Publications
My papers span a range of different disciplines, all driven by a better understanding of the causal mechanisms and reprogramming capabilities of dynamic biological and artificial systems.
In Journals
# means co-first author if not listed first. * means corresponding author. ^ means sorted alphabetically.
J58. Ab initio Causal Deconvolution of Intertwined Generating Mechanisms
H. Zenil*, N.A. Kiani, A. Zea, J. Tegnér
submitted [preprint]
J57. Training-free DNA Sequence Complexity Reveals Structure Beyond GC Content in Nucleosome Occupancy
H. Zenil*, P. Minary
submitted [preprint]
J56. Numerical Explorations of Resource-bounded Measures of Sophistication and Logical Depth with Application to Deep Pattern Classification
H. Zenil*, L. Badillo and F. Soler-Toscano
submitted [preprint coming soon]
J55. Unsupervised and Universal Data Reduction and Network Sparsification Methods By Minimal Algorithmic Information Loss
H. Zenil*, N.A. Kiani, A. Rueda-Toicen, J. Tegnér
submitted [preprint]
J54. An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
H Zenil*, N.A. Kiani, F. Marabita, Y. Deng, S. Elias, A. Schmidt, G. Ball, J. Tegnér
submitted [preprint, video]
J53. Algorithmically probable mutations reproduce aspects of evolution such as convergence rate, genetic memory, modularity, diversity explosions, and mass extinction
S. Hernández-Orozco, H. Zenil* and N.A. Kiani
submitted [preprint]
J52. A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity
H. Zenil*, S. Hernández-Orozco, N.A. Kiani, F. Soler-Toscano, A. Rueda-Toicen
submitted [preprint]
J51. Algorithmic Information Dynamics of Persistent Patterns and Colliding Particles in the Game of Life
H. Zenil*, N.A. Kiani and J. Tegnér
Entropy (forthcoming) [preprint]
J50. Information-theoretic Guided Machine Learning Approach to Low-cost Microscopy Image Analysis in the Evaluation of Tissue Complexity and Population Cell Repertoire
H. Zenil*, S. Rad Pour, N.A. Kiani and J. Tegnér
submitted [preprint coming soon]
J49. Observability and Sensitivity in the Reconstruction of Generative Models of Dynamical Systems
H. Zenil*, Y. Zhang and N.A. Kiani
submitted [preprint coming soon]
J48. Symmetry and Algorithmic Information of Graphs and Polyhedral Networks in Application to Molecular Complexity
H. Zenil*, N.A. Kiani and J. Tegnér
submitted [preprint]
J47. Coding-theorem Like Behaviour and Emergence of the Universal Distribution from Resource-bounded Algorithmic Probability
H. Zenil*, L. Badillo, S. Hernández-Orozco and F. Hernandez-Quiroz
International Journal of Parallel Emergent and Distributed Systems, 2018 DOI: 10.1080/17445760.2018.1448932 [online]
J46. Rule Primality, Minimal Generating Sets, Turing-Universality and Causal Decomposition in Elementary Cellular Automata
J. Riedel and H. Zenil^*
accepted Journal of Cellular Automata [preprint]
J45. Algorithmic Complexity and Reprogrammability of Chemical Structure Networks
H. Zenil*, N.A. Kiani, M-M. Shang, J. Tegnér
accepted Parallel Processing Letters [preprint]
J44. Cross-boundary Behavioural Reprogrammability Reveals Evidence of Pervasive Universality
J. Riedel, H. Zenil^*
accepted International Journal of Unconventional Computing [preprint]
J43. Slime mould: the fundamental mechanisms of biological cognition
J. Vallverdú, O. Castro, R. Mayne, M. Talanov, M. Levine, F. Baluska, Y. Gunji, A. Dussutourg, H. Zenil, A. Adamatzky
BioSystems, vol. 165, pp 57-70, 2018. [online, preprint] (Elsevier)
J42. Approximations of Algorithmic and Structural Complexity Validate Cognitive-behavioural Experimental Results
H. Zenil*, J.A.R. Marshall, J. Tegnér
submitted [preprint]
J41. Rare Speed-up in Automatic Theorem Proving Reveals Tradeoff Between Computational Time and Information Value
S. Hernández-Orozco, H. Zenil*, F. Hernández-Quiroz, W. Sieg
submitted [preprint]
J40. The Limits of Decidable States on Open-Ended Evolution and Emergence
S. Hernández-Orozco, F. Hernández-Quiroz and H. Zenil*
Artificial Life, vol. 24:1, pp. 56--70, 2018 [online, preprint] (MIT)
J39. A Computable Measure of Algorithmic Probability by Finite Approximations with an Application to Integer Sequences
F. Soler-Toscano, H. Zenil*
Complexity vol. 2017 (2017), Article ID 7208216 [online, preprint] (Wiley/Hindawi)
J38. Reprogramming Matter, Life and Purpose
H. Zenil
International Journal of Unconventional Computing, vol. 13.3, p. 221--233, 2017. [online, preprint] (OCP)
J37. HiDi: An efficient reverse engineering schema for large scale dynamic regulatory network reconstruction using adaptive differentiation
Y. Deng, H. Zenil*, J. Tegnér, N.A. Kiani
Bioinformatics btx501, 2017. [preprint, online] (Oxford)
J36. East-West Paths to Unconventional Computing: Complexity in Causality
S. Akl, M. Burgin, C.S. Calude, M.M. Dehshibi, Y. Gunji, Z. Konkoli, B. Maclenna, B. Marchal, M. Margenstern, G.J. Martinez, R. Mayne, K. Morita, A. Schumann, G.Ch. Sirakoulis, K. Svozil, H. Zenil, A. Adamatzky
Progress in Biophysics & Molecular Biology, 131:469--493, 2017. doi: 10.1016/j.pbiomolbio.2017.08.004. [online, preprint] (Elsevier)
J35. Low Algorithmic Complexity Entropy-deceiving Graphs
H. Zenil*, N.A. Kiani and J. Tegnér
Physical Review E 96, 012308, 2017. [online] (APS)
J34. Formal Definitions of Unbounded Evolution and Innovation Reveal Universal Mechanisms for Open-Ended Evolution in Dynamical Systems
A. Adams, H. Zenil, P.W.C. Davies, S.I. Walker
Scientific Reports 7, No:997, 2017. [online] (NPG)
J33. Human Behavioral Complexity Peaks at Age 25
N. Gauvrit, H. Zenil*, F. Soler-Toscano, J.-P. Delahaye, P. Brugger
PLoS Comput Biol 13(4): e1005408, 2017. [online, video] (PLOS)
