = "119", - journal = "Proceedings of machine learning research", - year = "2020", - pages = "11639–11649" +@article{Zanna.2010, + author = "Zanna, Laure and Heimbach, Patrick and Moore, Andrew M. and Tziperman, Eli", + year = "2010", + rating = "0", + title = "{The Role of Ocean Dynamics in the Optimal Growth of Tropical SST Anomalies}", + journal = "Journal of Physical Oceanography", + issn = "0022-3670", + doi = "10.1175/2009jpo4196.1", + url = "http://journals.ametsoc.org/doi/abs/10.1175/2009JPO4196.1", + abstract = "{The role of ocean dynamics in optimally exciting interannual variability of tropical sea surface temperature (SST) anomalies is investigated using an idealized-geometry ocean general circulation model. Initial temperature and salinity perturbations leading to an optimal growth of tropical SST anomalies, typically arising from the nonnormal dynamics, are evaluated. The structure of the optimal perturbations is characterized by relatively strong deep salinity anomalies near the western boundary generating a transient amplification of equatorial SST anomalies in less than four years. The associated growth mechanism is linked to the excitation of coastal and equatorial Kelvin waves near the western boundary following a rapid geostrophic adjustment owing to the optimal initial temperature and salinity perturbations. The results suggest that the nonnormality of the ocean dynamics may efficiently create large tropical SST variability on interannual time scales in the Atlantic without the participation of air–sea processes or the meridional overturning circulation. An optimal deep initial salinity perturbation of 0.1 ppt located near the western boundary can result in a tropical SST anomaly of approximately 0.45°C after nearly four years, assuming the dynamics are linear. Possible mechanisms for exciting such deep perturbations are discussed. While this study is motivated by tropical Atlantic SST variability, its relevance to other basins is not excluded. The optimal initial conditions leading to the tropical SST anomalies’ growth are obtained by solving a generalized eigenvalue problem. The evaluation of the optimals is achieved by using the Massachusetts Institute of Technology general circulation model (MITgcm) tangent linear and adjoint models as well the the Arnoldi Package (ARPACK) software for solving large-scale eigenvalue problems.}", + pages = "983--1003", + number = "5", + volume = "40", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2010/2010-Zanna-Journal\%20of\%20Physical\%20Oceanography.pdf" } -@article{laurie1997calculation, - author = "Laurie, Dirk", - title = "Calculation of Gauss-Kronrod quadrature rules", - journal = "Mathematics of Computation", - volume = "66", - number = "219", - pages = "1133--1145", - year = "1997" +@article{Zanna:2011ge, + author = "Zanna, Laure and Heimbach, Patrick and Moore, Andrew M and Tziperman, Eli", + year = "2011", + rating = "0", + title = "{Optimal Excitation of Interannual Atlantic Meridional Overturning Circulation Variability}", + journal = "Journal of Climate", + issn = "0894-8755", + doi = "10.1175/2010jcli3610.1", + url = "http://journals.ametsoc.org/doi/abs/10.1175/2010JCLI3610.1", + pages = "413 -- 427", + number = "2", + volume = "24", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2011/2011-Zanna-Journal\%20of\%20Climate.pdf" } -@article{gonnet2012review, - author = "Gonnet, Pedro", - title = "A review of error estimation in adaptive quadrature", - journal = "ACM Computing Surveys (CSUR)", - volume = "44", - number = "4", - pages = "1--36", +@article{Zanna:2012dw, + author = "Zanna, L and Heimbach, P and Moore, A M and Tziperman, E", year = "2012", - publisher = "ACM New York, NY, USA" + rating = "0", + title = "{Upper-ocean singular vectors of the North Atlantic climate with implications for linear predictability and variability}", + journal = "Quarterly Journal of the Royal Meteorological Society", + doi = "10.1002/qj.937", + url = "http://doi.wiley.com/10.1002/qj.937", + pages = "500 -- 513", + number = "663", + volume = "138", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2012/2012-Zanna-Quarterly\%20Journal\%20of\%20the\%20Royal\%20Meteorological\%20Society.pdf" } @article{Weaver.2003, @@ -1671,21 +1709,21 @@ @article{Marotzke:1999 keywords = "" } -@article{Wunsch.2007, - author = "Wunsch, Carl and Heimbach, Patrick", - year = "2007", +@article{Heimbach.2005, + author = "Heimbach, Patrick and Hill, Chris and Giering, Ralf", + year = "2005", rating = "0", - title = "{Practical global oceanic state estimation}", - journal = "Physica D: Nonlinear Phenomena", - issn = "0167-2789", - doi = "10.1016/j.physd.2006.09.040", - url = "http://linkinghub.elsevier.com/retrieve/pii/S0167278906003496", - abstract = "{The problem of oceanographic state estimation, by means of an ocean general circulation model (GCM) and a multitude of observations, is described and contrasted with the meteorological process of data assimilation. In practice, all such methods reduce, on the computer, to forms of least-squares. The global oceanographic problem is at the present time focussed primarily on smoothing, rather than forecasting, and the data types are unlike meteorological ones. As formulated in the consortium Estimating the Circulation and Climate of the Ocean (ECCO), an automatic differentiation tool is used to calculate the so-called adjoint code of the GCM, and the method of Lagrange multipliers used to render the problem one of unconstrained least-squares minimization. Major problems today lie less with the numerical algorithms (least-squares problems can be solved by many means) than with the issues of data and model error. Results of ongoing calculations covering the period of the World Ocean Circulation Experiment, and including among other data, satellite altimetry from TOPEX/POSEIDON, Jason-1, ERS- 1/2, ENVISAT, and GFO, a global array of profiling floats from the Argo program, and satellite gravity data from the GRACE mission, suggest that the solutions are now useful for scientific purposes. Both methodology and applications are developing in a number of different directions.}", - pages = "197--208", - number = "1-2", - volume = "230", + title = "{An efficient exact adjoint of the parallel MIT General Circulation Model, generated via automatic differentiation}", + journal = "Future Generation Computer Systems", + issn = "0167-739X", + doi = "10.1016/j.future.2004.11.010", + url = "http://linkinghub.elsevier.com/retrieve/pii/S0167739X04001797", + abstract = "{We describe computational aspects of automatic differentiation applied to global ocean circulation modeling and state estimation. The task of minimizing a cost function measuring the ocean simulation versus observation misfit is achieved through efficient calculation of the cost gradient w.r.t. a set of controls via the adjoint technique. The adjoint code of the parallel MIT general circulation model is generated using TAMC or its successor TAF. To achieve a tractable problem in both CPU and memory requirements, in the light of control flow reversal, the adjoint code relies heavily on the balancing of storing versus recomputation via the checkpointing method. Further savings are achieved by exploiting self-adjointness of part of the computation. To retain scalability of domain decomposition-based parallelism, hand-written adjoint routines are provided. These complement routines of the parallel support package to perform corresponding operations in reverse mode. The unique feature of the TAF tool which enables the dumping of the adjoint state and restart the adjoint integration is exploited to overcome batch execution limitations on HPC machines for large-scale ocean and climate simulations. Strategies to test the correctness of the adjoint-generated gradient are presented. The size of a typical adjoint application is illustrated for the case of the global ocean state estimation problem undertaken by the SIO-JPL-MIT Consortium “Estimating the Circulation and Climate of the Ocean” (ECCO). Results are given by way of example.