Computational Mechanics Publications

Jim Crutchfield

Computational Mechanics

Dynamics of Learning

Evolving Cellular Automata

Evolutionary Dynamics

About

arXiv.org

General

Spatially-Extended Systems

Stochastic and Quantum Computation

Earlier Related Work

Dissertations

General

A. M. Jurgens and N. Brodu, “Inferring Kernel ε-Machines: Discovering Structure in Complex Systems”, arxiv.org:2410.01076.
[Abstract] [pdf]
arxiv.org:2410.01076. doi:.
K. W. Tang, K. J. Ray, and J. P. Crutchfield, “Nonequilibrium Thermodynamics of a Superconducting Szilard Engine”, arxiv.org:2407.20418.
[Abstract] [pdf]
arxiv.org:2407.20418. doi:.
C. Pratt, K. J. Ray, and J. P. Crutchfield, “Controlled Erasure as a Building Block for Universal Thermodynamically-Robust Superconducting Computing”, arxiv.org:2406.12153.
[Abstract] [pdf]
arxiv.org:2406.12153. doi:.
J. Lyu, K. J. Ray, and J. P. Crutchfield, “Entropy Production by Underdamped Langevin Dynamics”, arxiv.org:2405.12305.
[Abstract] [pdf]
arxiv.org:2405.12305. doi:.
A. B. Boyd, J. P. Crutchfield, M. Gu, and F. C. Binder, “Thermodynamic Overfitting and Generalization: Energetic Limits on Predictive Complexity”, arxiv.org:2402.16995.
[Abstract] [pdf]
arxiv.org:2402.16995. doi:.
J. P. Crutchfield, D. D. Dunn, and A. M. Jurgens, “Whales in Space: Experiencing Aquatic Animals in Their Natural Place with the Hydroambiphone” bioRxiv.org (2023) 2023.12.27.573441.
[Abstract] [pdf]
arxiv.org:2312.16662. doi:10.1101/2023.12.27.573441.
A. T. Rupe and J. P. Crutchfield, “On Principles of Emergent Organization”, Physics Reports 1071 (2024) 1-47.
[Abstract] [pdf]
arxiv.org:2311.13749. doi:10.1016/j.physrep.2024.04.001. [Podcast]
K. J. Ray, A. B. Boyd, G. Guarneiri, and J. P. Crutchfield, “The Thermodynamic Uncertainty Theorem”, Physical Review E 108:5 (2023) 054126.
[Abstract] [pdf]
arxiv.org:2210.00914. doi:10.1103/PhysRevE.108.054126.
C. Z. Pratt, K. J. Ray, and J. P. Crutchfield, “Extracting Equations of Motion from Superconducting Circuits” (2023).
[Abstract] [pdf]
arxiv.org:2307.01926. doi:.
J. Lyu, A. B. Boyd, and J. P. Crutchfield, “Efficient Quantum Work Reservoirs at the Nanoscale” Physical Review A 110:1 (2024) 012225.
[Abstract] [pdf]
arxiv.org:2305.17815. doi:10.1103/PhysRevA.110.012225.
A. Rupe and J. P. Crutchfield, “Physics-Informed Representation Learning for Emergent Organization in Complex Dynamical Systems” (2023).
[Abstract] [pdf]
arxiv.org:2304.12586. doi:.
A. Touil, F. Anza, S. Deffner, and J. P. Crutchfield, “Branching States as The Emergent Structure of a Quantum Universe”, Quantum (2024) in press.
[Abstract] [pdf]
arxiv.org:2208.05497. doi:.
S. E. Marzen, P. M. Riechers, and J. P. Crutchfield, “Complexity-calibrated Benchmarks for Machine Learning Reveal When Next-Generation Reservoir Computer Predictions Succeed and Mislead” Scientific Reports 14 (2024) 8727.
[Abstract] [pdf]
arxiv.org:2303.14553. doi:10.1038/s41598-024-58814-0.
D. Gier and J. P. Crutchfield, “Intrinsic and Measured Information in Separable Quantum Processes” .
[Abstract] [pdf]
arxiv.org:2303.00162. doi:.

J. P. Crutchfield and A. M. Jurgens, “Whale Casting: Remote mobile streaming humpback whale vocalizations to the world” .
[Abstract] [pdf]
arxiv.org:2212.02462. doi:.

