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Assembly Theory is an approximation to algorithmic complexity based on LZ compression that does not explain selection or evolution
F.S. Abrahão, S. Hernández-Orozco, N.A. Kiani, J. Tegnér, H. Zenil PLOS Complex Systems, 1(1): e0000014, 2024 [online] |
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On the Salient Limitations of the Methods of Assembly Theory and their Classification of Molecular Biosignatures
A. Uthamacumaran, F.S. Abrahão, N.A. Kiani, H. Zenil npj Systems Biology and Applications 10, 82, 2024. [online]. |
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A Review of Mathematical and Computational Methods in Cancer Dynamics
A. Uthamacumaran and H. Zenil Frontiers in Oncology, 25 July 2022 [online] |
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Emergence and Algorithmic Information Dynamics of Systems and Observers
F. S. Abrahão and H. Zenil Philosophical Transactions of the Royal Society A, 2022 [online] |
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Artificial Intelligence in Medicine and Causality for Precision and Value-based Healthcare
H. Zenil In N. Lidströmer and H. Ashrafian (eds.) Artificial Intelligence in Medicine, Springer Verlag, 2021 [online] |
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Causal Diagnostics for Cancer and Complex Diseases
H. Zenil In I. Balaz and A. Adamatzky, Cancer, Complexity, Computation, World Scientific Publishing Company, 2021 [Amazon] |
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Algorithmic Information Dynamics
H. Zenil, N.A. Kiani, F.S. Abrahao and J. Tegnér Scholarpedia, 15(7):53143, 2020. [online] |
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A Review of Methods for Estimating Algorithmic Complexity: Options, Challenges, and New Directions
H. Zenil Entropy, 22, 612, 2020. (special issue on Shannon Entropy and Kolmogorov complexity) [online] |
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Evolving Neural Networks through a Reverse Encoding Tree
H. Zhang, C-H. Huck Yang, H. Zenil, N.A. Kiani, Y. Shen and J. Tegnér IEEE World Congress on Computational Intelligence 2020. [preprint] |
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Algorithmic Information Distortions in Node-Aligned and Node-Unaligned Multidimensional Networks
F.S. Abrahao, K. Wehmuth, H. Zenil, and A. Ziviani Entropy 2021, 23(7), 835 [online] |
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MAPK Pathway and B Cells Overactivation in Multiple Sclerosis: A Phosphoproteomics–Genomic Analysis
Ekaterina Kotelnikova, Narsis Aftab Kiani, et al. In Proceedings of the National Academy of Sciences of the United States of America (PNAS), Vol. 116, No. 19, pp. 9672–9677. National Academy of Sciences, 2019. [online] |
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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
Michael P. Menden, Dennis Wang, Yuanfang Guan, (…) i.a. N.A. Kiani (DREAM Challenge Consortium) (…), G. Stolovitzky, et al. In Nature Communications, 2019. [online] |
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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
S.M Hill, L.M. Heiser, (…) i.a. H. Zenil (DREAM Challenge Consortium) (…), G. Stolovitzky, J. Guinney, J.R Dry, J. Saez-Rodriguez Nature Communications, vol. 10, Article number: 2674, 2019. [online] (NPG) |
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The Thermodynamics of Network Coding, and Algorithmic Refinement of the principle of Maximum Entropy
H. Zenil, N.A. Kiani, J. Tegnér Entropy, 21(6), 560, 2019 [online] (MDPI) |
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Time-Resolved Transcriptome and Proteome Landscape of Human Regulatory T Cell (Treg) Differentiation Reveals Novel Regulators of FOXP3
Angelika Schmidt, Francesco Marabita, Narsis A. Kiani, et al. In BMC Biology, Vol. 16, Article 51, 2018. [online] |
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Network Modules Uncover Mechanisms of Skeletal Muscle Dysfunction in COPD Patients
Ákos Tényi, Isaac Cano, Francesco Marabita, Narsis Kiani, et al. In Journal of Translational Medicine, Vol. 16, No. 1, February 2018, pp. 34. 2018. [online] |
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A Review of Graph and Network Complexity from an Algorithmic Information Perspective
H. Zenil, N.A. Kiani, J. Tegnér Entropy, 20(8):551, 2018. [online] |
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Algorithmically Probable Mutations Reproduce Aspects of Evolution, such as Convergence Rate, Genetic Memory, and Modularity
S. Hernández-Orozco, N.A. Kiani, H. Zenil Royal Society Open Science, 5:180399, 2018 [online] |
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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 Entropy 20(8), 605, 2018. [online] (MDPI) |
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Model Discovery and Discrete Inverse Problems with Cellular Automata and Boolean Networks
H. Zenil, Y. Zhang and N.A. Kiani In A. Adamatzky, Automata and Complexity, Eric Goles festschrift, Springer, 2022. [Amazon] |
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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 [online, preprint] (Taylor & Francis) |
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Rule Primality, Minimal Generating Sets and Turing-Universality in the Causal Decomposition of Elementary Cellular Automata