}", + pages = "1356--1371", + number = "8", + volume = "21", keywords = "", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2007/2007-Wunsch-Physica\%20D.pdf" + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2005/2005-Heimbach-Future\%20Generation\%20Computer\%20Systems.pdf" } @article{Forget.2015m9i, @@ -1705,40 +1743,51 @@ @article{Forget.2015m9i local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2015/2015-Forget-Geoscientific\%20Model\%20Development.pdf" } -@article{Griewank_1989, - author = "Griewank, Andreas", - title = "On Automatic Differentiation", - journal = "Mathematical Programming: Recent Developments and Applications", - year = "1989" +@article{Dutkiewicz:2006gw, + author = "Dutkiewicz, S and Follows, M J and Heimbach, P and Marshall, J", + year = "2006", + rating = "0", + title = "{Controls on ocean productivity and air-sea carbon flux: An adjoint model sensitivity study}", + journal = "Geophysical Research Letters", + issn = "0094-8276", + doi = "10.1029/2005gl024987", + url = "http://doi.wiley.com/10.1029/2005GL024987", + abstract = "{Oceanography: General: Numerical modeling; Oceanography: Biological and Chemical: Biogeochemical cycles, processes, and modeling; Oceanography: Biological and Chemical: Carbon cycling; Oceanography: Biological and Chemical: Nutrients and nutrient cycling; Oceanography: Biological and Chemical: Trace elements}", + pages = "159 -- 4", + number = "2", + volume = "33", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2006/2006-Dutkiewicz-Geophysical\%20Research\%20Letters.pdf" } -@article{clifford1871dualnumbers, - author = "Clifford", - title = "Preliminary sketch of biquaternions", - journal = "Proceedings of the London Mathematical Society", - volume = "1", - number = "1", - pages = "381--395", - year = "1871", - publisher = "Oxford University Press" +@article{Heimbach:2010fz, + author = "Heimbach, Patick and Menemenlis, Dimitris and Losch, Martin and Campin, Jean-Michel and Hill, Chris", + year = "2010", + rating = "0", + title = "{On the formulation of sea-ice models. Part 2: Lessons from multi-year adjoint sea-ice export sensitivities through the Canadian Arctic Archipelago}", + journal = "Ocean Modelling", + doi = "10.1016/j.ocemod.2010.02.002", + url = "http://dx.doi.org/10.1016/j.ocemod.2010.02.002", + pages = "145 -- 158", + number = "1-2", + volume = "33", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2010/2010-Heimbach-Ocean\%20Modelling.pdf" } -@inproceedings{Karczmarczuk2001, - author = "Karczmarczuk, Jerzy", - title = "Functional Differentiation of Computer Programs", - year = "1998", - isbn = "1581130244", - publisher = "Association for Computing Machinery", - address = "New York, NY, USA", - url = "https://doi.org/10.1145/289423.289442", - doi = "10.1145/289423.289442", - abstract = "We present two purely functional implementations of the computational differentiation tools -- the well known numeric (not symbolic!) techniques which permit to compute pointwise derivatives of functions defined by computer programs economically and exactly. We show how the co-recursive (lazy) algorithm formulation permits to construct in a transparent and elegant manner the entire infinite tower of derivatives of higher order for any expressions present in the program, and we present a purely functional variant of the reverse (or adjoint) mode of computational differentiation, using a chain of delayed evaluations represented by closures. Some concrete applications are also discussed.", - booktitle = "Proceedings of the Third ACM SIGPLAN International Conference on Functional Programming", - pages = "195–203", - numpages = "9", - keywords = "Haskell, arithmetic, lazy semantics, derivatives, differentiation", - location = "Baltimore, Maryland, USA", - series = "ICFP '98" +@article{Heimbach:2012iu, + author = "Heimbach, Patrick and Losch, Martin", + year = "2012", + rating = "0", + title = "{Adjoint sensitivities of sub-ice-shelf melt rates to ocean circulation under the Pine Island Ice Shelf, West Antarctica}", + journal = "Annals of Glaciology", + doi = "10.3189/2012/aog60a025", + url = "http://openurl.ingenta.com/content/xref?genre=article\&issn=0260-3055\&volume=53\&issue=60\&spage=59", + pages = "59 -- 69", + number = "60", + volume = "53", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2012/2012-Heimbach-Annals\%20of\%20Glaciology.pdf" } @article{Goldberg:2020dl, @@ -1773,124 +1822,116 @@ @article{Ferreira.2005 local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2005/2005-Ferreira-Journal\%20of\%20Physical\%20….pdf" } -@article{RevelsLubinPapamarkou2016, - author = "{Revels}, J. and {Lubin}, M. and {Papamarkou}, T.", - title = "Forward-Mode Automatic Differentiation in {J}ulia", - journal = "arXiv:1607.07892 [cs.MS]", - year = "2016", - url = "https://arxiv.org/abs/1607.07892" +@article{Stammer:2005dw, + author = "Stammer, Detlef", + year = "2005", + rating = "0", + title = "{Adjusting Internal Model Errors through Ocean State Estimation}", + journal = "Journal of Physical Oceanography", + issn = "0022-3670", + doi = "10.1175/jpo2733.1", + url = "http://journals.ametsoc.org/doi/abs/10.1175/JPO2733.1", + pages = "1143 -- 1153", + number = "6", + volume = "35", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2005/2005-Stammer-Journal\%20of\%20Physical\%20Oceanography.pdf" } -@phdthesis{fike2013multi, - author = "Fike, Jeffrey Alan", - title = "Multi-objective optimization using hyper-dual numbers", - year = "2013", - publisher = "Stanford university" +@article{Liu:2012jd, + author = "Liu, Chuanyu and Köhl, A and Stammer, Detlef", + year = "2012", + rating = "0", + title = "{Adjoint-Based Estimation of Eddy-Induced Tracer Mixing Parameters in the Global Ocean}", + journal = "Journal of Physical Oceanography", + issn = "1520-0485", + doi = "10.1175/jpo-d-11-0162.1", + url = "http://journals.ametsoc.org/doi/abs/10.1175/JPO-D-11-0162.1", + pages = "1186 -- 1206", + number = "7", + volume = "42", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2012/2012-Liu-Journal\%20of\%20Physical\%20Oceanography.pdf" } -@inproceedings{kantorovich1957mathematical, - author = "Kantorovich, Leonid Vitalevich", - title = "On a mathematical symbolism convenient for performing machine calculations", - booktitle = "Dokl. Akad. Nauk SSSR", - volume = "113", +@article{Utke:2008ko, + author = "Utke, Jean and Naumann, Uwe and Fagan, Mike and Tallent, Nathan and Strout, Michelle and Heimbach, Patrick and Hill, Chris and Wunsch, Carl", + year = "2008", + rating = "0", + title = "{OpenAD/F: A Modular Open-Source Tool for Automatic Differentiation of Fortran Codes}", + journal = "ACM Transactions on Mathematical Software (TOMS)", + issn = "0098-3500", + doi = "10.1145/1377596.1377598", + url = "http://portal.acm.org/citation.cfm?doid=1377596.1377598", + abstract = "{The Open/ADF tool allows the evaluation of derivatives of functions defined by a Fortran program. The derivative evaluation is performed by a Fortran code resulting from the analysis and transformation of the original program that defines the function of interest. Open/ADF has been designed with a particular emphasis on modularity, flexibility, and the use of open source components. While the code transformation follows the basic principles of automatic differentiation, the tool implements new algorithmic approaches at various levels, for example, for basic block preaccumulation and call graph reversal. Unlike most other automatic differentiation tools, Open/ADF uses components provided by the Open/AD framework, which supports a comparatively easy extension of the code transformations in a language-independent fashion. It uses code analysis results implemented in the OpenAnalysis component. The interface to the language-independent transformation engine is an XML-based format, specified through an XML schema. The implemented transformation algorithms allow efficient derivative computations using locally optimized cross-country sequences of vertex, edge, and face elimination steps. Specifically, for the generation of adjoint codes, Open/ADF supports various code reversal schemes with hierarchical checkpointing at the subroutine level. As an example from geophysical fluid dynamics, a nonlinear time-dependent scalable, yet simple, barotropic ocean model is considered. OpenAD/F's reverse mode is applied to compute sensitivities of some of the model's transport properties with respect to gridded fields such as bottom topography as independent (control) variables.}", + pages = "18", number = "4", - pages = "738--741", - year = "1957" + volume = "34", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2008/2008-Utke-ACM\%20Transactions\%20on\%20Mathematical\%20Software\%20(TOMS).pdf" } -@article{Wengert_1964, - author = "Wengert, R. E.", - title = "A simple automatic derivative evaluation program", - volume = "7", - ISSN = "0001-0782", - DOI = "10.1145/355586.364791", - number = "8", - journal = "Communications of the ACM", - year = "1964", - pages = "463–464" +@article{Hascoet.2013, + author = "Hascoet, Laurent and Pasqual, Valerie", + year = "2013", + rating = "0", + title = "{The Tapenade Automatic Differentiation Tool: Principles, Model, and Specification}", + journal = "ACM Transactions on Mathematical Software", + doi = "10.1145/2450153.2450158", + url = "https://doi.org/10.1145/2450153.2450158", + pages = "1 -- 43", + number = "3", + volume = "39", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2013/2013-Hascoet-ACM\%20Transactions\%20on\%20Mathematical\%20Software.pdf" } -@article{Bauer_1974, - author = "Bauer, F L", - title = "Computational Graphs and Rounding Error", - volume = "11", - ISSN = "0036-1429", - DOI = "10.1137/0711010", - number = "1", - journal = "SIAM Journal on Numerical Analysis", - year = "1974", - pages = "87–96" +@article{Gaikwad.2023, + author = "Gaikwad, Shreyas Sunil and Hascoet, Laurent and Narayanan, Sri Hari Krishna and Curry-Logan, Liz and Greve, Ralf and Heimbach, Patrick", + year = "2023", + title = "{SICOPOLIS-AD v2: tangent linear and adjoint modeling framework for ice sheet modeling enabled by automatic differentiation tool Tapenade}", + journal = "Journal of Open Source Software", + doi = "10.21105/joss.04679", + pages = "4679", + number = "83", + volume = "8", + local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/Gaikwad-SICOPOLIS-AD\%20v2-\%20tangent\%20linear\%20and\%20adjoint\%20modeling\%20framework\%20for\%20ice\%20sheet\%20modeling\%20enabled\%20by\%20automatic\%20differentiation\%20tool\%20Tapenade-2023-Journal\%20of\%20Open\%20Source\%20Software.pdf" } -@article{Oktay_randomized-AD, - author = "Oktay, Deniz and McGreivy, Nick and