M. T. Semaan and J. P. Crutchfield, “First and Second Laws of Information Processing by Nonequilibrium Dynamical States”, Physical Review E 107 (2023) 054132.
[Abstract] [pdf]
arxiv.org:2211.05849 [cond-mat.stat-mech]. doi:10.1103/PhysRevE.107.054132.
J. B. Rundle, J. Yazbeck, A. Donnellan, G. Fox, L. G. Ludwig, M. Heflin, and J. Crutchfield, “Optimizing Earthquake Nowcasting With Machine Learning: The Role of Strain Hardening in the Earthquake Cycle”, Earth and Space Science 9 (2022) e2022EA002343.
doi:10.1029/2022EA002343.
J. P. Crutchfield and A. M. Jurgens, “Twainspotting: Identity Revealed During a Simple, but Extended Conversation with a Humpback Whale”, bioRxiv.org 2023.02.12.528197.
[Abstract] [pdf]
2023.02.12.528197. doi:10.1101/2023.02.12.528197.
J. P. Crutchfield, A. M. Jurgens, J. M. Straley, and T. Cheeseman, “A Whale With A History: Sighting Twain The Humpback Over Three Decades”, bioRxiv.org 2022.10.07.511372.
[Abstract] [pdf]
2022.10.07.511372. doi:10.1101/2022.10.07.511372.
G. Wimsatt, A. B. Boyd, and J. P. Crutchfield, “Trajectory Class Fluctuation Theorem”, (2022).
[Abstract] [pdf]
arxiv.org:2207.03612 [cond-mat.stat-mech]. doi:.
A. Rupe and J. P. Crutchfield, “Algebraic Theory of Patterns as Generalized Symmetries”, Symmetry 14:8 (2022) 1636.
[Abstract] [pdf]
arxiv.org:2206.15050 [cond-mat.stat-mech]. doi:10.3390/sym14081636.
S. P. Loomis and J. P. Crutchfield, “Exploring Predictive States via Cantor Embeddings and Wasserstein Distance”, Chaos 32:12 (2022) 123115.
[Abstract] [pdf]
2206.04198 [cond-mat.stat-mech]. doi:10.1063/5.0102603.
A. Venegas-Li and J. P. Crutchfield, “Optimality and Complexity in Measured Quantum-State Stochastic Processes”, Journal of Statistical Physics 190 (2023) 106.
[Abstract] [pdf]
arxiv.org:2205.03958 [quant-ph]. doi:10.1007/s10955-023-03112-8.
A. Rupe and V. V. Vesselinov and J. P. Crutchfield, “Nonequilibrium Statistical Mechanics and Optimal Prediction of Partially-Observed Complex Systems”, New Journal of Physics 24 (2022) 103033.
[Abstract] [pdf]
arxiv.org:2203.16048 [cond-mat.stat-mech]. doi:10.1088/1367-2630/ac95b7.
M. Semaan and J. P. Crutchfield, “Homeostatic and Adaptive Energetics: Nonequilibrium Fluctuations Beyond Detailed Balance in Voltage-Gated Ion Channels”, Physical Review E 106:4 (2022) 044410.
[Abstract] [pdf]
arxiv.org:2202.13038 [cond-mat.stat-mech]. doi:10.1103/PhysRevE.106.044410.
K. J. Ray and J. P. Crutchfield, “Gigahertz Sub-Landauer Momentum Computing”, Physical Review Applied 19 (2023) 014049.
[Abstract] [pdf]
arxiv.org:2202.07122 [cond-mat.stat-mech]. doi:10.1103/PhysRevApplied.19.014049.
F. Anza and J. P. Crutchfield, “Quantum Information Dimension and Geometric Entropy”, Physical Revew X Quantum 3 (2021) 020355.
[Abstract] [pdf]
2111.06374 [quant-phys]. doi:10.1103/PRXQuantum.3.020355.
S. P. Loomis and J. P. Crutchfield, “Topology, Convergence, and Reconstruction of Predictive States”, Physica D 445 (2023) 133621.
[Abstract] [pdf]
2109.09203 [cond-mat.stat-mech]. doi:10.1016/j.physd.2022.133621.
S. P. Loomis and J. P. Crutchfield, “Nonequilibrium Thermodynamics in Measuring Carbon Footprints: Disentangling Structure and Artifact in Input-Output Accounting”, (2021).
[Abstract] [pdf]
2106.03948 [cond-mat.stat-mech]. doi:.
A. M Jurgens and J. P. Crutchfield, “Ambiguity Rate of Hidden Markov Processes”, Physical Review E 104 (2021) 064107.
[Abstract] [pdf]
2105.07294 [cond-mat.stat-mech]. doi:10.1103/PhysRevE.104.064107.
A. B. Boyd, P. M. Riechers, G. W. Wimsatt, J. P. Crutchfield, and M. Gu, “Time Symmetries of Memory Determine Thermodynamic Efficiency”, (2021).
[Abstract] [pdf]
arxiv.org:2104.12072 [cond-mat.stat-mech]. doi:.
A. M Jurgens and J. P. Crutchfield, “Divergent Predictive States: The Statistical Complexity Dimension of Stationary, Ergodic Hidden Markov Processes”, Chaos 31:8 (2021) 0050460.
[Abstract] [pdf]
arxiv.org:2102.10487 [cond-mat.stat-mech]. doi:10.1063/5.0050460.
Sulimon Sattari, Udoy S. Basak, James P. Crutchfield, and Tamiki Komatsuzaki, “Modes of Information Flow in Collective Cohesion”, Science Advances 8:6 (2021) 1-13.
[Abstract] [pdf]
arxiv.org:2012.00293 [cond-mat.stat-mech]. doi:10.1126/sciadv.abj1720.
G. W. Wimsatt, A. B. Boyd, P. M. Riechers, and J. P. Crutchfield, “Refining Landauer's Stack: Balancing Error and Dissipation When Erasing Information”, Journal of Statistical Physics 183:16 (2021) 1-23.
[Abstract] [pdf]
arxiv.org:2011.14235 [cond-mat.stat-mech]. doi:10.1007/s10955-021-02733-1.
N. Brodu and J. P. Crutchfield, “Discovering Causal Structure with Reproducing-Kernel Hilbert Space ε-Machines”, Chaos 32 (2022) 023103.
[Abstract] [pdf]
arxiv.org:2011.14821 [cond-mat.stat-mech]. doi:10.1063/5.0062829.
M. Ashrafi, F. Anza, and J. P. Crutchfield, “Szilard Engines as Quantum Thermodynamical Systems”, (2020).
[Abstract] [pdf]
arxiv.org:2010.14652 [quant-phys]. doi:.
J. Emenheiser, A. Salova, J. Snyder, J. P. Crutchfield, and R. M. D'Souza, “Network and Phase Symmetries Reveal That Amplitude Dynamics Stabilize Decoupled Oscillator Clusters”, (2020).
[Abstract] [pdf]
arxiv.org:2010.09131 [cond-mat.stat-mech]. doi:.
K. J. Ray, G. W. Wimsatt, A. B. Boyd, and J. P. Crutchfield, “Non-Markovian Momentum Computing: Thermodynamically Efficient and Computation Universal”, Physical Review Research 3:2 (2021) 023164.
[Abstract] [pdf]
arxiv.org:2010.01152 [cond-mat.stat-mech]. doi: 10.1103/PhysRevResearch.3.023164.
A. M. Jurgens and J. P. Crutchfield, “Shannon Entropy Rate of Hidden Markov Processes”, Journal of Statistical Physics 183:32 (2020) 1-18.
[Abstract] [pdf]
arxiv.org:2008.12886 [cond-mat.stat-mech]. doi:10.1007/s10955-021-02769-3.
F. Anza and J. P. Crutchfield, “Maximum Geometric Quantum Entropy”, Entropy 26 (2024) 225.
[Abstract] [pdf]
arxiv.org:2008.08679 [quan-phys]. doi:.
F. Anza and J. P. Crutchfield, “Geometric Quantum Thermodynamics”, Physical Review E 106 (2022) 054103.
[Abstract] [pdf]
arxiv.org:2008.08683 [quant-phys]. doi:10.1103/PhysRevE.106.054102.
F. Anza and J. P. Crutchfield, “Beyond Density Matrices: Geometric Quantum States”, Physical Review Research 103:6 (2020) 062218.
[Abstract] [pdf]
arxiv.org:2008.08682 [quant-phys]. doi:10.1103/PhysRevA.103.062218 .
A. Rupe and J. P. Crutchfield, “Spacetime Autoencoders Using Local Causal States”, AAAI (2020).
[Abstract] [pdf]
arxiv.org:2010.05451 [non-lin.adap-org]. doi:.
A. B. Boyd, J. P. Crutchfield, and M. Gu, “Thermodynamic Machine Learning through Maximum Work Production”, New J. Physics 24 (2021) 083040.
[Abstract] [pdf]
arxiv.org:2006.15416 [cond-mat.stat-mech]. doi:10.1088/1367-2630/ac4309.
S. E. Marzen and J. P. Crutchfield, “Inference, Prediction, and Entropy-Rate Estimation of Continuous-time, Discrete-event Processes”, Entropy 24 (2022) 1675.
[Abstract] [pdf]
arxiv.org:2005.03750 [cond-mat.stat-mech]. doi:10.3390/e24111675.
K. Ray and J. P. Crutchfield, “Variations on a Demonic Theme: Szilard's Other Engines”, Chaos 30:9 (2020) 0012052.
[Abstract] [pdf]
arxiv.org:2003.09990 [cond-mat.stat-mech]. doi:10.1063/5.0012052.
A. M. Jurgens and J. P. Crutchfield, “The Functional Thermodynamics of Finite-State Maxwellian Ratchets”, Physical Review Research 2:3 (2020) 033334.
[Abstract] [pdf]
arxiv.org:2003.00139 [cond-mat.stat-mech].
doi:10.1103/PhysRevResearch.2.033334.
S. P. Loomis and J. P. Crutchfield, “Thermodynamically-Efficient Local Computation and the Inefficiency of Quantum Memory Compression”, Physical Review Research 2:2 (2020) 023039.
[Abstract] [pdf]
arxiv.org:2001.02258 [quant-ph]. doi:10.1103/PhysRevResearch.2.023039.
S. P. Loomis and J. P. Crutchfield, “Thermal Efficiency of Quantum Memory Compression”, Physical Review Letters 125 (2020) 020601.
[Abstract] [pdf]
arxiv.org:1911.00998 [quant-ph]. doi:10.1103/PhysRevLett.125.020601.
S. P. Loomis, J. R. Mahoney, C. Aghamohammadi, and J. P. Crutchfield, “Optimizing Quantum Models of Classical Channels: The reverse Holevo problem”, Journal of Statistical Physics 181 (2020) 1966--1985.
[Abstract] [pdf]
arxiv.org:1709.08101 [quant-ph]. doi:10.1007/s10955-020-02649-2.
S. E. Marzen and J. P. Crutchfield, “Probabilistic Deterministic Finite Automata and Recurrent Networks, Revisited”, Entropy 24:1 (2022) 90. (2019).
[Abstract] [pdf]
arxiv.org:1910.07663 [cs.LG]. doi:10.3390/e24010090.
O-P. Saira, M. H. Matheny, R. Katti, W. Fon, G. Wimsatt, S. Han, J. P. Crutchfield, and M. L. Roukes, “Nonequilibrium thermodynamics of erasure with superconducting flux logic”, Physical Review Research 2 (2020) 013249.
[Abstract] [pdf]
arxiv.org:1909.13828. doi:10.1103/PhysRevResearch.2.013249.
A. Rupe, N. Kumar, V. Epifanov, K. Kashinath, O. Pavlyk, F. Schimbach, M. Patwary, S. Maidanov, V. Lee, Prabhat, and J. P. Crutchfield, “DisCo: Physics-Based Unsupervised Discovery of Coherent Structures in Spatiotemporal Systems”, MLHPC (2019).
