Curriculum Vitae

Luis Mateus Rocha

School of Informatics, Cognitive Science Program, and The Biocomplexity Institute
Indiana University
919 East Tenth Street, Bloomington IN 47406
e-mail: rocha@indiana.edu
and
Computational Biology Collaboratorium, Director
Instituto Gulbenkian da Ciencia, Portugal.

Contents

The most recent version of the full CV and a short version are available (last updated August 7, 2014) in Adobe Acrobat (.pdf) format. Selected elements of the CV are available below.






Personal Data

Luis M. Rocha is Professor of Informatics and Cognitive Science at Indiana University. He is director of the Complex Systems graduate Program in Informatics, member of the Center for Complex Networks and Systems, and core faculty of the Cognitive Science Program at Indiana University, Bloomington, USA. He is also the director of the Computational Biology Collaboratorium and in the Direction of PhD program in Computational Biology at the Instituto Gulbenkian da Ciencia, Portugal. His research is on complex systems, computational biology, artificial life, embodied cognition and bio-inspired computing. He received his Ph.D in Systems Science in 1997 from the State University of New York at Binghamton. From 1998 to 2004 he was a permanent 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 major conferences in the field such as the Tenth International Conference on the Simulation and Synthesis of Living Systems (Alife X) and the Ninth European Conference on Artificial Life (ECAL 2007). He has published many articles in scientific and technology journals, and has been the recipient of several scholarships and awards. At Indiana University, he has received the School of Informatics Teaching Excellence Award for 2006 after developing a new syllabus for an introductory undergraduate course on Informatics and a new graduate course on biologically-inspired computing.

Research Interests


For additional information see my research projects and my research group (CASCI).

Complex adaptive systems:

Agent-based modeling, artificial life, automata, bio-inspired computing, discrete dynamical systems, embodied cognition, collective behavior and dynamics, evolutionary and adaptive systems, network dynamics, origin of information, theoretical biology.

Computational and Systems biology:

Automatic functional annotation, bioinformatics, literature and text mining, microarray analysis, models of biochemical regulation, RNA editing.

Computational intelligence and complex networks:

Collective and adaptive behavior, connectionism, evolutionary computation, fuzzy set theory, generalized information theory, information retrieval, literature and text mining, machine learning, network science, recommender systems, uncertainty modeling.


List of Publications


Volumes

Seabra Lopes, L.; Lau, N.; Mariano, P.; Rocha, L.M. (Eds.) [2009]. Progress in Artificial Intelligence: 14th Portuguese Conference on Artificial Intelligence (EPIA 2009). Lecture Notes in Artificial Intelligence (LNAI), 5816. Springer-Verlag. doi:10.1007/978-3-642-04686-5 (Online Fulltext Content)

Almeida e Costa, F., L.M. Rocha, E. Costa, I. Harvey, A. Coutinho (Eds.) [2007]. Advances in Artificial Life: Proceedings of the 2007 European Conference on Artificial Life. Lecture Notes in Artificial Intelligence (LNAI), 4648. Springer-Verlag.

Rocha, L.M., L. Yaeger, M. Bedau, D. Floreano, R. Goldstone, and A. Vespignani (Eds.) [2006]. Artificial Life 10: Tenth International Conference on the Simulation and Synthesis of Living Systems. MIT Press.

Almeida e Costa, F. and Rocha, Luis M. (Eds.) [2005]. Special Issue on Embodied and Situated Cognition. Artificial Life. 11 (1-2).

Rocha, Luis M. (Ed.)[2001]. The Physics and Evolution of Symbols and Codes. BioSystems Vol. 60, No. 1-3. Editorial: Biosystems Vol. 60, pp. 1-4.

Rocha, Luis M. [1997]. Evidence Sets and Contextual Genetic Algorithms: Exploring Uncertainty, Context, and Embodiment in Cognitive and Biological Systems. PhD Dissertation. State University of New York at Binghamton.