Aduol, Joshua and Beatson, Alex and Adams, Ryan P", - title = "Randomized Automatic Differentiation", - DOI = "10.48550/arxiv.2007.10412", - journal = "arXiv", - year = "2020" -} - -@article{griewank2012invented, - author = "Griewank, Andreas", - title = "Who invented the reverse mode of differentiation", - journal = "Documenta Mathematica, Extra Volume ISMP", - volume = "389400", - year = "2012" -} - -@article{Wolfe_1982, - author = "Wolfe, Philip", - title = "Checking the Calculation of Gradients", - volume = "8", - ISSN = "0098-3500", - DOI = "10.1145/356012.356013", - abstractNote = "An abstract is not available.", - number = "4", - journal = "ACM Transactions on Mathematical Software (TOMS)", - year = "1982", - pages = "337–343" -} - -@article{Giering_Kaminski_1998, - author = "Giering, Ralf and Kaminski, Thomas", - title = "Recipes for adjoint code construction", - volume = "24", - ISSN = "0098-3500", - DOI = "10.1145/293686.293695", - number = "4", - journal = "ACM Transactions on Mathematical Software (TOMS)", - year = "1998", - pages = "437–474" -} - -@article{Gaikwad.2024, - author = "Gaikwad, Shreyas Sunil and Narayanan, Sri Hari Krishna and Hascoet, Laurent and Campin, Jean-Michel and Pillar, Helen and Nguyen, An and Hückelheim, Jan and Hovland, Paul and Heimbach, Patrick", - year = "2024", - title = "{MITgcm-AD v2: Open source tangent linear and adjoint modeling framework for the oceans and atmosphere enabled by the Automatic Differentiation tool Tapenade}", +@article{Gaikwad.2024, + author = "Gaikwad, Shreyas Sunil and Narayanan, Sri Hari Krishna and Hascoet, Laurent and Campin, Jean-Michel and Pillar, Helen and Nguyen, An and Hückelheim, Jan and Hovland, Paul and Heimbach, Patrick", + year = "2024", + title = "{MITgcm-AD v2: Open source tangent linear and adjoint modeling framework for the oceans and atmosphere enabled by the Automatic Differentiation tool Tapenade}", journal = "arXiv", eprint = "2401.11952", abstract = "{The Massachusetts Institute of Technology General Circulation Model (MITgcm) is widely used by the climate science community to simulate planetary atmosphere and ocean circulations. A defining feature of the MITgcm is that it has been developed to be compatible with an algorithmic differentiation (AD) tool, TAF, enabling the generation of tangent-linear and adjoint models. These provide gradient information which enables dynamics-based sensitivity and attribution studies, state and parameter estimation, and rigorous uncertainty quantification. Importantly, gradient information is essential for computing comprehensive sensitivities and performing efficient large-scale data assimilation, ensuring that observations collected from satellites and in-situ measuring instruments can be effectively used to optimize a large uncertain control space. As a result, the MITgcm forms the dynamical core of a key data assimilation product employed by the physical oceanography research community: Estimating the Circulation and Climate of the Ocean (ECCO) state estimate. Although MITgcm and ECCO are used extensively within the research community, the AD tool TAF is proprietary and hence inaccessible to a large proportion of these users. The new version 2 (MITgcm-AD v2) framework introduced here is based on the source-to-source AD tool Tapenade, which has recently been open-sourced. Another feature of Tapenade is that it stores required variables by default (instead of recomputing them) which simplifies the implementation of efficient, AD-compatible code. The framework has been integrated with the MITgcm model main branch and is now freely available.}" } -@article{Huang_Smith_Henry_Geijn_2016, - author = "Huang, Jianyu and Smith, Tyler M. and Henry, Greg M. and Geijn, Robert A. Van De", - title = "Strassen’s Algorithm Reloaded", - DOI = "10.1109/sc.2016.58", - journal = "SC16: International Conference for High Performance Computing, Networking, Storage and Analysis", - year = "2016", - pages = "690–701" +@article{Meehl.2021, + author = "Meehl, Gerald A and Richter, Jadwiga H and Teng, Haiyan and Capotondi, Antonietta and Cobb, Kim and Doblas-Reyes, Francisco and Donat, Markus G and England, Matthew H and Fyfe, John C and Han, Weiqing and Kim, Hyemi and Kirtman, Ben P and Kushnir, Yochanan and Lovenduski, Nicole S and Mann, Michael E and Merryfield, William J and Nieves, Veronica and Pegion, Kathy and Rosenbloom, Nan and Sanchez, Sara C and Scaife, Adam A and Smith, Doug and Subramanian, Aneesh C and Sun, Lantao and Thompson, Diane and Ummenhofer, Caroline C and Xie, Shang-Ping", + year = "2021", + rating = "0", + title = "{Initialized Earth System prediction from subseasonal to decadal timescales}", + journal = "Nature Reviews Earth \& Environment", + doi = "10.1038/s43017-021-00155-x", + url = "http://dx.doi.org/10.1038/s43017-021-00155-x", + abstract = "{Nature Reviews Earth \& Environment, doi:10.1038/s43017-021-00155-x}", + pages = "1 -- 18", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2021/2021-Meehl-Nature\%20Reviews\%20Earth\%20\&\%20Environment.pdf" } -@article{Bennett_1973, - author = "Bennett, C H", - title = "Logical Reversibility of Computation", - volume = "17", - ISSN = "0018-8646", - DOI = "10.1147/rd.176.0525", - number = "6", - journal = "IBM Journal of Research and Development", - year = "1973", - pages = "525–532" +@article{Frolov.2023, + author = "Frolov, Sergey and Rousseaux, Cécile S and Auligne, Tom and Dee, Dick and Gelaro, Ron and Heimbach, Patrick and Simpson, Isla and Slivinski, Laura", + year = "2023", + title = "{Road Map for the Next Decade of Earth System Reanalysis in the United States}", + journal = "Bulletin of the American Meteorological Society", + issn = "0003-0007", + doi = "10.1175/bams-d-23-0011.1", + pages = "E706--E714", + number = "3", + volume = "104", + local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/Frolov-Road\%20Map\%20for\%20the\%20Next\%20Decade\%20of\%20Earth\%20System\%20Reanalysis\%20in\%20the\%20United\%20States-2023-Bulletin\%20of\%20the\%20American\%20Meteorological\%20Society.pdf" } @article{lea2000sensitivity, @@ -1905,46 +1946,69 @@ @article{lea2000sensitivity doi = "https://doi.org/10.3402/tellusa.v52i5.12283" } -@book{ascher2008-numerical-methods, - author = "Ascher, Uri M. and Greif, Chen", - title = "A First Course in Numerical Methods", - publisher = "Society for Industrial and Applied Mathematics", - year = "2011", - doi = "10.1137/9780898719987", - address = "Philadelphia, PA", - edition = "" +@article{Lea:2002cv, + author = "Lea, Daniel J and Haine, Thomas W N and Allen, Myles R and Hansen, James A", + year = "2002", + rating = "0", + title = "{Sensitivity analysis of the climate of a chaotic ocean circulation model}", + journal = "Quarterly Journal of the Royal Meteorological Society", + doi = "10.1256/qj.01.180", + url = "http://doi.wiley.com/10.1256/qj.01.180", + abstract = "{Quarterly Journal of the Royal Meteorological Society 2002.128:2587-2605}", + pages = "2587 -- 2605", + number = "586", + volume = "128", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2002/2002-Lea-Quarterly\%20Journal\%20of\%20the\%20Royal\%20Meteorological\%20Society.pdf" } -@article{Fornberg1988, - author = "Fornberg, Bengt", - ISSN = "00255718, 10886842", - URL = "http://www.jstor.org/stable/2008770", - journal = "Mathematics of Computation", - number = "184", - pages = "699--706", - publisher = "American Mathematical Society", - title = "Generation of Finite Difference Formulas on Arbitrarily Spaced Grids", - urldate = "2024-03-20", - volume = "51", - year = "1988" +@article{Blessing.2014, + author = "Blessing, Simon and Kaminski, Thomas and Lunkeit, Frank and Matei, Ion and Giering, Ralf and Köhl, Armin and Scholze, Marko and Herrmann, P. and Fraedrich, Klaus and Stammer, Detlef", + year = "2014", + rating = "0", + title = "{Testing variational estimation of process parameters and initial conditions of an earth system model}", + journal = "Tellus A", + issn = "0280-6495", + doi = "10.3402/tellusa.v66.22606", + url = "http://www.tellusa.net/index.php/tellusa/article/view/22606", + abstract = "{We present a variational assimilation system around a coarse resolution Earth System Model (ESM) and apply it for estimating initial conditions and parameters of the model. The system is based on derivative information that is efficiently provided by the ESM's adjoint, which has been generated through automatic differentiation of the model's source code. In our variational approach, the length of the feasible assimilation window is limited by the size of the domain in control space over which the approximation by the derivative is valid. This validity domain is reduced by non-smooth process representations. We show that in this respect the ocean component is less critical than the atmospheric component. We demonstrate how the feasible assimilation window can be extended to several weeks by modifying the implementation of specific process representations and by switching off processes such as precipitation.