[Abstract] [pdf]
arxiv.org: 1909.11822 [physics.comp-ph]. doi:.
P. M. Riechers, A. B. Boyd, G. W. Wimsatt, and J. P. Crutchfield, “Balancing Error and Dissipation in Computing”, Physical Review Research 2:3 (2020) 033524.
[Abstract] [pdf]
arxiv.org:1909.06650 [cond-mat.stat-mech].
doi:10.1103/PhysRevResearch.2.033524.
P. M. Riechers and J. P. Crutchfield, “Fraudulent White Noise: Flat power spectra belie arbitrarily complex processes”, Physical Review Research 3:1 (2021) 013170.
[Abstract] [pdf]
arxiv.org:1908.11405 [nlin.CD]. doi: 10.1103/PhysRevResearch.3.013170.
A. E. Venegas-Li, A. M. Jurgens, and J. P. Crutchfield, “Measurement-Induced Randomness and Structure in Controlled Qubit Processes” Physical Review E, 102:4 (2020) 040102(R).
[Abstract] [pdf]
arxiv.org:1908.09053. doi:10.1103/PhysRevE.102.040102.
K. Finn, E. Bliss-Moreau, and J. P. Crutchfield, “Macaques preferentially attend to visual patterns with higher fractal dimension contours”, Scientific Reports 9 (2019) 10592.
[Abstract] [pdf]
doi:10.1038/s41598-019-46799-0.
G. Wimsatt, O-P. Saira, A. B. Boyd, M. H. Matheny, S. Han, M. L. Roukes, and J. P. Crutchfield, “Harnessing Fluctuations in Thermodynamic Computing via Time-Reversal Symmetries”, Physical Review Research 3:3 (2021) 033115.
[Abstract] [pdf]
arxiv.org:1906.11973. doi:10.1103/PhysRevResearch.3.033115.
A. Salova, J. Emenheiser, J. P. Crutchfield, and R. M. D'Souza, “Koopman Operator and its Approximations for Systems with Symmetries”, Chaos 29 (2019) 093128.
[Abstract] [pdf]
arxiv.org:1904.11472. doi:10.1063/1.5099091.
M. H. Matheny, J. Emenheiser, W. Fon, A. Chapman, A. Salova, M. Rohden, J. Li, M. Hudoba de Badyn, M. Posfai, L. Duenas-Osorio, M. Mesbahi, J. P. Crutchfield, M. C. Cross, R. M. D'Souza, and M. L. Roukes, “Exotic states in a simple network of nanoelectromechanical oscillators”, Science 363:6431 (2019) eaav7932.
[article pdf]
doi:10.1126/science.aav7932.
A. Rupe and J. P. Crutchfield, “Spacetime Symmetries, Invariant Sets, and Additive Subdynamics of Cellular Automata”, (2018).
[Abstract] [pdf]
arxiv.org:1812.11597. doi:.
A. B. Boyd, A. Patra, C. Jarzynski, and J. P. Crutchfield, “Shortcuts to Thermodynamic Computing: The Cost of Fast and Faithful Erasure”, Journal of Statistical Physics 187:17 (2022) 1-34.
[Abstract] [pdf]
arXiv.org:1812.11241. doi: 10.1007/s10955-022-02871-0.
J. B. Rundle and A. Giguere and D. L. Turcotte and J. P. Crutchfield, “Global Seismic Nowcasting with Shannon Information Entropy”, Earth and Space Science 6 (2019) 1-7.
[Abstract] [pdf]
doi: 10.1029/2018EA000464.
R. G. James, J. Emenheiser, and J. P. Crutchfield, “Unique Information and Secret Key Agreement”, Entropy 21 (2019) 1-12.
[Abstract] [pdf]
arXiv.org:1811.01745. doi: 10.3390/e21010012.
S. P. Loomis and J. P. Crutchfield, “Strong and Weak Optimizations in Classical and Quantum Models of Stochastic Processes”, Journal of Statistical Physics 176:6 (2019) 1317-1342.
[Abstract] [pdf]
arXiv.org:1808.08639. doi: 10.1007/s10955-019-02344-x.
R. G. James, J. Emenheiser, and J. P. Crutchfield, “A Perspective on Unique Information: Directionality, Intuitions, and Secret Key Agreement”, (2018).
[Abstract] [pdf]
arXiv.org:1808.08606. doi: .
Ryan G. James, Christopher J. Ellison, and James P. Crutchfield, “dit: a Python package for discrete information theory”, The Journal of Open Source Software 3:25 (2018) 738.
[Abstract] [pdf]
doi: 10.21105/joss.00738.
Ryan G. James, Blanca Daniella Mansante Ayala, Bahti Zakirov, and James P. Crutchfield, “Modes of Information Flow”, (2018).
[Abstract] [pdf]
arXiv.org:1808.06723. doi: XXXX.
S. E. Marzen and J. P. Crutchfield, “Optimized Bacteria are Environmental Prediction Engines”, Physical Review E 98 (2018) 012408.
[Abstract] [pdf]
arXiv.org:1802.03105 [q-bio]. doi: 10.1103/PhysRevE.98.012408.
J. Thompson, A. J. P. Garner, J. R. Mahoney, J. P. Crutchfield, V. Vedral, and M. Gu, “Causal Asymmetry in a Quantum World”, Physical Review X 8 (2018) 031013.
[Abstract] [pdf]
arxiv.org:1712.02368 [quant-ph]. doi: 10.1103/PhysRevX.8.031013.
J. P. Crutchfield, “The Origins of Computational Mechanics: A Brief Intellectual History and Several Clarifications”, (2017).
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-10-23. arxiv.org:1710.06832 [cond-mat.stat-mech].
J. R. Mahoney, C. Aghamohammadi, and J. P. Crutchfield, “Classical and Quantum Factors of Channels”, (2017).
[Abstract] [pdf]
arxiv.org:1709.08101 [quant-ph]. doi:.
W. Fon, M. H. Matheny, J. Li, L. Krayzman, M. C. Cross, R. M. D'Souza, J. P. Crutchfield, and M. L. Roukes, “Complex Dynamical Networks Constructed with Fully Controllable Nonlinear Nanomechanical Oscillators”, NanoLetters 17 (2017) 5977-5983.
[Abstract] [pdf]
doi:10.1021/acs.nanolett.7b02026.
R. G. James, J. Emenhesier, and J. P. Crutchfield, “Unique Information via Dependency Constraints”, Journal of Physics A 52 (2019) 014002.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-09-034. arxiv.org:1709.06653 [cond-mat.stat-mech]. doi:10.1088/1751-8121/aaed53.
A. Rupe, J. P. Crutchfield, K. Kashinath, and Prabhat, “A Physics-Based Approach to Unsupervised Discovery of Coherent Structures in Spatiotemporal Systems”, Lyubchich, V., N. C. Oza, A. Rhines, and E. Szekely, eds., Proceedings of the 7th International Workshop on Climate Informatics: CI 2017. NCAR Technical Note NCAR/TN-536+PROC.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-09-033. arxiv.org:1709.03184 [physics.flu-dyn]. doi:10.5065/D6222SH7.
A. Rupe and J. P. Crutchfield, “Local Causal States and Discrete Coherent Structures”, Chaos 28:7 (2018) 1-22.
[Abstract] [pdf]
arxiv.org:1801.00515 [cond-mat.stat-mech]. doi:10.1063/1.5021130.
A. B. Boyd, D. Mandal, and J. P. Crutchfield, “Thermodynamics of Modularity: Structural Costs Beyond the Landauer Bound”, Physical Review X 8:3 (2018) 031036.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-08-030. arxiv.org:1708.03030 [cond-mat.stat-mech]. doi:10.1103/PhysRevX.8.031036.
J. Ruebeck, R. G. James, J. R. Mahoney, and J. P. Crutchfield, “Prediction and Generation of Binary Markov Processes: Can a Finite-State Fox Catch a Markov Mouse?”, CHAOS 28 (2018) 013109.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-08-027. arxiv.org:1708.00113 [cond-mat.stat-mech]. doi:10.1063/1.5003041.
C. Aghamohammadi, S. P. Loomis, J. R. Mahoney, and J. P. Crutchfield, “Extreme Quantum Memory Advantage for Rare-Event Sampling”, Physical Review X 8 (2018) 011025.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-08-029. arxiv.org:1707.09553 [quant-ph]. doi:10.1103/PhysRevX.8.011025.
X. Lei, D. P. Varn, and J. P. Crutchfield, “Islands in the Gap: Intertwined Transport and Localization in Structurally Complex Materials”, (2017) submitted.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-07-025. arxiv.org:1707.05894 [cond-mat.mtrl-sci].
S. E. Marzen and J. P. Crutchfield, “Prediction and Dissipation in Nonequilibrium Molecular Sensors: Conditionally Markovian Channels Driven by Memoryful Environments”, Bulletin of Mathematical Biology 82:25 (2020) 1-46.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-07-020. arxiv.org:1707.03962 [cond-mat.stat-mech]. doi:10.1007/s11538-020-00694-2.
P. M. Riechers and J. P. Crutchfield, “Spectral Simplicity of Apparent Complexity, Part II: Exact Complexities and Complexity Spectra”, Chaos 28 (2018) 033116.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-06-019. arxiv.org:1706.00883 [nlin.CD]. doi:10.1063/1.4986248.
P. M. Riechers and J. P. Crutchfield, “Spectral Simplicity of Apparent Complexity, Part I: The Nondiagonalizable Metadynamics of Prediction”, Chaos 28 (2018) 033115.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-05-018. arxiv.org:1705.08042 [cond-mat.stat-mech]. doi:10.1063/1.4985199.
S. E. Marzen and J. P. Crutchfield, “Structure and Randomness of Continuous-Time Discrete-Event Processes”, Journal of Statistical Physics 169:2 (2017) 303-315.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-04-009. arxiv.org:1704.04707 [cond-mat.stat-mech]. doi:10.1007/s10955-017-1859-y.
S. E. Marzen and J. P. Crutchfield, “Nearly Maximally Predictive Features and Their Dimensions”, Phys. Rev. E (Rapid Communication) 95:5 (2017) 051301(R).
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-02-007. arxiv.org:1702.08565 [cond-mat.stat-mech].
R. G. James, J. R. Mahoney, and J. P. Crutchfield, “Information Trimming: Sufficient Statistics, Mutual Information, and Predictability from Effective Channel States”, Physical Review E 95:6 (2017) 060102(R).