Rocha, Luis M. (Ed.) [1995]. Self-Reference in Biological and Cognitive Systems. Special issue of Communication and Cognition - Artificial Intelligence. Vol. 12, nos. 1-2. Contributors: Howard Pattee, Robert Rosen, George Kampis, Peter Cariani, Pedro Medina-Martins, Charles Henry, and Luis Rocha.

Journal papers

T. Simas and L.M. Rocha [2014]."Distance Closures on Complex Networks". Network Science, In Press.

A. Kolchinsky, M. P. Van Den Heuvel, A. Griffa, P. Hagmann, L.M. Rocha, O. Sporns, J. Goni [2014]. "Multi-scale Integration and Predictability in Resting State Brain Activity". Frontiers in Neuroinformatics, 8:66. doi: 10.3389/fninf.2014.00066.

M. Marques-Pita and L.M. Rocha [2013]. "Canalization and control in automata networks: body segmentation in Drosophila Melanogaster". PLoS ONE, 8(3): e55946. doi:10.1371/journal.pone.0055946.

Wu, Hengyi, S. Karnik, A. Subhadarshini, Z. Wang, S. Philips, X. Han, C. Chiang, L. Liu, M. Boustani, L.M. Rocha, S.K. Quinney, D.A. Flockhart and L. Li [2013]. "An Integrated Pharmacokinetics Ontology and Corpus for Text Mining”. BMC Bioinformatics. 14:35. DOI:10.1186/1471-2105-14-35. (Highly Accessed)

A. Lourenço, M. Conover, A. Wong, A. Nematzadeh, F. Pan, H. Shatkay, and L.M. Rocha [2011]."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.

M. Krallinger, et al [2011]."The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text". BMC Bioinformatics. 12(Suppl 8):S3.

A. Abi-Haidar and L.M. Rocha [2011]. "Collective Classification of Textual Documents by Guided Self-Organization in T-Cell Cross-Regulation Dynamics". Evolutionary Intelligence. 4(2):69-80.

A. Kolchinsky, A. Abi-Haidar, J. Kaur, A.A. Hamed and L.M. Rocha [2010]. "Classification of protein-protein interaction full-text documents using text and citation network features." IEEE/ACM Transactions On Computational Biology And Bioinformatics, 7(3):400-411. DOI: doi.ieeecomputersociety.org/10.1109/TCBB.2010.55

A. Lourenço; R.C. Carreira; D. Glez-Peña; J.R. Méndez; S.A. Carneiro; L.M. Rocha; F. Díaz; E.C. Ferreira; I.P. Rocha; F. Fdez-Riverola; M. Rocha [2009]. "BioDR: Semantic Indexing Networks for Biomedical Document Retrieval." Expert Systems with Applications, 37, 3444–3453.

Z. Wang, S. Kim, S.K. Quinney, Y. Guo, S.D. Hall, L.M. Rocha, and L. Li [2009]. "Literature mining on pharmacokinetics numerical data: A feasibility study". Journal of Biomedical Informatics. 42 (4): 726-735.

T. Simas and L.M. Rocha [2008]."Stochastic model for scale-free networks with cutoffs". Physical Review E, 78(6):066116.

A. Abi-Haidar, J. Kaur, A. Maguitman, P. Radivojac, A. Retchsteiner, K. Verspoor, Z. Wang, and L.M. Rocha [2008]. Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks". Genome Biology. 9(Suppl 2):S11

C. Huang, J. Kaur, A. Maguitman, L.M. Rocha[2007]."Agent-Based Model of Genotype Editing". Evolutionary Computation, 15(3): 253-89.

