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My current expertise is focused on the field of Artificial Intelligence, more specifically on the application of Optimization and Machine Learning methods to problems arising in different domains. My research group at the Centre for Informatics and Systems of the University of Coimbra has longstanding multidisciplinary collaborations with researchers from the areas of chemistry, physics and biochemistry. In the chemistry/physics areas we have been working for the past 15 years with groups from Portugal, Spain and Brazil in the development of bio-inspired optimization methods for prediction of the optimal 3-dimensional structures of atomic and molecular clusters and also for the fitting of potential energy functions. This collaboration is supported by several national and international scientific projects and has been presented in a solid publication record. As for the collaboration with the biochemistry area, we have been applying our expertise in the development of innovative exploratory techniques for unveiling relevant patterns in biological data and to the creation of prediction/diagnosis computational classifiers
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Identification

Personal identification

Full name
Francisco Baptista Pereira

Citation names

  • Pereira, Francisco
  • Francisco B. Pereira
  • Francisco Baptista Pereira

Author identifiers

Ciência ID
1D17-8FBA-A9D9
ORCID iD
0000-0002-1937-6548

Email addresses

  • xico@dei.uc.pt (Professional)
  • xico@isec.pt (Professional)

Addresses

  • Instituto Superior de Engenharia de Coimbra. Rua Pedro Nunes - Quinta da Nora , 3030-199, Coimbra, Coimbra, Portugal (Professional)
  • Centro de Informática e Sistemas da Universidade de Coimbra (CISUC), Polo 2, Pinhal de Marrocos , 3030-290, Coimbra, Coimbra, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
French Intermediate (B1) Upper intermediate (B2) Elementary (A2) Upper intermediate (B2) Intermediate (B1)
Education
Degree Classification
2002
Concluded
 Engenharia Informática (Doutoramento)
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
 Distinção e Louvor
1995
Concluded
 Mestrado em Engenharia Informática (Mestrado)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
 Muito Bom
1992/07/29
Concluded
 Engenharia Informática (Licenciatura)
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
 16 valores
Affiliation

Teaching in Higher Education

Category
Host institution 		Employer
2022/03 - Current Teacher Coordinator (Polytechnic Teacher) Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
1999/09/01 - 2022/03 Adjunct Teacher (Polytechnic Teacher) Instituto Politécnico de Coimbra, Portugal
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
1995/12/01 - 1999/09/01 Assistant (Polytechnic Teacher) Instituto Politécnico de Coimbra, Portugal
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
Projects

Contract

Designation Funders
2023/06/01 - 2028/05/31 PASGRAS: DE-RISKING METABOLIC, ENVIRONMENTAL AND BEHAVIORAL DETERMINANTS OF OBESITY IN CHILDREN, ADOLESCENTS AND YOUNG ADULTS
101080329-2
Researcher
Horizon 2020
Ongoing
2022/01/15 - 2025/01/15 NeuroTool4ALS : Human Neuronal Cells Differentiated from Urine-derived Stem Cells as a Platform for Personalized Medicine in Amyotrophic Lateral Sclerosis
PTDC/BTM-ORG/0327/2020
Researcher
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2020/01/01 - 2022/01/01 CôaMedPlants: Preservation of natural and cultural heritage and scientific validation of practices with medicinal plants from Côa Valley
COA/BRB/0019/2019
Researcher
Universidade de Coimbra Faculdade de Medicina, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/07 - 2021/12/04 MitoScreening: Development and Validation of Innovative Screening Methods for Mitochondrial Health Modulators
POCI-01-0145-FEDER-029297
 Fundação para a Ciência e a Tecnologia
Ongoing
2016/03/01 - 2018/02/28 Study of the energetic landscapes of atomic clusters by applying novel bio-inspired algorithms
88887.125439/2016-00/CAPES
Researcher
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2013/01/01 - 2015/06/01 iCIS: Intelligent Computing in the Internet of Services
iCIS
Researcher
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
Concluded
2010/05/01 - 2013/10/31 Computação de alto desempenho em grande escala sobre a Internet
PTDC/EIA-EIA/102212/2008
Universidade de Coimbra, Portugal