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-03-008. arxiv.org:1702.01831 [cond-mat.stat-mech]. doi:10.1103/PhysRevE.95.060102.
C. Aghamohammadi and J. P. Crutchfield, “Thermodynamics of Random Number Generation”, Physical Review E 95:6 (2017) 062139.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-01-02. arxiv.org:1612.08459 [cond-mat.stat-mech]. doi:10.1103/PhysRevE.95.062139.
A. B. Boyd, D. Mandal, P. M. Riechers, and J. P. Crutchfield, “Transient Dissipation and Structural Costs of Physical Information Transduction”, Physical Review Letters 118 (2017) 220602.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2017-01-01. arxiv.org:1612.08616 [cond-mat.stat-mech].
S. E. Marzen and J. P. Crutchfield, “Informational and Causal Architecture of Continuous-Time Renewal Processes”, Journal of Statistical Physics 168:1 (2017) 109-127.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2016-11-024. arxiv.org:1611.01099 [cond-mat.stat-mech]. Online. 10.1007/s10955-017-1793-z.
P. M. Riechers and J. P. Crutchfield, “Fluctuations When Driving Between Nonequilibrium Steady States”, Journal of Statistical Physics 168:4 (2017) 873-918.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2016-10-023. arxiv.org:1610.09444 [cond-mat.stat-mech]. 10.1007/s10955-017-1822-y.
C. Aghamohammadi and J. P. Crutchfield, “Minimum Memory for Generating Rare Events”, Physical Review E 95:3 (2017) 032101.
[Abstract] [pdf] doi:10.1103/PhysRevE.95.032101
Santa Fe Institute Working Paper 2016-10-022. arxiv.org:1610.07685 [cond-mat.stat-mech].
A. B. Boyd, D. Mandal, and J. P. Crutchfield, “Leveraging Environmental Correlations: The Thermodynamics of Requisite Variety”, Journal of Statistical Physics 167:6 (2017) 1555-1585.
[Abstract] [pdf] doi:10.1007/s10955-017-1776-0
Santa Fe Institute Working Paper 2016-09-021. arxiv.org:1609.05353 [cond-mat.stat-mech].
C. Aghamohammadi, J. R. Mahoney, and J. P. Crutchfield, “Extreme Quantum Advantage when Simulating Strongly Coupled Classical Systems”, Scientific Reports 7 (2017) 6735.
[Abstract] [pdf] Corrigendum [pdf]
Santa Fe Institute Working Paper 2016-09-019. arxiv.org:1609.03650 [quant-ph]. http://rdcu.be/uwVo. doi:10.1038/s41598-017-04928-7.
J. P. Crutchfield and C. Aghamohammadi, “Not All Fluctuations are Created Equal: Spontaneous Variations in Thermodynamic Function”, Entropy 26:11 (2024) 894.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2016-09-018. arxiv.org:1609.02519 [cond-mat,stat-mech]. doi:10.3390/e26110894.
R. G. James and J. P. Crutchfield, “Multivariate Dependence Beyond Shannon Information”, Entropy 19 (2017) 531.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2016-09-017. arxiv.org:1609.01233 [math.IT]. doi:10.3390/e19100531.
P. M. Riechers and J. P. Crutchfield, “Beyond the Spectral Theorem: Spectrally Decomposing Arbitrary Functions of Nondiagonalizable Operators”, AIP Advances 8 (2018) 065305.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2016-07-015. arxiv.org:1607.06526 [math-ph]. doi:10.1063/1.5040705.
J. Emenheiser, A. Chapman, M. Posfai, J. P. Crutchfield, M. Mesbahi, and R. M. D'Souza, “Patterns of patterns of synchronization: Noise induced attractor switching in rings of coupled nonlinear oscillators”, Chaos 26:9 (2016) 094816.
[Abstract] [pdf]
arxiv.org:1606.01435 [cond-mat.stat-mech].
A. B. Boyd, D. Mandal, and J. P. Crutchfield, “Correlation-powered Information Engines and the Thermodynamics of Self-Correction”, Physical Review E 95:1 (2017) 012152.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2016-06-013. arxiv.org:1606.08506 [cond-mat.stat-mech].
C. Aghamohammadi, J. R. Mahoney, and J. P. Crutchfield, “The Ambiguity of Simplicity”, Physics Letters A 381:14 (2017) 1223-1227.
[Abstract] [pdf] doi:10.1016/j.physleta.2016.12.036
Santa Fe Institute Working Paper 16-02-005. arxiv.org:1602.08646 [quant-ph].
R. G. James, N. Barnett, and J. P. Crutchfield, “Information Flows? A Critique of Transfer Entropies”, Physical Review Letters 116 (2016) 238701.
[Abstract] [pdf]
Santa Fe Institute Working Paper 16-01-001. arxiv.org:1512.06479 [cond-mat.stat-mech].
S. E. Marzen and J. P. Crutchfield, “Statistical Signatures of Structural Organization: The case of long memory in renewal processes”, Physics Letters A 380:17 (2016) 1517-1525.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-12-046. arxiv.org:1512.01859 [cond-mat.stat-mech].
V. S. Vijayaraghavan, R. G. James, and J. P. Crutchfield, “Anatomy of a Spin: The Information-Theoretic Structure of Classical Spin Systems”, Entropy 19 (2017) 214.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-10-042. arxiv.org:1510.08954 [cond-mat.stat-mech].
P. M. Riechers, J. R. Mahoney, C. Aghamohammadi, and J. P. Crutchfield, “Minimized State-Complexity of Quantum-Encoded Cryptic Processes”, Physical Review A 93:5 (2016) 052317.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-10-041. arxiv.org:1510.08186 [quant-ph].
D. P. Varn and J. P. Crutchfield, “What did Erwin Mean? The Physics of Information from the Materials Genomics of Aperiodic Crystals & Water to Molecular Information Catalysts & Life”, Philosophical Transactions of the Royal Society A 374 (2016) 20150067.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-10-035. arxiv.org:1510.02778 [cond-mat.stat-mech].
D. Mandal, A. B. Boyd, and J. P. Crutchfield, “Memoryless Thermodynamics? A Reply”, (2015) submitted.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-08-031. arxiv.org:1508.03311 [cond-mat.stat-mech].
J. R. Mahoney, C. Aghamohammadi, and J. P. Crutchfield, “Occam's Quantum Strop: Synchronizing and Compressing Classical Cryptic Processes via a Quantum Channel”, Scientific Reports 6 (2016) 20495.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-08-030. arxiv.org:1508.02760 [quant-ph].
A. B. Boyd, D. Mandal, and J. P. Crutchfield, “Identifying Functional Thermodynamics in Autonomous Maxwellian Ratchets”, New Journal of Physics 18 (2016) 023149.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-07-025. arxiv.org:1507.01537 [cond-mat.stat-mech].
P. M. Ara, R. G. James, and J. P. Crutchfield, “The Elusive Present: Hidden Past and Future Dependency and Why We Build Models”, Physical Review E 93:2 (2016) 022143.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-07-024. arxiv.org:1507.00672 [cond-mat.stat-mech].
A. B. Boyd and J. P. Crutchfield, “Demon Dynamics: Deterministic Chaos, the Szilard Map, and the Intelligence of Thermodynamic Systems”, Physical Review Letters 116 (2016) 190601.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-06-019. arxiv.org:1506.04327 [cond-mat.stat-mech].
S. E. Marzen, M. R. DeWeese, and J. P. Crutchfield, “Time Resolution Dependence of Information Measures for Spiking Neurons: Scaling and Universality”, Frontiers in Computational Neuroscience 9 (2015) 109.
[Abstract] [pdf]
Santa Fe Institute Working Paper 15-04-012. arxiv.org:1504.04756 [q-bio.NC].
J. P. Crutchfield and S. Marzen, “Signatures of Infinity: Nonergodicity and Resource Scaling in Prediction, Complexity, and Learning”, Physical Review E 91 (2015) 050106(R).
[Abstract] [pdf] PRE Editor's Suggestion
Santa Fe Institute Working Paper 15-04-010. arxiv.org:1504.00386 [cond-mat.stat-mech].
J. P. Crutchfield, R. G. James, S. Marzen and D. P. Varn, “Understanding and Designing Complex Systems: Response to ‘A framework for optimal high-level descriptions in science and engineering---preliminary report’”, (2014).
[Abstract] [pdf]
Santa Fe Institute Working Paper 14-12-048. arxiv.org:1412.8520 [cond-mat.stat-mech].
S. Marzen and J. P. Crutchfield, “Predictive Rate-Distortion for Infinite-Order Markov Processes”, Journal of Statistical Physics 163:6 (2016) 1312-1338.
[Abstract] [pdf]
Santa Fe Institute Working Paper 14-12-047. arxiv.org:1412.2859 [cond-mat.stat-mech].
N. Barnett and J. P. Crutchfield, “Computational Mechanics of Input-Output Processes: Structured transformations and the ε-transducer”, Journal of Statistical Physics 161:2 (2015) 404-451.
[Abstract] [pdf]
Santa Fe Institute Working Paper 14-12-046. arxiv.org:1412.2690 [cond-mat.stat-mech].
P. M. Riechers, D. P. Varn, and J. P. Crutchfield, “Diffraction Patterns of Layered Close-packed Structures from Hidden Markov Models”, (2014) submitted.
[Abstract] [pdf]
Santa Fe Institute Working Paper 2014-10-038. arxiv.org:1410.5028 [cond-mat.mtrl-sci].
D. P. Varn and J. P. Crutchfield, “Chaotic Crystallography: How the physics of information reveals structural order in materials”, Current Opinion in Chemical Engineering 7 (2015) 47-56.
[Abstract] [pdf]
Santa Fe Institute Working Paper 14-09-036. arxiv.org:1409.5930 [cond-mat.stat-mech].
S. Marzen and J. P. Crutchfield, “Informational and Causal Architecture of Discrete-Time Renewal Processes”, Entropy 17:7 (2015) 4891-4917.