J32. Perspective on Bridging Scales and Design of Models using Low-Dimensional Manifolds & Data-driven Model Inference
J. Tegner, H. Zenil, N.A. Kiani, G. Ball, D. Gomez-Cabrero
Philosophical Transactions of the Royal Society A, volume 374, issue 2080, 2016. [online] (Royal Society)
J31. Empirical Assessment of Causal Network Learning through a Community-based Effort
i.a. H. Zenil (DREAM Challenge Consortium)
Nature Methods 13, pp. 310–318, 2016. doi:10.1038/nmeth.3773 [online] (NPG)
J30. Methods of Information Theory and Algorithmic Complexity for Network Biology
H. Zenil*, N.A. Kiani and J. Tegnér
Seminars in Cell and Developmental Biology, vol. 51, pp. 32-43, 2016. doi:10.1016/j.semcdb.2016.01.011 [online, preprint] (Elsevier)
J29. Fractal Dimension versus Process Complexity
J.J. Joosten, F. Soler-Toscano, and H. Zenil*
Advances in Mathematical Physics vol. 2016, Article ID 5030593 [online] (Hindawi)
J28. Flow of Information in Biological Systems (editorial to special issue)
A. Masoudi-Nejad and H. Zenil*
Seminars in Cell and Developmental Biology, vol. 51 pp 1-2, 2016. [online] (Elsevier)
J27. Quantifying Loss of Information in Network-based Dimensionality Reduction Techniques
H. Zenil*, N.A. Kiani, J. Tegnér
Journal of Complex Networks, vol. 4:(3) pp. 342-362, 2016. [online, preprint] (Oxford)
J26. Evaluating Network Inference Methods in Terms of Their Ability to Preserve the Topology and Complexity of Genetic Networks
N.A. Kiani, H. Zenil*#, J. Olczak and J. Tegnér
Seminars in Cell and Developmental Biology, vol. 51, pp. 44-52, 2016. doi:10.1016/j.semcdb.2016.01.012, [online, preprint] (Elsevier)
J25. Algorithmic complexity for psychology: A user-friendly implementation of the coding theorem method
N. Gauvrit, H. Singmann, F. Soler-Toscano, H. Zenil*
Behavior Research Methods, Volume 48, Issue 1, pp. 1-16, 2015. doi:10.3758/s13428-015-0574-3 [preprint, online] (Springer)
J24. Algorithmicity and Programmability in Natural Computing with the Game of Life as an In Silico Case Study
H. Zenil
Journal of Experimental & Theoretical Artificial Intelligence, Volume 27, Issue 1, pp. 109-121, 2015. [online] (Taylor & Francis)
J23. Complexity Measurement Based on Information Theory and Kolmogorov Complexity
L. Ting Lui, G. Terrazas, H. Zenil, C. Alexander and N. Krasnogor
Artificial Life, vol. 21:2, pp. 205-24 2015. (MIT Press)
J22. Two-Dimensional Kolmogorov Complexity and Validation of the Coding Theorem Method by Compressibility
H. Zenil, F. Soler-Toscano, J.-P. Delahaye and N. Gauvrit
PeerJ Computer Science, 1:e23, 2015. [online] (PeerJ)
J21. Natural Scene Statistics Mediate the Perception of Image Complexity
N. Gauvrit, F. Soler-Toscano, H. Zenil*
Visual Cognition, Volume 22, Issue 8, pp. 1084-1091, 2014. [preprint, online] doi: 10.1080/13506285.2014.950365 (Taylor & Francis)
J20. Calculating Kolmogorov Complexity from the Output Frequency Distributions of Small Turing Machines
F. Soler-Toscano, H. Zenil#*^, J.-P. Delahaye and N. Gauvrit
PLoS ONE 9(5): e96223, 2014. [online, data, online program, Mathematica API, R package] doi:10.1371/journal.pone.0096223 (PLOS)
J19. Correlation of Automorphism Group Size and Topological Properties with Program-size Complexity Evaluations of Graphs and Complex Networks
H. Zenil, F. Soler-Toscano, K. Dingle and A. Louis
Physica A: Statistical Mechanics and its Applications, vol. 404, pp. 341–358, 2014. [online, preprint, video]
doi: 10.1016/j.physa.2014.02.060 (Elsevier)
J18. Algorithmic complexity for short binary strings applied to psychology: a primer
N. Gauvrit, H. Zenil*, F. Soler-Toscano and J.-P. Delahaye
Behavior Research Methods, vol. 46-3, pp 732-744, 2014. [preprint, online] doi: 10.3758/s13428-013-0416-0 (Springer)
J17. Correspondence and Independence of Numerical Evaluations of Algorithmic Information Measures
F. Soler-Toscano, H. Zenil#*, J.-P. Delahaye and N. Gauvrit
Computability, vol. 2, no. 2, pp 125-140, 2013. doi:10.3233/COM-13019 [online, preprint] (IOS)
J16. Exploring Programmable Self-Assembly in Non DNA-based Computing
G. Terrazas, H. Zenil and N. Krasnogor
Natural Computing, vol 12(4): 499--515, 2013. doi:10.1007/s11047-013-9397-2 [online, preprint] (Springer)
J15. Asymptotic Behaviour and Ratios of Complexity in Cellular Automata Rule Spaces
H. Zenil
International Journal of Bifurcation and Chaos vol. 23, no. 9, 2013. doi:10.1142/S0218127413501599 [preprint] (WSPC)
J14. Algorithmic Complexity of Financial Motions
L. Ma, O. Brandouy, J.-P. Delahaye and H. Zenil
Research in International Business and Finance, vol. 30, pp. 336-347, 2014. doi:10.1016/j.ribaf.2012.08.001 [online,preprint] (Elsevier)
J13. Turing Patterns with Turing Machines: Emergence and Low-level Structure Formation
H. Zenil
Natural Computing, vol. 12(2): 291-303, 2013, doi:10.1007/s11047-013-9363-z [online, preprint] (Springer)
J12. Computation and Universality: Class IV versus Class III Cellular Automata
G.J. Martinez, J.C. Seck-Touh-Mora and H. Zenil
Journal of Cellular Automata, vol. 7, no. 5-6, pp. 393-430, 2013. (OCP)
J11. Some Aspects of Computation Essential to Evolution and Life
H. Zenil and J.A.R. Marshall
Ubiquity, vol. 2013, no. April, pp 1-16. [online, preprint] (ACM)
J10. Life as Thermodynamic Evidence of Algorithmic Structure in Natural Environments
H. Zenil*, C. Gershenson, J.A.R. Marshall and D. Rosenblueth
Entropy, 14(11), 2173-2191, 2012. [online] doi:10.3390/e14112173 (MDPI)
J9. What is Nature-like Computation? A Behavioural Approach and a Notion of Programmability
H. Zenil
Philosophy & Technology, vol 27-3, pp 399--421, 2014. (online: 2012). [online, preprint] doi:10.1007/s13347-012-0095-2 (Springer)
J8. Sloane’s Gap: Do Mathematical and Social Factors Explain the Distribution of Numbers in the OEIS?