Universidade de Coimbra Departamento de Engenharia Civil, Portugal

Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010/05 - 2013/10 High-Performance Computing over the Large-Scale Internet
102212
Provided by PTCRIS: 102212
 Fundação para a Ciência e a Tecnologia, I.P.
2010/05 - 2013/10 COSMO - COllaborative System for Mobility Optimization
Provided by PTCRIS: 108785
108785
 Fundação para a Ciência e a Tecnologia, I.P.
2010/04 - 2013/10 EnviGP - Improving Genetic Programming for the Environment and Other Applications
103363
Provided by PTCRIS: 103363
 Fundação para a Ciência e a Tecnologia, I.P.
2010/04 - 2013/09 MOSAL - Multi-objective Sequence Alignment
98674
Provided by PTCRIS: 98674
 Fundação para a Ciência e a Tecnologia, I.P.
2009/01 - 2012/06 Theoretical and computational studies of dissociation reactions occurring in hyperthermal conditions: from small ionic systems to clusters
Provided by PTCRIS: 69422
69422
 Fundação para a Ciência e a Tecnologia, I.P.
2005/07 - 2008/09 Development of New Evolutionary Computation Approaches for Applications in Theoretical Chemistry
Provided by PTCRIS: 55951
55951
Principal investigator
Fundação para a Ciência e a Tecnologia
2000/12/01 - 2002/06/30 Study and Application of Evolutionary Computation Techniques to Non-Computable and NP-Complete Problems
POSI/SRI/34493/99
Researcher
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2022/01/15 - 2025/01/14 Human Neuronal Cells Differentiated from Urine-derived Stem Cells as a Platform for Personalized Medicine in Amyotrophic Lateral Sclerosis
PTDC/BTM-ORG/0055/2021
Universidade de Coimbra, Portugal

Universidade de Coimbra Instituto de Investigação Clínica e Biomédica de Coimbra, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
Outputs

