% =============================================================================
% Phasic Supplementary Online Material — Bibliography
% =============================================================================

% ---------------------------------------------------------------------------
% Core phasic references
% ---------------------------------------------------------------------------

@article{roikjer2022,
  author    = {R{\o}ikjer, Thomas and Hobolth, Asger and Munch, Kasper},
  title     = {Graph-based algorithms for phase-type distributions},
  journal   = {Statistics and Computing},
  volume    = {32},
  number    = {6},
  pages     = {85},
  year      = {2022},
  doi       = {10.1007/s11222-022-10155-6},
  publisher = {Springer}
}

@book{bladt2017,
  author    = {Bladt, Mogens and Nielsen, Bo Friis},
  title     = {Matrix-Exponential Distributions in Applied Probability},
  publisher = {Springer},
  series    = {Probability Theory and Stochastic Modelling},
  volume    = {81},
  year      = {2017},
  doi       = {10.1007/978-1-4939-7049-0}
}

@book{neuts1981,
  author    = {Neuts, Marcel F.},
  title     = {Matrix-Geometric Solutions in Stochastic Models: An Algorithmic Approach},
  publisher = {Johns Hopkins University Press},
  address   = {Baltimore},
  year      = {1981}
}

@article{hobolth2024,
  author    = {Hobolth, Asger and Rivas-Gonz{\'a}lez, Iker and Bladt, Mogens and Futschik, Andreas},
  title     = {Phase-type distributions in mathematical population genetics: An emerging framework},
  journal   = {Theoretical Population Biology},
  volume    = {157},
  pages     = {14--32},
  year      = {2024},
  doi       = {10.1016/j.tpb.2024.03.001},
  publisher = {Elsevier}
}

% ---------------------------------------------------------------------------
% Graph algorithms
% ---------------------------------------------------------------------------

@article{tarjan1972,
  author    = {Tarjan, Robert},
  title     = {Depth-first search and linear graph algorithms},
  journal   = {SIAM Journal on Computing},
  volume    = {1},
  number    = {2},
  pages     = {146--160},
  year      = {1972},
  doi       = {10.1137/0201010},
  publisher = {SIAM}
}

@article{kahn1962,
  author    = {Kahn, Arthur B.},
  title     = {Topological sorting of large networks},
  journal   = {Communications of the ACM},
  volume    = {5},
  number    = {11},
  pages     = {558--562},
  year      = {1962},
  doi       = {10.1145/368996.369025},
  publisher = {ACM}
}

@article{adelsonvelsky1962,
  author    = {Adelson-Velsky, Georgy M. and Landis, Evgenii M.},
  title     = {An algorithm for the organization of information},
  journal   = {Soviet Mathematics Doklady},
  volume    = {3},
  pages     = {1259--1263},
  year      = {1962}
}

@article{weisfeiler1968,
  author    = {Weisfeiler, Boris and Leman, Andrei},
  title     = {A reduction of a graph to a canonical form and an algebra arising during this reduction},
  journal   = {Nauchno-Technicheskaya Informatsia},
  volume    = {2},
  number    = {9},
  pages     = {12--16},
  year      = {1968}
}

% ---------------------------------------------------------------------------
% Numerical methods
% ---------------------------------------------------------------------------

@article{kahan1965,
  author    = {Kahan, William},
  title     = {Pracniques: Further remarks on reducing truncation errors},
  journal   = {Communications of the ACM},
  volume    = {8},
  number    = {1},
  pages     = {40},
  year      = {1965},
  doi       = {10.1145/363707.363723},
  publisher = {ACM}
}

@book{higham2002,
  author    = {Higham, Nicholas J.},
  title     = {Accuracy and Stability of Numerical Algorithms},
  edition   = {2nd},
  publisher = {SIAM},
  address   = {Philadelphia},
  year      = {2002},
  doi       = {10.1137/1.9780898718027}
}