[Abstract] [pdf]
Santa Fe Institute Working Paper 14-08-032. arxiv.org:1408.6876 [cond-mat.stat-mech].
P. M. Riechers, D. P. Varn, and J. P. Crutchfield, “Pairwise Correlations in Layered Close-Packed Structures”, Acta Crystallographica Section A: Foundations and Advances 71:4 (2015) 423-443.
[Abstract] [pdf]
Santa Fe Institute Working Paper 14-08-026. arxiv.org:1407.7159 [cond-mat].
S. Marzen and J. P. Crutchfield, “Information Anatomy of Stochastic Equilibria”, Entropy 16 (2014) 4713-4748.
[Abstract] [pdf]
Santa Fe Institute Working Paper 14-04-005. arXiv:1403.3864 [cond-mat].
V. Griffith, E. K. P. Chong, R. G. James, C. J. Ellison, and J. P. Crutchfield, “Intersection Information based on Common Randomness”, Entropy 16 (2014) 1985-2000.
[Abstract] [pdf]
Santa Fe Institute Working Paper 13-10-031. arXiv:1310.1538 [cs.IT].
R. G. James, K. Burke, and J. P. Crutchfield, “Chaos Forgets and Remembers: Measuring Information Creation, Destruction, and Storage”, Physics Letters A 378 (2014) 2124-2127.
[Abstract] [pdf]
Santa Fe Institute Working Paper 13-10-030. arXiv:1309.5504 [nlin.CD].
J. P. Crutchfield, C. J. Ellison, and P. M. Riechers, “Exact Complexity: The Spectral Decomposition of Intrinsic Computation”, Physics Letters A 380 (2016) 998-1002.
[Abstract] [pdf]
Santa Fe Institute Working Paper 13-09-028. arXiv:1309.3792 [cond-mat.stat-mech].
C. C. Strelioff and J. P. Crutchfield, “Bayesian Structural Inference for Hidden Processes”, Physical Review E 89 (2014) 042119.
[Abstract] [pdf]
Santa Fe Institute Working Paper 13-09-027. arXiv:1309.1392 [stat.ML].
J. P. Crutchfield, “Between Order and Chaos”, Nature Physics 8 (January 2012) 17-24.
[Abstract] Abstract at Nature Physics Addendum Corrected version
N. F. Travers and J. P. Crutchfield, “Equivalence of History and Generator ε-Machines”, submitted (2011).
[Abstract] [pdf]
Santa Fe Institute Working Paper 11-11-051. arXiv:1111.4500 [math.PR].
N. F. Travers and J. P. Crutchfield, “Infinite Excess Entropy Processes with Countable-State Generators”, Entropy 16 (2014) 1396-1413.
[Abstract] [pdf]
Santa Fe Institute Working Paper 11-11-052. arXiv:1111.3393 [math.PR].
J. P. Crutchfield and J. Machta, `Toward a Physics of Pattern—Focus Issue on “Randomness, Structure, and Causality: Measures of Complexity from Theory to Applications”', CHAOS 21:3 (2011) 037101.
[Abstract] [pdf]
Santa Fe Institute Working Paper 11-08-XXX. arXiv:1108.XXXX [cond-mat.stat-mech].
J. R. Mahoney, C. J. Ellison, R. G. James, and J. P. Crutchfield, "How Hidden are Hidden Processes? A Primer on Crypticity and Entropy Convergence", CHAOS 21:3 (2011) 037112.
[Abstract] [pdf]
Santa Fe Institute Working Paper 11-08-029. arXiv:1108.1510 [cond-mat.stat-mech].
C. J. Ellison, J. R. Mahoney, R. G. James, J. P. Crutchfield, and Joerg Reichardt, "Information Symmetries in Irreversible Processes", CHAOS 21:3 (2011) 037107.
[Abstract] [pdf]
Santa Fe Institute Working Paper 11-07-028. arXiv:1107.2168 [cond-mat.stat-mech].
R. G. James, C. J. Ellison, and J. P. Crutchfield, "Anatomy of a Bit: Information in a Time Series Measurement", CHAOS 21 (2011) 037109.
[Abstract] [pdf]
Santa Fe Institute Working Paper 11-05-019. arXiv:1105.2988 [math.IT].
J. P. Crutchfield and C. J. Ellison, "The Past and the Future in the Present", (2010) submitted.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-12-034. arXiv:1012.0356 [nlin.CD].
J. P. Crutchfield, "The Dreams of Theory", (23 June 2009). Wiley Reviews (WIREs) in Computational Statistics 6 (March/April 2014) 75-79. doi: 10.10002/wics.1290.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-11-033.
N. F. Travers and J. P. Crutchfield, "Asymptotic Synchronization for Finite-State Sources", J. Stat. Phys. 145:5 (2011) 1202-1223.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-11-029. arXiv:1011.1581 [nlin.CD].
B. D. Johnson, J. P. Crutchfield, C. J. Ellison, and C. S. McTague, "Enumerating Finitary Processes", Theo. Comp. Sci. (2012) in press.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-11-027. arXiv:1011.0036 [cs.FL].
R. G. James, J. R. Mahoney, C. J. Ellison, and J. P. Crutchfield, "Many Roads to Synchrony: Natural Time Scales and Their Algorithms", Physical Review E 89 (2014) 042135.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-11-025. arXiv:1010.5545 [nlin.CD].
S. T. Piantadosi and J. P. Crutchfield, "How the Dimension of Space Affects the Products of Pre-Biotic Evolution: The Spatial Population Dynamics of Structural Complexity and The Emergence of Membranes", PLoS Comp. Bio. (2010) submitted.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-11-023. arXiv:1010.5019 [q-bio.PE].
J. P. Crutchfield, W. Ditto, and S. Sinha, "Beyond the Digital Hegemony—Intrinsic and Designed Computation: Information Processing in Dynamical Systems", CHAOS 20:3 (2010) 037101.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-11-024.
AIP CHAOS Special Issue.
N. F. Travers and J. P. Crutchfield, "Exact Synchronization for Finite-State Sources", J. Stat. Phys. 145:5 (2011) 1181-1201.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-11-031. arXiv:1008.4182 [nlin.CD].
A. Hubler and J. P. Crutchfield, "Order and Disorder in Open Systems", Complexity 15:7 (2010) 3-7.
[Abstract] [pdf]
Online: article.
J. P. Crutchfield, Christopher J. Ellison, Ryan G. James, and John R. Mahoney, "Synchronization and Control in Intrinsic and Designed Computation: An Information-Theoretic Analysis of Competing Models of Stochastic Computation", CHAOS 20:3 (2010) 037105.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-08-015. arXiv:1007.5354 [cond-mat.stat-mech].
J. P. Crutchfield and S. Whalen, "Structural Drift: The Population Dynamics of Sequential Learning", PLoS Computational Biology 8:6 (2012) e1002510.
[Abstract] [pdf] [Journal]
Santa Fe Institute Working Paper 10-05-011. arXiv:1005.2714 [q-bio.PE].
J. P. Crutchfield and K. Wiesner, "Simplicity and Complexity", Physics World (February 2010) 36-38.
[Abstract] [pdf]
Santa Fe Institute Working Paper 10-02-XXX.
J. P. Crutchfield, "The Hidden Fragility of Complex Systems—Consequences of Change, Changing Consequences", in Cultures of Change: Social Atoms and Electronic Lives, G. Ascione, C. Massip, and J. Perello, editors, ACTAR D Publishers, Barcelona, Spain (2009) 98-111.
[Abstract] [pdf]
Santa Fe Institute Working Paper 09-12-045. arXiv:2003.11153.
S. Whalen, M. Bishop, and J. P. Crutchfield, "Hidden Markov Models for Automated Protocol Learning", S. Jajodia and J. Zhou (Eds.), SecureComm 2010, LNICST 50 (2010) 415-428.
[Abstract] [pdf]
Santa Fe Institute Working Paper 09-11-XXX. arXiv:0911.XXXX [cs.NI].
J. R. Mahoney, C. J. Ellison, J. P. Crutchfield, "Information Accessibility and Cryptic Processes: Linear Combinations of Causal States", (2009).
[Abstract] [pdf]
Santa Fe Institute Working Paper 09-06-019. arXiv:0906.5099 [cond-mat].
J. R. Mahoney, C. J. Ellison, J. P. Crutchfield, "Information Accessibility and Cryptic Processes", Journal of Physics A: Math. Theo. 42 (2009) 362002.
[Abstract] [pdf]
Santa Fe Institute Working Paper 09-05-018. arXiv:0905.4787 [cond-mat].
C. J. Ellison, J. R. Mahoney, J. P. Crutchfield, "Prediction, Retrodiction, and The Amount of Information Stored in the Present", Journal of Statistical Physics 136:6 (2009) 1005-1034.
[Abstract] [pdf]
Santa Fe Institute Working Paper 09-05-017. arXiv:0905.3587 [cond-mat].
J. P. Crutchfield, C. J. Ellison, J. R. Mahoney, "Time's Barbed Arrow: Irreversibility, Crypticity, and Stored Information", Physical Review Letters 103:9 (2009) 094101.
[Abstract] [pdf]
Santa Fe Institute Working Paper 09-02-002; arXiv:0902.1209 [cond-mat]; Physical Review Letters; DOI: 10.1103/PhysRevLett.103.094101.
David P. Feldman, Carl S. McTague, and J. P. Crutchfield, "The Organization of Intrinsic Computation: Complexity-Entropy Diagrams and the Diversity of Natural Information Processing", CHAOS 18:4 (2008) 53-73.
[Abstract] [pdf]
Santa Fe Institute Working Paper 08-07-028. arXiv:0806.4789 [nlin.CD].
C. C. Strelioff and J. P. Crutchfield, "Optimal Instruments and Models for Noisy Chaos", CHAOS 17 (2007) 043127.
[Abstract] [pdf]
Santa Fe Institute Working Paper 06-11-042. arxiv.org e-print cs.LG/0611054.
S. Still, J. P. Crutchfield, and C. J. Ellison, "Optimal Causal Inference: Estimating Stored Information and Approximating Causal Architecture", CHAOS 20:3 (2010) 037111.
[Abstract] [pdf]
Santa Fe Institute Working Paper 07-08-024. arxiv.org e-print 0708.1580 [cs.IT].
Susanne Still and J. P. Crutchfield, "Structure or Noise?", Physics Letters A (2008) submitted.
[Abstract] [pdf]
Santa Fe Institute Working Paper 07-08-020. arxiv.org e-print physics.gen-ph/0708.0654.