Publications

Book chapter
  1. Henriques, Jorge; Ribeiro, Caio; Rocha, Teresa; Paredes, Simão; de Carvalho, Paulo; Duarte, Ana I.; Freitas, Alex A.; Cunha-Oliveira, Teresa; Pereira, Francisco B.. "Machine learning in the context of better healthcare in aging". In Aging, 625-647. Elsevier, 2023.
    10.1016/b978-0-12-823761-8.00015-x
  2. Lourenço, Nuno; Assunção, Filipe; Pereira, Francisco B.; Costa, Ernesto; Machado, Penousal. "Structured Grammatical Evolution: A Dynamic Approach". In Handbook of Grammatical Evolution, 137-161. Springer International Publishing, 2018.
    10.1007/978-3-319-78717-6_6
  3. Jorge M. C. Marques; Wanderson Jesus; Frederico Prudente; Pereira, Francisco; Nuno Lourenço. "Revealing energy landscapes of atomic clusters by applying adaptive bio- inspired algorithms". In Physical Chemistry for Chemists and Chemical Engineers: Multidisciplinary Research Perspectives. 2018.
  4. Pereira, Francisco B.; Marques, Jorge M. C.. "Analysis of Crossover Operators for Cluster Geometry Optimization". In Computational Intelligence for Engineering Systems, 77-89. Springer Netherlands, 2010.
    10.1007/978-94-007-0093-2_5
  5. Pereira, Francisco; Jorge Tavares. "Preface". In Bio-inspired Algorithms for the Vehicle Routing Problem, V-IX. Studies in Computational Intelligence series, Springer Verlag, 2009.
  6. Pereira, Francisco B.; Marques, JorgeM.C.; Leitão, Tiago; Tavares, Jorge. "Designing Efficient Evolutionary Algorithms for Cluster Optimization: A Study on Locality". In Advances in Metaheuristics for Hard Optimization, 223-250. Springer Berlin Heidelberg, 2007.
    10.1007/978-3-540-72960-0_11
  7. Machado, Penousal; Pereira, Francisco B.; Tavares, Jorge; Costa, Ernesto; Cardoso, Amílcar. "Evolutionary Turing Machines". In Recent Developments in Biologically Inspired Computing, 9-40. IGI Global, 2005.
    10.4018/978-1-59140-312-8.ch002
Conference paper
  1. Monteiro, Mariana; Lourenço, Nuno; Pereira, Francisco B.. "FERMAT: Feature Engineering with Grammatical Evolution". Paper presented in EPIA -2021 - 20th Portuguese Conference on Artificial Intelligence, 2021.
    10.1007/978-3-030-86230-5_19
  2. Lourenço, Nuno; Ferrer, Joaquim; Pereira, Francisco B.; Costa, Ernesto. "A Comparative Study of Different Grammar-Based Genetic Programming Approaches". Paper presented in EuroGP-2017: 20th European Conference on Genetic Programming - EvoStar, 2017.
    10.1007/978-3-319-55696-3_20
  3. Lourenço, Nuno; Pereira, Francisco B.; Costa, Ernesto. "An Evolutionary Approach to the Full Optimization of the Traveling Thief Problem". Paper presented in EvoCOP-2016: Evolutionary Computation in Combinatorial Optimization - Evostar, 2016.
    10.1007/978-3-319-30698-8_3
  4. Lourenço, Nuno; Pereira, Francisco B.; Costa, Ernesto. "SGE: A Structured Representation for Grammatical Evolution". Paper presented in EA-2015: International Conference on Artificial Evolution, 2016.
    10.1007/978-3-319-31471-6_11
  5. Lourenço, Nuno; Pereira, Francisco B.; Costa, Ernesto. "The Optimization Ability of Evolved Strategies". Paper presented in EPIA 2015: 17th Portuguese Conference on Artificial Intelligence, 2015.
    10.1007/978-3-319-23485-4_23
  6. Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B.. "Local Search for Multiobjective Multiple Sequence Alignment". Paper presented in IWBBIO 2015: International Conference on Bioinformatics and Biomedical Engineering, 2015.
    10.1007/978-3-319-16480-9_18
  7. Melo, Leonor; Pereira, Francisco; Costa, Ernesto. "Extended Experiments with Ant Colony Optimization with Heterogeneous Ants for Large Dynamic Traveling Salesperson Problems". Paper presented in ICCSA-2014: 14th International Conference on Computational Science and Its Applications, 2014.
    10.1109/iccsa.2014.39
  8. Lourenço, Nuno; Pereira, Francisco Baptista; Costa, Ernesto. "The importance of the learning conditions in hyper-heuristics". Paper presented in GECCO-2013: 15th Annual Conference on Genetic and Evolutionary Computation, 2013.
    10.1145/2463372.2463558
  9. Lourenço, Nuno; Pereira, Francisco; Costa, Ernesto. "Learning Selection Strategies for Evolutionary Algorithms". Paper presented in EA-2013: International Conference on Artificial Evolution, 2013.
    10.1007/978-3-319-11683-9_16
  10. Melo, Leonor; Pereira, Francisco; Costa, Ernesto. "Effective Multi-caste Ant Colony System for Large Dynamic Traveling Salesperson Problems". Paper presented in EA-2013: International Conference on Artificial Evolution, 2013.
    10.1007/978-3-319-11683-9_6
  11. Melo, Leonor; Pereira, Francisco; Costa, Ernesto. "Multi-caste Ant Colony Algorithm for the Dynamic Traveling Salesperson Problem". Paper presented in ICANNGA-2013: International Conference on Adaptive and Natural Computing Algorithms, 2013.