Almeida e Costa, F. and Rocha, Luis M. [2005]. "Embodied and Situated Cognition". Artificial Life. 11 (1-2), pp. 5 - 11

Rocha, Luis M. and W. Hordijk [2005]. "Material Representations: From the Genetic Code to the Evolution of Cellular Automata". Artificial Life. 11 (1-2), pp. 189 - 214

Verspoor, K., J. Cohn, C. Joslyn, S. Mniszewski, A. Rechtsteiner, L.M. Rocha, T. Simas [2005]. "Protein Annotation as Term Categorization in the Gene Ontology using Word Proximity Networks". BMC Bioinformatics, 6(Suppl 1):S20. doi:10.1186/1471-2105-6-S1-S20

Challacombe, J,, A. Rechtsteiner, G. Gottardo, L.M. Rocha, E.P. Brown, T. Shenk, M. Altherr, T. Brettin [2004]. "Evaluation of the host transcriptional response to human cytomegalovirus infection". Physiol. Genomics (April 6, 2004). 10.1152/physiolgenomics.00155.2003. In Press.

Rocha, Luis M. and A. Rechtsteiner [2004]. "Review of Bioinformatics for Geneticists." Clinical Chemistry 50 (9), pp. 2471 - 2472. CLINCHEM/2003/020909.

Rocha, Luis M. [2001]. "Evolution with material symbol systems". Biosystems. Vol. 60, pp. 95-121.

Rocha, Luis M. [2001]. "Adaptive Recommendation and Open-Ended Semiosis". Kybernetes. Vol. 30, No. 5-6.

Rocha, Luis M. [1999]." Evidence Sets: Modeling Subjective Categories." In: International Journal of General Systems. Vol. 27, pp. 457-494.

Joslyn, Cliff and Luis Rocha [1998] "Towards a Formal Taxonomy of Hybrid Uncertainty Representations" (pdf). Information Sciences. Vol. 110, pp. 255-277

Rocha, Luis M. [1998]." Where is the progress?. " Cybernetics and Human Knowing. Vol.5, No. 4, pp. 86-90.

Rocha, Luis M. and Cliff Joslyn [1998]." "Simulations of Evolving Embodied Semiosis: Emergent Semantics in Artificial Environments" Simulation Series; Vol. 30, (2), pp. 233-238.

Rocha, Luis M. [1997]." Relative Uncertainty and Evidence Sets: A Constructivist Framework." In: International Journal of General Systems. Vol. 26. (1-2), pp. 35-61.

Rocha, Luis M. (Ed.) [1997]. "Obituary for Professor Gordon Pask." In: International Journal of General Systems. Vol. 26, no. 3, pp. 219-222.

Rocha, Luis M., V. Kreinovich, and R. Kearfott[1996]. " Computing Uncertainty in Interval Based Sets." Applied Optimization. Vol. 3, pp. 337-380. Also appears In: Applications of Interval Computation. R.B. Kearfott and V. Kreinovich (Eds.). Kluwer Academic Press. pp. 337-380.

Henry, Charles and Luis Rocha [1996] "Language Theory: Consensual Selection of Dynamics". Cybernetics and Systems: An International Journal. Vol. 27, pp. 541-553. Winner of the best paper award of the EMCSR96 and the Gordon Pask Memorial Award.

Rocha, Luis M. [1996]." Eigenbehavior and symbols." In: Systems Research Vol. 13, No 3, pp. 371-384.

Rocha, Luis M. [1995]. " Artificial semantically closed objects." Communication and Cognition - Artificial Intelligence. Vol. 12, nos. 1-2 ( Rocha [1995a]). pp. 63-90.

Conference Proceedings

A. Gates and L.M. Rocha [2014]. "Structure and dynamics affect the controllability of complex systems: a Preliminary Study". Artificial Life 14: Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems: 429-430, MIT Press.

M.R. Francisco, I. Wood, S. Sabanovic and L.M. Rocha [2014]. "Designing a minimalist socially aware robotic agent for the home". Artificial Life 14: Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems: 876-883, MIT Press.

A. Kolchinsky, A. Lourenço, L. Li, L.M. Rocha [2013]. "Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions". Pacific Symposium on Biocomputing 18:409-420.

T. Simas and L.M. Rocha [2012]."Semi-metric networks for recommender systems". 2012 IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology, pp. 175-179.

J. Goni, A. Kolchinsky, M. Van den Heuvel, A. Griffa, L. M. Rocha, O. Sporns [2012]. "Information, Space and Structure in the Human Brain Resting State". In: Physics, Computation, and the Mind, 12th Granada Seminar, September 17-21, 2012.

