Publications

2022

JOURNAL PAPERS
  • Fournier, B., Steiner, M., Brochet, X., Degrune, F., Mammeri, J., Carvalho, D. L., Siliceo, S. L., Bacher, S., Peña-Reyes, C. A., & Heger, T. J. (2022). Toward the use of protists as bioindicators of multiple stresses in agricultural soils: A case study in vineyard ecosystems. In Ecological Indicators (Vol. 139, p. 108955). Elsevier BV. DOI https://doi.org/10.1016/j.ecolind.2022.108955
  • Mungloo-Dilmohamud, Z.; Heenaye-Mamode Khan, M.; Jhumka, K.; Beedassy, B.N.; Mungloo, N.Z.; Peña-Reyes, C. Balancing Data through Data Augmentation Improves the Generality of Transfer Learning for Diabetic Retinopathy Classification. Appl. Sci.2022, 12, 5363. DOI

2019

JOURNAL PAPERS
  • Ramírez López DV, Melo Escobar MI, Peña-Reyes CA, Rojas Arciniegas ÁJ, Neuta Arciniegas PA. Isolation, Characterization, and Agent-Based Modeling of Mesenchymal Stem Cells in a Bio-construct for Myocardial Regeneration Scaffold Design. Data. 2019; 4(2):71. DOI
PEER REVIEWED CONFERENCES
  • Z. Mungloo-Dilmohamud, Y. Jaufeerally-Fakim and C. Peña-Reyes. “Exploring the Stability of Feature Selection Methods Across a Palette of Gene Expression Datasets”. 6th International Conference on Biomedical and Bioinformatics Engineering (ICBBE 2019). 2019.DOI
  • J.F. López, J. López, D. Leite and C. Peña. “Applying one-class learning algorithms to predict phage-bacteria interactions”. 6th IEEE Latin American Conference on Computational Intelligence LA-CCI. 2019.DOI
BOOK CHAPTERS
  • Despraz J., Gomez S., Satizábal H.F., Peña-Reyes C.A. (2019) Exploring Internal Representations of Deep Neural Networks. In: Sabourin C., Merelo J., Madani K., Warwick K. (eds) Computational Intelligence. IJCCI 2017. Studies in Computational Intelligence, vol 829. Springer, Cham. First Online 30 May 2019.DOI

2018

PEER REVIEWED CONFERENCES
  • S. Gomez, J. Despraz, CA Pena-Reyes. Improving Neural Network Interpretability via Rule Extraction. ICANN 2018 (Accepted), 2018
JOURNAL PAPERS
  • Leite et al., “Exploration of multiclass and one-class learning methods for prediction of phage-bacteria interaction at strain level,” 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 1818-1825. doi: 10.1109/BIBM.2018.8621433
  • Despraz, S. Gomez, CA Pena-Reyes. Exploring Internal Representations of Deep Neural Networks. Studies in Computational Intelligence (Springer, to appear). 2018
  • Carvalho Leite, D.M., Brochet, X., Resch, G., Que, Y.-A., Pena-Reyes, C.A.; Computational prediction of inter-species relationships through omics data analysis and machine learning. BMC Bioinformatics (to appear). 2018

2017

PEER REVIEWED CONFERENCES
  • D. Leite, X. Brochet, G. Resch, Y. Que, A. Neves, and C. Peña, Computational Prediction of Host-Pathogen Interactions Through Omics Data Analysis and Machine Learning, IWBBIO 2017. Bioinformatics and Biomedical Engineering pp 360-371, 2017. DOI
  • Z. Mungloo, Y. Jaufeerally, and C. Peña, A Meta-Review of Feature Selection Techniques in the Context of Microarray Data, IWBBIO 2017. Bioinformatics and Biomedical Engineering pp 33-49, 2017. DOI
  • J. Despraz, S. Gomez, H.F. Satizábal and C. Peña, Towards a Better Understanding of Deep Neural Networks Representations using Deep Generative Networks, IJCCI 2017. SCITEPRESS 215-222, 2017 .DOI

2014

PEER REVIEWED CONFERENCES
  • N. Jakob, and C. Peña, Living Emerging Worlds for Games, WIVACE 2014. Advances in Artificial Life and Evolutionary Computation, Communications in Computer and Information Science, Vol. 445, pp 37-46, 2014. DIWBBIO 2017OI

2012

PEER REVIEWED CONFERENCES
  • M.-A. Barreto-Sanz, A. Bujard and C. Peña, Evolving very compact fuzzy systems for gene expression data analysis. Proceedings of the IEEE 12th International Conference on BioInformatics and BioEngineering, BIBE 2012, pp. 356-361, 2012.
    DOI – PDF-iconPDF

2010

PEER REVIEWED CONFERENCES
  • J. Rossier, C.A. Peña-Reyes, Extrinsic evolution of fuzzy systems applied to disease diagnosis, ICES 2010. Lecture Notes in Computer Science, Vol. 6274/2010, 226-237, 2010. DOI