    10.1007/978-3-642-37213-1_19
  12. Lourenço, N.; Pereira, F.B.; Costa, E.. "Evolving evolutionary algorithms". Paper presented in GECCO-2012: 14th Annual Conference on Genetic and Evolutionary Computation, 2012.
    10.1145/2330784.2330794
  13. Leitao, Antonio; Pereira, Francisco B.; Machado, Penousal. "Enhancing cluster geometry optimization with Island Models". Paper presented in CEC-2012: IEEE Congress on Evolutionary Computation, 2012.
    10.1109/cec.2012.6256544
  14. Tavares, Jorge; Pereira, Francisco B.. "Automatic Design of Ant Algorithms with Grammatical Evolution". Paper presented in EuroGP-2012: 15th European Conference on Genetic Programming - EvoStar, 2012.
    10.1007/978-3-642-29139-5_18
  15. Lourenço, Nuno; Pereira, Francisco B.. "DACCO". Paper presented in GECCO-2012: 14th Annual Conference on Genetic and Evolutionary Computation, 2012.
    10.1145/2330163.2330170
  16. Leonor Albuquerque Melo; Pereira, Francisco; Ernesto Costa. "Multi-caste Ant Colony Optimization Algorithms". Paper presented in EPIA-2011: 15th Portuguese Conference on Artificial Intelligence, 2011.
  17. Tavares, J.; Pereira, F.B.. "Designing pheromone update strategies with strongly typed genetic programming". Paper presented in EuroGP-2011: 14th European Conference on Genetic Programming - EvoStar, 2011.
    10.1007/978-3-642-20407-4_8
  18. Tavares, J.; Pereira, F.B.. "Towards the development of self-ant systems". Paper presented in GECCO-2011: 13th Annual Conference on Genetic and Evolutionary Computation, 2011.
    10.1145/2001576.2001838
  19. Tavares, J.; Pereira, F.B.. "Evolving strategies for updating pheromone trails: A case study with the TSP". Paper presented in PPSN-2010: Parallel Problem Solving from Nature, PPSN XI, 2010.
    10.1007/978-3-642-15871-1_53
  20. Pereira, F.B.; Marques, J.M.C.. "Towards an effective evolutionary approach for binary Lennard-Jones clusters". Paper presented in CEC-2010: IEEE Congress on Evolutionary Computation, 2010.
    10.1109/CEC.2010.5586220
  21. Melo, L.; Pereira, F.; Costa, E.. "MC-ANT: A multi-colony ant algorithm". Paper presented in EA-2009: International Conference on Artificial Evolution, 2009.
    10.1007/978-3-642-14156-0_3
  22. Tavares, J.; Pereira, F.B.; Costa, E.. "Golomb rulers: A fitness landscape analysis". Paper presented in CEC-2008: IEEE Congress on Evolutionary Computation, 2008.
    10.1109/CEC.2008.4631298
  23. Pereira, F.B.; Marques, J.M.C.. "A hybrid evolutionary algorithm for cluster geometry optimization: The importance of structural elitism". Paper presented in HIS-2008: Eighth International Conference on Hybrid Intelligent Systems, 2008.
    10.1109/HIS.2008.98
  24. Pereira, F.B.; Marques, J.M.C.. "A self-adaptive evolutionary algorithm for cluster geometry optimization". Paper presented in HIS-2008: Eighth International Conference on Hybrid Intelligent Systems, 2008.
    10.1109/HIS.2008.96
  25. Leitão, T.; Pereira, F.B.; Tavares, J.; Costa, E.. "Niching techniques: A study on the cluster geometry optimization problem". Paper presented in GECCO-2007: 9th Annual Conference on Genetic and Evolutionary Computation, 2007.
    10.1145/1276958.1277253
  26. Tavares, J.; Pereira, F.B.; Costa, E.. "The Role of Representation on the Multidimensional Knapsack Problem by means of Fitness Landscape Analysis". Paper presented in CEC-2006: IEEE Congress on Evolutionary Computation, 2006.
    10.1109/cec.2006.1688593
  27. Pereira, F.B.; Marques, J.M.C.; Leitao, T.; Tavares, J.. "Analysis of Locality in Hybrid Evolutionary Cluster Optimization". Paper presented in CEC-2006: IEEE Congress on Evolutionary Computation, 2006.
    10.1109/cec.2006.1688590
  28. Tavares, Jorge; Pereira, Francisco B.; Costa, Ernesto. "Golomb Rulers: Experiments with Marks Representation". Paper presented in ICANNGA-2005: International Conference on Adaptive and Natural Computing Algorithms, 2005.
    10.1007/3-211-27389-1_56
  29. Tavares, Jorge; Leitão, Tiago; Pereira, Francisco B.; Costa, Ernesto. "Evolving Segments Length in Golomb Rulers". Paper presented in ICANNGA-2005: International Conference on Adaptive and Natural Computing Algorithms, 2005.
    10.1007/3-211-27389-1_57
  30. Penousal Machado; Jorge Tavares; F. Amilcar Cardoso; Pereira, Francisco; Ernesto Costa. "Evolving creativity". Paper presented in Third Computational Creativity Workshop (CC-04), Seventh European Conference on Case Based Reasoning (ECCBR-04)., 2004.
  31. Tavares, J.; Pereira, F.B.; Costa, E.. "Evolving Golomb rulers". Paper presented in GECCO-2004: 6th Annual Conference on Genetic and Evolutionary Computation, 2004.