N. Gauvrit, J.-P. Delahaye and H. Zenil
Journal of Humanistic Mathematics, vol. 3, no. 1, pp. 3-19, 2013. [preprint, featured in Numberphile] doi:10.5642/jhummath.201301.03 (Claremont College)
J7. On the Dynamic Qualitative Behaviour of Universal Computation
H. Zenil
Complex Systems, 20-3, pp 265-277, 2012. [online,preprint] (Complex Systems)
J6. Numerical Evaluation of the Complexity of Short Strings: A Glance Into the Innermost Structure of Algorithmic Randomness
J.-P. Delahaye and H. Zenil#*^
Applied Mathematics and Computation 219, pp. 63-77, 2012. [preprint] doi:10.1016/j.amc.2011.10.006 (online 2011) (Elsevier)
J5. Empirical Encounters with Computational Irreducibility and Unpredictability
H. Zenil, F. Soler-Toscano and J.J. Joosten
Minds and Machines, vol. 22, Number 3, pp. 149-165, 2012. [preprint]. doi: 10.1007/s11023-011-9262-y (Springer)
J4. Image Information Content Characterization and Classification by Physical Complexity
H. Zenil*, J.-P. Delahaye and C. Gaucherel
Complexity, vol. 17-3, pages 26-42, 2012. [preprint] doi:10.1002/cplx.20388 (Wiley)
J3. Program-size versus Time complexity, Slowdown and speed-up phenomena in the micro-cosmos of small Turing machines
J.J. Joosten, F. Soler Toscano and H. Zenil#*
International Journal of Unconventional Computing, vol. 7, no. 5, pp. 353-387, 2011. [preprint] (OCP)
J2. An Algorithmic Information-theoretic Approach to the Behaviour of Financial Markets
H. Zenil* and J.-P. Delahaye
Journal of Economic Surveys, vol. 25-3, pp. 431-463, 2011. [preprint] doi:10.1111/j.1467-6419.2010.00666.x (Wiley)
J1. Compression-based Investigation of the Dynamical Properties of Cellular Automata and Other Systems
H. Zenil
Complex Systems, vol. 19, No. 1, pp. 1-28, 2010. [online]
In Proceedings and Chapters
P36. Predictive Systems Toxicology
N.A. Kiani, M. Shang, H. Zenil and J. Tegnér
In Orazio Nicolotti (ed.), Computational Toxicology - Methods and Protocols, Methods in Molecular Biology, Springer, 2017 [preprint]
P35. Approximations to Algorithmic Probability
H. Zenil
In Robert A. Meyers (ed), 2nd. Edition of the Springer Encyclopedia of Complexity and Systems Science, 2017
P34. Cognition and the Algorithmic Nature of the Mind
H. Zenil
In Robert A. Meyers (ed), 2nd. Edition of the Springer Encyclopedia of Complexity and Systems Science, 2017
P33. Is there any Real Substance to the Claims for a 'New Computationalism'?
A. Hernández-Espinosa, F. Hernández-Quiroz and H. Zenil (invited paper)
In J. Kari, F. Manea, I. Petre (eds) Unveiling Dynamics and Complexity (Computability in Europe 2017), Springer Verlag, 2017. [preprint]
P32. Quantifying Non-trivial Open-Ended Evolution Reveals Necessary and Sufficient Conditions
A. Adams, H. Zenil, P.C.W. Davies and S.I. Walker
Second Workshop on Open-Ended Evolution, 15th International Conference on the Synthesis and Simulation of Living Systems (ALIFE), 2016. [online, preprint]
P31. Undecidability and Irreducibility Conditions for Open-Ended Evolution and Emergence
S. Hernández-Orozco, F. Hernández-Quiroz and H. Zenil*
15th International Conference on the Synthesis and Simulation of Living Systems, Artificial Life Conference (ALIFE), MIT Press, 2016. [online, preprint]
P30. Causality, Information and Biological Computation
H. Zenil, A. Schmidt, J. Tegnér
In S I. Walker, P.C.W. Davies and G. Ellis (eds.), Information and Causality: From Matter to Life,
Cambridge University Press, pp. 244-279, 2017 [preprint, Amazon]
P29. Algorithmic Data Analytics, Small Data Matters and Correlation versus Causation
H. Zenil
In M. Ott, W. Pietsch, J. Wernecke (eds.), Berechenbarkeit der Welt? Philosophie und Wissenschaft im Zeitalter von Big Data (Computability of the World? Philosophy and Science in the Age of Big Data)
Springer Verlag, pp 453-475, 2017 [preprint]
P28. Asymptotic Intrinsic Universality and Reprogrammability by Behavioural Emulation
H. Zenil and J. Riedel
Invited contribution in Advances in Unconventional Computation. A. Adamatzky (ed)
Springer Verlag, pp. 205-220, 2016. [preprint]
P27. Topological Evaluation of Methods for Reconstruction of Genetic Regulatory Networks
J. Olczak, N.A. Kiani, H. Zenil* and J. Tegnér
Proceedings of the IEEE Workshop on Complex Networks, SITIS, Bangkok 2015. [online program]
P26. The Information-theoretic and Algorithmic Approach to Human, Animal and Artificial Cognition
N. Gauvrit, H. Zenil#, J. Tegnér
In G. Dodig-Crnkovic and R. Giovagnoli (Eds.) Representation and reality : Humans, animals and machines.
Springer, pp 117-139, 2017 [preprint]
P25. Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues
H. Zenil, N.A. Kiani, J. Tegnér
In F. Ortuño & I. Rojas (Eds.): 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO) 2015, Part II,
LNCS 9044, pp. 395--405. Springer, 2015. [preprint, online]
P24. The Effects of Global Rules on Interacting Cellular Automata
A. Adams, H. Zenil, E. Reyes, J. Joosten
In J. Kari, I. Törmä, M. Szabados (Eds.), 21st International Workshop on Cellular Automata and Discrete Complex Systems
AUTOMATA 2015, TUCS Lecture Notes, 2015. [slides online]
P23. Quantifying Natural and Artificial Intelligence in Robots and Natural Systems with an Algorithmic Behavioural Test
H. Zenil
In F.P. Bonsignorio, A.P. del Pobil, E. Messina, J. Hallam (eds.), Metrics of sensory motor integration in robots and animals
Springer Cosmos Series, Cognitive Systems Monographs, Springer, (to appear) [preprint]
P22. Programmability: A Turing Test Approach to Computation
H. Zenil
In L. De Mol and G. Primiero (eds.), Turing in Context, Koninklijke Vlaamse Academie van België voor Wetenschappen en Kunsten
(Belgian Academy of Sciences and Arts), Contactforum, 2014.
P21. Gene Sequence Walks
H. Zenil, V. Kannan, J. Tegnér
Visualizing Biological Data conference
EMBO - EMBL VizBi 2014, Heidelberg, Germany (poster and lighting talk).
P20. Algorithmic complexity of motifs clusters superfamilies of networks
H. Zenil, N.A. Kiani and J. Tegner
IEEE International Conference on Bioinformatics and Biomedicine, pp 74 - 76, Shanghai, China 2013. [online] DOI: 10.1109/BIBM.2013.6732768
P19. Algorithmic Complexity of Animal Behaviour: From Communication to Cognition
H. Zenil
International Conference on the Theory and Practice of Natural Computing (TPNC) 2013. Cáceres, Spain, (poster), Cáceres, Spain
P18. Fractal Dimension of Space-time Diagrams and the Runtime Complexity of Small Turing Machines
J.J. Joosten, F. Soler-Toscano, H. Zenil
In T. Neary and M. Cook (Eds.), Machines, Computations and Universality (MCU 2013),
EPTCS 128, 2013, pp. 29-30, DOI: 10.4204/EPTCS.128.9. [abstract, presentation]
P17. Testing Biological Models for Non-linear Sensitivity with a Programmability Test
H. Zenil, G. Ball and J. Tegnér
In P. Liò, O. Miglino, G. Nicosia, S. Nolfi and M. Pavone (eds), Advances in Artificial Intelligence, ECAL 2013, pp. 1222-1223,
MIT Press, 2013. DOI: http://dx.doi.org/10.7551/978-0-262-31719-2-ch188 [online]
P16. Sparsity of Non-trivial Proving Speed-up in Random Systems of Propositional Calculus
S. Hernández-Orozco, F. Hernández-Quiroz and H. Zenil*
In Paola Bonizzoni, Vasco Brattka, Benedikt Löwe (eds.), The Nature of Computation, Logic, Algorithms, Applications,
Proceedings 9th. conference Computability in Europe, CiE 2013.
P15. A Turing Test-Inspired Approach to Natural Computation
H. Zenil
In G. Primiero and L. De Mol (eds.), Turing in Context II, Historical and Contemporary Research in Logic, Computing Machinery and Artificial Intelligence. Proceedings by the Royal Flemish Academy of Belgium for Science and the Arts, Belgium, 2013.