@article{vanloan1978,
  author    = {Van Loan, Charles F.},
  title     = {Computing integrals involving the matrix exponential},
  journal   = {IEEE Transactions on Automatic Control},
  volume    = {23},
  number    = {3},
  pages     = {395--404},
  year      = {1978},
  doi       = {10.1109/TAC.1978.1101743},
  publisher = {IEEE}
}

% ---------------------------------------------------------------------------
% Markov chains and phase-type theory
% ---------------------------------------------------------------------------

@book{norris1997,
  author    = {Norris, James R.},
  title     = {Markov Chains},
  publisher = {Cambridge University Press},
  series    = {Cambridge Series in Statistical and Probabilistic Mathematics},
  year      = {1997},
  doi       = {10.1017/CBO9780511810633}
}

@article{jensen1953,
  author    = {Jensen, Arne},
  title     = {Markoff chains as an aid in the study of {Markoff} processes},
  journal   = {Skandinavisk Aktuarietidskrift},
  volume    = {36},
  pages     = {87--91},
  year      = {1953},
  doi       = {10.1080/03461238.1953.10419459}
}

@article{kingman1982,
  author    = {Kingman, John F. C.},
  title     = {The coalescent},
  journal   = {Stochastic Processes and their Applications},
  volume    = {13},
  number    = {3},
  pages     = {235--248},
  year      = {1982},
  doi       = {10.1016/0304-4149(82)90011-4},
  publisher = {Elsevier}
}

@article{kulkarni1989,
  author    = {Kulkarni, Vidyadhar G.},
  title     = {A new class of multivariate phase type distributions},
  journal   = {Operations Research},
  volume    = {37},
  number    = {1},
  pages     = {151--158},
  year      = {1989},
  doi       = {10.1287/opre.37.1.151},
  publisher = {INFORMS}
}

% ---------------------------------------------------------------------------
% Inference: SVGD, MCMC, optimization
% ---------------------------------------------------------------------------

@inproceedings{liu2016svgd,
  author    = {Liu, Qiang and Wang, Dilin},
  title     = {Stein Variational Gradient Descent: A General Purpose {Bayesian} Inference Algorithm},
  booktitle = {Advances in Neural Information Processing Systems},
  volume    = {29},
  year      = {2016},
  pages     = {2378--2386},
  publisher = {Curran Associates}
}

@inproceedings{stein1972,
  author    = {Stein, Charles},
  title     = {A bound for the error in the normal approximation to the distribution of a sum of dependent random variables},
  booktitle = {Proceedings of the Sixth Berkeley Symposium on Mathematical Statistics and Probability},
  volume    = {2},
  pages     = {583--602},
  year      = {1972},
  publisher = {University of California Press}
}

@inproceedings{kingma2015adam,
  author    = {Kingma, Diederik P. and Ba, Jimmy},
  title     = {Adam: A Method for Stochastic Optimization},
  booktitle = {Proceedings of the 3rd International Conference on Learning Representations (ICLR)},
  year      = {2015}
}

@article{gelman2006,
  author    = {Gelman, Andrew},
  title     = {Prior distributions for variance parameters in hierarchical models},
  journal   = {Bayesian Analysis},
  volume    = {1},
  number    = {3},
  pages     = {515--534},
  year      = {2006},
  doi       = {10.1214/06-BA117A},
  publisher = {International Society for Bayesian Analysis}
}

@article{haario2001,
  author    = {Haario, Heikki and Saksman, Eero and Tamminen, Johanna},
  title     = {An adaptive {Metropolis} algorithm},
  journal   = {Bernoulli},
  volume    = {7},
  number    = {2},
  pages     = {223--242},
  year      = {2001},
  doi       = {10.2307/3318737},
  publisher = {Bernoulli Society}
}

@article{roberts1997,
  author    = {Roberts, Gareth O. and Gelman, Andrew and Gilks, Walter R.},
  title     = {Weak convergence and optimal scaling of random walk {Metropolis} algorithms},
  journal   = {Annals of Applied Probability},
  volume    = {7},
  number    = {1},
  pages     = {110--120},
  year      = {1997},
  doi       = {10.1214/aoap/1034625254}
}

