Publications

Journal Articles

2019 S. M. Kandathil, M. Garza-Fabre, J. Handl, and S. C. Lovell, Reliable Generation of Native-Like Decoys Limits Predictive Ability in Fragment-Based Protein Structure Prediction, Biomolecules, vol. 9, no. 10, 2019. ISSN: 2218-273X. DOI: 10.3390/biom9100612.

2018 S. M. Kandathil, M. Garza-Fabre, J. Handl, and S. C. Lovell, Improved Fragment-Based Protein Structure Prediction by Redesign of Search Heuristics, Scientific Reports, vol. 8, no. 1, pp. 13694, 2018. ISSN: 2045-2322. DOI: 10.1038/s41598-018-31891-8.

2018 M. Garza-Fabre, J. Handl, and J. Knowles, An Improved and More Scalable Evolutionary Approach to Multiobjective Clustering, IEEE Transactions on Evolutionary Computation, vol. 22, no. 4, pp. 515-535, 2018. ISSN: 1089-778X. DOI: 10.1109/TEVC.2017.2726341.

2016 M. Garza-Fabre, S. M. Kandathil, J. Handl, J. Knowles, and S. C. Lovell, Generating, Maintaining, and Exploiting Diversity in a Memetic Algorithm for Protein Structure Prediction, Evolutionary Computation, vol. 24, no. 4, pp. 577-607, 2016. ISSN: 1063-6560. DOI: 10.1162/EVCO_a_00176.

2015 M. Garza-Fabre, E. Rodriguez-Tello, and G. Toscano-Pulido, Constraint-Handling Through Multi-Objective Optimization: the Hydrophobic-Polar Model for Protein Structure Prediction, Computers & Operations Research, vol. 53, pp. 128-153, 2015. ISSN: 0305-0548. DOI: 10.1016/j.cor.2014.07.010.

2015 M. Garza-Fabre, G. Toscano-Pulido, and E. Rodriguez-Tello, Multi-objectivization, Fitness Landscape Transformation and Search Performance: A Case of Study on the HP model for Protein Structure Prediction, European Journal of Operational Research, vol. 243, no. 2, pp. 405-422, 2015. ISSN: 0377-2217. DOI: 10.1016/j.ejor.2014.06.009.

2013 M. Garza-Fabre, E. Rodriguez-Tello, and G. Toscano-Pulido, Comparative Analysis of Different Evaluation Functions for Protein Structure Prediction Under the HP Model, Journal of Computer Science and Technology, vol. 28, no. 5, pp. 868-889, 2013. ISSN: 1860-4749. DOI: 10.1007/s11390-013-1384-7.

Conferences and Workshops

2019 A. José-García, J. Handl, W. Gómez-Flores, M. Garza-Fabre, Many-view Clustering: An Illustration Using Multiple Dissimilarity Measures, Proceedings of the Companion Publication of the 2019 Genetic and Evolutionary Computation Conference (GECCO 2019), Prague, Czech Republic, Jul. 2019, pp. 213-214. DOI: 10.1145/3319619.3323365.

2017 J. Handl, M. Garza-Fabre, S. Kandathil, and S. C. Lovell, On Heuristic Bias in Fragment-assembly Methods for Protein Structure Prediction, Proceedings of the Companion Publication of the 2017 Genetic and Evolutionary Computation Conference (GECCO 2017), Berlin, Germany, Jul. 2017, pp. 1652-1656. DOI: 10.1145/3067695.3082545.

2017 M. Garza-Fabre, J. Handl, and J. Knowles, A New Reduced-Length Genetic Representation for Evolutionary Multiobjective Clustering, Evolutionary Multi-Criterion Optimization (EMO), Münster, Germany, Mar. 2017, pp. 236-251. DOI: 10.1007/978-3-319-54157-0_17.

2015 M. Garza-Fabre, S. M. Kandathil, J. Handl, J. D. Knowles, and S. C. Lovell, Using Machine Learning to Explore the Relevance of Local and Global Features During Conformational Search in Rosetta, Proceedings of the Companion Publication of the 2015 Genetic and Evolutionary Computation Conference (GECCO 2015), Madrid, Spain, Jul. 2015, pp. 935-938. DOI: 10.1145/2739482.2768441.