J. Riedel and H. Zenil Journal of Cellular Automata, vol. 13, pp. 479–497, 2018 [online, preprint] |
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Algorithmic Complexity and Reprogrammability of Chemical Structure Networks
H. Zenil, N.A. Kiani, M-M. Shang, J. Tegnér Parallel Processing Letters, vol. 28, 2018. [online, preprint] (World Scientific) |
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Cross-boundary Behavioural Reprogrammability Reveals Evidence of Pervasive Universality
J. Riedel, H. Zenil International Journal of Unconventional Computing, vol 13:14-15 pp. 309-357, 2018 [online, preprint] |
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Approximations of Algorithmic and Structural Complexity Validate Cognitive-behavioural Experimental Results
H. Zenil, J.A.R. Marshall, J. Tegnér vol. 16 Frontiers In Computational Neuroscience, 2023 [online] |
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Undecidability and Irreducibility Conditions for 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) |
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Dynamics and Heterogeneity of Brain Damage in Multiple Sclerosis
Ekaterina Kotelnikova, Narsis A. Kiani, et al. In PLoS Computational Biology, Vol. 13, No. 10, October 2017, Article e1005757. Public Library of Science (PLoS), 2017. [online] |
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A Minimal Unified Model of Disease Trajectories Captures Hallmarks of Multiple Sclerosis
Venkateshan Kannan, Narsis A. Kiani, Fredrik Piehl, Jesper Tegnér. In Mathematical Biosciences, Vol. 289, July 2017. Elsevier BV, 2017. |
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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) |
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Low Algorithmic Complexity Entropy-deceiving Graphs
H. Zenil, N.A. Kiani and J. Tegnér Physical Review E 96, 012308, 2017. [online] |
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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] |
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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, supplementary information (SI)] (PLOS) |
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Causality, Information and Biological Computation: An algorithmic software approach to life, disease and the immune system
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] |
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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. [online, preprint] |
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Emergence of Network Motifs in the Context of Multiple Sclerosis
Narsis A. Kiani, Ming-Mei Shang, Jesper Tegnér. In Current Pharmaceutical Design, Vol. 22, No. 46, 2016, pp. 6911-6917. Bentham Science Publishers, 2016. |
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Conditional Disease Development Extracted from Longitudinal Health Care Cohort Data Using Layered Network Construction
Venkateshan Kannan, Fredrik Swartz, Narsis A. Kiani, Gilad Silberberg, Giorgos Tsipras, David Gomez-Cabrero, Kristina Alexanderson, Jesper Tegnér. In Scientific Reports, Vol. 6, May 2016. [online] |
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P4 Systems Medicine: From Molecular Features and Models to the Clinic in COPD
David Gomez-Cabrero, Jörg Menche, Isaac Cano, Narsis A. Kiani, et al. In Journal of Translational Medicine, 2016. |
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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) |
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Inferring causal molecular networks: Empirical Assessment of Causal Network Learning through a Community-based Effort
S.M Hill, L.M. Heiser, (…) i.a. H. Zenil (DREAM Challenge Consortium) (…), S. Mukherjee, G. Stolovitzky, J. Saez-Rodriguez Nature Methods 13, pp. 310–318, 2016. [online] |
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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. [online, preprint] |
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Fractal Dimension versus Process Complexity
J.J. Joosten, F. Soler-Toscano, and H. Zenil Advances in Mathematical Physics vol. 2016, Article ID 5030593 [online] |
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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. [online, preprint] |
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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] |
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Extended Predictor-Corrector Methods for Solving Fuzzy Differential Equations Under Generalized Differentiability
Narsis A. Kiani, Mahnaz Barkhordarii, Nasser Mikaeilvand. In International Journal of Mathematical Modelling and Computations, Vol. 5, No. 2, Spring 2015, pp. 149-171. Vira Science, 2015. |
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Signaling Pathways in MS: A Systems-Based Approach to Developing New Pharmacological Therapies
Ekaterina Kotelnikova, Marti Bernardo-Faura, Gilad Silberberg, Narsis A. Kiani, et al. In Multiple Sclerosis Journal, Vol. 21, No. 2, 2015. |
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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. [preprint, online] |
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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] |