A. Kolchinsky, and L.M. Rocha [2011]."Prediction and modularity in complex dynamical systems" (pdf). In: Proc. of the 8th Int. Conf. on Complex Systems. June 26 - July 1, 2011, Quincy, MA, USA. In Press.

S. Karnik, A. Subhadarshini, Z. Wang, L.M. Rocha, and L. Li [2011]."Extraction of drug-drug interactions using all paths graph kernel." (pdf). In: Proceedings of the 1st Challenge task on Drug-Drug Interaction Extraction. I. Segura-Bedmar, P. Martínez, D. Sánchez. September, 7th, 2011, Huelva, Spain, pp. 83-88.

A. Kolchinsky, and L.M. Rocha [2011]."Prediction and Modularity in Dynamical Systems". In: Advances in Artificial Life, Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems (ECAL 2011). August 8 – 12, 2011, Paris, France,. MIT Press, pp. 423-430.

M. Marques-Pita and L.M. Rocha [2011]. "Schema Redescription in Cellular Automata: Revisiting Emergence in Complex Systems". In: The 2011 IEEE Symposium on Artificial Life, at the IEEE Symposium Series on Computational Intelligence 2011. April 11 – 15, 201, Paris, France,. IEEE Press, pp: 233-240.

A. Lourenço, M. Conover, A. Wong, F. Pan, Alaa Abi-Haidar, A. Nematzadeh, H. Shatkay, and L.M. Rocha [2010]."Testing Extensive Use of NER tools in Article Classification and a Statistical Approach for Method Interaction Extraction in the Protein-Protein Interaction Literature" (pdf). Proceedings of the BioCreative III Workshop 2010, Bethesda, Maryland, September 13-15, 2010.

A. Abi-Haidar and L.M. Rocha [2010]. "Collective Classification of Biomedical Articles using T-Cell Cross-regulation". In: Artificial Life XII: Twelfth International Conference on the Simulation and Synthesis of Living Systems. H. Fellermann et al et al (Eds.). MIT Press, pp. 706-713.

A. Abi-Haidar and L.M. Rocha [2010]. "Biomedical Article Classification Using an Agent-Based Model of T-Cell Cross-Regulation". In: Artificial Immune Systems: 9th International Conference, (ICARIS 2010). E. Hart, C. McEwan, J. Timmis, and A. Hone (Eds.) Lecture Notes in Computer Science. Springer-Verlag, 6209: 237-249. Recipient of Best Paper Award. for ICARIS 2010

A. Lourenço, L.M. Rocha, and H. Shatkay [2010]. " Establishing an evaluation baseline for document classifiers in biomedical curation". Biolink@ISMB, Washington DC, September, 2010.

A. Kolchinsky, A. Abi-Haidar, J. Kaur, A.A. Hamed and L.M. Rocha [2009]."Classification of protein-protein interaction documents using text and citation network features". A. Lourenço, S. Carneiro, E.C. Ferreira, R. Carreira, L.M. Rocha, D. Glez-Peña, J.R. Méndez, F. Fdez-Riverola, F. Diaz, I. Rocha and M. Rocha [2009]. "Biomedical Text Mining Applied To Document Retrieval and Semantic Indexing.". In: Proc. of the 3rd International Workshop on Practical Applications of Computational Biology & Bioinformatics (IWPACBB'09). Lecture Notes in Computer Science. Springer-Verlag, 5518: 954-963.

M. Marques-Pita, M. Mitchell, and L.M. Rocha [2008]. "The Role of Conceptual Structure in Learning Cellular Automata to Perform Collective Computation". In: Unconventional Computation: 7th International Conference (UC 2008). Lecture Notes in Computer Science. Springer-Verlag, 5204: 146-163.

A. Abi-Haidar and L.M. Rocha [2008]. Adaptive Spam Detection Inspired by a Cross-Regulation Model of Immune Dynamics: A Study of Concept Drift". In: Artificial Immune Systems: 7th International Conference, (ICARIS 2008). Bentley, Peter; Lee, Doheon; Jung, Sungwon (Eds.) Lecture Notes in Computer Science. Springer-Verlag, 5132: 36-47.

