Luis M. Rocha

For other people named Luis Rocha, see Luis Rocha (disambiguation).
Luis M. Rocha
Born (1966-10-05) October 5, 1966
Luanda, Angola
Residence
Fields
Institutions
Alma mater Instituto Superior Técnico, Portugal Lic. (B.A. plus M.S.), 1990
Binghamton University Ph.D., 1997
Thesis Evidence Sets and Contextual Genetic Algorithms: Exploring Uncertainty, Context, and Embodiment in Cognitive and Biological Systems. SUNY Binghamton. (1997)
Academic advisors
Influences
Notable awards
Website
www.informatics.indiana.edu/rocha/

Luis M. Rocha is a Professor and director of the Complex Systems graduate Program in Informatics, member of the Indiana University Network Science Institute, and core faculty of the Cognitive Science Program at Indiana University, Bloomington, USA. He is a Fulbright Scholar and is also the director of the Computational Biology Collaboratorium and in the Direction of the PhD program in Computational Biology at the Instituto Gulbenkian de Ciencia, Portugal. His research is on complex systems and networks,[1][2][3][4] computational and systems biology,[1][5][6][7][8] and computational intelligence (including Artificial Life and Embodied Cognition).[9][10][11][12][13][14][15][16][17]

Biography

He received his Ph.D in Systems Science in 1997 from the Binghamton University. From 1998 to 2004 he was a staff scientist at the Los Alamos National Laboratory, where he founded and led a Complex Systems Modeling Team during 1998-2002, and was part of the Santa Fe Institute research community. He has organized the Tenth International Conference on the Simulation and Synthesis of Living Systems (Alife X)[18] and the Ninth European Conference on Artificial Life (ECAL 2007).[19]

Research

Dr. Rocha studies the informational properties of natural and artificial systems which enable them to adapt and evolve. He has approached this general topic by investigating how information is fundamental for controlling the behavior and evolutionary capabilities of complex systems,[11][12][13] as well as abstracting principles from natural systems to produce adaptive information technology.[14][15][17]

Accepting Von Neumann's principle of self-replication and Turing's universal computation as a general principle for generating open-ended complexity that encompasses Natural Selection, Dr. Rocha has developed the work of Howard Pattee,[20] Sydney Brenner,[21] and others who regard computation and information as fundamental to understanding life, cognition and other complex systems (a good overview is Gleick's Book). From this viewpoint, he has approached several questions: how do cells and collectives of cells compute?[1] Is language an evolutionary system operating under the same principle?[9][12][13] Can artificial systems implement the same principle?[9][11] Namely, can collective intelligence on the web become a super-organism implementing this principle?[10][14][22][23] From these questions, he has worked on various specific research projects ranging from Biomedical Literature Mining [6][7][8] to understanding redundancy, robustness, modularity and control in Complex Networks,[1][2][3][4] Collective Intelligence on the Web and in Social Systems,[9][10][2][14][16][22][23] and Agent-based models of Evolutionary Systems such as RNA Editing[15] and Artificial Immune Systems.[17]

Philosophical views

Rocha is a proponent of embodied and situated cognition and has defended the grounded epistemological stance of evolutionary constructivism. He is a proponent of the view that the threshold of complexity required for open-ended evolution requires an interplay between symbolic memory and dynamical machinery, i.e. a strict genotype-phenotype separation. This idea has been labeled semiotic closure[24] and is generally understood to fit in the area of biosemiotics. He has defended that this principle of organization is at play in cognition and human collective behavior, having developed web technology to implement the principle [9][10][2][11][14]