}", + pages = "22606", + number = "0", + volume = "66", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2014/2014-Blessing-Tellus\%20A.pdf" } -@article{Goldberg_1991_floatingpoint, - author = "Goldberg, David", - title = "What every computer scientist should know about floating-point arithmetic", - volume = "23", - ISSN = "0360-0300", - DOI = "10.1145/103162.103163", +@article{Lyu.2018, + author = "Lyu, Guokun and Köhl, Armin and Matei, Ion and Stammer, Detlef", + year = "2018", + rating = "0", + title = "{Adjoint‐Based Climate Model Tuning: Application to the Planet Simulator}", + journal = "Journal of Advances in Modeling Earth Systems", + issn = "1942-2466", + doi = "10.1002/2017ms001194", + url = "http://doi.wiley.com/10.1002/2017MS001194", + abstract = "{The adjoint method is used to calibrate the medium complexity climate model “Planet Simulator” through parameter estimation. Identical twin experiments demonstrate that this method can retrieve default values of the control parameters when using a long assimilation window of the order of 2 months. Chaos synchronization through nudging, required to overcome limits in the temporal assimilation window in the adjoint method, is employed successfully to reach this assimilation window length. When assimilating ERA‐Interim reanalysis data, the observations of air temperature and the radiative fluxes are the most important data for adjusting the control parameters. The global mean net longwave fluxes at the surface and at the top of the atmosphere are significantly improved by tuning two model parameters controlling the absorption of clouds and water vapor. The global mean net shortwave radiation at the surface is improved by optimizing three model parameters controlling cloud optical properties. The optimized parameters improve the free model (without nudging terms) simulation in a way similar to that in the assimilation experiments. Results suggest a promising way for tuning uncertain parameters in nonlinear coupled climate models. Through chaos synchronization, adjoint method is successfully applied to calibrate the “Planet Simulator” Air temperature and radiative fluxes are the most important observations for tuning parameters controlling clouds and water vapor properties The optimized parameters may either reduce or increase the RMSE of variables that are not explicitly included in the cost function}", + pages = "207--222", number = "1", - journal = "ACM Computing Surveys (CSUR)", - year = "1991", - pages = "5–48" + volume = "10", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2018/2018-Lyu-J\%20Adv\%20Model\%20Earth\%20Syst.pdf" } -@phdthesis{mathur2012stepsize-finitediff, - author = "Mathur, Ravishankar", - title = "An analytical approach to computing step sizes for finite-difference derivatives", - year = "2012" +@article{Stammer:2018de, + author = "Stammer, D and Köhl, A and Vlasenko, A and Matei, I and Lunkeit, F and Schubert, S", + year = "2018", + rating = "0", + title = "{A Pilot Climate Sensitivity Study Using the CEN Coupled Adjoint Model (CESAM)}", + journal = "Journal of Climate", + doi = "10.1175/jcli-d-17-0183.1", + url = "http://journals.ametsoc.org/doi/10.1175/JCLI-D-17-0183.1", + pages = "2031 -- 2056", + number = "5", + volume = "31", + keywords = "", + local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2018/2018-Stammer-Journal\%20of\%20Climate.pdf" } @article{Kochkov.2023, @@ -1958,16 +2022,15 @@ @article{Kochkov.2023 local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/Kochkov-Neural\%20General\%20Circulation\%20Models\%20for\%20Weather\%20and\%20Climate-2023-arXiv.pdf" } -@article{Ipsen_Meyer_1998, - author = "Ipsen, Ilse C. F. and Meyer, Carl D.", - title = "The Idea Behind Krylov Methods", - volume = "105", - ISSN = "0002-9890", - DOI = "10.1080/00029890.1998.12004985", - number = "10", - journal = "The American Mathematical Monthly", - year = "1998", - pages = "889–899" +@article{macayeal1992basal, + author = "MacAyeal, Douglas R", + title = "The basal stress distribution of Ice Stream E, Antarctica, inferred by control methods", + journal = "Journal of Geophysical Research: Solid Earth", + volume = "97", + number = "B1", + pages = "595--603", + year = "1992", + publisher = "Wiley Online Library" } @article{Vieli.2006, @@ -1999,26 +2062,26 @@ @article{goldberg2013parameter publisher = "Copernicus GmbH" } -@article{Butcher_Wanner_1996, - author = "Butcher, J.C. and Wanner, G.", - title = "Runge-Kutta methods: some historical notes", - volume = "22", - ISSN = "0168-9274", - DOI = "10.1016/s0168-9274(96)00048-7", - abstractNote = "This centenary history of Runge-Kutta methods contains an appreciation of the early work of Runge, Heun, Kutta, and Nyström and a survey of some significant developments of these methods over the last hundred years. In particular, the order conditions, as they are now understood, will be outlined, as will the introduction and practical implementation of implicit Runge-Kutta methods, the use of linear and nonlinear stability analysis in the assessment of Runge-Kutta methods, and the theory and applications of the composition of methods. Of the many further developments that have arisen, most are discussed only briefly; however, the recent interest in Runge-Kutta methods for Hamiltonian systems will be surveyed in more detail.", - number = "1–3", - journal = "Applied Numerical Mathematics", - year = "1996", - pages = "113–151" +@article{heimbach2009greenland, + author = "Heimbach, Patrick and Bugnion, Veronique", + title = "Greenland ice-sheet volume sensitivity to basal, surface and initial conditions derived from an adjoint model", + journal = "Annals of Glaciology", + volume = "50", + number = "52", + pages = "67--80", + year = "2009", + publisher = "Cambridge University Press" } -@article{Butcher_2001, - author = "Butcher, J C", - title = "Numerical Analysis: Historical Developments in the 20th Century", - DOI = "10.1016/b978-0-444-50617-7.50018-5", - abstractNote = "Numerical methods for the solution of initial value problems in ordinary differential equations made enormous progress during the 20th century for several reasons. The first reasons lie in the impetus that was given to the subject in the concluding years of the previous century by the seminal papers of Bashforth and Adams for linear multistep methods and Runge for Runge–Kutta methods. Other reasons, which of course apply to numerical analysis in general, are in the invention of electronic computers half way through the century and the needs in mathematical modelling of efficient numerical algorithms as an alternative to classical methods of applied mathematics. This survey paper follows many of the main strands in the developments of these methods, both for general problems, stiff systems, and for many of the special problem types that have been gaining in significance as the century draws to an end. © 2000 Elsevier Science B.V. All rights reserved.", - year = "2001", - pages = "449–477" +@article{mosbeux2016comparison, + author = "Mosbeux, Cyrille and Gillet-Chaulet, Fabien and Gagliardini, Olivier", + title = "Comparison of adjoint and nudging methods to initialise ice sheet model basal conditions", + journal = "Geoscientific Model Development", + volume = "9", + number = "7", + pages = "2549--2562", + year = "2016", + publisher = "Copernicus GmbH" } @article{Petra.2012, @@ -2049,15 +2112,15 @@ @article{morlighem2013inversion publisher = "Wiley Online Library" } -@article{van1980internal, - author = "van Der Houwen, Pieter J and Sommeijer, Ben P", - title = "On the internal stability of explicit, m-stage Runge-Kutta methods for large m-values", - journal = {ZAMM-Journal of Applied Mathematics and Mechanics/Zeitschrift f{\"u}r Angewandte Mathematik und Mechanik}, - volume = "60", - number = "10", - pages = "479--485", - year = "1980", - publisher = "Wiley Online Library" +@article{hascoet2018source, + author = {Hasco{\"e}t, Laurent and Morlighem, Mathieu}, + title = "Source-to-source adjoint Algorithmic Differentiation of an ice sheet model written in C", + journal = "Optimization Methods and Software", + volume = "33", + number = "4-6", + pages = "829--843", + year = "2018", + publisher = "Taylor \& Francis" } @article{Petra.2014, @@ -2103,35 +2166,43 @@ @article{Morlighem.2023 local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/misc\_morlighem\_goldberg\_2023\_data\_assimilation\_in\_glaciology.pdf" } -@book{hastie2009elements, - author = "Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome H and Friedman, Jerome H", - title = "The elements of statistical learning: data mining, inference, and prediction", - volume = "2", - year = "2009", - publisher = "Springer" +@Article{BolibarSapienza_UDEs, + AUTHOR = "Bolibar, J. and Sapienza, F. and Maussion, F. and Lguensat, R. and Wouters, B. and P\'erez, F.", + TITLE = "Universal differential equations for glacier ice flow modelling", + JOURNAL = "Geoscientific Model Development", + VOLUME = "16", + YEAR = "2023", + NUMBER = "22", + PAGES = "6671--6687", + URL = "https://gmd.copernicus.org/articles/16/6671/2023/", + DOI = "10.5194/gmd-16-6671-2023" } -@book{pml1Book, - author = "Murphy, Kevin P.", - title = "Probabilistic Machine Learning: An introduction", - publisher = "MIT Press", - year = "2022", - url = "probml.ai" +@article{wang2022discovering, + author = "Wang, Yongji and Lai, Ching-Yao and Cowen-Breen, Charlie", + title = "Discovering the rheology of Antarctic Ice Shelves via physics-informed deep learning", + year = "2022" } -@book{gelman2013bayesian, - author = "Gelman, Andrew and Carlin, John B and Stern, Hal S and Dunson, David B and Vehtari, Aki and Rubin, Donald B", - title = "Bayesian data analysis", - year = "2013", - publisher = "CRC press" +@article{Jouvet_Cordonnier_Kim_Lüthi_Vieli_Aschwanden_2021, + author = "Jouvet, Guillaume and Cordonnier, Guillaume and Kim, Byungsoo and Lüthi, Martin and Vieli, Andreas and Aschwanden, Andy", + title = "Deep learning speeds up ice flow modelling by several orders of magnitude", + ISSN = "0022-1430", + DOI = "10.1017/jog.2021.120", + journal = "Journal of Glaciology", + year = "2021", + pages = "1–14" } -@article{Betancourt_2017, - author = "Betancourt, Michael", - title = "A Conceptual Introduction to Hamiltonian Monte Carlo", - DOI = "10.48550/arxiv.1701.02434", - journal = "arXiv", - year = "2017" +@article{jouvet2023inversion, + author = "Jouvet, Guillaume", + title = "Inversion of a Stokes glacier flow model emulated by deep learning", + journal = "Journal of Glaciology", + volume = "69", + number = "273", + pages = "13--26", + year = "2023", + publisher = "Cambridge University Press" } @article{hodgkin1952quantitative, @@ -2432,199 +2503,89 @@ @article{Ipsen_Meyer_1998 pages = "889–899" } -@inproceedings{abadi-tensorflow, - author = "Abadi, Mart\'{\i}n and Barham, Paul and Chen, Jianmin and Chen, Zhifeng and Davis, Andy and Dean, Jeffrey and Devin, Matthieu and Ghemawat, Sanjay and Irving, Geoffrey and Isard, Michael and Kudlur, Manjunath and Levenberg, Josh and Monga, Rajat and Moore, Sherry and Murray, Derek G. and Steiner, Benoit and Tucker, Paul and Vasudevan, Vijay and Warden, Pete and Wicke, Martin and Yu, Yuan and Zheng, Xiaoqiang", - title = "TensorFlow: A System for Large-Scale Machine Learning", - year = "2016", - isbn = "9781931971331", - publisher = "USENIX Association", - address = "USA", - booktitle = "Proceedings of the 12th USENIX Conference on Operating Systems Design and Implementation", - pages = "265–283", - numpages = "19", - location = "Savannah, GA, USA", - series = "OSDI'16" +@article{clifford1871dualnumbers, + author = "Clifford", + title = "Preliminary sketch of biquaternions", + journal = "Proceedings of the London Mathematical Society", + volume = "1", + number = "1", + pages = "381--395", + year = "1871", + publisher = "Oxford University Press" } -@article{Moses.2021, - author = "Moses, William S and Churavy, Valentin and Paehler, Ludger and Hückelheim, Jan and Narayanan, Sri Hari Krishna and Schanen, Michel and Doerfert, Johannes", - year = "2021", - title = "{Reverse-Mode Automatic Differentiation and Optimization of GPU Kernels via Enzyme}", - journal = "SC21: International Conference for High Performance Computing, Networking, Storage and Analysis", - doi = "10.1145/3458817.3476165", - abstract = "{Computing derivatives is key to many algorithms in scientific computing and machine learning such as optimization, uncertainty quantification, and stability analysis. Enzyme is a LL VM compiler plugin that performs reverse-mode automatic differentiation (AD) and thus generates high performance gradients of programs in languages including \$\textbackslashmathrm\{C\}/\textbackslashmathrm\{C\}++\$, Fortran, Julia, and Rust. Prior to this work, Enzyme and other AD tools were not capable of generating gradi-ents of GPU kernels. Our paper presents a combination of novel techniques that make Enzyme the first fully automatic reverse-mode AD tool to generate gradients of GPU kernels. Since unlike other tools Enzyme performs automatic differentiation within a general-purpose compiler, we are able to introduce several novel GPU and AD-specific optimizations. To show the generality and efficiency of our approach, we compute gradients office GPU-based HPC applications, executed on NVIDIA and AMD GPUs. All bench-marks run within an order of magnitude of the original program's execution time. Without GPU and AD-specific optimizations, gra-dients of GPU kernels either fail to run from a lack of resources or have infeasible overhead. Finally, we demonstrate that increasing the problem size by either increasing the number of threads or increasing the work per thread, does not substantially impact the overhead from differentiation.}", - pages = "1--18", - volume = "00", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2021/misc\_moses\_etal\_2021\_reverse\_mode\_ad\_gpu\_kernels\_enzyme.pdf" +@inproceedings{Karczmarczuk2001, + author = "Karczmarczuk, Jerzy", + title = "Functional Differentiation of Computer Programs", + year = "1998", + isbn = "1581130244", + publisher = "Association for Computing Machinery", + address = "New York, NY, USA", + url = "https://doi.org/10.1145/289423.289442", + doi = "10.1145/289423.289442", + abstract = "We present two purely functional implementations of the computational differentiation tools -- the well known numeric (not symbolic!) techniques which permit to compute pointwise derivatives of functions defined by computer programs economically and exactly. We show how the co-recursive (lazy) algorithm formulation permits to construct in a transparent and elegant manner the entire infinite tower of derivatives of higher order for any expressions present in the program, and we present a purely functional variant of the reverse (or adjoint) mode of computational differentiation, using a chain of delayed evaluations represented by closures. Some concrete applications are also discussed.", + booktitle = "Proceedings of the Third ACM SIGPLAN International Conference on Functional Programming", + pages = "195–203", + numpages = "9", + keywords = "Haskell, arithmetic, lazy semantics, derivatives, differentiation", + location = "Baltimore, Maryland, USA", + series = "ICFP '98" } -@article{Schäfer_Tarek_White_Rackauckas_2021, - author = "Schäfer, Frank and Tarek, Mohamed and White, Lyndon and Rackauckas, Chris", - title = "AbstractDifferentiation.jl: Backend-Agnostic Differentiable Programming in Julia", - DOI = "10.48550/arxiv.2109.12449", +@article{Neuenhofen_2018, + author = "Neuenhofen, Martin", + title = "Review of theory and implementation of hyper-dual numbers for first and second order automatic differentiation", + DOI = "10.48550/arxiv.1801.03614", journal = "arXiv", - year = "2021" + year = "2018" } -@inproceedings{kantorovich1957mathematical, - author = "Kantorovich, Leonid Vitalevich", - title = "On a mathematical symbolism convenient for performing machine calculations", - booktitle = "Dokl. Akad. Nauk SSSR", - volume = "113", +@article{RevelsLubinPapamarkou2016, + author = "{Revels}, J. and {Lubin}, M. and {Papamarkou}, T.", + title = "Forward-Mode Automatic Differentiation in {J}ulia", + journal = "arXiv:1607.07892 [cs.MS]", + year = "2016", + url = "https://arxiv.org/abs/1607.07892" +} + +@inproceedings{kantorovich1957mathematical, + author = "Kantorovich, Leonid Vitalevich", + title = "On a mathematical symbolism convenient for performing machine calculations", + booktitle = "Dokl. Akad. Nauk SSSR", + volume = "113", number = "4", pages = "738--741", year = "1957" } -@article{Checkpoiting_2023, - author = "Schanen, Michel and Narayanan, Sri Hari Krishna and Williamson, Sarah and Churavy, Valentin and Moses, William S. and Paehler, Ludger", - editor = "Miky{\v{s}}ka, Ji{\v{r}}{\'i} and de Mulatier, Cl{\'e}lia and Paszynski, Maciej and Krzhizhanovskaya, Valeria V. and Dongarra, Jack J. and Sloot, Peter M.A.", - title = "Transparent Checkpointing for Automatic Differentiation of Program Loops Through Expression Transformations", - booktitle = "Computational Science -- ICCS 2023", - year = "2023", - publisher = "Springer Nature Switzerland", - address = "Cham", - pages = "483--497", - isbn = "978-3-031-36024-4" -} - -@article{Martins_Sturdza_Alonso_2003_complex_differentiation, - author = "Martins, Joaquim R. R. A. and Sturdza, Peter and Alonso, Juan J.", - title = "The complex-step derivative approximation", - volume = "29", - ISSN = "0098-3500", - DOI = "10.1145/838250.838251", - journal = "ACM Transactions on Mathematical Software (TOMS)", - year = "2003", - pages = "245–262" -} - -@article{Lyness_1967, - author = "Lyness, J N", - title = "Numerical algorithms based on the theory of complex variable", - DOI = "10.1145/800196.805983", - journal = "Proceedings of the 1967 22nd national conference on -", - year = "1967", - pages = "125–133" +@article{Wengert_1964, + author = "Wengert, R. E.", + title = "A simple automatic derivative evaluation program", + volume = "7", + ISSN = "0001-0782", + DOI = "10.1145/355586.364791", + number = "8", + journal = "Communications of the ACM", + year = "1964", + pages = "463–464" } -@article{Lyness_Moler_1967, - author = "Lyness, J N and Moler, C B", - title = "Numerical Differentiation of Analytic Functions", - volume = "4", +@article{Bauer_1974, + author = "Bauer, F L", + title = "Computational Graphs and Rounding Error", + volume = "11", ISSN = "0036-1429", - DOI = "10.1137/0704019", - number = "2", + DOI = "10.1137/0711010", + number = "1", journal = "SIAM Journal on Numerical Analysis", - year = "1967", - pages = "202–210" -} - -@article{Squire_Trapp_1998_complex_diff, - author = "Squire, William and Trapp, George", - title = "Using Complex Variables to Estimate Derivatives of Real Functions", - volume = "40", - ISSN = "0036-1445", - DOI = "10.1137/s003614459631241x", - year = "1998", - pages = "110–112" -} - -@book{stein2010complex, - author = "Stein, Elias M and Shakarchi, Rami", - title = "Complex analysis", - volume = "2", - year = "2010", - publisher = "Princeton University Press" -} - -@article{Bezanson_Karpinski_Shah_Edelman_2012, - author = "Bezanson, Jeff and Karpinski, Stefan and Shah, Viral B and Edelman, Alan", - title = "Julia: A Fast Dynamic Language for Technical Computing", - DOI = "10.48550/arxiv.1209.5145", - journal = "arXiv", - year = "2012" -} - -@article{allaire2015review, - author = "Allaire, Gr{\'e}goire", - title = "A review of adjoint methods for sensitivity analysis, uncertainty quantification and optimization in numerical codes", - journal = "Ing{\'e}nieurs de l'Automobile", - volume = "836", - pages = "33--36", - year = "2015" -} - -@article{gronwall1919note, - author = "Gronwall, Thomas Hakon", - title = "Note on the derivatives with respect to a parameter of the solutions of a system of differential equations", - journal = "Annals of Mathematics", - pages = "292--296", - year = "1919", - publisher = "JSTOR" -} - -@Article{math8111947, - AUTHOR = "Palmieri, Giacomo and Tiboni, Monica and Legnani, Giovanni", - TITLE = "Analysis of the Upper Limitation of the Most Convenient Cadence Range in Cycling Using an Equivalent Moment Based Cost Function", - JOURNAL = "Mathematics", - VOLUME = "8", - YEAR = "2020", - NUMBER = "11", - ARTICLE-NUMBER = "1947", - URL = "https://www.mdpi.com/2227-7390/8/11/1947", - ISSN = "2227-7390", - DOI = "10.3390/math8111947" -} - -@article{Cox:2017hv, - author = "Cox, D R and Efron, Bradley", - year = "2017", - rating = "0", - title = "{Statistical thinking for 21st century scientists}", - journal = "Science Advances", - doi = "10.1126/sciadv.1700768", - url = "http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1700768", - pages = "e1700768", - number = "6", - volume = "3", - keywords = "", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2017/2017-Cox-Science\%20Advances.pdf" -} - -@article{zdeborova_understanding_2020, - author = "Zdeborová, Lenka", - title = "Understanding deep learning is also a job for physicists", - issn = "1745-2473, 1745-2481", - url = "http://www.nature.com/articles/s41567-020-0929-2", - doi = "10.1038/s41567-020-0929-2", - language = "en", - urldate = "2020-05-29", - journal = "Nature Physics", - month = "May", - year = "2020" -} - -@article{Coveney:2016eb, - author = "Coveney, Peter V and Dougherty, Edward R and Highfield, Roger R", - year = "2016", - rating = "0", - title = "{Big data need big theory too}", - journal = "Philosophical Transactions of the Royal Society of London. Series A: Physical and Engineering Sciences", - issn = "1364-503X", - doi = "10.1098/rsta.2016.0153", - url = "http://rsta.royalsocietypublishing.org/lookup/doi/10.1098/rsta.2016.0153", - pages = "20160153 -- 11", - number = "2080", - volume = "374", - keywords = "", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2016/2016-Coveney-Philosophical\%20Transactions\%20of\%20the\%20Royal\%20Society\%20of\%20London.\%20Series\%20A-\%20Physical\%20and\%20Engineering\%20Sciences.pdf" + year = "1974", + pages = "87–96" } -@article{Molnar.2020sisk, - author = "Molnar, Christoph and Casalicchio, Giuseppe and Bischl, Bernd", - year = "2020", - title = "{Interpretable Machine Learning -- A Brief History, State-of-the-Art and Challenges}", +@article{Oktay_randomized-AD, + author = "Oktay, Deniz and McGreivy, Nick and Aduol, Joshua and Beatson, Alex and Adams, Ryan P", + title = "Randomized Automatic Differentiation", + DOI = "10.48550/arxiv.2007.10412", journal = "arXiv", year = "2020" } @@ -2828,215 +2789,182 @@ @article{Wang2012-chaos-adjoint url = "https://www.sciencedirect.com/science/article/pii/S0021999114001715" } -@article{Georgieva_Glavic_Bakr_Bandler_2002, - author = "Georgieva, Natalia K. and Glavic, Snezana and Bakr, Mohamed H. and Bandler, John W.", - title = "Feasible Adjoint Sensitivity Technique for Em Design Optimization", - volume = "50", - ISSN = "0018-9480", - DOI = "10.1109/tmtt.2002.805131", - number = "12", - journal = "IEEE Transactions on Microwave Theory and Techniques", - year = "2002", - pages = "2751" +@article{eyink2004ruelle, + author = "Eyink, GL and Haine, TWN and Lea, DJ1115", + title = "Ruelle's linear response formula, ensemble adjoint schemes and {L{\'e}vy} flights", + journal = "Nonlinearity", + volume = "17", + number = "5", + pages = "1867", + year = "2004", + publisher = "IOP Publishing", + url = "https://iopscience.iop.org/article/10.1088/0951-7715/17/5/016/meta" } -@article{McGreivy_stellarator_2021, - author = "McGreivy, N. and Hudson, S.R. and Zhu, C.", - title = "Optimized finite-build stellarator coils using automatic differentiation", - volume = "61", - ISSN = "0029-5515", - DOI = "10.1088/1741-4326/abcd76", - journal = "Nuclear Fusion", - year = "2021", - pages = "026020" +@article{thuburn2005climate, + author = "Thuburn, John", + title = "{Climate sensitivities via a Fokker--Planck adjoint approach}", + journal = "Quarterly Journal of the Royal Meteorological Society: A journal of the atmospheric sciences, applied meteorology and physical oceanography", + volume = "131", + number = "605", + pages = "73--92", + year = "2005", + publisher = "Wiley Online Library", + doi = "https://doi.org/10.1256/qj.04.46" } -@article{jirari:2009, - author = "Jirari, Hamza", - title = "Optimal control approach to dynamical suppression of decoherence of a qubit", - journal = "Europhysics Letters", - volume = "87", - number = "4", - pages = "40003", - year = "2009", - publisher = "IOP Publishing", - doi = "10.1209/0295-5075/87/40003" +@article{blonigan2014probability, + author = "Blonigan, Patrick J and Wang, Qiqi", + title = "Probability density adjoint for sensitivity analysis of the mean of chaos", + journal = "Journal of Computational Physics", + volume = "270", + pages = "660--686", + year = "2014", + publisher = "Elsevier", + doi = "https://doi.org/10.1016/j.jcp.2014.04.027" } -@article{leung:2017, - author = "Leung, Nelson and Abdelhafez, Mohamed and Koch, Jens and Schuster, David", - title = "Speedup for quantum optimal control from automatic differentiation based on graphics processing units", - journal = "Physical Review A", - volume = "95", - number = "4", - pages = "042318", - year = "2017", - publisher = "APS", - doi = "10.1103/PhysRevA.95.042318", - url = "https://doi.org/10.1103/PhysRevA.95.042318" +@article{leith1975climate, + author = "Leith, Cecil E", + title = "Climate response and fluctuation dissipation", + journal = "Journal of Atmospheric Sciences", + volume = "32", + number = "10", + pages = "2022--2026", + year = "1975", + doi = "https://doi.org/10.1175/1520-0469(1975)032<2022:CRAFD>2.0.CO;2" } -@article{abdelhafez:2019, - author = "Abdelhafez, Mohamed and Schuster, David I and Koch, Jens", - title = "Gradient-based optimal control of open quantum systems using quantum trajectories and automatic differentiation", - journal = "Phys. Rev. A", - volume = "99", - number = "5", - pages = "052327", - year = "2019", - publisher = "APS", - url = "https://journals.aps.org/pra/abstract/10.1103/PhysRevA.99.052327", - doi = "10.1103/PhysRevA.99.052327" +@article{abramov2007blended, + author = "Abramov, Rafail V and Majda, Andrew J", + title = "Blended response algorithms for linear fluctuation-dissipation for complex nonlinear dynamical systems", + journal = "Nonlinearity", + volume = "20", + number = "12", + pages = "2793", + year = "2007", + publisher = "IOP Publishing", + doi = "https://iopscience.iop.org/article/10.1088/0951-7715/20/12/004" } - -@article{jirari2019quantum, - author = "Jirari, Hamza", - title = "From quantum optimal control theory to coherent destruction of tunneling", - journal = "The European Physical Journal B", - volume = "92", - pages = "1--8", - year = "2019", + +@article{abramov2008new, + author = "Abramov, Rafail V and Majda, Andrew J", + title = "New approximations and tests of linear fluctuation-response for chaotic nonlinear forced-dissipative dynamical systems", + journal = "Journal of Nonlinear Science", + volume = "18", + pages = "303--341", + year = "2008", publisher = "Springer", - url = "https://doi.org/10.1140/epjb/e2018-90231-5", - doi = "10.1140/epjb/e2018-90231-5" + doi = "https://doi.org/10.1007/s00332-007-9011-9" } -@article{abdelhafez:2020, - author = "Abdelhafez, Mohamed and Baker, Brian and Gyenis, Andr{\'a}s and Mundada, Pranav and Houck, Andrew A and Schuster, David and Koch, Jens", - title = "Universal gates for protected superconducting qubits using optimal control", - journal = "Physical Review A", - volume = "101", - number = "2", - pages = "022321", - year = "2020", - publisher = "APS", - url = "https://doi.org/10.1103/PhysRevA.101.022321", - doi = "10.1103/PhysRevA.101.022321" +@article{wang2013forward, + author = "Wang, Qiqi", + title = "Forward and adjoint sensitivity computation of chaotic dynamical systems", + journal = "Journal of Computational Physics", + volume = "235", + pages = "1--13", + year = "2013", + publisher = "Elsevier", + doi = "https://doi.org/10.1016/j.jcp.2012.09.007" } -@article{schaefer:2020, - author = {Sch{\"a}fer, Frank and Kloc, Michal and Bruder, Christoph and L{\"o}rch, Niels}, - title = "A differentiable programming method for quantum control", - journal = "Machine Learning: Science and Technology", - volume = "1", - number = "3", - pages = "035009", - year = "2020", - publisher = "IOP Publishing", - doi = "10.1088/2632-2153/ab9802", - url = "https://doi.org/10.1088/2632-2153/ab9802" +@article{wang2014least, + author = "Wang, Qiqi and Hu, Rui and Blonigan, Patrick", + title = "Least squares shadowing sensitivity analysis of chaotic limit cycle oscillations", + journal = "Journal of Computational Physics", + volume = "267", + pages = "210--224", + year = "2014", + publisher = "Elsevier", + doi = "https://doi.org/10.1016/j.jcp.2014.03.002" } -@article{goerz:2022, - author = "Goerz, Michael H and Carrasco, Sebasti{\'a}n C and Malinovsky, Vladimir S", - title = "Quantum optimal control via semi-automatic differentiation", - journal = "Quantum", - volume = "6", - pages = "871", - year = "2022", - publisher = {Verein zur F{\"o}rderung des Open Access Publizierens in den Quantenwissenschaften}, - doi = "10.22331/q-2022-12-07-871" +@article{wang2014convergence, + author = "Wang, Qiqi", + title = "Convergence of the least squares shadowing method for computing derivative of ergodic averages", + journal = "SIAM Journal on Numerical Analysis", + volume = "52", + number = "1", + pages = "156--170", + year = "2014", + publisher = "SIAM", + doi = "https://doi.org/10.1137/130917065" } -@article{schaefer:2021, - author = {Sch{\"a}fer, Frank and Sekatski, Pavel and Koppenh{\"o}fer, Martin and Bruder, Christoph and Kloc, Michal}, - title = "Control of stochastic quantum dynamics by differentiable programming", - journal = "Machine Learning: Science and Technology", - volume = "2", - number = "3", - pages = "035004", - year = "2021", - publisher = "IOP Publishing", - doi = "10.1088/2632-2153/abec22", - url = "https://doi.org/10.1088/2632-2153/abec22" +@article{ni2017sensitivity, + author = "Ni, Angxiu and Wang, Qiqi", + title = "{Sensitivity analysis on chaotic dynamical systems by Non-Intrusive Least Squares Shadowing (NILSS)}", + journal = "Journal of Computational Physics", + volume = "347", + pages = "56--77", + year = "2017", + publisher = "Elsevier", + doi = "https://doi.org/10.1016/j.jcp.2017.06.033" } -@article{Vallis:2016kv, - author = "Vallis, Geoffrey K", - year = "2016", - rating = "0", - title = "{Geophysical fluid dynamics: whence, whither and why?}", - journal = "Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences", - doi = "10.1098/rspa.2016.0140", - url = "http://rspa.royalsocietypublishing.org/lookup/doi/10.1098/rspa.2016.0140", - pages = "20160140 -- 23", - number = "2192", - volume = "472", - keywords = "", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2016/2016-Vallis-Proceedings\%20of\%20the\%20Royal\%20Society\%20of\%20London.\%20Series\%20A.\%20Mathematical\%20and\%20Physical\%20Sciences.pdf" +@article{blonigan2017adjoint, + author = "Blonigan, Patrick J", + title = "Adjoint sensitivity analysis of chaotic dynamical systems with non-intrusive least squares shadowing", + journal = "Journal of Computational Physics", + volume = "348", + pages = "803--826", + year = "2017", + publisher = "Elsevier", + doi = "https://doi.org/10.1016/j.jcp.2017.08.002" } -@article{Errico_1997, - author = "Errico, Ronald M.", - title = "What Is an Adjoint Model?", - volume = "78", - ISSN = "0003-0007", - DOI = "10.1175/1520-0477(1997)078<2577:wiaam>2.0.co;2", - number = "11", - journal = "Bulletin of the American Meteorological Society", - year = "1997", - pages = "2577–2591" +@article{blonigan2018multiple, + author = "Blonigan, Patrick J and Wang, Qiqi", + title = "Multiple shooting shadowing for sensitivity analysis of chaotic dynamical systems", + journal = "Journal of Computational Physics", + volume = "354", + pages = "447--475", + year = "2018", + publisher = "Elsevier", + doi = "https://doi.org/10.1016/j.jcp.2017.10.032" } -@article{Talagrand.1987, - author = "Talagrand, Olivier and Courtier, Philippe", - year = "1987", - title = "{Variational Assimilation of Meteorological Observations With the Adjoint Vorticity Equation. I: Theory}", - journal = "Quarterly Journal of the Royal Meteorological Society", - issn = "1477-870X", - doi = "10.1002/qj.49711347812", - abstract = "{The following variational approach is taken to the problem of assimilation of meteorological observations: find the solution of the assimilating model which minimizes a given scalar function measuring the ‘distance’ between a model solution and the available observations. It is shown how the ‘adjoint equations’ of the model can be used to compute explicitly the ‘gradient’ of the distance function with respect to the model's initial conditions. the computation of one gradient requires one forward integration of the full model equations over the time interval on which the observations are available, followed by one backward integration of the adjoint equations. Successive gradients thus computed are introduced into a descent algorithm in order to determine the initial conditions which define the minimizing model solution. The theory is applied to the vorticity equation. Successful numerical experiments performed on a Haurwitz wave are described.}", - pages = "1311--1328", - number = "478", - volume = "113", - local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/Talagrand-Variational\%20Assimilation\%20of\%20Meteorological\%20Observations\%20With\%20the\%20Adjoint\%20Vorticity\%20Equation.\%20I-\%20Theory-1987-Quarterly\%20Journal\%20of\%20the\%20Royal\%20Meteorological\%20Society.pdf" +@article{ni2019adjoint, + author = "Ni, Angxiu and Talnikar, Chaitanya", + title = "{Adjoint sensitivity analysis on chaotic dynamical systems by Non-Intrusive Least Squares Adjoint Shadowing (NILSAS)}", + journal = "Journal of Computational Physics", + volume = "395", + pages = "690--709", + year = "2019", + publisher = "Elsevier", + doi = "https://doi.org/10.1016/j.jcp.2019.06.035" } -@article{Courtier.1987, - author = "Courtier, Philippe and Talagrand, Olivier", - year = "1987", - title = "{Variational Assimilation of Meteorological Observations With the Adjoint Vorticity Equation. Ii: Numerical Results}", - journal = "Quarterly Journal of the Royal Meteorological Society", - issn = "0035-9009", - doi = "10.1002/qj.49711347813", - abstract = "{The adjoint variational approach to data assimilation described in the first part of this paper is used, with the same vorticity equation model, to assimilate northern hemisphere radiosonde observations of wind and geopotential distributed over a 24‐hour period. Except over the eastern Pacific Ocean, where no observations are available, the variational assimilation reconstructs all structures of the flow resolvable by the model to an accuracy of about 30 m for geopotential heights and 8 m s−1 for wind vectors. A particular structure, the Aleutian depression, is reconstructed even though it was not covered by the available observations. The assimilation produces unrealistic small‐scale noise which can be reduced by adding an appropriate smoothing term to the distance function minimized in the variational process. Detailed study of the minimization strongly suggests that the distance function varies quadratically with respect to the model's initial conditions. This implies that the tangent linear equation of the model suffices to describe the 24‐hour evolution of the forecast error.}", - pages = "1329--1347", - number = "478", - volume = "113", - local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/Courtier-Variational\%20Assimilation\%20of\%20Meteorological\%20Observations\%20With\%20the\%20Adjoint\%20Vorticity\%20Equation.\%20Ii-\%20Numerical\%20Results-1987-Quarterly\%20Journal\%20of\%20the\%20Royal\%20Meteorological\%20Society.pdf" +@article{ni2019sensitivity, + author = "Ni, Angxiu and Wang, Qiqi and Fernandez, Pablo and Talnikar, Chaitanya", + title = "{Sensitivity analysis on chaotic dynamical systems by finite difference non-intrusive least squares shadowing (FD-NILSS)}", + journal = "Journal of Computational Physics", + volume = "394", + pages = "615--631", + year = "2019", + publisher = "Elsevier", + doi = "https://doi.org/10.1016/j.jcp.2019.06.004" } -@article{Dimet.2002, - author = "Dimet, Francois-Xavier Le and Navon, I. M. and Daescu, Dacian N.", - year = "2002", - rating = "0", - title = "{Second-Order Information in Data Assimilation*}", - journal = "Monthly Weather Review", - issn = "0027-0644", - doi = "10.1175/1520-0493(2002)130<0629:soiida>2.0.co;2", - url = "http://journals.ametsoc.org/doi/abs/10.1175/1520-0493\\%282002\\%29130\\%3C0629\\%3ASOIIDA\\%3E2.0.CO\\%3B2", - abstract = "{In variational data assimilation (VDA) for meteorological and/or oceanic models, the assimilated fields are deduced by combining the model and the gradient of a cost functional measuring discrepancy between model solution and observation, via a first-order optimality system. However, existence and uniqueness of the VDA problem along with convergence of the algorithms for its implementation depend on the convexity of the cost function. Properties of local convexity can be deduced by studying the Hessian of the cost function in the vicinity of the optimum. This shows the necessity of second-order information to ensure a unique solution to the VDA problem. In this paper a comprehensive review of issues related to second-order analysis of the problem of VDA is presented along with many important issues closely connected to it. In particular issues of existence, uniqueness, and regularization through second-order properties are examined. The focus then shifts to second-order information related to statistical properties and to issues related to preconditioning and optimization methods and second-order VDA analysis. Predictability and its relation to the structure of the Hessian of the cost functional is then discussed along with issues of sensitivity analysis in the presence of data being assimilated. Computational complexity issues are also addressed and discussed. Automatic differentiation issues related to second-order information are also discussed along with the computational complexity of deriving the second-order adjoint. Finally an application aimed at illustrating the use of automatic differentiation for deriving the second-order adjoint as well as the Hessian/vector product applied to minimizing a cost functional of a meteorological problem using the truncated-Newton method is presented. Results verifying numerically the computational cost of deriving the second-order adjoint as well as results related to the spectrum of the Hessian of the cost functional are displayed and discussed.