% Shared Bibliography for Computational Mechanics Publications
% ============================================================

% === FOUNDATIONAL PAPERS ===

@article{shalizi2001computational,
  author    = {Shalizi, Cosma Rohilla and Crutchfield, James P.},
  title     = {Computational Mechanics: Pattern and Prediction, Structure and Simplicity},
  journal   = {Journal of Statistical Physics},
  volume    = {104},
  number    = {3/4},
  pages     = {817--879},
  year      = {2001},
  doi       = {10.1023/A:1010388907793}
}

@article{crutchfield1989inferring,
  author    = {Crutchfield, James P. and Young, Karl},
  title     = {Inferring Statistical Complexity},
  journal   = {Physical Review Letters},
  volume    = {63},
  number    = {2},
  pages     = {105--108},
  year      = {1989},
  doi       = {10.1103/PhysRevLett.63.105}
}

@article{crutchfield1994calculi,
  author    = {Crutchfield, James P.},
  title     = {The Calculi of Emergence: Computation, Dynamics, and Induction},
  journal   = {Physica D: Nonlinear Phenomena},
  volume    = {75},
  number    = {1-3},
  pages     = {11--54},
  year      = {1994},
  doi       = {10.1016/0167-2789(94)90273-9}
}

@article{crutchfield2012between,
  author    = {Crutchfield, James P.},
  title     = {Between Order and Chaos},
  journal   = {Nature Physics},
  volume    = {8},
  number    = {1},
  pages     = {17--24},
  year      = {2012},
  doi       = {10.1038/nphys2190}
}

% === CSSR ALGORITHM ===

@article{shalizi2004algorithm,
  author    = {Shalizi, Cosma Rohilla and Klinkner, Kristina Lisa},
  title     = {Blind Construction of Optimal Nonlinear Recursive Predictors for Discrete Sequences},
  booktitle = {Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference},
  pages     = {504--511},
  year      = {2004},
  publisher = {AUAI Press}
}

% === SPECTRAL LEARNING ===

@inproceedings{hsu2012spectral,
  author    = {Hsu, Daniel and Kakade, Sham M. and Zhang, Tong},
  title     = {A Spectral Algorithm for Learning Hidden Markov Models},
  booktitle = {Journal of Computer and System Sciences},
  volume    = {78},
  number    = {5},
  pages     = {1460--1480},
  year      = {2012},
  doi       = {10.1016/j.jcss.2011.12.025}
}

@inproceedings{boots2011closing,
  author    = {Boots, Byron and Siddiqi, Sajid M. and Gordon, Geoffrey J.},
  title     = {Closing the Learning-Planning Loop with Predictive State Representations},
  booktitle = {International Journal of Robotics Research},
  volume    = {30},
  number    = {7},
  pages     = {954--966},
  year      = {2011}
}

% === INFORMATION THEORY ===

@article{shannon1948mathematical,
  author    = {Shannon, Claude E.},
  title     = {A Mathematical Theory of Communication},
  journal   = {Bell System Technical Journal},
  volume    = {27},
  number    = {3},
  pages     = {379--423},
  year      = {1948},
  doi       = {10.1002/j.1538-7305.1948.tb01338.x}
}

@book{cover2006elements,
  author    = {Cover, Thomas M. and Thomas, Joy A.},
  title     = {Elements of Information Theory},
  edition   = {2nd},
  publisher = {Wiley-Interscience},
  year      = {2006},
  isbn      = {978-0471241959}
}

% === HIDDEN MARKOV MODELS ===

@article{rabiner1989tutorial,
  author    = {Rabiner, Lawrence R.},
  title     = {A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition},
  journal   = {Proceedings of the IEEE},
  volume    = {77},
  number    = {2},
  pages     = {257--286},
  year      = {1989},
  doi       = {10.1109/5.18626}
}

@book{bishop2006pattern,
  author    = {Bishop, Christopher M.},
  title     = {Pattern Recognition and Machine Learning},
  publisher = {Springer},
  year      = {2006},
  isbn      = {978-0387310732}
}

