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Information Theory and Programmable Medicine

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Invited talk given at the IEEE International Conference on Bioinformatics and Biomedicine 2013 in Shanghai, China.

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Information Theory and Programmable Medicine

  1. 1. Information Theory and Programmable Medicine Hector Zenil hector.zenil@ki.se Unit of Computational Medicine, Stockholm, Sweden Invited Talk IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013) December 20, 2013, Shanghai, China Hector Zenil Information and Programmable Medicine 1 / 27
  2. 2. Complexity and Computation in Nature Natural computing Contents What is computation Small computing machines and emergent properties The Turing test and what is (artificial) life Information theory and spatial molecular computation Kolmogorov complexity and programmable medicine Hector Zenil Information and Programmable Medicine 2 / 27
  3. 3. Complexity and Computation in Nature Natural computing The origins of modern computation J. von Neuman’s self-replication interest (1950s). von Neumann (with S. Ulam) started the field of Cellular Automata Hector Zenil Information and Programmable Medicine 3 / 27
  4. 4. Complexity and Computation in Nature Natural computing Cellular Automata Hector Zenil Information and Programmable Medicine 4 / 27
  5. 5. Complexity and Computation in Nature Natural computing Rule 30 continuation Hector Zenil Information and Programmable Medicine 5 / 27
  6. 6. Complexity and Computation in Nature Natural computing von Neumann’s universal constructor Hector Zenil Information and Programmable Medicine 6 / 27
  7. 7. Complexity and Computation in Nature Natural computing Life as self-replication? Langton’s loop shows that self-replication does not require Turing universality. But crystals self-replicate too, so it cannot be a sufficient condition for life. Hector Zenil Information and Programmable Medicine 7 / 27
  8. 8. Complexity and Computation in Nature Natural computing What is life? An informational definition (Gerald F. Joyce, Bit by Bit: The Darwinian Basis of Life, PloS, Bio. 2012) of life: A genetic system that contains more bits than the number that were required to initiate its operation. A computational view (John Hopfield, J. Theor. Biol. 171, 53-60, 1994): All biological systems perform some kind of computation. Computation is inherent to adaptive systems and makes biology different from physics. A mechanistic view (Leroy Cronin, TED conference, 2011) proposes that: Life is anything that can undergo evolution (survival of the fittest). Matter that can evolve is alive. Borderline case: Virus evolve (not exactly by their own though) yet they are only matter (encapsulated genetic material). Hector Zenil Information and Programmable Medicine 8 / 27
  9. 9. Complexity and Computation in Nature A behavioural approach to computation A behavioural approach to what is computation (and life) The Turing test is a reformulation of a question of non-factual character into a measurable one: something is intelligent if it behaves like so. It is a clever strategy to tackle difficult questions! Figure : A Turing-test like test strategy to the question of life (instead of machine intelligence) [Zenil, Philosophy & Technology, Springer (2013)] Hector Zenil Information and Programmable Medicine 9 / 27
  10. 10. Complexity and Computation in Nature A behavioural approach to computation A Turing test like approach to computation and life [Zenil in Computing Nature, & SAPERE Series, Springer (2013)] How to chemically recognize artificial life? (Cronin, Krasnogor, et al, Nature Biotechnology 2006). Talking to the cells with chells. How closely simulators emulate the properties of real data (e.g. in silico reconstruction of genetic networks from synthetically generated gene expression data) (Maier et al., A Turing test for artificial expression data, Bioinformatics (2013) 29 (20): 2603-2609, 2013). Hector Zenil Information and Programmable Medicine 10 / 27
  11. 11. Complexity and Computation in Nature A behavioural approach to computation Algorithmic information theory to the rescue? Which string looks more random? (a) 1111111111111111111111111111111111111111 (b) 0011010011010010110111010010100010111010 (c) 0101010101010101010101010101010101010101 Definition KU (s) = min{|p|, U(p) = s} (1) Compressibility and algorithmic randomness A string with low Kolmogorov complexity is c-compressible if |p| + c = |s|. A string is random if K(s) ≈ |s|. [Kolmogorov (1965); Chaitin (1966)] Hector Zenil Information and Programmable Medicine 11 / 27