M. Marques-Pita and L.M. Rocha [2008]. "Conceptual Structure in Cellular Automata: The Density Classification Task". In: Artificial Life XI: Eleventh International Conference on the Simulation and Synthesis of Living Systems. S. Bullock, J. Noble, R. A. Watson, and M. A. Bedau (Eds.). MIT Press, pp. 390-397.

A. Abi-Haidar and L.M. Rocha [2008]. Adaptive Spam Detection Inspired by the Immune System". In: Artificial Life XI: Eleventh International Conference on the Simulation and Synthesis of Living Systems. S. Bullock, J. Noble, R. A. Watson, and M. A. Bedau (Eds.). MIT Press, pp. 1-8.

L.M. Rocha and J. Kaur [2007]."Genotype Editing and the Evolution of Regulation and Memory". Proceedings of the 9th European Conference on Artificial Life. Lecture Notes in Artificial Intelligence (LNAI), 4648: 63-73 (Springer-Verlag).

A. Abi-Haidar, J. Kaur, A. Maguitman, P. Radivojac, A. Retchsteiner, K. Verspoor, Z. Wang, and L.M. Rocha [2007]."Uncovering Protein-Protein Interactions in the Bibliome". Proceedings of the Second BioCreative Challenge Evaluation Workshop (ISBN 84-933255-6-2), pp.247-255.

Rechtsteiner, A., Luinstra, J., Rocha, L.M., Strauss, C.E., [2006]. "Use of Text Mining for Protein Structure Prediction and Functional Annotation in Lack of Sequence Homology". In: Joint BioLINK and Bio-Ontologies Meeting 2006 (ISMB Special Interest Group).In Press.

Rocha, L.M., A. Maguitman, C. Huang, J. Kaur, and S. Narayanan. [2006].""An Evolutionary Model of Genotype Editing". In: Artificial Life 10: Tenth International Conference on the Simulation and Synthesis of Living SystemsL.M.Rocha, L. Yaeger, M. Bedau, D. Floreano, R. Goldstone, and A. Vespignani (Eds.). MIT Press, pp. 105-111.

Maguitman, A. G., Rechtsteiner, A., Verspoor, K., Strauss, C.E., Rocha, L.M. [2006]. "Large-Scale Testing Of Bibliome Informatics Using Pfam Protein Families". In: Pacific Symposium on Bioinformatics 2006. In Press.

Huang, Chien-Feng and Luis M. Rocha [2005]. "Tracking Extrema in Dynamic Environments using a Coevolutionary Agent-based Model of Genotype Edition". In: Genetic and Evolutionary Computation Conference: GECCO 2005. ACM Press, pp. 545-552.

Rocha, L.M., T. Simas, A. Rechtsteiner, M. DiGiacomo, R. Luce [2005]. "MyLibrary@LANL: Proximity and Semi-metric Networks for a Collaborative and Recommender Web Service". In: Proc. 2005 IEEE/WIC/ACM International Conference on Web Intelligence (WI'05), IEEE Press, pp. 565-571.

Huang, Chien-Feng and Luis M. Rocha [2004]. "A Systematic Study of Genetic Algorithms with Genotype Editing". In: Genetic and Evolutionary Computation: GECCO 2004. Lecture Notes in Computer Science Vol. 3102, pp.1233 - 1245. Springer-Verlag.

Rocha, Luis M. [2004]. "Evolving Memory: Logical Tasks for Cellular Automata". Ninth International Conference on the Simulation and Synthesis of Living Systems (ALIFE9). Boston, Massachusetts, September 12-15th 2004.

Rocha, Luis M. and Chien-feng Huang [2004]. "The Role of RNA Editing in Dynamic Environments". In: Ninth International Conference on the Simulation and Synthesis of Living Systems (ALIFE9). Boston, Massachusetts, September 12-15th 2004.