% === COMPLEXITY & CHAOS ===

@book{strogatz2015nonlinear,
  author    = {Strogatz, Steven H.},
  title     = {Nonlinear Dynamics and Chaos},
  edition   = {2nd},
  publisher = {Westview Press},
  year      = {2015},
  isbn      = {978-0813349107}
}

@article{grassberger1986toward,
  author    = {Grassberger, Peter},
  title     = {Toward a Quantitative Theory of Self-Generated Complexity},
  journal   = {International Journal of Theoretical Physics},
  volume    = {25},
  number    = {9},
  pages     = {907--938},
  year      = {1986},
  doi       = {10.1007/BF00668821}
}

% === RELATED FRAMEWORKS ===

@article{rissanen1978modeling,
  author    = {Rissanen, Jorma},
  title     = {Modeling by Shortest Data Description},
  journal   = {Automatica},
  volume    = {14},
  number    = {5},
  pages     = {465--471},
  year      = {1978},
  doi       = {10.1016/0005-1098(78)90005-5}
}

@article{kolmogorov1965three,
  author    = {Kolmogorov, Andrei N.},
  title     = {Three Approaches to the Quantitative Definition of Information},
  journal   = {Problems of Information Transmission},
  volume    = {1},
  number    = {1},
  pages     = {1--7},
  year      = {1965}
}

% === APPLICATIONS ===

@article{james2011anatomy,
  author    = {James, Ryan G. and Ellison, Christopher J. and Crutchfield, James P.},
  title     = {Anatomy of a Bit: Information in a Time Series Observation},
  journal   = {Chaos},
  volume    = {21},
  number    = {3},
  pages     = {037109},
  year      = {2011},
  doi       = {10.1063/1.3637494}
}

@article{marzen2015informational,
  author    = {Marzen, Sarah E. and Crutchfield, James P.},
  title     = {Informational and Causal Architecture of Discrete-Time Renewal Processes},
  journal   = {Entropy},
  volume    = {17},
  number    = {7},
  pages     = {4891--4917},
  year      = {2015},
  doi       = {10.3390/e17074891}
}

% === QUANTUM EXTENSIONS ===

@article{gu2012quantum,
  author    = {Gu, Mile and Wiesner, Karoline and Rieper, Elisabeth and Vedral, Vlatko},
  title     = {Quantum Mechanics Can Reduce the Complexity of Classical Models},
  journal   = {Nature Communications},
  volume    = {3},
  pages     = {762},
  year      = {2012},
  doi       = {10.1038/ncomms1761}
}

@article{thompson2018causal,
  author    = {Thompson, Jayne and Garner, Andrew J. P. and Mahoney, John R. and Crutchfield, James P. and Vedral, Vlatko and Gu, Mile},
  title     = {Causal Asymmetry in a Quantum World},
  journal   = {Physical Review X},
  volume    = {8},
  number    = {3},
  pages     = {031013},
  year      = {2018},
  doi       = {10.1103/PhysRevX.8.031013}
}

% === BAYESIAN INFERENCE ===

@article{strelioff2014bayesian,
  author    = {Strelioff, Christopher C. and Crutchfield, James P.},
  title     = {Bayesian Structural Inference for Hidden Processes},
  journal   = {Physical Review E},
  volume    = {89},
  number    = {4},
  pages     = {042119},
  year      = {2014},
  doi       = {10.1103/PhysRevE.89.042119}
}

% === SOFTWARE ===

@software{emic2026,
  author    = {{emic developers}},
  title     = {emic: A Python Library for Computational Mechanics},
  version   = {0.1.1},
  year      = {2026},
  url       = {https://github.com/johnazariah/emic}
}

% === CYBERNETICS ===

@book{ashby1956introduction,
  author    = {Ashby, W. Ross},
  title     = {An Introduction to Cybernetics},
  publisher = {Chapman \& Hall},
  year      = {1956},
  address   = {London}
}