@article{robbins1951,
  author    = {Robbins, Herbert and Monro, Sutton},
  title     = {A stochastic approximation method},
  journal   = {Annals of Mathematical Statistics},
  volume    = {22},
  number    = {3},
  pages     = {400--407},
  year      = {1951},
  doi       = {10.1214/aoms/1177729586}
}

@article{roberts2007,
  author    = {Roberts, Gareth O. and Rosenthal, Jeffrey S.},
  title     = {Coupling and ergodicity of adaptive {Markov} chain {Monte Carlo} algorithms},
  journal   = {Journal of Applied Probability},
  volume    = {44},
  number    = {2},
  pages     = {458--475},
  year      = {2007},
  doi       = {10.1239/jap/1183667414}
}

@article{gelman1992,
  author    = {Gelman, Andrew and Rubin, Donald B.},
  title     = {Inference from iterative simulation using multiple sequences},
  journal   = {Statistical Science},
  volume    = {7},
  number    = {4},
  pages     = {457--472},
  year      = {1992},
  doi       = {10.1214/ss/1177011136}
}

@incollection{neal2011,
  author    = {Neal, Radford M.},
  title     = {{MCMC} using {Hamiltonian} dynamics},
  booktitle = {Handbook of {Markov} Chain {Monte Carlo}},
  editor    = {Brooks, Steve and Gelman, Andrew and Jones, Galin L. and Meng, Xiao-Li},
  publisher = {Chapman and Hall/CRC},
  chapter   = {5},
  pages     = {113--162},
  year      = {2011}
}

@article{metropolis1953,
  author    = {Metropolis, Nicholas and Rosenbluth, Arianna W. and Rosenbluth, Marshall N. and Teller, Augusta H. and Teller, Edward},
  title     = {Equation of state calculations by fast computing machines},
  journal   = {Journal of Chemical Physics},
  volume    = {21},
  number    = {6},
  pages     = {1087--1092},
  year      = {1953},
  doi       = {10.1063/1.1699114}
}

@article{hastings1970,
  author    = {Hastings, W. Keith},
  title     = {{Monte Carlo} sampling methods using {Markov} chains and their applications},
  journal   = {Biometrika},
  volume    = {57},
  number    = {1},
  pages     = {97--109},
  year      = {1970},
  doi       = {10.1093/biomet/57.1.97}
}

% ---------------------------------------------------------------------------
% BFFG / importance sampling / guided proposals
% ---------------------------------------------------------------------------

@article{schauer2017,
  author    = {Schauer, Moritz and van der Meulen, Frank and van Zanten, Harry},
  title     = {Guided proposals for simulating multi-dimensional diffusion bridges},
  journal   = {Bernoulli},
  volume    = {23},
  number    = {4A},
  pages     = {2917--2950},
  year      = {2017},
  doi       = {10.3150/16-BEJ833}
}

% ---------------------------------------------------------------------------
% Method of moments / estimation theory
% ---------------------------------------------------------------------------

@article{hansen1982,
  author    = {Hansen, Lars Peter},
  title     = {Large sample properties of generalized method of moments estimators},
  journal   = {Econometrica},
  volume    = {50},
  number    = {4},
  pages     = {1029--1054},
  year      = {1982},
  doi       = {10.2307/1912775}
}

@incollection{newey1994,
  author    = {Newey, Whitney K. and McFadden, Daniel},
  title     = {Large sample estimation and hypothesis testing},
  booktitle = {Handbook of Econometrics},
  editor    = {Engle, Robert F. and McFadden, Daniel},
  volume    = {4},
  pages     = {2111--2245},
  year      = {1994},
  publisher = {Elsevier},
  doi       = {10.1016/S1573-4412(05)80005-4}
}

@book{vandervaart1998,
  author    = {{van der Vaart}, Aad W.},
  title     = {Asymptotic Statistics},
  publisher = {Cambridge University Press},
  series    = {Cambridge Series in Statistical and Probabilistic Mathematics},
  year      = {1998},
  doi       = {10.1017/CBO9780511802256}
}