References

  1. 1 2 3 4 M. Marques-Pita and L.M. Rocha,. "Canalization and control in automata networks: body segmentation in Drosophila Melanogaster" PLoS ONE, 8(3): e55946. doi:10.1371/journal.pone.0055946. 2013
  2. 1 2 3 4 T. Simas and L.M. Rocha. "Distance Closures on Complex Networks." Network Science, doi:10.1017/nws.2015.11, 2015
  3. 1 2 A. Kolchinsky, M. P. Van Den Heuvel, A. Griffa, P. Hagmann, L.M. Rocha, O. Sporns, J. Goni. "Multi-scale Integration and Predictability in Resting State Brain Activity". Frontiers in Neuroinformatics, 8:66. doi: 10.3389/fninf.2014.00066, 2014
  4. 1 2 Gates, A. and L.M. Rocha. "Control of complex networks requires both structure and dynamics". Scientific Reports., 6:24456. doi: 10.1038/srep244564, 2016
  5. ↑ M.E. Wall, A. Rechtesteiner, and L. M. Rocha, Singular Value Decomposition and Principal Component Analysis "A Practical Approach to Microarray Data Analysis". D. P. Berrar, W. Dubitzky, and M. Granzow (Eds.). Kluwer Academic Publishers, pp. 91-109. 2003
  6. 1 2 A. Kolchinsky, A. Lourenço, H. Wu, L. Li, L.M. Rocha. "Extraction of Pharmacokinetic Evidence of Drug-drug Interactions from the literature" PLoS ONE 10(5): e0122199. doi:10.1371/journal.pone.0122199. 2015.
  7. 1 2 A. Lourenco, M. Conover, A. Wong, A. Nematzadeh, F. Pan, H. Shatkay, and L.M. Rocha, A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature. "BMC Bioinformatics.12(Suppl 8):S12." 2011
  8. 1 2 A. Abi-Haidar, J. Kaur, A. Maguitman, P. Radivojac, A. Retchsteiner, K. Verspoor, Z. Wang, and L.M. Rocha, Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks. "Genome Biology. 9(Suppl 2):S11" 2008
  9. 1 2 3 4 5 Clark, A. Natural-Born Cyborgs:Minds, Technologies, and the Future of Human Intelligence. Oxford University Press, 2003.
  10. 1 2 3 4 Stark, D. The Sense of Dissonance: Accounts of Worth in Economic Life. Princeton University Press, 2011.
  11. 1 2 3 4 L.M. Rocha. and W. Hordijk, Material Representations: From the Genetic Code to the Evolution of Cellular Automata. "Artificial Life. 11 (1-2), pp. 189 - 214" 2005
  12. 1 2 3 L.M. Rocha, Evolution with material symbol systems. "Biosystems. Vol. 60, pp. 95-121." 2001
  13. 1 2 3 L.M. Rocha, Selected Self-Organization and the Semiotics of Evolutionary Systems. "In: Evolutionary Systems: Biological and Epistemological Perspectives on Selection and Self-Organization." S. Salthe, G. Van de Vijver, and M. Delpos (eds.). Kluwer Academic Publishers, pp. 341-358. 1998
  14. 1 2 3 4 5 L.M. Rocha, Adaptive Recommendation and Open-Ended Semiosis. "Kybernetes. Vol. 30, No. 5-6." 2001
  15. 1 2 3 C. Huang, J. Kaur, A. Maguitman, L.M. Rocha, Agent-Based Model of Genotype Editing. "Evolutionary Computation, 15(3): 253-89." 2007
  16. 1 2 L.M. Rocha, Evidence Sets: Modeling Subjective Categories. "In: International Journal of General Systems. Vol. 27, pp. 457-494." 1997
  17. 1 2 3 A. Abi-Haidar and L.M. Rocha. "Collective Classification of Textual Documents by Guided Self-Organization in T-Cell Cross-Regulation Dynamics". Evolutionary Intelligence. 4(2):69-80, 2011
  18. ↑ L.M. Rocha (Editor), L. S. Yaeger (Editor), M. A. Bedau (Editor), D. Floreano (Editor), R. L. Goldstone (Editor), A. Vespignani (Editor), "Artificial Life X: Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems (Bradford Books).". 2006
  19. ↑ F. Almeida e Costa , "Advances in Artificial Life: 9th European Conference, ECAL 2007, Lisbon, Portugal, September 10–14, 2007, Proceedings (Lecture Notes in Computer Science / Lecture Notes in Artificial Intelligence).". 2007
  20. ↑ Rocha, Luis M. (Ed.) The Physics and Evolution of Symbols and Codes: Reflections on the Work of Howard Pattee . BioSystems 60 (1-3), 2001.
  21. ↑ Brenner, Sydney. "Turing centenary: Life’s code script." Nature 482 (7386) (February 22): 461-461, 2012.
  22. 1 2 Rocha, Luis M. and Johan Bollen. "Biologically Motivated Distributed Designs for Adaptive Knowledge Management". In: Design Principles for the Immune System and other Distributed Autonomous Systems. L. Segel and I. Cohen (Eds.) Santa Fe Institute Series in the Sciences of Complexity. Oxford University Press, pp. 305-334, 2001
  23. 1 2 G.L. Ciampaglia, P. Shiralkar, L.M. Rocha, J. Bollen, F. Menczer, A. Flammini.Computational fact checking from knowledge networks. PLoS One. 10(6): e0128193. doi:10.1371/journal.pone.0128193, 2015.
  24. ↑ Pattee, H.H. "The Physics and Metaphysics of Biosemiotics." Journal of Biosemiotics. 1:281-301, 2005.
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