Olof Görnerup and J. P. Crutchfield, "Primordial Evolution in the Finitary Process Soup", Electronic Journal of Theoretical Physics 4:16 (2007) 297-311. Reprinted in Physics of Emergence and Organization, Eds. I. Licata and A. Sakaji, World Scientific (2008) 297-311.
[Abstract] [pdf]
Santa Fe Institute Working Paper 07-05-008. arxiv.org e-print q-bio.PE/0704.3771.

C. C. Strelioff, J. P. Crutchfield, and A. Hubler, "Inferring Markov Chains: Bayesian Estimation, Model Comparison, Entropy Rate, and Out-of-class Modeling", Physical Review E 76:1 (2007) 011106.
[Abstract] [pdf]
Santa Fe Institute Working Paper 07-04-005. arxiv.org e-print math.ST/0703715.

C. C. Strelioff and J. P. Crutchfield, "How Random Is a Coin Toss? Bayesian Inference and the Symbolic Dynamcs of Deterministic Chaos", Conference on Neural Information Processing, Workshop on Dynamical Systems, Stochastic Processes and Bayesian Inference (2006) Online Proceedings.
[Abstract] [pdf]
Santa Fe Institute Working Paper 06-11-042. arxiv.org e-print cs.LG/0611054.

O. Görnerup and J. P. Crutchfield, "Hierarchical Self-Organization in the Finitary Process Soup", Special Issue on the Evolution of Complexity, Artificial Life Journal 14:3 (2008) 245-254.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 06-03-001. arxiv.org e-print nlin.AO/0603001.

D. J. Albers, J. C. Sprott, and J. P. Crutchfield, "Persistent Chaos in High Dimensions", Physical Review E 74:5 (2006) 057201.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 05-04-011. arxiv.org e-print nlin.CD/0504040.

Carl S. McTague and J. P. Crutchfield, "Automated Pattern Detection---An Algorithm for Constructing Optimally Synchronizing Multi-Regular Language Filters", Theoretical Computer Science 359 (2006) 306-328.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 04-09-027. arxiv.org e-print cs.CV/0410017.

J. P. Crutchfield and O. Görnerup, "Objects That Make Objects: The Population Dynamics of Structural Complexity", Journal of the Royal Society Interface 3 (2006) 345-349.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 04-06-020. arxiv.org e-print adap-org/0406058.

Nihat Ay and J. P. Crutchfield, "Reductions of Hidden Information Sources", Journal of Statistical Physics 210:3-4 (2005) 659-684.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 04-06-011. arxiv.org/abs/math.PR/0405425.

Cosma Rohilla Shalizi, Kristina Lisa Shalizi, and J. P. Crutchfield, "Pattern Discovery in Time Series, Part I: Theory, Algorithm, Analysis, and Convergence", Journal of Machine Learning Research (2002), in preparation.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Insitute Working Paper 02-10-060. arXiv.org/abs/cs.LG/0210025.

D. P. Feldman and J. P. Crutchfield, "Synchronizing to Periodicity: The Transient Information and Synchronization Times of Periodic Sequences", Advances in Complex Systems 7:3-4 (2004) 329-355.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Insitute Working Paper 02-08-043. arXiv.org/abs/nlin.AO/0208040.

J. P. Crutchfield and D. P. Feldman, "Synchronizing to the Environment: Information Theoretic Constraints on Agent Learning", Advances in Complex Systems 4:2 (2001) 251-264.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Insitute Working Paper 01-03-020. arXiv.org/abs/nlin.AO/0103038.

J. P. Crutchfield and D. P. Feldman, "Regularities Unseen, Randomness Observed: Levels of Entropy Convergence", CHAOS 13:1 (2003) 25-54.
[Abstract] [ps.gz] [ps] [pdf] Addenda [pdf]
Santa Fe Insitute Working Paper 01-02-012. arXiv.org/abs/cond-mat/0102181.

C. R. Shalizi and J. P. Crutchfield, "Information Bottlenecks, Causal States, and Statistical Relevance Bases: How to Represent Relevant Information in Memoryless Transduction", Advances in Complex Systems 5 (2002): 1-5.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Insitute Working Paper 00-07-035. arXiv.org/abs/nlin.AO/0006025.

C. R. Shalizi and J. P. Crutchfield, "Pattern Discovery and Computational Mechanics".
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Insitute Working Paper 00-01-008. arXiv.org/abs/cs.LG/0001027.

C. R. Shalizi and J. P. Crutchfield, "Computational Mechanics: Pattern and Prediction, Structure and Simplicity", Journal of Statistical Physics 104 (2001) 819--881.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Insitute Working Paper 99-07-044. arXiv.org/abs/cond-mat/9907176.

J. P. Crutchfield, D. P. Feldman, and C. R. Shalizi, 'Comment on "Simple Measure for Complexity"', Physical Review E 62 (2000) 2996-2997.
[Abstract] [ps] [pdf]
Santa Fe Insitute Working Paper 99-06-040.

J. P. Crutchfield and C. R. Shalizi, "Thermodynamic Depth of Causal States: Objective Complexity via Minimal Representations", Physical Review E 59 (1999) 275-283.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Insitute Working Paper 98-06-047.