P14. Algorithmic Information Theory
H. Zenil
In The Philosophy of Information An Introduction, The Π Research Network
The UK Society for the Philosophy of Information, 2013 [online]
P13. A Behavioural Foundation for Natural Computing and a Programmability Test
H. Zenil
In G. Dodig-Crnkovic and R. Giovagnoli (eds), Computing Nature: Turing Centenary Perspective, Springer SAPERE Series vol. 7, pp. 87-113, 2013. [online, preprint] [conference picture]
From invited talk at AISB/IACAP Turing World Congress 2012, Birmingham, UK
P12. Wolfram's Classification and Computation in Cellular Automata Classes III and IV
G.J. Martinez, J.C. Seck-Touh-Mora and H. Zenil
In H. Zenil (ed), Irreducibility and Computational Equivalence: Wolfram Science 10 Years After the Publication of A New Kind of Science, Springer, 2013 [preprint]
P11. El Universo Algorítmico
H. Zenil
In, O. Miramontes and K. Volke (eds.) Fronteras de la Física en el Siglo XXI, CopIt arXives, UNAM, 2013 [PDF]
P10. From Computer Runtimes to the Length of Proofs: With an Algorithmic Probabilistic Application to Waiting Times in Automatic Theorem Proving
H. Zenil
In M.J. Dinneen, B. Khousainov, and A. Nies (Eds.), Computation, Physics and Beyond International Workshop on Theoretical Computer Science, WTCS 2012, LNCS 7160, pp. 223-240, Springer, 2012. [preprint] DOI:10.1007/978-3-642-27654-5_17
P9. Fractal Dimension as an Indication of the Terminating Runtime of Discrete Dynamical Systems
J.J. Joosten, H. Zenil and F. Soler-Toscano
In S. Thurner M. Szell (eds), Löcker Verlag, European Conference on Complex Systems (ECCS'11), 2011.
P8. Un método estable para la evaluación de la complejidad algorítmica de cadenas cortas (A Stable Method for the Evaluation of the Algorithmic Complexity of Short Strings).
H. Zenil, and J.-P. Delahaye
In G.J. Martinez, H. Zenil and C.R. Stevens (eds), Complex Systems as Computing Models, Luniver Press, 2011. [preprint]
P7. Complejidad descriptiva y computacional en máquinas de Turing pequeñas
J.J. Joosten, F. Soler-Toscano, H. Zenil#
In Lógica Universal e Unidade da Ciência, Centro de Filosofia das Ciências da Universidade de Lisboa, pp. 11--32, 2011. [preprint]
P6. An Algorithmic Information-theoretic Approach to the Behaviour of Financial Markets.
H. Zenil and J.-P. Delahaye
In S. Zambelli, D.A.R. George (eds.) Nonlinearity, Complexity and Randomness in Economics: Towards Algorithmic Foundations for Economics, Wiley-Blackwell, 2011. [preprint]
P5. Complejidad descriptiva y computacional en máquinas de Turing pequeñas
J.J. Joosten, F. Soler-Toscano and H. Zenil
Actas de las V Jornadas Ibéricas, Lógica Universal e Unidade da Ciência, CFCU 2010. [preprint]
P4. Program-size versus Time complexity, Slowdown and speed-up phenomena in the micro-cosmos of small Turing machines
J.J. Joosten, F. Soler-Toscano and H. Zenil
In H. Guerra (ed.). Physics and Computation 2010, CAMIT, 3rd International Workshop on Physics and Computation 2010. [PDF]
P3. On the Algorithmic Nature of the World
H. Zenil and J-P. Delahaye
In G. Dodig-Crnkovic and M. Burgin (eds), Information and Computation, World Scientific Publishing Company, 2010. [preprint]
P2. On the Kolmogorov-Chaitin complexity for short sequences
J-P. Delahaye and H. Zenil#
In C. Calude (ed) Randomness and Complexity: From Leibniz to Chaitin, World Scientific Publishing Company, 2007. [preprint]
P1. On the Possible Computational Power of the Human Mind
H. Zenil and F. Hernandez-Quiroz
In Worldviews, Science and Us, Philosophy and Complexity, C. Gershenson, D. Aerts, and B. Edmonds (eds),
World Scientific Publishing Company, 2007. [preprint]
Books & Edited Volumes
Theses
Selected Essays and Reviews
Software
Network and Computational Biology
Information Theory, Computational Lingustics & Complexity Theory
Discrete Math, Mathematical Logic & Combinatorics
Automata, Normality & Pseudorandomness
My papers span a range of different disciplines, all driven by a better understanding of the causal mechanisms and reprogramming capabilities of dynamic biological and artificial systems.
In Journals
# means co-first author if not listed first. * means corresponding author. ^ means sorted alphabetically.
J58. Ab initio Causal Deconvolution of Intertwined Generating Mechanisms
H. Zenil*, N.A. Kiani, A. Zea, J. Tegnér
submitted [preprint]
J57. Training-free DNA Sequence Complexity Reveals Structure Beyond GC Content in Nucleosome Occupancy
H. Zenil*, P. Minary
submitted [preprint]
J56. Numerical Explorations of Resource-bounded Measures of Sophistication and Logical Depth with Application to Deep Pattern Classification
H. Zenil*, L. Badillo and F. Soler-Toscano
submitted [preprint coming soon]
J55. Unsupervised and Universal Data Reduction and Network Sparsification Methods By Minimal Algorithmic Information Loss
H. Zenil*, N.A. Kiani, A. Rueda-Toicen, J. Tegnér
submitted [preprint]
J54. An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
H Zenil*, N.A. Kiani, F. Marabita, Y. Deng, S. Elias, A. Schmidt, G. Ball, J. Tegnér
submitted [preprint, video]
J53. Algorithmically probable mutations reproduce aspects of evolution such as convergence rate, genetic memory, modularity, diversity explosions, and mass extinction
S. Hernández-Orozco, H. Zenil* and N.A. Kiani
submitted [preprint]
J52. A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity
H. Zenil*, S. Hernández-Orozco, N.A. Kiani, F. Soler-Toscano, A. Rueda-Toicen
submitted [preprint]
J51. Algorithmic Information Dynamics of Persistent Patterns and Colliding Particles in the Game of Life
H. Zenil*, N.A. Kiani and J. Tegnér
Entropy (forthcoming) [preprint]
J50. Information-theoretic Guided Machine Learning Approach to Low-cost Microscopy Image Analysis in the Evaluation of Tissue Complexity and Population Cell Repertoire
H. Zenil*, S. Rad Pour, N.A. Kiani and J. Tegnér
submitted [preprint coming soon]
J49. Observability and Sensitivity in the Reconstruction of Generative Models of Dynamical Systems
H. Zenil*, Y. Zhang and N.A. Kiani
submitted [preprint coming soon]
J48. Symmetry and Algorithmic Information of Graphs and Polyhedral Networks in Application to Molecular Complexity
H. Zenil*, N.A. Kiani and J. Tegnér
submitted [preprint]
J47. Coding-theorem Like Behaviour and Emergence of the Universal Distribution from Resource-bounded Algorithmic Probability
H. Zenil*, L. Badillo, S. Hernández-Orozco and F. Hernandez-Quiroz
International Journal of Parallel Emergent and Distributed Systems, 2018 DOI: 10.1080/17445760.2018.1448932 [online]
J46. Rule Primality, Minimal Generating Sets, Turing-Universality and Causal Decomposition in Elementary Cellular Automata