  32. Tavares, J.; Pereira, F.B.; Costa, E.. "Understanding the role of insertion and correction in the evolution of Golomb rulers". Paper presented in CEC-2004: IEEE Congress on Evolutionary Computation, 2004.
    10.1109/cec.2004.1330839
  33. Tavares, J.; Machado, P.; Cardoso, A.; Pereira, F.B.; Costa, E.. "On the evolution of evolutionary algorithms". Paper presented in EuroGP-2004: 7th European Conference on Genetic Programming - EvoStar, 2004.
  34. Jorge Tavares; Pereira, Francisco; Penousal Machado; Ernesto Costa. "Crossover and Diversity: A Study about GVR". Paper presented in Genetic and Evolutionary Computation Conference (GECCO-2003) Workshops – Analysis and Design of Representations and Operators track (AdoRo 2003), 2003.
  35. Tavares, Jorge; Machado, Penousal; Pereira, Francisco B.; Costa, Ernesto. "On the influence of GVR in vehicle routing". Paper presented in SAC-2003: ACM symposium on Applied computing, 2003.
    10.1145/952532.952679
  36. Pereira, F.B.; Tavares, J.; Costa, E.. "Golomb rulers: The advantage of evolution". Paper presented in EPIA-2003: Portuguese Conference on Artificial Intelligence, 2003.
  37. Penousal Machado; Jorge Tavares; Pereira, Francisco; Ernesto Costa. "Vehicle Routing Problem: Doing it the Evolutionary Way". Paper presented in GECCO-2002: 4th Annual Conference on Genetic and Evolutionary Computation, 2002.
  38. Jorge Tavares; Pereira, Francisco; Penousal Machado; Ernesto Costa. "GVR Delivers It On Time". Paper presented in Fourth Asia-Pacific Conference on Simulated Evolution And Learning (SEAL'02), 2002.
  39. Pereira, Francisco B.; Tavares, Jorge; Machado, Penousal; Costa, Ernesto. "GVR: A New Genetic Representation for the Vehicle Routing Problem". Paper presented in AICS-2002: Irish Conference on Artificial Intelligence and Cognitive Science, 2002.
    10.1007/3-540-45750-x_12
  40. Pereira, Francisco; Ernesto Costa. "Understanding the Role of Learning in the Evolution of Busy Beavers: a Comparison Between the Baldwin Effect and a Lamarckian Strategy". Paper presented in GECCO-2001: 3rd Annual Conference on Genetic and Evolutionary Computation, 2001.
  41. Pereira, Francisco; Ernesto Costa. "The Influence of Learning in the Evolution of Busy Beavers". Paper presented in Applications of Evolutionary Computing: EvoWorkshops 2001 (First European Workshop on Evolutionary Learning),, 2001.
  42. Pereira, Francisco; Ernesto Costa. "How Learning Improves the Performance of Evolutionary Agents: a Case Study with an Information Retrieval System for a Distributed Environment". Paper presented in the Third International Symposium on Adaptive Systems: Evolutionary Computation and Probabilistic Graphical Models, 2001.
  43. Pereira, F.B.; Costa, E.. "How adaptive agents learn to deal with incomplete queries in distributed information environments". Paper presented in CEC-2000: IEEE Congress on Evolutionary Computation, 2001.
    10.1109/cec.2000.870805
  44. Roberto Santana; Alberto Ochoa-Rodriguez; Marta Soto; Pereira, Francisco; Penousal Machado; Ernesto Costa; F. Amilcar Cardoso. "Probabilistic Evolution and the Busy Beaver Problem". Paper presented in Late Breaking Papers of the Genetic and Evolutionary Computation Conference (GECCO-2000), 2000.
  45. Pereira, Francisco B.; Costa, Ernesto. "The influence of learning in the behavior of information retrieval adaptive agents". Paper presented in SAC-00: 2000 ACM symposium on Applied computing, 2000.
    10.1145/335603.335906
  46. Pereira, F.B.; Machado, P.; Costa, E.; Cardoso, A.; Ochoa-Rodriguez, A.; Santana, R.; Soto, M.. "Too busy to learn [individual learning interaction with evolutionary algorithm in Busy Beaver problem]". Paper presented in CEC-2000: IEEE Congress on Evolutionary Computation, 2000.
    10.1109/cec.2000.870369
  47. Oliveira, M.; Barreiros, J.; Costa, E.; Pereira, F.. "LamBaDa: an artificial environment to study the interaction between evolution and learning". Paper presented in CEC-1999: IEEE Congress on Evolutionary Computation, 1999.
    10.1109/cec.1999.781919
  48. Pereira, Francisco; Penousal Machado; Ernesto Costa; Amilcar Cardoso. "Graph-Based Crossover: A Case Study with the Busy Beaver Problem". Paper presented in GECCO-1999: 1st Annual Conference on Genetic and Evolutionary Computation, 1999.
  49. Machado, Penousal; Pereira, Francisco B.; Cardoso, Amílcar; Costa, Ernesto. "Busy Beaver - The Influence of Representation". Paper presented in EuroGP-1999: 2nd European Conference on Genetic Programming, 1999.
    10.1007/3-540-48885-5_3
  50. Pereira, Francisco; Penousal Machado; Ernesto Costa; Amílcar Cardoso. "Busy Beaver: an Evolutionary Approach". Paper presented in Second Symposium on Artificial Intelligence (CIMAF-99), 1999.