% ---------------------------------------------------------------------------
% Sampling
% ---------------------------------------------------------------------------

@article{gillespie1977,
  author    = {Gillespie, Daniel T.},
  title     = {Exact stochastic simulation of coupled chemical reactions},
  journal   = {Journal of Physical Chemistry},
  volume    = {81},
  number    = {25},
  pages     = {2340--2361},
  year      = {1977},
  doi       = {10.1021/j100540a008}
}

@article{doob1957,
  author    = {Doob, Joseph L.},
  title     = {Conditional {Brownian} motion and the boundary limits of harmonic functions},
  journal   = {Bulletin de la Soci{\'e}t{\'e} Math{\'e}matique de France},
  volume    = {85},
  pages     = {431--458},
  year      = {1957},
  doi       = {10.24033/bsmf.1494}
}

@book{rogers2000,
  author    = {Rogers, L. C. G. and Williams, David},
  title     = {Diffusions, {Markov} Processes and Martingales},
  volume    = {1: Foundations},
  edition   = {2nd},
  publisher = {Cambridge University Press},
  year      = {2000},
  doi       = {10.1017/CBO9781107590120}
}

% ---------------------------------------------------------------------------
% JAX / automatic differentiation
% ---------------------------------------------------------------------------

@software{bradbury2018jax,
  author    = {Bradbury, James and Frostig, Roy and Hawkins, Peter and Johnson, Matthew James and Leary, Chris and Maclaurin, Dougal and Necula, George and Paszke, Adam and Vander{P}las, Jake and Wanderman-{M}ilne, Skye and Zhang, Qiao},
  title     = {{JAX}: Composable transformations of {Python}+{NumPy} programs},
  url       = {http://github.com/jax-ml/jax},
  version   = {0.3.13},
  year      = {2018}
}

@article{baydin2018,
  author    = {Baydin, Atilim Gunes and Pearlmutter, Barak A. and Radul, Alexey Andreyevich and Siskind, Jeffrey Mark},
  title     = {Automatic differentiation in machine learning: A survey},
  journal   = {Journal of Machine Learning Research},
  volume    = {18},
  number    = {153},
  pages     = {1--43},
  year      = {2018}
}

@book{nocedal2006,
  author    = {Nocedal, Jorge and Wright, Stephen J.},
  title     = {Numerical Optimization},
  edition   = {2nd},
  publisher = {Springer},
  series    = {Springer Series in Operations Research},
  year      = {2006},
  doi       = {10.1007/978-0-387-40065-5}
}

% ---------------------------------------------------------------------------
% Automatic differentiation / trace-based computation
% ---------------------------------------------------------------------------

@book{griewank2008,
  author    = {Griewank, Andreas and Walther, Andrea},
  title     = {Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation},
  edition   = {2nd},
  publisher = {SIAM},
  address   = {Philadelphia},
  year      = {2008},
  doi       = {10.1137/1.9780898717761}
}

% ---------------------------------------------------------------------------
% Sparse matrix theory and graph elimination
% ---------------------------------------------------------------------------

@article{yannakakis1981,
  author    = {Yannakakis, Mihalis},
  title     = {Computing the minimum fill-in is {NP}-complete},
  journal   = {SIAM Journal on Algebraic Discrete Methods},
  volume    = {2},
  number    = {1},
  pages     = {77--79},
  year      = {1981},
  doi       = {10.1137/0602010}
}

@article{george1973,
  author    = {George, Alan},
  title     = {Nested dissection of a regular finite element mesh},
  journal   = {SIAM Journal on Numerical Analysis},
  volume    = {10},
  number    = {2},
  pages     = {345--363},
  year      = {1973},
  doi       = {10.1137/0710032}
}

@article{liptonrosetarjan1979,
  author    = {Lipton, Richard J. and Rose, Donald J. and Tarjan, Robert Endre},
  title     = {Generalized nested dissection},
  journal   = {SIAM Journal on Numerical Analysis},
  volume    = {16},
  number    = {2},
  pages     = {346--358},
  year      = {1979},
  doi       = {10.1137/0716027}
}