C. R. Shalizi, "Summer School Lectures on Computational Mechanics", notes for lectures given 18--19 June 1998, plus reading list.
[Abstract]

J. P. Crutchfield, "Dynamical Embodiments of Computation in Cognitive Processes", Behavioral and Brain Sciences 21:5 (1998) 635-637.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 98-02-016.

D. P. Feldman and J. P. Crutchfield, "Measures of Statistical Complexity: Why?", Physics Letters A 238 (1998) 244-252.
[Abstract] [ps.gz] [ps] [pdf]

J. P. Crutchfield and N. Kahn, "Turbulent Landscapes--A Dialogue", Complexity 2:2 (1996) 3-7.
[Abstract]

J. P. Crutchfield, "Is Anything Ever New? Considering Emergence", in Complexity: Metaphors, Models, and Reality, G. Cowan, D. Pines, and D. Melzner, editors, SFI Series in the Sciences of Complexity XIX, Addison-Wesley, Redwood City (1994) 479-497.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 94-03-011.

J. P. Crutchfield, "The Calculi of Emergence: Computation, Dynamics, and Induction", Physica D 75 (1994) 11-54.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 94-03-016.

J. P. Crutchfield, "Critical Computation, Phase Transitions, and, Hierarchical Learning" in Towards the Harnessing of Chaos, Proceedings of the 7th Toyota Conference, M. Yamaguti, editor, Elsevier Science, Amsterdam (1994) in press.
[Abstract] [ps] [pdf]
Santa Fe Institute Working Paper 93-06-035.

J. P. Crutchfield, "Observing Complexity and The Complexity of Observation", in Inside versus Outside, H. Atmanspacher, editor, Springer-Verlag, Berlin (1994) 234-272.
[Abstract] [ps] [pdf]
Santa Fe Institute Working Paper 93-06-035.

J. P. Crutchfield, "What Lies Between Order and Chaos?" in Art and Complexity, J. Casti, editor, Oxford University Press (2002).
[Abstract] [ps.gz] [ps] [pdf]

K. Young and J. P. Crutchfield, "Fluctuation Spectroscopy", Chaos, Solitons, and Fractals 4 (1993) 5-39.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 93-05-028.

J. P. Crutchfield, "Semantics and Thermodynamics", in Nonlinear Modeling and Forecasting, SFI Studies in the Sciences of Complexity, Proc. Vol. XII, M. Casdagli and S. Eubank, editors, Addison-Wesley, Reading, Massachusetts (1992) 317-360.
[Abstract] [pdf]
Santa Fe Institute Working Paper 91-09-033.

J. P. Crutchfield, "Knowledge and Meaning...Chaos and Complexity", in Modeling Complex Systems, L. Lam and H. C. Morris, editors, Springer-Verlag, Berlin (1992) 66 -101.
[Abstract]
Santa Fe Institute Working Paper 91-09-035.

J. P. Crutchfield, "Reconstructing Language Hierarchies", in Information Dynamics, NATO ASI Series, 256, H. A. Atmanspracher and H. Scheingraber, editors, Plenum Press, New York (1990) 45-60.
[Abstract] [pdf] zipped [pdf]

J. P. Crutchfield, "Complexity: Order contra Chaos", in Proceedings of the International Conference on Fuzzy Logic and Neural Networks, S. Yasui and T. Yamakawa, editors, Iizuka, Japan (July 1990) World Scientific Publishers, Singapore (1990) 127.
[Abstract] [ps.gz] [ps] [pdf]

J. P. Crutchfield, "Chaos and Complexity", in Handbook of Metaphysics and Ontology, Philosophia Verlag, München (1990).
[Abstract] [ps.gz] [ps] [pdf]

J. P. Crutchfield, "Information and Its Metric", in Nonlinear Structures in Physical Systems — Pattern Formation, Chaos, and Waves, L. Lam and H. C. Morris, editors, Springer-Verlag, Berlin (1990) 119-130.
[Abstract] [ps.gz] [ps] [pdf]

J. P. Crutchfield, "Inferring the Dynamic, Quantifying Physical Complexity", in Measures of Complexity and Chaos, A. M. Albano, N. B. Abraham, P. E. Rapp, and A. Passamante, editors, Plenum Press, New York (1989) 327.
[Abstract] [pdf] zipped [pdf]

J. P. Crutchfield and K. Young, "Computation at the Onset of Chaos", in Entropy, Complexity, and Physics of Information, W. Zurek, editor, SFI Studies in the Sciences of Complexity, VIII, Addison-Wesley, Reading, Massachusetts (1990) 223-269.
[Abstract] [ps.gz] [ps] [pdf]

J. P. Crutchfield and K. Young, "Inferring Statistical Complexity", Physical Review Letters 63 (1989) 105-108.
[Abstract] [zipped pdf] [pdf]

Spatially-Extended Systems

D. P. Varn, G. S. Canright, and J. P. Crutchfield, "Inferring planar disorder in close-packed structures via ε-machine spectral reconstruction theory: Examples from simulated diffraction patterns", Acta Crystallographica Section A 69:4 (2013) 413-426.
[Abstract] [pdf]
Santa Fe Institute Working Paper 03-03-021. arXiv.org/abs/cond-mat/0302585.

D. P. Varn, G. S. Canright, and J. P. Crutchfield, "ε-Machine spectral reconstruction theory: A direct method for inferring planar disorder and structure from X-ray diffraction studies", Acta Crystallographica Section A 69:2 (2013) 197-206.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 03-03-021. arXiv.org/abs/cond-mat/0302585.

D. P. Varn and J. P. Crutchfield, "From Finite to Infinite Range Order via Annealing: The Causal Architecture of Deformation Faulting in Annealed Close-Packed Crystals". Physics Letters A 234:4 (2004) 299-307.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 03-07-045. arXiv.org/abs/cond-mat/0307296.

D. P. Varn, G. S. Canright, and J. P. Crutchfield, "Inferring Pattern and Disorder in Close-Packed Structures from X-ray Diffraction Studies, Part II: Structure and Intrinsic Computation in Zinc Sulphide", Acta Crystallographica Section B 63:2 (2006) 169-182.
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 03-03-022. arXiv.org/abs/cond-mat/0302587.

D. P. Varn, G. S. Canright, and J. P. Crutchfield, "Inferring Pattern and Disorder in Close-Packed Structures from X-ray Diffraction Studies, Part I: epsilon-Machine Spectral Reconstruction Theory",
[Abstract] [ps.gz] [ps] [pdf]
Santa Fe Institute Working Paper 03-03-021. arXiv.org/abs/cond-mat/0302585.

D. P. Feldman and J. P. Crutchfield, "Structural Information in Two-Dimensional Patterns: Entropy Convergence and Excess Entropy", Physical Review E 67 (2003) 051104.
[Abstract] [pdf] [ps] [ps.gz]
Santa Fe Institute Working Paper 02-12-065. arXiv.org/abs/cond-mat/0212078.

D. P. Varn, G. S. Canright, and J. P. Crutchfield, "Discovering Planar Disorder in Close-Packed Structures from X-Ray Diffraction: Beyond the Fault Model", Physical Review B 66:17 (2002) 174110-3. Santa Fe Institute Working Paper 02-03-014.
[Abstract] [ps.gz]� [ps] [pdf]
arXiv.org/abs/cond-mat/0203290.

W. Hordijk, J. P. Crutchfield, and C. R. Shalizi,"Upper Bound on the Products of Particle Interactions in Cellular Automata", Physica D 154 (2001) 240--258.
[Abstract] [pdf] [ps.gz] [ps]
Santa Fe Institute Working Paper 00-09-052. arXiv.org/abs/nlin.CG/0008038.

D. P. Feldman and J. P. Crutchfield, "Discovering Noncritical Organization: Statistical Mechanical, Information Theoretic, and Computational Views of Patterns in One-Dimensional Spin Systems", Entropy 24 (2022) 1282.
[Abstract] [ps.gz] [pdf]
doi:10.3390/e24091282 .
Santa Fe Institute Working Paper 98-04-026.

J. P. Crutchfield and D. P. Feldman, "Statistical Complexity of Simple 1D Spin Systems", Physical Review E 55:2 (1997) 1239R-1243R.
[Abstract] [ps.gz]

J. E. Hanson and J. P. Crutchfield, "Computational Mechanics of Cellular Automata: An Example", Physica D 103 (1997) 169-189.
[Abstract] [pdf] [ps.gz]
Santa Fe Institute Working Paper 95-10-95.

J. E. Hanson and J. P. Crutchfield, "Postscript to 'The Attractor-Basin Portrait of a Cellular Automaton'", Research Note (February 1994) unpublished.
[Abstract] [ps.gz]

J. P. Crutchfield and J. E. Hanson, "Turbulent Pattern Bases for Cellular Automata", Physica D 69 (1993) 279-301.
[Abstract] [ps.gz] [pdf]
Santa Fe Institute Working Paper 93-03-010.