  51. Pereira, Francisco. "An Artificial Life Model for Information Retrieval in a Distributed Environment". Paper presented in ECAI-1998: Thirteenth European Conference on Artificial Intelligence, 1998.
  52. Pereira, Francisco; Ernesto Costa. "The Influence of Learning in the Optimization of Royal Road Functions". Paper presented in Third International Mendel Conference on Genetic, Optimization Problems, Fuzzy Logic, Neural Networks, Rough Sets (Mendel 97), 1997.
  53. Paulo Gomes; Pereira, Francisco; Arlindo Silva. "Empirical Study of the Influences of Genetic Parameters in the Training of a Neural Network". Paper presented in International Conference on Artificial Neural Nets and Genetic Algorithms (ICANNGA-97), 1997.
Conference poster
  1. Simões, Rui F.; Cunha-Oliveira, Teresa; Oliveira, Paulo; Pereira, Francisco. "Differentiated SH-SY5Y cells as a cellular model to study mitochondrial physiology and dynamics". Paper presented in 54th Annual Scientific Meeting of the European Society for Clinical Investigation, COVID Edition, 2020.
  2. Simões, Rui F.; Cunha-Oliveira, Teresa; Oliveira, Paulo; Pereira, Francisco. "Dose-dependent analysis of mitochondrial parameters in differentiated SH-SY5Y cells exposed to mitochondrial toxicants". Paper presented in 2nd Edition MitoPorto, 2018.
  3. João Campos; Pereira, Francisco; Ernesto Costa; Sardão, Vilma; Teresa Cunha-Oliveira; Tiago Silva; Rui Simões; et al. "Extracting Knowledge from Data to Predict Mitochondrial Toxicity Indexes for Pharmacological Compounds". Paper presented in MitoPorto International Symposium, Porto, Portugal, 2017 2017, 2017.
Edited book
  1. Pereira, Francisco; Penousal Machado; Ernesto Costa; F. Amilcar Cardoso. Progress in Artificial Intelligence. Springer International Publishing. 2015.
    10.1007/978-3-319-23485-4
  2. Pereira, Francisco; Jorge Tavares. Bio-inspired Algorithms for the Vehicle Routing Problem. Springer Berlin Heidelberg. 2009.
    10.1007/978-3-540-85152-3
Journal article
  1. Ferreiro, Elisabete; Monteiro, Mariana; Pereira, Francisco; Barroso, Cristina; Egas, Conceição; Macedo, Paula; Valero, Jorge; Sardão, Vilma A.; Oliveira, Paulo J.. "Age-dependent energy metabolism and transcriptome changes in urine-derived stem cells". Mechanisms of Ageing and Development 218 (2024): 111912. http://dx.doi.org/10.1016/j.mad.2024.111912.
    10.1016/j.mad.2024.111912
  2. Rosendo-Silva, Daniela; Gomes, Pedro Bastos; Rodrigues, Tiago; Viana, Sofia; da Costa, André Nogueira; Scherer, Philipp E.; Reis, Flávio; et al. "Clinical and molecular profiling of human visceral adipose tissue reveals impairment of vascular architecture and remodeling as an early hallmark of dysfunction". Metabolism 153 (2024): 155788. http://dx.doi.org/10.1016/j.metabol.2024.155788.
    10.1016/j.metabol.2024.155788
  3. Marques-Carvalho, Adriana; Silva, Beatriz; Pereira, Francisco B.; Kim, Ha-Neui; Almeida, Maria; Sardão, Vilma A.. "Oestradiol and osteoclast differentiation: Effects on p53 and mitochondrial metabolism". European Journal of Clinical Investigation 54 6 (2024): http://dx.doi.org/10.1111/eci.14195.
    10.1111/eci.14195
  4. Cunha-Oliveira, Teresa; Carvalho, Marcelo; Sardão, Vilma; Ferreiro, Elisabete; Mena, Débora; Pereira, Francisco B.; Borges, Fernanda; Oliveira, Paulo J.; Silva, Filomena S. G.. "Integrative Profiling of Amyotrophic Lateral Sclerosis Lymphoblasts Identifies Unique Metabolic and Mitochondrial Disease Fingerprints". Molecular Neurobiology 59 10 (2022): 6373-6396. http://dx.doi.org/10.1007/s12035-022-02980-7.
    10.1007/s12035-022-02980-7
  5. Rui F. Simões; Paulo J. Oliveira; Teresa Cunha-Oliveira; Francisco B. Pereira. "Evaluation of 6-Hydroxydopamine and Rotenone In Vitro Neurotoxicity on Differentiated SH-SY5Y Cells Using Applied Computational Statistics". International Journal of Molecular Sciences 23 6 (2022): 3009-3009. https://doi.org/10.3390/ijms23063009.
    10.3390/ijms23063009
  6. Carvalho, A.; Silva, B.; Pereira, Francisco; Ha-Neui, K.; Oliveira, P.; Almeida, M.; Sardão, V.. "Metabolic fingerprint during early stages of osteoclastogenesis and the modulator role of estradiol: new insights in bone metabolism". European Journal of Clinical Investigation 52 S1 (2022): 43.
  7. Silva, B.; Pereira, Francisco; Lourenço, Nuno. "Synthetic data augmentation for biological datasets". European Journal of Clinical Investigation 52 S1 (2022): 102.
  8. Rui F. Simões; Rute Pino; Maurício Moreira-Soares; Jaromira Kovarova; Jiri Neuzil; Rui Travasso; Paulo J. Oliveira; Teresa Cunha-Oliveira; Francisco B. Pereira. "Quantitative analysis of neuronal mitochondrial movement reveals patterns resulting from neurotoxicity of rotenone and 6-hydroxydopamine". The FASEB Journal 35 12 (2021): https://doi.org/10.1096/fj.202100899R.
