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Luis M. Rocha

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For other people named Luis Rocha, see Luis Rocha (disambiguation).
Luís M. Rocha
Luis M. Rocha, 2014
Born (1966-10-05) October 5, 1966 (age 58)
Luanda, Angola
Alma materInstituto Superior Técnico, Portugal Lic. (B.A. plus M.S.), 1990
Binghamton University Ph.D., 1997
Awards
Scientific career
Fields
Institutions
ThesisEvidence Sets and Contextual Genetic Algorithms: Exploring Uncertainty, Context, and Embodiment in Cognitive and Biological Systems. SUNY Binghamton. (1997)
Academic advisors
Websitecasci.binghamton.edu

Luis M. Rocha is the George J. Klir Professor of Systems Science at the Thomas J. Watson College of Engineering and Applied Science, Binghamton University (State University of New York). He has been director of the NSF-NRT Complex Networks and Systems graduate Program in Informatics at Indiana University, Bloomington, USA. He is also director of the Center for Social and Biomedical Complexity, between Binghamton University and Indiana University, Bloomington, a Fulbright Scholar, and Principal Investigator at the Instituto Gulbenkian de Ciência, Portugal. His research is on complex systems and networks,[1][2][3][4] computational and systems biology,[1][5][6][7][8] biomedical complexity and digital health,[9][10][11][12] and computational intelligence (including Artificial Life and Embodied Cognition).[13][14][15][16][17][18][19][20][21]

Biography

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He was born in Luanda, Angola, moving to Lisbon, Portugal in his teens and completing an Licentiate (B.A. plus M.S.) in Mechanical and Systems Engineering at the Instituto Superior Técnico. 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 been the director of the NSF-NRT Interdisciplinary Training Program in Complex Networks and Systems, and Professor of Informatics in the Luddy School of Informatics, Computing, and Engineering at Indiana University, where he was a member of the advisory council of the Indiana University Network Science Institute, and core faculty of the Cognitive Science Program. From 2005 to 2015 he was the director of the Computational Biology Collaboratorium and in the Direction of the PhD program in Computational Biology at the Instituto Gulbenkian de Ciencia, where he remains a Principal Investigator. He has organized the Tenth International Conference on the Simulation and Synthesis of Living Systems (Alife X)[22] and the Ninth European Conference on Artificial Life (ECAL 2007).[23]

Research

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Dr. Rocha studies the systems properties of natural and artificial systems which enable them to adapt and evolve. He has approached this general topic by investigating how information and redundancy are fundamental for controlling the behavior and evolutionary capabilities of complex systems,[1][15][16][17] as well as abstracting principles from natural systems to produce adaptive information technology.[18][19][21]

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,[24] Sydney Brenner,[25] 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?[13][16][17] Can artificial systems implement the same principle?[13][15] Namely, can collective intelligence on the web become a super-organism implementing this principle?[14][18][26][27] From these questions, he has worked on various specific research projects ranging from Biomedical Literature Mining and Social Media Mining[9][10][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,[13][14][2][18][20][26][27] and Agent-based models of Evolutionary Systems such as RNA Editing[19] and Artificial Immune Systems.[21]

Philosophical views

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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[28] 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.[13][14][2][15][18] In addition to scientific work often mentioned in the media, he regularly publishes opinion articles in the popular media to disseminate scientific thinking.[29]

References

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  1. ^ a b c d e A.J. Gates, R.B. Correia, X. Wang, L.M. Rocha. "The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling" PNAS, 118(12): e2022598118. doi:10.1371/journal.pone.0055946. 2013
  2. ^ a b c d T. Simas, R.B. Correia, and L.M. Rocha. "The distance backbone of complex networks." Journal of Complex Networks, 9 (6): cnab021, DOI:10.1093/comnet/cnab021, 2021
  3. ^ a b 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. ^ a b 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. ^ a b 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. ^ a b 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. ^ a b 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. ^ a b R.B. Correia, L. Li, L.M. Rocha "Monitoring potential drug interactions and reactions via network analysis of Instagram user timelines". Pacific Symposium on Biocomputing., 21:492-503. DOI: 10.1073/pnas.2022598118, 2021
  10. ^ a b I.B Wood, P.L. Varela, J. Bollen, L.M. Rocha, J. Gonçalves-Sá "Human Sexual Cycles are Driven by Culture and Match Collective Moods". Scientific Reports., 7:17973. doi: 10.1038/s41598-017-18262-5, 2017
  11. ^ R.B. Correia, I.B Wood, J. Bollen, L.M. Rocha "Mining social media data for biomedical signals and health-related behavior". Annual Review of Biomedical Data Science., 3(1): 433-458. DOI: 10.1146/annurev-biodatasci-030320-040844, 2020.
  12. ^ R.B. Correia, L.P. de Araújo, M.M. Mattos, L.M. Rocha "City-wide Analysis of Electronic Health Records Reveals Gender and Age Biases in the Administration of Known Drug-Drug Interactions". npj Digital Medicine., 2: 74. DOI: 10.1038/s41746-019-0141-x, 2029.
  13. ^ a b c d e Clark, A. Natural-Born Cyborgs:Minds, Technologies, and the Future of Human Intelligence. Oxford University Press, 2003.
  14. ^ a b c d Stark, D. The Sense of Dissonance: Accounts of Worth in Economic Life. Princeton University Press, 2011.
  15. ^ a b c d 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
  16. ^ a b c L.M. Rocha, Evolution with material symbol systems. "Biosystems. Vol. 60, pp. 95-121." 2001
  17. ^ a b c 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
  18. ^ a b c d e L.M. Rocha, Adaptive Recommendation and Open-Ended Semiosis. "Kybernetes. Vol. 30, No. 5-6." 2001
  19. ^ a b c C. Huang, J. Kaur, A. Maguitman, L.M. Rocha, Agent-Based Model of Genotype Editing. "Evolutionary Computation, 15(3): 253-89." 2007
  20. ^ a b L.M. Rocha, Evidence Sets: Modeling Subjective Categories. "In: International Journal of General Systems. Vol. 27, pp. 457-494." 1997
  21. ^ a b c 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
  22. ^ 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
  23. ^ 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
  24. ^ Rocha, Luis M. (Ed.) The Physics and Evolution of Symbols and Codes: Reflections on the Work of Howard Pattee . BioSystems 60 (1-3), 2001.
  25. ^ Brenner, Sydney. "Turing centenary: Life’s code script." Nature 482 (7386) (February 22): 461-461, 2012.
  26. ^ a b 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
  27. ^ a b 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.
  28. ^ Pattee, H.H. "The Physics and Metaphysics of Biosemiotics." Journal of Biosemiotics. 1:281-301, 2005.
  29. ^ Luis M. Rocha in the News and Media
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