J. Riedel and H. Zenil^*
accepted Journal of Cellular Automata [preprint]
J45. Algorithmic Complexity and Reprogrammability of Chemical Structure Networks
H. Zenil*, N.A. Kiani, M-M. Shang, J. Tegnér
accepted Parallel Processing Letters [preprint]
J44. Cross-boundary Behavioural Reprogrammability Reveals Evidence of Pervasive Universality
J. Riedel, H. Zenil^*
accepted International Journal of Unconventional Computing [preprint]
J43. Slime mould: the fundamental mechanisms of biological cognition
J. Vallverdú, O. Castro, R. Mayne, M. Talanov, M. Levine, F. Baluska, Y. Gunji, A. Dussutourg, H. Zenil, A. Adamatzky
BioSystems, vol. 165, pp 57-70, 2018. [online, preprint] (Elsevier)
J42. Approximations of Algorithmic and Structural Complexity Validate Cognitive-behavioural Experimental Results
H. Zenil*, J.A.R. Marshall, J. Tegnér
submitted [preprint]
J41. Rare Speed-up in Automatic Theorem Proving Reveals Tradeoff Between Computational Time and Information Value
S. Hernández-Orozco, H. Zenil*, F. Hernández-Quiroz, W. Sieg
submitted [preprint]
J40. The Limits of Decidable States on Open-Ended Evolution and Emergence
S. Hernández-Orozco, F. Hernández-Quiroz and H. Zenil*
Artificial Life, vol. 24:1, pp. 56--70, 2018 [online, preprint] (MIT)
J39. A Computable Measure of Algorithmic Probability by Finite Approximations with an Application to Integer Sequences
F. Soler-Toscano, H. Zenil*
Complexity vol. 2017 (2017), Article ID 7208216 [online, preprint] (Wiley/Hindawi)
J38. Reprogramming Matter, Life and Purpose
H. Zenil
International Journal of Unconventional Computing, vol. 13.3, p. 221--233, 2017. [online, preprint] (OCP)
J37. HiDi: An efficient reverse engineering schema for large scale dynamic regulatory network reconstruction using adaptive differentiation
Y. Deng, H. Zenil*, J. Tegnér, N.A. Kiani
Bioinformatics btx501, 2017. [preprint, online] (Oxford)
J36. East-West Paths to Unconventional Computing: Complexity in Causality
S. Akl, M. Burgin, C.S. Calude, M.M. Dehshibi, Y. Gunji, Z. Konkoli, B. Maclenna, B. Marchal, M. Margenstern, G.J. Martinez, R. Mayne, K. Morita, A. Schumann, G.Ch. Sirakoulis, K. Svozil, H. Zenil, A. Adamatzky
Progress in Biophysics & Molecular Biology, 131:469--493, 2017. doi: 10.1016/j.pbiomolbio.2017.08.004. [online, preprint] (Elsevier)
J35. Low Algorithmic Complexity Entropy-deceiving Graphs
H. Zenil*, N.A. Kiani and J. Tegnér
Physical Review E 96, 012308, 2017. [online] (APS)
J34. Formal Definitions of Unbounded Evolution and Innovation Reveal Universal Mechanisms for Open-Ended Evolution in Dynamical Systems
A. Adams, H. Zenil, P.W.C. Davies, S.I. Walker
Scientific Reports 7, No:997, 2017. [online] (NPG)
J33. Human Behavioral Complexity Peaks at Age 25
N. Gauvrit, H. Zenil*, F. Soler-Toscano, J.-P. Delahaye, P. Brugger
PLoS Comput Biol 13(4): e1005408, 2017. [online, video] (PLOS)
J32. Perspective on Bridging Scales and Design of Models using Low-Dimensional Manifolds & Data-driven Model Inference
J. Tegner, H. Zenil, N.A. Kiani, G. Ball, D. Gomez-Cabrero
Philosophical Transactions of the Royal Society A, volume 374, issue 2080, 2016. [online] (Royal Society)
J31. Empirical Assessment of Causal Network Learning through a Community-based Effort
i.a. H. Zenil (DREAM Challenge Consortium)
Nature Methods 13, pp. 310–318, 2016. doi:10.1038/nmeth.3773 [online] (NPG)
J30. Methods of Information Theory and Algorithmic Complexity for Network Biology
H. Zenil*, N.A. Kiani and J. Tegnér
Seminars in Cell and Developmental Biology, vol. 51, pp. 32-43, 2016. doi:10.1016/j.semcdb.2016.01.011 [online, preprint] (Elsevier)
J29. Fractal Dimension versus Process Complexity
J.J. Joosten, F. Soler-Toscano, and H. Zenil*
Advances in Mathematical Physics vol. 2016, Article ID 5030593 [online] (Hindawi)
J28. Flow of Information in Biological Systems (editorial to special issue)
A. Masoudi-Nejad and H. Zenil*
Seminars in Cell and Developmental Biology, vol. 51 pp 1-2, 2016. [online] (Elsevier)
J27. Quantifying Loss of Information in Network-based Dimensionality Reduction Techniques
H. Zenil*, N.A. Kiani, J. Tegnér
Journal of Complex Networks, vol. 4:(3) pp. 342-362, 2016. [online, preprint] (Oxford)
J26. Evaluating Network Inference Methods in Terms of Their Ability to Preserve the Topology and Complexity of Genetic Networks
N.A. Kiani, H. Zenil*#, J. Olczak and J. Tegnér
Seminars in Cell and Developmental Biology, vol. 51, pp. 44-52, 2016. doi:10.1016/j.semcdb.2016.01.012, [online, preprint] (Elsevier)
J25. Algorithmic complexity for psychology: A user-friendly implementation of the coding theorem method
N. Gauvrit, H. Singmann, F. Soler-Toscano, H. Zenil*
Behavior Research Methods, Volume 48, Issue 1, pp. 1-16, 2015. doi:10.3758/s13428-015-0574-3 [preprint, online] (Springer)
J24. Algorithmicity and Programmability in Natural Computing with the Game of Life as an In Silico Case Study
H. Zenil
Journal of Experimental & Theoretical Artificial Intelligence, Volume 27, Issue 1, pp. 109-121, 2015. [online] (Taylor & Francis)
J23. Complexity Measurement Based on Information Theory and Kolmogorov Complexity
L. Ting Lui, G. Terrazas, H. Zenil, C. Alexander and N. Krasnogor
Artificial Life, vol. 21:2, pp. 205-24 2015. (MIT Press)
J22. Two-Dimensional Kolmogorov Complexity and Validation of the Coding Theorem Method by Compressibility
H. Zenil, F. Soler-Toscano, J.-P. Delahaye and N. Gauvrit
PeerJ Computer Science, 1:e23, 2015. [online] (PeerJ)
J21. Natural Scene Statistics Mediate the Perception of Image Complexity
N. Gauvrit, F. Soler-Toscano, H. Zenil*
Visual Cognition, Volume 22, Issue 8, pp. 1084-1091, 2014. [preprint, online] doi: 10.1080/13506285.2014.950365 (Taylor & Francis)
J20. Calculating Kolmogorov Complexity from the Output Frequency Distributions of Small Turing Machines
F. Soler-Toscano, H. Zenil#*^, J.-P. Delahaye and N. Gauvrit
PLoS ONE 9(5): e96223, 2014. [online, data, online program, Mathematica API, R package] doi:10.1371/journal.pone.0096223 (PLOS)
J19. Correlation of Automorphism Group Size and Topological Properties with Program-size Complexity Evaluations of Graphs and Complex Networks
H. Zenil, F. Soler-Toscano, K. Dingle and A. Louis
Physica A: Statistical Mechanics and its Applications, vol. 404, pp. 341–358, 2014. [online, preprint, video]
doi: 10.1016/j.physa.2014.02.060 (Elsevier)
J18. Algorithmic complexity for short binary strings applied to psychology: a primer
N. Gauvrit, H. Zenil*, F. Soler-Toscano and J.-P. Delahaye