    10.1096/fj.202100899R
  9. Pereira, Francisco. "Machine Learning Basics". European Journal of Clinical Investigation 51 S1 (2021): 13-14. https://doi.org/10.1111/eci.13567.
    Open access • Published
  10. Simões, Rui F.; Oliveira, Teresa; Oliveira, P. ; Pereira, Francisco. "Evaluation of 6-Hydroxydopamine and Rotenone in Vitro Neurotoxicity in SH-SY5Y Cells using Computational Applied Statistics". European Journal of Clinical Investigation 51 S1 (2021): 95-95. https://doi.org/10.1111/eci.13567.
    Open access • Published
  11. Monteiro, Mariana; Lourenço, Nuno; Pereira, Francisco. "Automatic feature engineering for drug discovery". European Journal for Clinical Investigation 51 S1 (2021): https://doi.org/10.1111/eci.13567.
    Open access • Published
  12. Amorim, Ricardo; Simões, Inês C. M.; Veloso, Caroline; Carvalho, Adriana; Simões, Rui F.; Pereira, Francisco B.; Thiel, Theresa; et al. "Exploratory Data Analysis of Cell and Mitochondrial High-Fat, High-Sugar Toxicity on Human HepG2 Cells". Nutrients 13 5 (2021): 1723. http://dx.doi.org/10.3390/nu13051723.
    10.3390/nu13051723
  13. Jesus, Wanderson; Prudente, Frederico Vasconcellos; Marques, Jorge; Pereira, Francisco. "Modeling microsolvation clusters with electronic-structure calculations guided by analytical potentials and predictive machine learning techniques". Physical Chemistry Chemical Physics (2021): http://dx.doi.org/10.1039/d0cp05200k.
    10.1039/d0cp05200k
  14. Pino, R.; Simões R.; Moreira-Soares, M.; Teresa Cunha-Oliveira; Kovarova, J.; Neuzil, Jiri; Travasso, Rui; Oliveira, PJ; Pereira, Francisco. "Data Extraction from Mitochondrial Motility Tracking using Computational Algorithms". European Journal of Clinical Investigation 50 S1 (2020): 79-80.
    Open access
  15. Cláudia M. Deus; Susana P. Pereira; Teresa Cunha-Oliveira; Pereira, Francisco; Nuno Raimundo; Paulo J. Oliveira. "Mitochondrial remodeling in human skin fibroblasts from sporadic male Parkinson's disease patients uncovers metabolic and mitochondrial bioenergetic defects". Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease (2020): http://dx.doi.org/10.1016/j.bbadis.2019.165615.
    10.1016/j.bbadis.2019.165615
  16. Rui Simões; Teresa Cunha-Oliveira; Paulo J. Oliveira; Pereira, Francisco. "Non-supervised analysis of neurotoxicity of mitochondrial poisons 6-OHDA and rotenone". European Journal of Clinical Investigation 50 S1 (2020): 76. https://doi.org/10.1111/eci.13369.
    Open access
  17. Elisabete Ferreiro; Mariana Monteiro; Guida Bento; Pereira, Francisco; Vilma Sardão; Paula Macedo; Paulo J. Oliveira. "Exploratory data analysis applied to metabolic profiling of urine-derived stem cells from young and elderly women". European Journal of Clinical Investigation 50 S1 (2020): 77. https://doi.org/10.1111/eci.13369.
    Open access
  18. Gonçalo C Pereira; Susana P Pereira; Francisco B Pereira; Nuno Lourenço; José A Lumini; Claudia V Pereira; James A Bjork; et al. "Early Cardiac Mitochondrial Molecular and Functional Responses to Acute Anthracycline Treatment in Wistar Rats". Toxicological Sciences (2019): https://doi.org/10.1093/toxsci/kfz026.
    10.1093/toxsci/kfz026
  19. Rui Simões; Teresa Cunha-Oliveira; Jaromira Kovarova; Neuzil, Jiri; Paulo J. Oliveira; Pereira, Francisco. "Early mitochondrial metabolism and dynamics changes as predictors of neurodegeneration and neuronal cell death.". European Journal of Clinical Investigation 49 (2019): 180-181. https://doi.org/10.1111/eci.13109.
    Open access • Published
  20. Pereira, Francisco; Nuno Lourenço; Wanderson Jesus; Frederico V. Prudente; Jorge M. C. Marques. "Discovering low-energy atomic clusters with machine learning". European Journal of Clinical Investigation 49 (2019): 41. https://doi.org/10.1111/eci.13107.
    Open access • Published
  21. Jesus, Wanderson S.; Marques, Jorge M. C.; Prudente, Frederico V.; Pereira, Francisco B.. "Exploring the first-shell and second-shell structures arising in the microsolvation of Li + by rare gases". International Journal of Quantum Chemistry 119 13 (2018): e25860. http://dx.doi.org/10.1002/qua.25860.
    10.1002/qua.25860
  22. Frederico V. Prudente; Jorge M. C. Marques; Francisco B. Pereira. "Correction: Solvation of Li+ by argon: how important are three-body forces?". Physical Chemistry Chemical Physics (2018): https://doi.org/10.1039/C8CP91778G.
    10.1039/C8CP91778G