@article{liptontarjan1979,
  author    = {Lipton, Richard J. and Tarjan, Robert Endre},
  title     = {A separator theorem for planar graphs},
  journal   = {SIAM Journal on Applied Mathematics},
  volume    = {36},
  number    = {2},
  pages     = {177--189},
  year      = {1979},
  doi       = {10.1137/0136016}
}

@article{rose1970,
  author    = {Rose, Donald J.},
  title     = {Triangulated graphs and the elimination process},
  journal   = {Journal of Mathematical Analysis and Applications},
  volume    = {32},
  pages     = {597--609},
  year      = {1970},
  doi       = {10.1016/0022-247X(70)90282-9}
}

@article{rosetarjan1978,
  author    = {Rose, Donald J. and Tarjan, Robert Endre},
  title     = {Algorithmic aspects of vertex elimination on directed graphs},
  journal   = {SIAM Journal on Applied Mathematics},
  volume    = {34},
  number    = {1},
  pages     = {176--197},
  year      = {1978},
  doi       = {10.1137/0134014}
}

@article{amestoy1996,
  author    = {Amestoy, Patrick R. and Davis, Timothy A. and Duff, Iain S.},
  title     = {An approximate minimum degree ordering algorithm},
  journal   = {SIAM Journal on Matrix Analysis and Applications},
  volume    = {17},
  number    = {4},
  pages     = {886--905},
  year      = {1996},
  doi       = {10.1137/S0895479894278952}
}

@article{tinneywalker1967,
  author    = {Tinney, William F. and Walker, John W.},
  title     = {Direct solutions of sparse network equations by optimally ordered triangular factorization},
  journal   = {Proceedings of the IEEE},
  volume    = {55},
  number    = {11},
  pages     = {1801--1809},
  year      = {1967},
  doi       = {10.1109/PROC.1967.6011}
}

@book{georgeliu1981,
  author    = {George, Alan and Liu, Joseph W. H.},
  title     = {Computer Solution of Large Sparse Positive Definite Systems},
  publisher = {Prentice-Hall},
  address   = {Englewood Cliffs, NJ},
  year      = {1981}
}

@article{hudson1983,
  author    = {Hudson, Richard R.},
  title     = {Properties of a neutral allele model with intragenic recombination},
  journal   = {Theoretical Population Biology},
  volume    = {23},
  number    = {2},
  pages     = {183--201},
  year      = {1983},
  doi       = {10.1016/0040-5809(83)90013-8}
}

@article{wiufhein1999,
  author    = {Wiuf, Carsten and Hein, Jotun},
  title     = {Recombination as a point process along sequences},
  journal   = {Genetics},
  volume    = {153},
  number    = {2},
  pages     = {999--1012},
  year      = {1999},
  doi       = {10.1093/genetics/153.2.999}
}

% ---------------------------------------------------------------------------
% Spatial / hex grids
% ---------------------------------------------------------------------------

@misc{patel2013,
  author       = {Patel, Amit},
  title        = {Hexagonal Grids},
  howpublished = {Red Blob Games},
  year         = {2013},
  url          = {https://www.redblobgames.com/grids/hexagons/}
}

% ---------------------------------------------------------------------------
% Algorithms textbook
% ---------------------------------------------------------------------------

@book{cormen2009,
  author    = {Cormen, Thomas H. and Leiserson, Charles E. and Rivest, Ronald L. and Stein, Clifford},
  title     = {Introduction to Algorithms},
  edition   = {3rd},
  publisher = {MIT Press},
  address   = {Cambridge, MA},
  year      = {2009}
}

% ---------------------------------------------------------------------------
% Cryptographic standards
% ---------------------------------------------------------------------------

@techreport{fips180,
  author      = {{National Institute of Standards and Technology}},
  title       = {Secure Hash Standard ({SHS})},
  institution = {U.S. Department of Commerce},
  number      = {FIPS PUB 180-4},
  year        = {2015},
  doi         = {10.6028/NIST.FIPS.180-4}
}
