formal luis rocha

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Publications On-Line

Latest Publications on the Web

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

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. 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.

L.M. Rocha. Biologically-inspired computing Lecture Notes (pdf document)

A. Lourenço, M. Conover, A. Wong, A. Nematzadeh, F. Pan, H. Shatkay, and L.M. Rocha [2012]."Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature". BMC Bioinformatics, 13180.

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.

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.

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.

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. 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. 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. 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 [2010]. "BioDR: Semantic Indexing Networks for Biomedical Document Retrieval." Expert Systems with Applications, 37, 3444–3453.

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.)

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". Proceedings of the BioCreative II.5 Workshop 2009: Special Session on Digital Annotations, Madrid, Spain, October 7-9, 2009. pp 34.

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.

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.

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

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

Full List of Publications with older papers.

Conference Organization

Current

The Alan Turing Centenary Symposium, Fundacao Calouste Gulbenkian, December 11, 2012, Lisbon, Portugal. A videocast of the symposium is available

Recent Past

9th European Conference on Artificial Life (ECAL 07), September 10-14, 2007, Lisbon, Portugal

Multi-Agents for modelling Complex Systems (MA4CS), Satellite Conference of the European Conference on Complex Systems (ECCS'07), Dresden, Germany, October 5-6, 2007

The 10th International Conference on the Simulation and Synthesis of Living Systems (Alife X), June 3-7, 2006, School of Informatics, Indiana University, Bloomington

European Conference on Artificial Life (ECAL 2005), Monday 5th to Friday 9th September 2005 University of Kent, Canterbury, Kent (UK). Includes the Active agents and their environments as dynamical systems Workshop

12th Portuguese Conference on Artificial Intelligence, University of Beira Interior, Covilhã, Portugal, 05 to 08 December, 2005. 2nd Portuguese Workshop on Artificial Life and Evolutionary Algorithms (ALEA 2005)

Genetic and Evolutionary Computation COnference (GECCO 2005), Washington, DC, June 25 - 29, 2005.

Agent-Based Simulation 5, Lisbon, Portugal, 3-5 May 2004.

Genetic Regulatory Networks: Theory and Practice, Canberra, Australia, 8th - 12th December 2003.

Oeiras Mathematical and Computational Biology Workshop, June 20, 2003, Instituto Gulbenkian de Ciência.

International interdisciplinary seminar on new robotics, evolution and embodied cognition. Lisbon, Portugal, November 12-15, 2002. Special Issue of Artificial Life.

Media Pieces

RDP-Antena 2, Portugal. Three episodes of the weekly science program devoted to Alan Turing and AI: December 24 and 31, 2012 and January 7, 2013 (in Portuguese). These interviews were in the context of The Alan Turing Centenary Symposium, whose English videocast is available

Público, Portugal, December 27, 2012: "O cérebro é uma máquina de Turing? E os computadores ficarão inteligentes?". Reprint available (pdf)

La Repubblica, Italy: "L'Italia, un paese felice e lo scrive su Facebook", December 23th, 2011.

Jornal de Letras, Portugal: on April 6th, 2010: Interview: "Somos todos Cyborgs." (pdf)

RTP2 (Bairro Alto), Portugal: on January 26th, 2010: Long interview to Portuguese TV network.

BBC Digital Planet, U.K.: World Service interview about immune-inspired spam-detection system.

SIC News, Portugal: TV interview about immune-inspired spam-detection system.

Rádio Renascença, Portugal: Radio interview about immune-inspired spam-detection system, October 5, 2008.

L'atelier, France: "Spams et bacteries : meme combat", August 22th, 2008.

Tecnomania, Spain: "Podemos hacer software que nazca a la vida?", August 12th, 2008.

Ciência Hoje, Portugal: "Cientistas portugueses criaram aspirador de lixo electronico", August 11th, 2008.

Portuguese Press on August 7th, 2008: Correio da Manhã (p20), Diario de Notícias (p15), Jornal de Notícias (p5), Público (p8), etc.

Silicon Republic, Ireland: "Fighting spam and thinking robots -- bio-inspired AI", August 6th, 2008.

The Daily Telegraph, U.K.: "Can we make software that comes to life?", August 5th, 2008.

Other International Press on August 5-6t, 2008. ACM TechNews (USA), Innovations Report (Germany), Science Daily (USA), Slashdot (USA), AlphaGalileo (European Union), SiloBreaker (UK), etc.

On Facebook, Scholars Link Up With Data, New York Times, December 17, 2007. A description of work pursued with Eliot Smith.

Tecendo Redes Para A Biologia Computacional, Fundacao Calouste Gulbenkian Newsletter, September 2007

Luis Rocha: FLAD and the Portuguese Scientists in America, Ciencia Hoje, October 1, 2006

Aposta na investigação em Portugal, Correio da Manha, June 22, 2006

IGC e FLAD criam laboratório de biologia computacional, Ciencia Hoje, June 22, 2006

Biologia Computacional: Parceria luso-americana para co-laboratório, Lusa News Agency, June 21, 2006

Interview (asf) given to Complexity Digest at the Alife X Conference.

IU to showcase AI technology. Indiana Daily Student: Thursday, June 1, 2006

The facts of Artificial Life. Research at Indiana University: Thursday, June 1, 2006

Luis Rocha, deFrente: May 29, 2006

Indiana noteworthy, Indystar.com: May 22, 2006

Integrating artificial life simulation with synthetic biology, Laboratorytalk: May 22, 2006

Integrating artificial life simulation with synthetic biology, School of Informatics Press Release: May 22, 2006

Integrating artificial life simulation with synthetic biology, biohealthmathematics.com: May 19, 2006

Scientists to Get ‘Alife’ at International Conference. Techpoint, March 15, 2006

Luís Rocha preside a conferência sobre duas décadas de Vida Artificial, Ciencia Hoje, March 15, 2006 Portugal

Artificial life conference set for June, IU Home pages, March 10, 2006

Scientists to Get ‘Alife’ at International Conference, Press Release, February 2006.

Interview (asf video) given to Complexity Digest at the Artificial Life 9 Conference, Boston, MA, 04/09/12-15.

Mentes Lusas. in Expresso, Portugal, July 2004.

Video piece from the 2010 program of the Portuguese National Television channel RTP2, November, 2002. For faster and slower connections

Newspaper article "Insetos, neurônios e sistema imunológico. Esses são os modelos das redes do futuro" in O Estado de Sao Paulo, September 16, 2002. There is also a piece about the Global Brain and Adaptive Webs where my work is mentioned, as well as a translation of the Washignton Post article below.

Newspaper article "Web May Hold the Key to Achieving Artificial Intelligence" in The Washington Post, September 6, 2002; Page A01. Pretty much the same article as"Creating a smarter computer" in the MSNBC web site.

Newspaper article "O português de Los Alamos" in Expresso, Portugal, August 31, 2002. Larger version of the article in the reporter's web site.

Newspaper article "Nova robótica apresenta-se em Lisboa" in Expresso, Portugal, August 17, 2002.

Interview (real video) given to Complexity Digest at the NECSI Complex Systems Conference.

Magazine article "Evolution and scientific literature: towards a decentralized adaptive web" in Nature: WebDebates, 2001.


For more information contact Luis Rocha at rocha@indiana.edu. Check the Web Design Credits, for due credit.
Last Modified: January 20, 2014
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