Verspoor, K., J. Cohn, C. Joslyn, S. Mniszewski, A. Rechtsteiner, L.M. Rocha, T. Simas [2004]. "Protein Annotation as Term Categorization in the Gene Ontology". EMBO Workshop: A critical assessment of text mining methods in molecular biology, Granada, Spain, March 28-31, 2004.

Rechtsteiner, A. and L.M. Rocha [2004]. "MeSH Key Terms for Validation and Annotation of Gene Expression Clusters" (pdf). Currents in Computational Molecular Biology. Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), San Diego, CA, March 2004. A. Gramada and Philip E. Bourne (Eds). pp. 212-213.

Rechtsteiner, A., R. Gottardo, L.M. Rocha, and M.E. Wall [2003]. "Singular Value Decomposition for Analysis of Gene Expression" (pdf). Currents in Computational Molecular Biology. Proceedings of the The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2003), Berlin, April 10-13, 2003. R. Spang, P.Beziat and M. Vingron (Eds).pp. 275-276

Rechtsteiner, A., R. Gottardo, L.M. Rocha, M.E. Wall and T. Brettin [2003]. "Three Algorithms for Filtering and Analysis of Gene Expression Data". Poster at Pacific Symposium on Biocomputing 2003.

Rocha Luis M. [2003]. "Extraction and Semi-metric Analysis of Social and Biological Networks". Poster at Networks: Structure, Dynamics and Function, May 12 - 16, 2003, Santa Fe, New Mexico, USA.

Rocha, Luis M. and Andreas Rechtsteiner [2003]. "Fast Cheap and Synthetic Oracle (FACSO): Proximity Measures to capture Expert Knowledge in the Bibliome". Poster at Pacific Symposium on Biocomputing 2003.

Huang, Chien-Feng and Luis M. Rocha [2003]. "Exploration of RNA Editing and Design of Robust Genetic Algorithms". 2003 IEEE Congress on Evolutionary Computation (CEC), Canberra, Australia, December 2003. R.Sarker et al (Eds). IEEE Press, pp. 2799-2806.

Rocha, Luis M. [2002]. "Combination of Evidence in Recommendation Systems Characterized by Distance Functions". In: Proceedings of the 2002 World Congress on Computational Intelligence: FUZZ-IEEE'02. Honolulu, Hawaii, May 2002. IEEE Press, pp. 203-208. LAUR 02-154.

Rocha, Luis M. [2001]. "Adaptive Webs for Heterarchies with Diverse Communities of Users". Paper prepared for the workshop From Intelligent Networks to the Global Brain: Evolutionary Social Organization through Knowledge Technology, Brussels, July 3-5, 2001. LAUR 005173.

Joslyn, Cliff and Luis M. Rocha [2000]. "Towards Semiotic Agent-Based Models of  Socio-Technical Organizations." Proc. AI, Simulation and Planning in High Autonomy Systems (AIS 2000) Conference, Tucson, Arizona, USA. ed. HS Sarjoughian et al., pp. 70-79.

Bollen, Johan, Luis M. Rocha [2000]. "An Adaptive Systems Approach to the Implementation and Evaluation of Digital Library Recommendation Systems." In: Research and Advanced Technology for Digital Libraries: 4th European Conference, ECDL 2000. Lectures Notes in Computer Science, Springer-Verlag, pp.356-359.

Bollen, Johan, Hebert Van de Sompel, and Luis M. Rocha [1999]. “Mining associative relations from website logs and their application to context-dependent retrieval using spreading activation” (adobe pdf). Workshop on Organizing Web Space (WOWS), ACM Digital Libraries 99, August 1999, Berkeley, California.

Rocha, Luis M. [1999]. "TalkMine and the Adaptive Recommendation Project". In: the Proceedings of the Association for Computing Machinery (ACM) - Digital Libraries 99. U.C. Berkely, August 1999. pp. 242-243.