Behavior Research Methods, vol. 46-3, pp 732-744, 2014. [preprint, online] doi: 10.3758/s13428-013-0416-0 (Springer)
J17. Correspondence and Independence of Numerical Evaluations of Algorithmic Information Measures
F. Soler-Toscano, H. Zenil#*, J.-P. Delahaye and N. Gauvrit
Computability, vol. 2, no. 2, pp 125-140, 2013. doi:10.3233/COM-13019 [online, preprint] (IOS)
J16. Exploring Programmable Self-Assembly in Non DNA-based Computing
G. Terrazas, H. Zenil and N. Krasnogor
Natural Computing, vol 12(4): 499--515, 2013. doi:10.1007/s11047-013-9397-2 [online, preprint] (Springer)
J15. Asymptotic Behaviour and Ratios of Complexity in Cellular Automata Rule Spaces
H. Zenil
International Journal of Bifurcation and Chaos vol. 23, no. 9, 2013. doi:10.1142/S0218127413501599 [preprint] (WSPC)
J14. Algorithmic Complexity of Financial Motions
L. Ma, O. Brandouy, J.-P. Delahaye and H. Zenil
Research in International Business and Finance, vol. 30, pp. 336-347, 2014. doi:10.1016/j.ribaf.2012.08.001 [online,preprint] (Elsevier)
J13. Turing Patterns with Turing Machines: Emergence and Low-level Structure Formation
H. Zenil
Natural Computing, vol. 12(2): 291-303, 2013, doi:10.1007/s11047-013-9363-z [online, preprint] (Springer)
J12. Computation and Universality: Class IV versus Class III Cellular Automata
G.J. Martinez, J.C. Seck-Touh-Mora and H. Zenil
Journal of Cellular Automata, vol. 7, no. 5-6, pp. 393-430, 2013. (OCP)
J11. Some Aspects of Computation Essential to Evolution and Life
H. Zenil and J.A.R. Marshall
Ubiquity, vol. 2013, no. April, pp 1-16. [online, preprint] (ACM)
J10. Life as Thermodynamic Evidence of Algorithmic Structure in Natural Environments
H. Zenil*, C. Gershenson, J.A.R. Marshall and D. Rosenblueth
Entropy, 14(11), 2173-2191, 2012. [online] doi:10.3390/e14112173 (MDPI)
J9. What is Nature-like Computation? A Behavioural Approach and a Notion of Programmability
H. Zenil
Philosophy & Technology, vol 27-3, pp 399--421, 2014. (online: 2012). [online, preprint] doi:10.1007/s13347-012-0095-2 (Springer)
J8. Sloane’s Gap: Do Mathematical and Social Factors Explain the Distribution of Numbers in the OEIS?
N. Gauvrit, J.-P. Delahaye and H. Zenil
Journal of Humanistic Mathematics, vol. 3, no. 1, pp. 3-19, 2013. [preprint, featured in Numberphile] doi:10.5642/jhummath.201301.03 (Claremont College)
J7. On the Dynamic Qualitative Behaviour of Universal Computation
H. Zenil
Complex Systems, 20-3, pp 265-277, 2012. [online,preprint] (Complex Systems)
J6. Numerical Evaluation of the Complexity of Short Strings: A Glance Into the Innermost Structure of Algorithmic Randomness
J.-P. Delahaye and H. Zenil#*^
Applied Mathematics and Computation 219, pp. 63-77, 2012. [preprint] doi:10.1016/j.amc.2011.10.006 (online 2011) (Elsevier)
J5. Empirical Encounters with Computational Irreducibility and Unpredictability
H. Zenil, F. Soler-Toscano and J.J. Joosten
Minds and Machines, vol. 22, Number 3, pp. 149-165, 2012. [preprint]. doi: 10.1007/s11023-011-9262-y (Springer)
J4. Image Information Content Characterization and Classification by Physical Complexity
H. Zenil*, J.-P. Delahaye and C. Gaucherel
Complexity, vol. 17-3, pages 26-42, 2012. [preprint] doi:10.1002/cplx.20388 (Wiley)
J3. Program-size versus Time complexity, Slowdown and speed-up phenomena in the micro-cosmos of small Turing machines
J.J. Joosten, F. Soler Toscano and H. Zenil#*
International Journal of Unconventional Computing, vol. 7, no. 5, pp. 353-387, 2011. [preprint] (OCP)
J2. An Algorithmic Information-theoretic Approach to the Behaviour of Financial Markets
H. Zenil* and J.-P. Delahaye
Journal of Economic Surveys, vol. 25-3, pp. 431-463, 2011. [preprint] doi:10.1111/j.1467-6419.2010.00666.x (Wiley)
J1. Compression-based Investigation of the Dynamical Properties of Cellular Automata and Other Systems
H. Zenil
Complex Systems, vol. 19, No. 1, pp. 1-28, 2010. [online]
In Proceedings and Chapters
P36. Predictive Systems Toxicology
N.A. Kiani, M. Shang, H. Zenil and J. Tegnér
In Orazio Nicolotti (ed.), Computational Toxicology - Methods and Protocols, Methods in Molecular Biology, Springer, 2017 [preprint]
P35. Approximations to Algorithmic Probability
H. Zenil
In Robert A. Meyers (ed), 2nd. Edition of the Springer Encyclopedia of Complexity and Systems Science, 2017
P34. Cognition and the Algorithmic Nature of the Mind
H. Zenil
In Robert A. Meyers (ed), 2nd. Edition of the Springer Encyclopedia of Complexity and Systems Science, 2017
P33. Is there any Real Substance to the Claims for a 'New Computationalism'?
A. Hernández-Espinosa, F. Hernández-Quiroz and H. Zenil (invited paper)
In J. Kari, F. Manea, I. Petre (eds) Unveiling Dynamics and Complexity (Computability in Europe 2017), Springer Verlag, 2017. [preprint]
P32. Quantifying Non-trivial Open-Ended Evolution Reveals Necessary and Sufficient Conditions
A. Adams, H. Zenil, P.C.W. Davies and S.I. Walker
Second Workshop on Open-Ended Evolution, 15th International Conference on the Synthesis and Simulation of Living Systems (ALIFE), 2016. [online, preprint]
P31. Undecidability and Irreducibility Conditions for Open-Ended Evolution and Emergence
S. Hernández-Orozco, F. Hernández-Quiroz and H. Zenil*
15th International Conference on the Synthesis and Simulation of Living Systems, Artificial Life Conference (ALIFE), MIT Press, 2016. [online, preprint]
P30. Causality, Information and Biological Computation
H. Zenil, A. Schmidt, J. Tegnér
In S I. Walker, P.C.W. Davies and G. Ellis (eds.), Information and Causality: From Matter to Life,
Cambridge University Press, pp. 244-279, 2017 [preprint, Amazon]
P29. Algorithmic Data Analytics, Small Data Matters and Correlation versus Causation
H. Zenil
In M. Ott, W. Pietsch, J. Wernecke (eds.), Berechenbarkeit der Welt? Philosophie und Wissenschaft im Zeitalter von Big Data (Computability of the World? Philosophy and Science in the Age of Big Data)
Springer Verlag, pp 453-475, 2017 [preprint]
P28. Asymptotic Intrinsic Universality and Reprogrammability by Behavioural Emulation
H. Zenil and J. Riedel
Invited contribution in Advances in Unconventional Computation. A. Adamatzky (ed)
Springer Verlag, pp. 205-220, 2016. [preprint]
P27. Topological Evaluation of Methods for Reconstruction of Genetic Regulatory Networks
J. Olczak, N.A. Kiani, H. Zenil* and J. Tegnér
Proceedings of the IEEE Workshop on Complex Networks, SITIS, Bangkok 2015. [online program]
P26. The Information-theoretic and Algorithmic Approach to Human, Animal and Artificial Cognition
N. Gauvrit, H. Zenil#, J. Tegnér
In G. Dodig-Crnkovic and R. Giovagnoli (Eds.) Representation and reality : Humans, animals and machines.