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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] |
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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. [online] |
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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] |
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Solving Two-Dimensional Fuzzy Partial Differential Equation by the Alternating Direction Implicit Method
Narsis A. Kiani, Nasser Mikaeilvand, Mahnaz Barkhordarii. In International Journal of Applied Mathematics, 2014. [online] |
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Dynamic Probabilistic Threshold Networks to Infer Signaling Pathways from Time-Course Perturbation Data
Narsis Aftab Kiani, Lars Kaderali. In BMC Bioinformatics, Vol. 15, 2014. [online] |
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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] |
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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] |
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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] |
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Laplace Transform Formula on Fuzzy Nth-Order Derivative and Its Application in Fuzzy Ordinary Differential Equations
Narsis A. Kiani, Mahnaz Barkhordarii, Nasser Mikaeilvand. In Soft Computing, 2013. Springer, 2013. |
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Integrative Analysis of High Throughput RNAi Screens: Towards a Comprehensive Understanding of the Virus-Host Interplay
Sandeep Amberkar, Narsis A. Kiani, Ralf Bartenschlager, Gualtiero Alvisi, Lars Kaderali. In World Journal of Virology, Vol. 2, No. 2, 2013. Baishideng Publishing Group, 2013. |
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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. [online, preprint] |
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Exploring Programmable Self-Assembly in Non DNA-based Computing
G. Terrazas, H. Zenil and N. Krasnogor Natural Computing, vol 12(4): 499–515, 2013. [online, preprint] |
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Asymptotic Behaviour and Ratios of Complexity in Cellular Automata Rule Spaces
H. Zenil International Journal of Bifurcation and Chaos vol. 23, no. 9, 2013. [online, preprint] |
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Toward the Existence and Uniqueness of Solutions of Second-Order Fuzzy Differential Equations
T. Allahviranloo, S. Salahshour, Narsis A. Kiani. In Neural Computing and Applications, 2012. [online] |
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Numerical Evaluation of Algorithmic 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. [online, preprint] |
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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] |
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Image Characterization and Classification by Physical Complexity
H. Zenil, J.-P. Delahaye and C. Gaucherel Complexity, vol. 17-3, pages 26-42, 2012. [online, preprint] |
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Molecular Mechanism of Signal Perception and Integration by the Innate Immune Sensor Retinoic Acid-Inducible Gene-I (RIG-I)
Marco Binder, Florian Eberle, Stefan Seitz, Norbert Mücke, Christian M. Hüber, Narsis Kiani, et al. In Journal of Biological Chemistry, Vol. 286, 2011. |
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Normalizing for Individual Cell Population Context in the Analysis of High-Content Cellular Screens
Bettina Knapp, Ilka Rebhan, Anil Kumar, Petr Matula, Narsis A. Kiani, Marco Binder, Holger Erfle, Karl Rohr, Roland Eils, Ralf Bartenschlager, Lars Kaderali. In BMC Bioinformatics, 2011. [online] |
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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] |
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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] |
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A New Method for Complex Decision Making Based on TOPSIS with Fuzzy Data
F. Hosseinzadeh Lotfi, T. Allahviranloo, M. Alimardani Jondabeh, Narsis A. Kiani. In International Journal of Computer and Information Engineering, 2009. World Academy of Science, Engineering and Technology, 2009. |
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Solving Fuzzy Differential Equations by Differential Transformation Method
T. Allahviranloo, Narsis A. Kiani, N. Motamedi. In Information Sciences, Vol. 179, 2009. |
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Solving Fuzzy Partial Differential Equation by Differential Transformation Method
Narsis A. Kiani, Nasser Mikaeilvand, Mahnaz Barkhordarii. In Information Sciences, 2009. |
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Signed Decomposition of Fully Fuzzy Linear Systems
Narsis A. Kiani, Rasol Mastani Shabestari. In Journal of Applied Mathematics, 2008. [online] |
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Homomorphic Solution of Fully Fuzzy Linear System
T. Allahviranloo, Narsis A. Kiani, M. Barkhordary, M. Mosleh. In Journal of Computational Mathematics and Modeling, 2008. [online] |
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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] |