Johnson, Norman, Steen Rasmussen, Cliff Joslyn, Luis Rocha, Steven Smith, and Marianna Kantor [1998] " Symbiotic intelligence: self-organizing knowledge on distributed networks, driven by human interaction"(postscript), (pdf). Proceedings of the Sixth International Conference on Artificial Life, C. Adami, R. K. Belew, H. Kitano, C. E. Taylor (Eds.), MIT Press, pp. 403-407.

Rocha, Luis M. [1998]. "Syntactic autonomy". In: Proceedings of the Joint Conference on the Science and Technology of Intelligent Systems (ISIC/CIRA/ISAS 98). National Institute of Standards and Technology, Gaithersburg, MD, September 1998. IEEE Press, pp. 706-711.

Rocha, Luis M. [1997]. "Evidence Sets: Contextual Categories". In: Proceedings of the meeting on Control Mechanisms for Complex Systems, Physical Science Laboratory, New Mexico State University, Las Cruces, New Mexico, January 1997. M. Coombs (ed.). NMSU Press, pp. 339-357.

Rocha, Luis M. [1996]." "Relative Uncertainty: Measuring Uncertainty in Discrete and Nondiscrete Domains". " In: Proceedings of the NAFIPS'96. M. Smith et al (Eds). IEEE Press, pp. 551-555.

Rocha, Luis M. [1995]." Contextual Genetic Algorithms: Evolving Developmental Rules ." In: Advances in Artificial Life: Proceedings of the European Conference on Artificial Life (ECAL 2005) . F. Moran, A. Moreno, J.J. Merelo, and P. Chacon (Eds.). Series: Lecture Notes in Artificial Intelligence, Springer-Verlag. pp. 368-382.

Rocha, Luis M. [1995]." Interval Based Evidence Sets." In: Proceedings of the ISUMA-NAFIPS'95. B. Ayyub (Ed.). IEEE Press. pp.624-629.

Rocha, Luis M. [1994]."Von Foerster's cognitive tiles: semantically closed building blocks for AI and Alife." In: Cybernetics and Systems ' 94. Robert Trappl (Ed.). Vol. 1, pp 621-628. World Scientific Press.

Rocha, Luis M. [1994]." Cognitive Categorization revisited: extending interval valued fuzzy sets as simulation tools for concept combination ." In: Proceedings of the 1994 International Conference of NAFIPS/IFIS/NASA. . IEEE. pp 400-404.

Medina-Martins, Pedro R., Luis Rocha, et al [1994]."Metalogues: an essay on computers' psychology - from childhood to adulthood." In: Cybernetics and Systems 94. R, Trappl (Ed.). World Scientific Press. pp. 565-572.

Medina-Martins, Pedro R. and Luis Rocha [1992]."The in and the out: an evolutionary approach." In: Cybernetics and Systems Research '92. Robert Trappl. World Scientific Press. pp 681-689.

Rocha, Luis M. [1991]."Fuzzification of Conversation Theory (pdf)." In: Principia Cybernetica Conference, Free University of Brussels, Brussels, June 1991. Ed. Francis Heylighen.

Book chapters

Rocha, L.M. [2003]. "Automatic Conversation Driven by Uncertainty Reduction and Combination of Evidence for Recommendation Agents ". In: Systematic Organization of Information in Fuzzy Systems. NATO Science Series. P. Melo-Pinto, H.N. Teodorescu and T. Fukuda (Eds.) IOS Press, pp 249-265.

Wall, Michael E., Andreas Rechtesteiner, and Luis M. Rocha [2003]. "Singular Value Decomposition and Principal Component Analysis ". In: A Practical Approach to Microarray Data Analysis. D. P. Berrar, W. Dubitzky, and M. Granzow (Eds.). Kluwer Academic Publishers, pp. 91-109.

Rocha, Luis M. [2002]. "Semi-metric Behavior in Document Networks and its Application to Recommendation Systems". In: Soft Computing Agents: A New Perspective for Dynamic Information Systems. V. Loia (Ed.) International Series Frontiers in Artificial Intelligence and Applications. IOS Press, pp. 137-163..

Rocha, Luis M. and Johan Bollen[2001]. 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.