Springer, pp 117-139, 2017 [preprint]
P25. Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues
H. Zenil, N.A. Kiani, J. Tegnér
In F. Ortuño & I. Rojas (Eds.): 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO) 2015, Part II,
LNCS 9044, pp. 395--405. Springer, 2015. [preprint, online]
P24. The Effects of Global Rules on Interacting Cellular Automata
A. Adams, H. Zenil, E. Reyes, J. Joosten
In J. Kari, I. Törmä, M. Szabados (Eds.), 21st International Workshop on Cellular Automata and Discrete Complex Systems
AUTOMATA 2015, TUCS Lecture Notes, 2015. [slides online]
P23. Quantifying Natural and Artificial Intelligence in Robots and Natural Systems with an Algorithmic Behavioural Test
H. Zenil
In F.P. Bonsignorio, A.P. del Pobil, E. Messina, J. Hallam (eds.), Metrics of sensory motor integration in robots and animals
Springer Cosmos Series, Cognitive Systems Monographs, Springer, (to appear) [preprint]
P22. Programmability: A Turing Test Approach to Computation
H. Zenil
In L. De Mol and G. Primiero (eds.), Turing in Context, Koninklijke Vlaamse Academie van België voor Wetenschappen en Kunsten
(Belgian Academy of Sciences and Arts), Contactforum, 2014.
P21. Gene Sequence Walks
H. Zenil, V. Kannan, J. Tegnér
Visualizing Biological Data conference
EMBO - EMBL VizBi 2014, Heidelberg, Germany (poster and lighting talk).
P20. Algorithmic complexity of motifs clusters superfamilies of networks
H. Zenil, N.A. Kiani and J. Tegner
IEEE International Conference on Bioinformatics and Biomedicine, pp 74 - 76, Shanghai, China 2013. [online] DOI: 10.1109/BIBM.2013.6732768
P19. Algorithmic Complexity of Animal Behaviour: From Communication to Cognition
H. Zenil
International Conference on the Theory and Practice of Natural Computing (TPNC) 2013. Cáceres, Spain, (poster), Cáceres, Spain
P18. Fractal Dimension of Space-time Diagrams and the Runtime Complexity of Small Turing Machines
J.J. Joosten, F. Soler-Toscano, H. Zenil
In T. Neary and M. Cook (Eds.), Machines, Computations and Universality (MCU 2013),
EPTCS 128, 2013, pp. 29-30, DOI: 10.4204/EPTCS.128.9. [abstract, presentation]
P17. Testing Biological Models for Non-linear Sensitivity with a Programmability Test
H. Zenil, G. Ball and J. Tegnér
In P. Liò, O. Miglino, G. Nicosia, S. Nolfi and M. Pavone (eds), Advances in Artificial Intelligence, ECAL 2013, pp. 1222-1223,
MIT Press, 2013. DOI: http://dx.doi.org/10.7551/978-0-262-31719-2-ch188 [online]
P16. Sparsity of Non-trivial Proving Speed-up in Random Systems of Propositional Calculus
S. Hernández-Orozco, F. Hernández-Quiroz and H. Zenil*
In Paola Bonizzoni, Vasco Brattka, Benedikt Löwe (eds.), The Nature of Computation, Logic, Algorithms, Applications,
Proceedings 9th. conference Computability in Europe, CiE 2013.
P15. A Turing Test-Inspired Approach to Natural Computation
H. Zenil
In G. Primiero and L. De Mol (eds.), Turing in Context II, Historical and Contemporary Research in Logic, Computing Machinery and Artificial Intelligence. Proceedings by the Royal Flemish Academy of Belgium for Science and the Arts, Belgium, 2013.
P14. Algorithmic Information Theory
H. Zenil
In The Philosophy of Information An Introduction, The Π Research Network
The UK Society for the Philosophy of Information, 2013 [online]
P13. A Behavioural Foundation for Natural Computing and a Programmability Test
H. Zenil
In G. Dodig-Crnkovic and R. Giovagnoli (eds), Computing Nature: Turing Centenary Perspective, Springer SAPERE Series vol. 7, pp. 87-113, 2013. [online, preprint] [conference picture]
From invited talk at AISB/IACAP Turing World Congress 2012, Birmingham, UK
P12. Wolfram's Classification and Computation in Cellular Automata Classes III and IV
G.J. Martinez, J.C. Seck-Touh-Mora and H. Zenil
In H. Zenil (ed), Irreducibility and Computational Equivalence: Wolfram Science 10 Years After the Publication of A New Kind of Science, Springer, 2013 [preprint]
P11. El Universo Algorítmico
H. Zenil
In, O. Miramontes and K. Volke (eds.) Fronteras de la Física en el Siglo XXI, CopIt arXives, UNAM, 2013 [PDF]
P10. From Computer Runtimes to the Length of Proofs: With an Algorithmic Probabilistic Application to Waiting Times in Automatic Theorem Proving
H. Zenil
In M.J. Dinneen, B. Khousainov, and A. Nies (Eds.), Computation, Physics and Beyond International Workshop on Theoretical Computer Science, WTCS 2012, LNCS 7160, pp. 223-240, Springer, 2012. [preprint] DOI:10.1007/978-3-642-27654-5_17
P9. Fractal Dimension as an Indication of the Terminating Runtime of Discrete Dynamical Systems
J.J. Joosten, H. Zenil and F. Soler-Toscano
In S. Thurner M. Szell (eds), Löcker Verlag, European Conference on Complex Systems (ECCS'11), 2011.
P8. Un método estable para la evaluación de la complejidad algorítmica de cadenas cortas (A Stable Method for the Evaluation of the Algorithmic Complexity of Short Strings).
H. Zenil, and J.-P. Delahaye
In G.J. Martinez, H. Zenil and C.R. Stevens (eds), Complex Systems as Computing Models, Luniver Press, 2011. [preprint]
P7. Complejidad descriptiva y computacional en máquinas de Turing pequeñas
J.J. Joosten, F. Soler-Toscano, H. Zenil#
In Lógica Universal e Unidade da Ciência, Centro de Filosofia das Ciências da Universidade de Lisboa, pp. 11--32, 2011. [preprint]
P6. An Algorithmic Information-theoretic Approach to the Behaviour of Financial Markets.