2013 M. Garza-Fabre, G. Toscano-Pulido, and E. Rodriguez-Tello, Handling Constraints in the HP Model for Protein Structure Prediction by Multiobjective Optimization, IEEE Congress on Evolutionary Computation (CEC), Cancún, México, Jun. 2013, pp. 2728-2735. DOI: 10.1109/CEC.2013.6557899.

2012 M. Garza-Fabre, E. Rodriguez-Tello, and G. Toscano-Pulido, An Improved Multiobjectivization Strategy for HP Model-Based Protein Structure Prediction, Parallel Problem Solving from Nature (PPSN), Taormina, Italy, Sep. 2012, pp. 82-92. DOI: 10.1007/978-3-642-32964-7_9.

2012 M. Garza-Fabre, G. Toscano-Pulido, and E. Rodriguez-Tello, Locality-based Multiobjectivization for the HP Model of Protein Structure Prediction, Genetic and Evolutionary Computation (GECCO), Philadelphia, PA, USA, Jul. 2012, pp. 473-480. DOI: 10.1145/2330163.2330231.

2012 M. Garza-Fabre, E. Rodriguez-Tello, and G. Toscano-Pulido, Multiobjectivizing the HP Model for Protein Structure Prediction, Evolutionary Computation in Combinatorial Optimization (EvoCOP), Málaga, Spain, Apr. 2012, pp. 182-193. DOI: 10.1007/978-3-642-29124-1_16.

2011 M. Garza-Fabre, G. Toscano-Pulido, and E. Rodriguez-Tello, Comparative Study of Alternative Energy Functions for the HP Model of Protein Structure Prediction, International Conference on Bioinformatics & Computational Biology (BIOCOMP), Las Vegas, NV, USA, Jul. 2011, pp. 618-624.

2011 M. Garza-Fabre, G. Toscano-Pulido, C. A. Coello Coello, and E. Rodriguez-Tello, Effective Ranking + Speciation = Many-Objective Optimization, IEEE Congress of Evolutionary Computation (CEC), New Orleans, LA, USA, Jun. 2011, pp. 2115-2122. DOI: 10.1109/CEC.2011.5949876.

2011 M. Garza-Fabre, E. Rodriguez-Tello, and G. Toscano-Pulido, Comparing Alternative Energy Functions for the HP Model of Protein Structure Prediction, IEEE Congress of Evolutionary Computation (CEC), New Orleans, LA, USA, Jun. 2011, pp. 2307-2314. DOI: 10.1109/CEC.2011.5949902.

2010 M. Garza-Fabre, G. Toscano-Pulido, and C. A. Coello Coello, Two Novel Approaches for Many-Objective Optimization, IEEE Congress on Evolutionary Computation (CEC), Barcelona, Spain, Jul. 2010, pp. 1-8. DOI: 10.1109/CEC.2010.5585930.

2009 M. Garza-Fabre, G. Toscano-Pulido, and C. A. Coello Coello, Ranking Methods for Many-Objective Optimization, Mexican International Conference on Artificial Intelligence (MICAI), Guanajuato, México, Nov. 2009, pp. 633-645. DOI: 10.1007/978-3-642-05258-3_56.

2009 M. Garza-Fabre, G. Toscano-Pulido, and C. A. Coello Coello, Alternative Fitness Assignment Methods for Many-Objective Optimization Problems, International Conference on Artificial Evolution (EA), Strasbourg, France, Oct. 2010, pp. 146-157. DOI: 10.1007/978-3-642-14156-0_13.

Theses

2014 M. Garza-Fabre, On the Use of Alternative Evaluation Schemes in Metaheuristics to Handle the Main Search Difficulties Involved with the Prediction of Protein Structures Under the HP Model, PhD thesis, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Ciudad Victoria, Tamaulipas, México, May 2014.

2009 M. Garza-Fabre, Many-Objective Optimization Through Evolutionary Algorithms (Spanish), Master's thesis, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Ciudad Victoria, Tamaulipas, México, Sep. 2009.