  12. 12. Complexity and Computation in Nature A behavioural approach to computation Behavioural classes of abstract computing machines Wolfram’s computational classes of behaviour: Class I: system evolves into a homogeneous state. Class II: system evolves in a periodic state. Class III: system evolves into random-looking states. Class IV: system evolves into localised complex structures. Living systems clearly fall in class IV systems. [Wolfram, (1994)] Hector Zenil Information and Programmable Medicine 12 / 27
  13. 13. Complexity and Computation in Nature A behavioural approach to computation Asymptotic behaviour of compressed evolutions [Zenil, Complex Systems (2010)] Hector Zenil Information and Programmable Medicine 13 / 27
  14. 14. Complexity and Computation in Nature A behavioural approach to computation A behavioural approach to computation (and life recognition) A Turing-test like test strategy to the question of life (instead of Turing’s original question of artificial intelligence): [Zenil, Philosophy & Technology and SAPERE, (2013)] Hector Zenil Information and Programmable Medicine 14 / 27
  15. 15. Complexity and Computation in Nature A behavioural approach to computation Answering Chalmer’s rock question Figure : ECA R4 has a low Ct value for any n and t (it doesn’t react much to external n stimuli). [Zenil, Philosophy & Technology, (2013)] Hector Zenil Information and Programmable Medicine 15 / 27
  16. 16. Complexity and Computation in Nature A behavioural approach to computation Turing universality Figure : ECA R110 has large asymptotic coefficient Ct value for large enough choices n of t and n, which is compatible with the fact that it is Turing universal (for particular semi-periodic initial configurations). Hector Zenil Information and Programmable Medicine 16 / 27
  17. 17. Complexity and Computation in Nature A behavioural approach to computation A hierarchical view of computing systems (and life?) The measure can be applied to other than computers. Programmability of physical and biological entities sorted by variability versus controllability: The diagonal determines the degree of programmability. [Zenil, Ball, Tegn´ r, ECAL MIT Press Proceedings, (2013)] e Hector Zenil Information and Programmable Medicine 17 / 27
  18. 18. Complexity and Computation in Nature A behavioural approach to computation Proof of concept: The EMBL-EBI BioModel’s Database The EMBL-EBI BioModel DB is a curated database of mathematical published (about 400) models related to living organisms. Hector Zenil Information and Programmable Medicine 18 / 27
  19. 19. Complexity and Computation in Nature A behavioural approach to computation Cell cycle versus metabolic pathways Variability analysis: Models cluster by their role in living processes. [Zenil, Ball, Tegn´ r, ECAL MIT Press Proceedings, (2013)] e Hector Zenil Information and Programmable Medicine 19 / 27
  20. 20. Complexity and Computation in Nature A behavioural approach to computation Variability and controllability of biological models Information content trajectories (from EMBL-EBI model simulations): Programmability is a combination of variability and controllability [Zenil, Ball, Tegn´ r, ECAL MIT Press Proceedings, (2013)] e Hector Zenil Information and Programmable Medicine 20 / 27
  21. 21. Complexity and Computation in Nature A behavioural approach to computation The main challenges in biology Parameter to conformational space mapping in biological systems from the fact that shape is function in biology! DNA sequence → protein structure mapping / Signalling → cells self-organization Environmental conds. → virus mutations / drugs → diseases reaction I call it the conformational space problem in biology. Hector Zenil Information and Programmable Medicine 21 / 27
  22. 22. Complexity and Computation in Nature A behavioural approach to computation Case study: Phorphyrin molecules simulation with Wang tiles Porphyrin interaction dynamics are extensively well known and accurate mathematical models exist. We ran a kinetic Monte Carlo simulation on 2 different porphyrin molecules deposited on a solid substrate. Porphyrins self-assemble in structures depending on the binding energy between: molecules of the same functional type molecules of different (2) functional type molecules and the substrate (They give red color to blood. They envelop hemes in hemoglobin that deliver nutrients (in particular oxygen!).) [Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNA based molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.] Hector Zenil Information and Programmable Medicine 22 / 27