}", - pages = "629--648", - number = "3", - volume = "130", - keywords = "", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2002/2002-Dimet-Monthly\%20Weather\%20Review.pdf" +@article{chandramoorthy2022efficient, + author = "Chandramoorthy, Nisha and Wang, Qiqi", + title = "Efficient computation of linear response of chaotic attractors with one-dimensional unstable manifolds", + journal = "SIAM Journal on Applied Dynamical Systems", + volume = "21", + number = "2", + pages = "735--781", + year = "2022", + publisher = "SIAM", + doi = "https://doi.org/10.1137/21M1405599" } -@article{Rabier.1992, - author = "Rabier, Florence and Courtier, Philippe", - year = "1992", - rating = "0", - title = "{Four‐Dimensional Assimilation In the Presence of Baroclinic Instability}", - journal = "Quarterly Journal of the Royal Meteorological Society", - doi = "10.1002/qj.49711850604", - url = "https://rmets.onlinelibrary.wiley.com/doi/full/10.1002/qj.49711850604", - abstract = "{Current operational assimilation methods have revealed deficiencies in cases of strong baroclinic development. Baroclinic conditions are therefore appropriate for evaluating the potential for improve...}", - pages = "649 -- 672", - number = "506", - volume = "118", - keywords = "", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/1992/1992-Rabier-Quarterly\%20Journal\%20of\%20the\%20Royal\%20Meteorological\%20Society.pdf" +@article{ni2020fast, + author = "Ni, Angxiu", + title = "Fast linear response algorithm for differentiating chaos", + journal = "arXiv preprint arXiv:2009.00595", + year = "2020", + doi = "https://arxiv.org/abs/2009.00595v5" } @article{ruelle1997differentiation, @@ -3181,20 +3109,16 @@ @article{Bockhorn.2020 local-url = "file://localhost/Users/heimbach/Documents/Papers\%20Library/siam\_bockhorn\_etal\_2020\_checkpointing\_approaches\_adjoints.pdf" } -@article{Thacker:1989jf, - author = "Thacker, William Carlisle", - year = "1989", - rating = "0", - title = "{The role of the Hessian matrix in fitting models to measurements}", - journal = "Journal of Geophysical Research: Oceans (1978–2012)", - doi = "10.1029/jc094ic05p06177", - url = "http://doi.wiley.com/10.1029/JC094iC05p06177", - abstract = "{A numerical model can be fit to data by minimizing a positive quadratic function of the differences between the data and their model counterparts. The rate at which algorithms for computing the best fit to data converge depends on the size of the condition number and ...}", - pages = "6177 -- 6196", - number = "C5", - volume = "94", - keywords = "", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/1989/1989-Thacker-Journal\%20of\%20Geophysical\%20Research-\%20Oceans\%20(1978–2012).pdf" +@article{Checkpoiting_2023, + author = "Schanen, Michel and Narayanan, Sri Hari Krishna and Williamson, Sarah and Churavy, Valentin and Moses, William S. and Paehler, Ludger", + editor = "Miky{\v{s}}ka, Ji{\v{r}}{\'i} and de Mulatier, Cl{\'e}lia and Paszynski, Maciej and Krzhizhanovskaya, Valeria V. and Dongarra, Jack J. and Sloot, Peter M.A.", + title = "Transparent Checkpointing for Automatic Differentiation of Program Loops Through Expression Transformations", + booktitle = "Computational Science -- ICCS 2023", + year = "2023", + publisher = "Springer Nature Switzerland", + address = "Cham", + pages = "483--497", + isbn = "978-3-031-36024-4" } @article{Eberhard_Bischof_1996, @@ -3289,36 +3213,26 @@ @article{Huang_Smith_Henry_Geijn_2016 pages = "690–701" } -@article{Zanna:2012dw, - author = "Zanna, L and Heimbach, P and Moore, A M and Tziperman, E", - year = "2012", - rating = "0", - title = "{Upper-ocean singular vectors of the North Atlantic climate with implications for linear predictability and variability}", - journal = "Quarterly Journal of the Royal Meteorological Society", - doi = "10.1002/qj.937", - url = "http://doi.wiley.com/10.1002/qj.937", - pages = "500 -- 513", - number = "663", - volume = "138", - keywords = "", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2012/2012-Zanna-Quarterly\%20Journal\%20of\%20the\%20Royal\%20Meteorological\%20Society.pdf" +@article{Zhu_Xu_Darve_Beroza_2021, + author = "Zhu, Weiqiang and Xu, Kailai and Darve, Eric and Beroza, Gregory C.", + title = "A general approach to seismic inversion with automatic differentiation", + volume = "151", + ISSN = "0098-3004", + DOI = "10.1016/j.cageo.2021.104751", + journal = "Computers \& Geosciences", + year = "2021", + pages = "104751" } -@article{Stammer.2002, - author = "Stammer, D. and Wunsch, C. and Giering, R. and Eckert, C. and Heimbach, P. and Marotzke, J. and Adcroft, A. and Hill, C. N. and Marshall, J.", - year = "2002", - rating = "0", - title = "{Global ocean circulation during 1992–1997, estimated from ocean observations and a general circulation model}", - journal = "Journal of Geophysical Research: Oceans", - issn = "0148-0227", - doi = "10.1029/2001jc000888", - url = "http://doi.wiley.com/10.1029/2001JC000888", - abstract = "{A three‐dimensional oceanic state is estimated for the period 1992–1997 as it results from combining large‐scale ocean data sets with a general circulation model. At the cost of increased computational load, the estimation (assimilation) method is chosen specifically so that the resulting state estimate is consistent with the model equations, having no artificial sources or sinks. To bring the model into close agreement with observations, its initial temperature and salinity conditions are permitted to change, as are the time‐dependent surface fluxes of momentum, heat and freshwater. Resulting changes of these “control vectors” are largely consistent with accepted uncertainties in the hydrographic climatology and meteorological analyses. The assimilation procedure is able to correct for many of the traditional shortcomings of the flow field by changing the surface boundary conditions. Changes in the resulting flow field are predominantly on the gyre scale and affect many features that are often poorly simulated in traditional numerical simulations, such as the strengths of the Gulf Stream and its extension, the Azores Current and the anticyclonic circulation associated with the Labrador Sea. Tests of the results and their consistency with prior error assumptions show that the constrained model has moved considerably closer to the observations imposed as constraints, but has also moved closer to independent data from the World Ocean Circulation Experiment not used in the assimilation procedure. In some regions where the comparisons remain indeterminate, not enough ocean observations are available, and it is difficult to ascribe the residuals to either the model or the observations. Although problems remain, a useful first solution to the global time‐dependent ocean state estimation problem has been found. The estimates will continue to improve through the evolution of numerical models, computer power increases, more data, and more efficient estimation methods.}", - pages = "1--1-1-27", - number = "C9", - volume = "107", - keywords = "", - local-url = "file://localhost/Users/heimbach/Documents/Library-Papers-ReadCube/2002/2002-Stammer-Journal\%20of\%20Geophysical\%20Research.pdf" +@article{li2020coupled, + author = "Li, Dongzhuo and Xu, Kailai and Harris, Jerry M and Darve, Eric", + title = "Coupled time-lapse full-waveform inversion for subsurface flow problems using intrusive automatic differentiation", + journal = "Water Resources Research", + volume = "56", + number = "8", + pages = "e2019WR027032", + year = "2020", + publisher = "Wiley Online Library" } @article{Alexe_Sandu_2009, diff --git a/tex/bibs/bibliography-facu.bib b/tex/bibs/bibliography-facu.bib index 428620a..9f0024e 100644 --- a/tex/bibs/bibliography-facu.bib +++ b/tex/bibs/bibliography-facu.bib @@ -114,7 +114,8 @@ @article{RevelsLubinPapamarkou2016 @article{ruder2016overview-gradient-descent, title={An overview of gradient descent optimization algorithms}, author={Ruder, Sebastian}, - journal={arXiv preprint arXiv:1609.04747}, + journal={arXiv}, + doi={10.48550/arXiv.1609.04747}, year={2016} } diff --git a/tex/main.tex b/tex/main.tex index 1f922fd..3431bcf 100644 --- a/tex/main.tex +++ b/tex/main.tex @@ -14,7 +14,6 @@ \titlespacing*{\paragraph} {0pt}{3.25ex plus 1ex minus .2ex}{1.5ex plus .2ex} - % IMPORTANT NOTE: % All the bib files are centralized here in bibliography.bib, which is % automatically created by compiling all the required cites in the references contained inside ./bibs/