H. Zenil and J.-P. Delahaye
In S. Zambelli, D.A.R. George (eds.) Nonlinearity, Complexity and Randomness in Economics: Towards Algorithmic Foundations for Economics, Wiley-Blackwell, 2011. [preprint]
P5. Complejidad descriptiva y computacional en máquinas de Turing pequeñas
J.J. Joosten, F. Soler-Toscano and H. Zenil
Actas de las V Jornadas Ibéricas, Lógica Universal e Unidade da Ciência, CFCU 2010. [preprint]
P4. Program-size versus Time complexity, Slowdown and speed-up phenomena in the micro-cosmos of small Turing machines
J.J. Joosten, F. Soler-Toscano and H. Zenil
In H. Guerra (ed.). Physics and Computation 2010, CAMIT, 3rd International Workshop on Physics and Computation 2010. [PDF]
P3. On the Algorithmic Nature of the World
H. Zenil and J-P. Delahaye
In G. Dodig-Crnkovic and M. Burgin (eds), Information and Computation, World Scientific Publishing Company, 2010. [preprint]
P2. On the Kolmogorov-Chaitin complexity for short sequences
J-P. Delahaye and H. Zenil#
In C. Calude (ed) Randomness and Complexity: From Leibniz to Chaitin, World Scientific Publishing Company, 2007. [preprint]
P1. On the Possible Computational Power of the Human Mind
H. Zenil and F. Hernandez-Quiroz
In Worldviews, Science and Us, Philosophy and Complexity, C. Gershenson, D. Aerts, and B. Edmonds (eds),
World Scientific Publishing Company, 2007. [preprint]
Books & Edited Volumes
- I. Zelinka, A. Sanayei, H. Zenil and O.E. Rössler (eds), How Nature Works, Complexity in Interdisciplinary Research and Applications, Series: Emergence, Complexity and Computation, Vol. 5, Springer, 2013.
- H. Zenil (ed), Irreducibility and Computational Equivalence: Ten Years After the Publication of Wolfram's A New Kind of Science, Series: Emergence, Complexity and Computation, Vol. 2, Springer, 2013. [book website]
- H. Zenil (ed.), A Computable Universe: Understanding Computation & Exploring Nature As Computation, with a Foreword by Sir R. Penrose, World Scientific/Imperial College Press, 2012. [book website, Amazon]
- G.J. Martínez, H. Zenil and C.R. Stephens (eds.), Sistemas Complejos Como Modelos de Computación (Complex Systems as Computing Models), Luniver, 2011. [Amazon]
- H. Zenil, Lo que cabe en el espacio: develando las propiedades geométricas de nuestra realidad, (in Spanish), Copit ArXives UNAM , 2011. [paper and Kindle versions will soon be available at Amazon.com]
- H. Zenil (ed.), Randomness Through Computation: Some Answers, More Questions, World Scientific/Imperial College Press, 2011. [book website]
- H. Zenil, F. Soler-Toscano and N. Gauvrit, Methods and Applications of Kolmogorov Complexity, Springer, forthcoming 2018.
- H. Zenil, N.A. Kiani and J. Tegnér, Algorithmic Information Dynamics: From Networks to Cells, Cambridge University Press, forthcoming 2018.
Theses
- L'approche algorithmique de l'aléatoire, thesis fulfilling the dissertation requirement for the Degree of Doctor of Philosophy under the direction of J. Mosconi, University of Paris 1 Panthéon-Sorbonne (IHPST/ENS Ulm/CNRS) 2015, with highest honours (très honorable). (Examiners: Andrew Adamatzky, Barry Cooper, Jean-Paul Delahaye and Cyrille Imbert). [jury report and thesis online here]
- Une approche experimentale à la théorie algorithmique de la complexité, doctoral dissertation, Computer Science, under supervision of J.-P. Delahaye and Cristian S. Calude (Examiners: Gregory Chaitin, Serge Grigorieff, Philippe Mathieu and Hervé Zwirn), University of Lille 1, 2011, with highest honours (très honorable). DOI 10.1.1.397.6875. All chapters were published as papers and are available sections papers and chapters above. [jury report, thesis online, alternative source]
- Calcul et hyper calcul, (mémoire) fulfilling the dissertation requirement for the degree of Masters (Logic) under the direction of Jacques Dubucs at the University of Paris 1 Panthéon-Sorbonne, 2006. 16/20.
- Encaje de las Redes Neuronales Recurrentes Analógicas en la Jerarquía Aritmética fulfilling the requirement for the B.Sc. (Math) degree, under advice of F. Hernández-Quiroz, Facultad de Ciencias, UNAM, 2005. [online]
Selected Essays and Reviews
- H. Zenil, The Seemingly Contradictory Philosophical Legacy of Turing and Shannon, AISB Quarterly no. 138 pp. 9--15, 2014. [PDF]
- H. Zenil, Complejidad y Aleatoriedad, Ciencia (número especial de Turing), Academia Mexicana de Ciencias, vol 64-4, 2013. [online]. The outstanding cover of the special issue here. And the full article here.
- A. German and H. Zenil, Afterword to Konrad Zuse's Calculating Space (Rechnender Raum)--The MIT translation--In A Computable Universe, World Scientific, 2012. [PDF]
- H. Zenil, Introducing the Computable Universe, Introduction to A Computable Universe (foreword by Roger Penrose), World Scientific, 2012. [PDF]
- H. Zenil, An Algorithmic Approach to Information and Meaning, APA Newsletter on Philosophy and Computers, vol. 11, No. 1, 2011. [online]
- H. Zenil, Information Theory and Computational Thermodynamics: Lessons for Biology from Physics, Information 3, no. 4: 739-750, 2012. [online] DOI: :10.3390/info3040739
- H. Zenil, The Complexity of Simple Programs: Workshop Report from Cork, Ireland, Bulletin of the European Association for Theoretical Computer Science (BEATCS), 2009.
- H. Zenil, The World is Either Algorithmic or Mostly Random, winning 3rd. Place in the International Essay Context of the FQXi, 2011. [PDF]
Software
Network and Computational Biology
- Cospectrality and duality (forthcoming)
- Complex Networks (random, scale-free and small world)
- Breadth-First Search Enumeration
- Euler's Polyhedral Formula
- World Metro Networks
- Generating Random DNA Sequences (with GC content per species)
- Network motifs and graphlets
Information Theory, Computational Lingustics & Complexity Theory
- Shannon's Noisy-Channel Coding Theorem
- Cellular Automaton Compressibility
- Kolmogorov Complexity of 3×3 and 4×4 Squares
- Prediction and Entropy of Languages
- Zipf's Law Applied to Word and Letter Frequencies
- Multilanguage Word Lengths
- Borel's Infinite Money Theorem and Algorithmic Probability
- Speedup and Slowdown Phenomena in Turing Machines
- Fractal Dimension versus Time Computational Complexity in Turing Machines
- Complexity: an R-package to enable measures of algorithmic complexity (with N.Gauvrit, H.Singmann and F.Soler)
- Block Decomposition Method (soon available in Perl, Python, Java, C++, Pascal and Mathematica, w/F.Soler)
Discrete Math, Mathematical Logic & Combinatorics
- Truth Tables
- Fundamental Theorem of Arithmetic
- Golden Ratio by the Fibonacci Sequence
- Visualizing the Goldbach Conjecture
- Predicate Calculus Formula Generator
- Skolemization of Quantified Formulae
- Applying the Pólya-Burnside Enumeration Theorem
Automata, Normality & Pseudorandomness
- Busy Beaver Turing Machines
- John von Neumann's First Pseudorandom Number Generator (middle-square method)
- Random Number Generation and Testing
- Country Data and Benford's Law
- Champernowne Constant
- Prime Numbers Gaps
- Collatz Sequence Paths
- Distribution of Primes
- Digit Frequencies in the Copeland-Erdos Constant
- Unveiling Mathematica's TuringMachine Function Step by Step
- Small Turing Machines with Halting State: Enumeration and Running on a Blank Tape