2009

BOOK CHAPTERS

2008

PEER REVIEWED CONFERENCES

2007

JOURNAL PAPERS

2006

PEER REVIEWED CONFERENCES
  • M.A. Melgarejo, C.A. Peña-Reyes, E. Sanchez. A genetic-fuzzy system approach to control a model of the HIV infection dynamics. Proceedings of the IEEE International Conference on Fuzzy Systems, pp. 2323 – 2330, 2006. DOI – PDF-iconPDF
  • E. Jodoin, C.A. Pena-Reyes, E. Sanchez. A method for the fuzzification of categorical variables. Proceedings of the IEEE International Conference on Fuzzy Systems, 2006, pp.831 – 838, 2006. DOI – PDF-iconPDF

2005

JOURNAL PAPERS
  • N. Grandjean, B. Charpiot, C.-A. Peña, M. C. Peitsch. Competitive Intelligence and Patent Analysis in Drug Discovery. Mining the competitive knowledge bases and patents. Drug Discovery Today: Technologies. 3:211-215, 2005. DOI
PEER REVIEWED CONFERENCES
  • G. Mermoud, A. Upegui, C. A. Peña-Reyes, and E. Sanchez, “A Dynamically-Reconfigurable FPGA Platform for Evolving Fuzzy Systems,” J. Cabestany, A. Prieto, F. Sandoval (Eds.), Computational Intelligence and Bioinspired Systems, IWANN 2005, Vol. 3512 of Lecture Notes in Computer Science, pp. 572-581. Springer-Verlag, Berlin, 2005. DOI

2004

JOURNAL PAPERS
  • C. A. Peña-Reyes. Evolutionary fuzzy modelling human diagnostic decisions. Annals of the New York Academy of Sciences, pages 190-211, May 2004. DOI – PDF-icon PDF
BOOK
  • C.-A. Peña-Reyes. Coevolutionary Fuzzy Modelling.
    Lecture Notes in Computer Science 3204. Springer, 2004. 129 pages. ISBN: 3540229949. DOI
PEER REVIEWED CONFERENCES
  • M. Melgarejo, A. Garcia, and C.-A. Peña-Reyes. Pro-Two: A hardware based platform for real-time type-2 fuzzy inference. Proceedings of the 2004 IEEE International Conference on Fuzzy Systems FUZZ-IEEE 2004, Volume: 2, pp. 977- 982. 2004. DOI – PDF-iconPDF
  • M. Melgarejo, C.-A. Peña-Reyes, and A. Garcia. Hardware architecture and FPGA implementation of a Type-2 fuzzy system. Proceedings of the 2004 Great Lakes Symposium on VLSI (GLSVLSI), 2004. pp. 458 – 461. DOI – PDF-iconPDF
  • M. Melgarejo, C.-A. Peña-Reyes, and A. Garcia. Computational model and architectural proposal for a hardware type-2 fuzzy system. Proceedings of the 2nd IASTED International Conference on Neural Networks and Computational Intelligence NCI 2004, pp. 279-284, 2004.
  • A. Upegui, C.-A. Peña-Reyes, and E. Sanchez. A hardware implementation of a network of functional spiking neurons with Hebbian learning. A. J. Ijspeert, D. Mange, M. Murata, S. Nishio, Eds., Bio-ADIT 2004 On-Conference Proceedings, pp. 399-409. Osaka University Forum 2004, Osaka, 2004.

2003

BOOK CHAPTERS
  • C.-A. Peña-Reyes and M. Sipper. Fuzzy CoCo: Balancing accuracy and interpretability of fuzzy models by means of coevolution. J. Casillas, O. Cordón, F. Herrera, and L. Magdalena, editors, Accuracy Improvements in Linguistic Fuzzy Modelling, volume 129 of Studies in Fuzziness and Soft Computing, pages 119-146. Physica-Verlag, 2003. DOI
PEER REVIEWED CONFERENCES
  • A. Upegui, C.-A. Peña-Reyes, and E. Sanchez. A methodology for evolving spiking neural network topologies on line using partial dynamic reconfiguration. Proceedings of the International Congress on Computational Intelligence – ICCI 2003. RedCIC – Colombian Network on Computational Intelligence, 2003.
  • C. A. Peña-Reyes. Incremental fuzzy coco: Incremental coevolution of fuzzy systems. Proceedings of the International Congress on Computational Intelligence – ICCI 2003. RedCIC – Colombian Network on Computational Intelligence, 2003.
  • C. A. Peña-Reyes. Island fuzzy coco: Island model-based coevolution of fuzzy systems. Proceedings of the Third European Symposium on Intelligent Technologies, Hybrid Systems and their implementation on Smart Adaptive Systems – EUNITE 2003, pages 353-362. ELITE Foundation, Verlag Mainz, 2003.
  • C.-A. Peña-Reyes, R. Villa, L. Prieto, and E. Sanchez. COBRA: an evolved online tool for mammography interpretation. J. Mira and J. R. _Alvarez, editors, Proceedings of the International Work-conference on Artificial and Natural Neural Networks – IWANN2003, number 2686 in Lecture Notes in Computer Science, pages 726-733. Springer, 2003. DOI
  • A. Upegui, C.-A. Peña-Reyes, and E. Sanchez. A functional spiking neuron hardware oriented model. J. Mira and J. R. _Alvarez, editors, Proceedings of the International Work-conference on Artificial and Natural Neural Networks IWANN2003, number 2686 in Lecture Notes in Computer Science, pages 136-143. Springer, 2003. DOI