Rocha, Luis M. [2001]. "TalkMine: a Soft Computing Approach to Adaptive Knowledge Recommendation". In: Soft Computing Agents: New Trends for Designing Autonomous Systems. Vincenzo Loia and Salvatore Sessa (Eds.). Series on Studies in Fuzziness and Soft Computing. Physica-Verlag, Springer, pp. 89-116

Rocha, Luis M. [2000]. "Syntactic autonomy, cellular automata, and RNA editing: or why self-organization needs symbols to evolve and how it might evolve them". In: Closure: Emergent Organizations and Their Dynamics. Chandler J.L.R. and G, Van de Vijver (Eds.) Annals of the New York Academy of Sciences. Vol. 901, pp 207-223.

Rocha, Luis M. [1998]." 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.

Media Writings

L.M. Rocha [2014]. "Ciência 2.0: do elitismo à decisão coletiva". Expresso. 8 Fevereiro, 2014, pp. 35.

L.M. Rocha [2014]. "Get in Sync". Herald Times, Bloomington, IN. August 7, 2014. Reprint available.

L.M. Rocha [2013]. "Summer Education". Herald Times, Bloomington, IN. August 29, 2013.

L.M. Rocha [2008]."The Logical Mechanisms of Life". In: Complex Biological Systems. Icfai University Press, 2008.

L.M. Rocha [2007]."Reality is Stranger than Fiction: What can Artificial Life do about Advances in Biology?". Invited presentation for the "Biocomplexity" discussion section at the 9th European Conference on Artificial Life, September 12, 2007 in Lisbon, Portugal. Reprinted in: Complex Biological Systems. Icfai University Press, 2008.

Rocha, Luis M. [2002]. “Partnership of Fools.Wired Magazine, (Rants and Raves) April 2002.

Rocha, Luis M. [2002]. “Path to Enlightenment?”. New York Times Book Review, (Letters) pp. 4, June 23.

Rocha, Luis M. [1999]. "Complex Systems Modeling: Using Metaphors From Nature in Simulation and Scientific Models". BITS: Computer and Communications News. Computing, Information, and Communications Division. Los Alamos National Laboratory. November 1999.

Blogs

Sciber [2008-Present].

Life Inspired [2007-Present].

Hey City Zen! [2004-Present].

InfoPort [2004-2008].

Electronic Publications

L.M. Rocha. Biologically-inspired computing Lecture Notes (pdf document), Lecture notes for course taught at Indiana University.

Rocha, Luis M. and S. Schnell [2005,2006]. "Introduction to Informatics", Lecture notes for course taught at Indiana University.

Rocha, Luis M. [2002] .Introduction to Bioinformatics. Lecture notes for PhD course at the Instituto Gulbenkian da Ciencia, Oeiras, Portugal.

L.M. Rocha [2000]. "O Caminho de Santa Fe."

Rocha, Luis M. [1999]. From Artificial Life to Semiotic Agent Models: Review and Research Directions. Los Alamos National Laboratory Internal Report. LAUR-99-5475.

Rocha, Luis M. [1995]. " Evolutionary Systems and Artificial Life. Lecture Notes for the course taught at the Department of Systems Science and Industrial Engineering at the State University of New York at Binghamton.

Translations

Varela F., E. Thompson and E. Rosch [1998]. A Mente Corporea: Ciencia Cognitiva e Experiencia Humana.. Editora Piaget. Translation and Scientific Editing by Luis M. Rocha from the original "The Embodied Mind".

Installations and Creative Productions

Marques Pita, M., S. Costa, A. Paio, M.J. Oliveira, S. Oliveira, Luis M. Rocha [2013-2014]. Morfogénese musical Visita-instalação interativa (Musical Morphogenesis: Interactive Installation). Opening: Fundação Calouste Gulbenkian Museum, Lisbon, October 5th, 2013. Also on Facebook.


For more information contact Luis Rocha at rocha@indiana.edu. Check the Web Design Credits, for due credit.
Last Modified: August 7, 2014