J. P. Crutchfield and J. E. Hanson, "Attractor Vicinity Decay for a Cellular Automaton", CHAOS 3:2 (1993) 215-224.
[Abstract] [pdf] [ps.gz]

J. P. Crutchfield, "Unreconstructible at Any Radius", Physics Letters A 171 (1992) 52-60.
[Abstract] [pdf] [ps.gz]

J. P. Crutchfield, "Discovering Coherent Structures in Nonlinear Spatial Systems", in Nonlinear Dynamics of Ocean Waves, A. Brandt, S. Ramberg, and M. Shlesinger, editors, World Scientific, Singapore (1992) 190-216.
[Abstract] [ps.gz] (Main portion)
Santa Fe Institute Working Paper 91-09-034.

J. E. Hanson and J. P. Crutchfield, "The Attractor-Basin Portrait of a Cellular Automaton", J. Statistical Physics 66 (1992) 1415-1462.
[Abstract] [pdf] [ps.gz]
Santa Fe Institute Working Paper 91-02-012.

Stochastic and Quantum Computation

K. Wiesner and J. P. Crutchfield, "Computation in Sofic Quantum Dynamical Systems", Natural Computing 7:1 (2008) doi:10.1007/978-3-540-73554-0_20. Reprinted in Unconventional Computing, S.G. Akl, C. S. Calude, M. J. Dinneen, G. Rozenberg, and H. T. Wareham, editors, Lecture Notes in Computer Science 4618 (2007) 214-225.
[Abstract] [pdf]
Santa Fe Institute Working Paper 07-05-007. arxiv.org e-print arxiv:0704.3075.
J. P. Crutchfield and K. Wiesner, "Intrinsic Quantum Computation", Physics Letters A 374:4 (2008) 375-380.
[Abstract] [pdf]
Santa Fe Institute Working Paper 06-11-045. arxiv.org e-print quant-ph/0611202.
K. Wiesner and J. P. Crutchfield, "Infinite Correlation in Measured Quantum Processes", Quantum Information Processing Workshop (2007) submitted.
[Abstract] [pdf]
Santa Fe Institute Working Paper 06-11-043. arxiv.org e-print quant-ph/0611143.
K. Wiesner and J. P. Crutchfield, "Computation in Finitary Stochastic and Quantum Processes", Physica D 237:9 (2008) 1173-1195.
[Abstract] [pdf]
Santa Fe Institute Working Paper 06-09-031. arxiv.org e-print quant-ph/0608206. Digital Object Identifier (DOI).
K. Wiesner and J. P. Crutchfield, "Language Diversity of Measured Quantum Processes", Intl. J. Unconventional Computing 4:1 (2008) 99-112, and in From Utopian to Genuine Unconventional Computers, A. Adamatzky and C. Teuscher, editors, Luniver Press, Beckington, United Kingdom (2006) 137-156.
[Abstract] [pdf]
Santa Fe Institute Working Paper 06-11-046. arxiv.org e-print quant-ph/0611203.
C. Moore and and J. P. Crutchfield, "Quantum Automata and Quantum Grammars", Theoretical Computer Science 237 (2000) 275-306.
[Abstract] [ps.gz]
Santa Fe Institute Working Paper 97-07-062.

Earlier Related Work

J. P. Crutchfield and B. McNamara, "Equations of Motion from a Data Series", Complex Systems 1:3 (1987) 417-452.
[Abstract] [pdf, no figures] [pdf, original scanned] [ps, no figures] [ps.gz]

J. P. Crutchfield, "Spatio-Temporal Complexity in Nonlinear Image Processing", IEEE Trans. Circuits Systems 35D:7 (1988) 770-780.
[Abstract] [pdf]
D. Campbell, J. P. Crutchfield, J. D. Farmer, and E. Jen, "Experimental Mathematics: The Role of Computation in Nonlinear Science", in Commun. Assoc. Comput. Mach. 28 (1985) 374-384.
[Abstract] [pdf]
J. P. Crutchfield, "Space-time Dynamics In Video Feedback", Physica 10D (1984) 229-245.
[Abstract] [pdf]

J. P. Crutchfield and N. H. Packard, "Symbolic Dynamics of Noisy Chaos", in Physica 7D (1983) 201-223.
[Abstract] [pdf]

J. P. Crutchfield, "Noisy Chaos", Ph.D. Dissertation, University of California, Santa Cruz (August 1983).
[Abstract] [ps.gz]

J. P. Crutchfield and N. H. Packard, "Noise Scaling of Symbolic Dynamics Entropies", in Evolution of Order and Chaos, ed. H. Haken, Springer-Verlag, Berlin (1982) 215-227.
[Abstract] [ps.gz]

P. Collet, J. P. Crutchfield, and J.-P. Eckmann, "Computing the Topological Entropy of Maps", Commun. Math. Phys. 88 (1983) 257-262.
[Abstract] [ps.gz]

J. P. Crutchfield and N. H. Packard, "Symbolic Dynamics of One-Dimensional Maps: Entropies, Finite Precision, and Noise", Intl. J. Theo. Phys. 21 (1982) 433-466.
[Abstract] [pdf]

N. H. Packard, J. P. Crutchfield, J. D. Farmer, and R. S. Shaw, "Geometry from a Time Series", Phys. Rev. Let. 45 (1980) 712-716.
[Abstract] [ps.gz]

Dissertations

C. Aghamohammadi, "Memory and Thermodynamic Costs of Sampling and Biased Sampling", Ph.D. Dissertation, Physics Department, University of California, Daivs (December 2018).
[Abstract] [pdf]

D. J. Albers, "A Qualitative Numerical Study of High Dimensional Dynamical Systems", Ph.D. Dissertation, Physics Department, University of Wisconsin, Madison (August 2004).
[Abstract] [pdf]

A. B. Boyd, "Thermodynamics of Correlations and Structure in Information Engines", Ph.D. Dissertation, Physics Department, University of California, Davis (December 2017).
[Abstract] [pdf]

J. P. Crutchfield, "Noisy Chaos", Ph.D. Dissertation, Physics Department, University of California, Santa Cruz (September 1983).
[Abstract] [pdf]

R. Das

D. P. Feldman, "Computational Mechanics of Classical Spin Systems", Ph.D. Dissertation, Physics Department, University of California, Davis (September, 1998).
[Abstract] [ps.gz]� [ps] [pdf]

D. Gier, "Stochastic Quantum Information Processing with Separable Qudit Processes", Ph.D. Dissertation, Physics Department, University of California, Davis (September, 2023).
[Abstract] [pdf]

A. M. Jurgens, "On Infinite Complexity: Quantifying the Randomness and Structure of Hidden Markov Processes", Ph.D. Dissertation, University of California, Davis (August 2021).
[Abstract] [pdf]
R. G. James, "Measures and Metrics of Information Processing in Complex Systems: A Rope of Sand", Ph.D. Dissertation, University of California, Davis (June 2013).
[Abstract] [pdf]

J. E. Hanson, "Computational Mechanics of Cellular Automata", Ph.D. Dissertation, University of California, Berkeley (August 1993).
[Abstract] [ps.gz]

W. Hordijk

P. M. Riechers, “Exact Results Regarding the Physics of Complex Systems via Linear Algebra, Hidden Markov Models, and Information Theory”, Ph.D. Dissertation, Physics Department, University of California at Davis, December 2016.
[Abstract] [pdf]

C. R. Shalizi, "Causal Architecture, Complexity and Self-Organization in Time Series and Cellular Automata", Ph.D. Dissertation, Physics Department, University of Wisconsin-Madison, May 2001.
[Abstract] [pdf]

N. F. Travers, "Bounds on Convergence of Entropy Rate Approximations in Hidden Markov Processes", Ph.D. Dissertation, University of California, Davis (June 2013).
[Abstract] [pdf]

D. R. Upper, "Theory and Algorithms for Hidden Markov Models and Generalized Hidden Markov Models", Ph.D. Dissertation, Mathematics Department, University of California (February 1997).
[Abstract] [ps.gz] [gzipped pdf]

D. P. Varn, "Languge Extraction from ZnS", Ph.D. Dissertation, Physics Department, University of Tennessee, Knoxville (December, 2001).
[Abstract] [pdf] [ps.gz]� [ps]

S. H. Whalen, "Security Applications of the ε-Machine", Ph.D. Dissertation, Computer Science Department, University of California, Davis (June, 2010).
[Abstract] [pdf]
K. Young, "The Grammar and Statistical Mechanics of Complex Physical Systems", Ph.D. Dissertation, University of California, Santa Cruz (August 1991).
[Abstract] [pdf]