2002

BOOK CHAPTERS
  • C.-A. Peña-Reyes and M. Sipper. Combining evolutionary and fuzzy techniques in medical diagnosis. M. Schmitt, H. N. Teodorescu, A. Jain, A. Jain, S. Jain, and L. C. Jain, editors, Computational Intelligence Techniques in Medical Diagnosis and Prognosis, volume 96 of Studies in Fuzziness and Soft Computing, chapter 14, pages 391-426. Springer-Verlag, Heidelberg, 2002. DOI
PH.D. THESIS
  • C. A. Peña-Reyes. Coevolutionary Fuzzy Modelling.
    PhD thesis, École Polytechnique Fédérale de Lausanne – EPFL, 2002. Nominee, 2002 Best thesis EPFL prize. PDF-iconPDF
PEER REVIEWED CONFERENCES
  • B. Mesot, C. A. Peña-Reyes, E. Sanchez, and A. Perez-Uribe. SOS++: Finding smart behaviors using learning and evolution. R. K. Standish, M. A. Bedau, and H. A. Abbass, editors, Artificial Life VIII. The 8th International Conference on the Simulation and Synthesis of Living Systems, pages 264-273. The MIT Press, 2002.
  • J.L. Bermúdez, C. A. Peña-Reyes, F. Rachidi, and F. Heidler. Use of genetic algorithms to extract primary lightning current parameters. 5th International Symposium on Electromagnetic Compatibility, pages 241-246, 2002.
  • C. A. Peña-Reyes, M. Sipper, and L. Prieto. Sensitive, specific, and interpretable: Evolving a fuzzy mammographic-interpretation assessment tool. 2002 IEEE International Fuzzy Systems Conference Proceedings, pages 837-842. IEEE Neural Network Society, 2002. DOI – PDF-iconPDF

2001

JOURNAL PAPERS
  • C. A. Peña-Reyes and M. Sipper. Fuzzy CoCo: A cooperative-coevolutionary approach to fuzzy modelling. IEEE Transactions on Fuzzy Systems, 9(5):727-737, October 2001. DOI – PDF-iconPDF
PEER REVIEWED CONFERENCES

C. A. Peña-Reyes and M. Sipper. The flowering of Fuzzy CoCo: Evolving fuzzy iris classifiers. V. Kurkova, N. C. Steele, R. Neruda, and M. Karny, editors, Proceedings of the 5th International Conference on Artificial Neural Networks and Genetic Algorithms (ICANNGA 2001), pages 304-307. Springer-Verlag, 2001. DOI

2000

JOURNAL PAPERS
  • C. A. Peña-Reyes and M. Sipper. Evolutionary computation in medicine: An overview. Artificial Intelligence in Medicine, 19(1):1-23, May 2000. DOI
PEER REVIEWED CONFERENCES
  • C. A. Peña-Reyes and M. Sipper. Applying Fuzzy CoCo to breast cancer diagnosis. Proceedings of the 2000 Congress on Evolutionary Computation (CEC00), volume 2, pages 1168-1175. IEEE Press, Piscataway, NJ, USA, 2000. DOI – PDF-iconPDF

1999

JOURNAL PAPERS
  • C. A. Peña-Reyes and M. Sipper. A fuzzy-genetic approach to breast cancer diagnosis. Artificial Intelligence in Medicine, 17(2):131-155, October 1999.
    DOI – PDF-iconPDF
PEER REVIEWED CONFERENCES
  • C. A. Peña-Reyes and M. Sipper. Designing breast cancer diagnostic systems via a hybrid fuzzy-genetic methodology.
    IEEE International Fuzzy Systems Conference Proceedings, volume 1, pages 135-139. IEEE Neural Network Council, 1999. DOI – PDF-iconPDF

1998

PEER REVIEWED CONFERENCES
  • C. A. Peña-Reyes and M. Sipper. Evolving fuzzy rules for breast cancer diagnosis. Proceedings of 1998 International Symposium on Nonlinear Theory and Applications (NOLTA’98), volume 2, pages 369-372. Presses Polytechniques et Universitaires Romandes, Lausanne, 1998.

1997

PEER REVIEWED CONFERENCES
  • K. Solano, R. A. Chavarriaga, R. A. Nuñez, and C. A. Peña-Reyes. Controladores adaptables basados en mecanismos de inferencia difusa. Memorias del Segundo Congreso Asociación Colombiana de Automática, 1997.
  • J. L. López, C. E. Quintero, M. Sacanamboy, J. O. Sánchez, O.M. Agudelo, and C. A. Peña-Reyes. Comparación entre sistemas difusos para el control de una banda transportadora dentro de un proceso de manufactura flexible. Memorias del Segundo Congreso Asociación Colombiana de Automática, 1997.