  23. 23. Complexity and Computation in Nature A behavioural approach to computation Self-assembly of porphyrin molecules How to map stimuli (energy binding) to conformational space? With information theory and Kolmogorov complexity. [Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNA based molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.] Hector Zenil Information and Programmable Medicine 23 / 27
  24. 24. Complexity and Computation in Nature A behavioural approach to computation Phorphyrins: mapping behaviour to stimuli Binding energies induced by chemical reactions with highest behavioural impact can be tested and programmed in silico and verified in the wet lab. (Hemes in hemoglobin. They give the red color to blood) [Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNA based molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.] Hector Zenil Information and Programmable Medicine 24 / 27
  25. 25. Complexity and Computation in Nature A behavioural approach to computation Phorphyrins: mapping behaviour to stimuli Binding energies induced by chemical reactions with highest behavioural impact can be tested and programmed in silico and verified in the wet lab. (Hemes in hemoglobin. They give the red color to blood) [Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNA based molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.] Hector Zenil Information and Programmable Medicine 25 / 27
  26. 26. Complexity and Computation in Nature A behavioural approach to computation Capturing and clustering behaviour The compressibility test retrieved phase transitions corresponding to changes in qualitative behaviour. Qualitative behaviour is captured by a quantitative measure. Corresponding to different stimuli [Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNA based molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.] Hector Zenil Information and Programmable Medicine 26 / 27
  27. 27. Complexity and Computation in Nature A behavioural approach to computation Towards programmable medicine Building on molecular such as porphyrin computation imagine, for example, the introduction of an array of these molecules with a simple logic to treatments releasing a payload if expressing certain conditions (e.g. cancer markers) are met. Hector Zenil Information and Programmable Medicine 27 / 27
  28. 28. Complexity and Computation in Nature A behavioural approach to computation H. Zenil, Compression-based Investigation of the Dynamical Properties of Cellular Automata and Other Systems, Complex Systems, Vol. 19, No. 1, pages 1-28, 2010. H. Zenil, What is Nature-like Computation? A Behavioural Approach and a Notion of Programmability, Philosophy & Technology (special issue on History and Philosophy of Computing), 2013. H. Zenil, On the Dynamic Qualitative Behavior of Universal Computation Complex Systems, vol. 20, No. 3, pp. 265-278, 2012. G. Terrazas, H. Zenil and N. Krasnogor, Exploring Programmable Self-Assembly in Non DNA-based Computing, Natural Computing, vol 12(4): 499–515, 2013. DOI: 10.1007/s11047-013-9397-2. H. Zenil and E. Villarreal-Zapata, Asymptotic Behaviour and Ratios of Complexity in Cellular Automata Rule Spaces, Journal of Bifurcation and Chaos (in press). H. Zenil, G. Ball and J. Tegn´ r, Testing Biological Models for Non-linear e Sensitivity with a Programmability Test. In P. Lio, O. Miglino, G. Nicosia, S. Nolfi ` and M. Pavone (eds), Advances in Artificial Intelligence, ECAL 2013, pp. 1222-1223, MIT Press, 2013. H. Zenil, A Turing Test-Inspired Approach to Natural Computation. In G. Primiero and L. De Mol (eds.), Turing in Context II (Brussels, 10-12 October 2012), Hector Zenil Information and Programmable Medicine 27 / 27
  29. 29. Complexity and Computation in Nature A behavioural approach to computation Historical and Contemporary Research in Logic, Computing Machinery and Artificial Intelligence, Proceedings published by the Royal Flemish Academy of Belgium for Science and Arts, 2013. A Behavioural Foundation for Natural Computing and a Programmability Test. In G. Dodig-Crnkovic and R. Giovagnoli (eds), Computing Nature: Turing Centenary Perspective, SAPERE Series vol. 7, Springer, 2013. H. Zenil, Turing Patterns with Turing Machines: Emergence and Low-level Structure Formation, Natural Computing, 12(2): 291-303 (2013), 2013. J.-P. Delahaye and H. Zenil, Numerical Evaluation of the Complexity of Short Strings: A Glance Into the Innermost Structure of Algorithmic Randomness, Applied Mathematics and Computation 219, pp. 63-77, 2012. Hector Zenil Information and Programmable Medicine 27 / 27

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