  23. Rui Simões; Teresa Cunha-Oliveira; Paulo J. Oliveira; Pereira, Francisco. "Optimization of experimental and computational processes to study mitochondrial trafficking and metabolic biomarkers". European Journal of Clinical Investigation 48 (2018): 89. https://doi.org/10.1111/eci.12926.
    Open access
  24. Rodríguez-Fernández, Roberto; Pereira, Francisco B.; Marques, Jorge M.C.; Martínez-Núñez, Emilio; Vázquez, Saulo A.. "GAFit: A general-purpose, user-friendly program for fitting potential energy surfaces". Computer Physics Communications 217 (2017): 89-98. http://dx.doi.org/10.1016/j.cpc.2017.02.008.
    10.1016/j.cpc.2017.02.008
  25. Marques JM; Pereira FB; Llanio-Trujillo JL; Abreu PE; Albertí M; Aguilar A; Pirani F; Bartolomei M. "A global optimization perspective on molecular clusters.". Philosophical transactions. Series A, Mathematical, physical, and engineering sciences (2017): http://europepmc.org/abstract/med/28320902.
    10.1098/rsta.2016.0198
  26. Frederico V. Prudente; Jorge M. C. Marques; Francisco B. Pereira. "Solvation of Li+ by argon: how important are three-body forces?". Physical Chemistry Chemical Physics 19 37 (2017): 25707-25716. https://doi.org/10.1039/C7CP04549B.
    10.1039/C7CP04549B
  27. Cruz, S. M. A.; Marques, J. M. C.; Pereira, F. B.. "Improved evolutionary algorithm for the global optimization of clusters with competing attractive and repulsive interactions". The Journal of Chemical Physics 145 15 (2016): 154109. http://dx.doi.org/10.1063/1.4964780.
    10.1063/1.4964780
  28. Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B.. "Heuristics for multiobjective multiple sequence alignment". BioMedical Engineering OnLine 15 S1 (2016): http://dx.doi.org/10.1186/s12938-016-0184-z.
    10.1186/s12938-016-0184-z
  29. Lourenço, Nuno; Pereira, Francisco B.; Costa, Ernesto. "Unveiling the properties of structured grammatical evolution". Genetic Programming and Evolvable Machines 17 3 (2016): 251-289. http://dx.doi.org/10.1007/s10710-015-9262-4.
    10.1007/s10710-015-9262-4
  30. Marques, J.M.C.; Pereira, F.B.. "Colloidal clusters from a global optimization perspective". Journal of Molecular Liquids 210 (2015): 51-63. http://dx.doi.org/10.1016/j.molliq.2015.03.009.
    10.1016/j.molliq.2015.03.009
  31. Leitão, António; Pereira, Francisco Baptista; Machado, Penousal. "Island models for cluster geometry optimization: how design options impact effectiveness and diversity". Journal of Global Optimization 63 4 (2015): 677-707. http://dx.doi.org/10.1007/s10898-015-0302-7.
    10.1007/s10898-015-0302-7
  32. Llanio-Trujillo, J.L.; Marques, J.M.C.; Pereira, F.B.. "New insights on lithium-cation microsolvation by solvents forming hydrogen-bonds: Water versus methanol". Computational and Theoretical Chemistry 1021 (2013): 124-134. http://www.scopus.com/inward/record.url?eid=2-s2.0-84884986960&partnerID=MN8TOARS.
    10.1016/j.comptc.2013.06.043
  33. Marques, J.M.C.; Pereira, F.B.. "A detailed investigation on the global minimum structures of mixed rare-gas clusters: Geometry, energetics, and site occupancy". Journal of Computational Chemistry 34 6 (2013): 505-517. http://www.scopus.com/inward/record.url?eid=2-s2.0-84873479217&partnerID=MN8TOARS.
    10.1002/jcc.23161
  34. Lourenço, Nuno; Pereira, Francisco Baptista. "PSO-CGO: A Particle Swarm Algorithm for Cluster Geometry Optimization". International Journal of Natural Computing Research 2 1 (2011): 1-20. http://dx.doi.org/10.4018/jncr.2011010101.
    10.4018/jncr.2011010101
  35. Abreu, P.E.; Marques, J.M.C.; Pereira, F.B.. "Electronic structure calculations on the Ar-C6H12 interaction: Application to the microsolvation of the chair conformer". Computational and Theoretical Chemistry 975 1-3 (2011): 83-91. http://www.scopus.com/inward/record.url?eid=2-s2.0-80955149677&partnerID=MN8TOARS.
    10.1016/j.comptc.2011.02.014
  36. Almeida, M.M.; Prudente, F.V.; Fellows, C.E.; Marques, J.M.C.; Pereira, F.B.. "Direct fit of spectroscopic data of diatomic molecules by using genetic algorithms: II. the ground state of RbCs". Journal of Physics B: Atomic, Molecular and Optical Physics 44 22 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80955141278&partnerID=MN8TOARS.
    10.1088/0953-4075/44/22/225102
  37. Llanio-Trujillo, J.L.; Marques, J.M.C.; Pereira, F.B.. "An evolutionary algorithm for the global optimization of molecular clusters: Application to water, benzene, and benzene cation". Journal of Physical Chemistry A 115 11 (2011): 2130-2138. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952770953&partnerID=MN8TOARS.
    10.1021/jp1117695
  38. Marques, J.M.C.; Llanio-Trujillo, J.L.; Abreu, P.E.; Pereira, F.B.. "How different are two chemical structures?". Journal of Chemical Information and Modeling 50 12 (2010): 2129-2140. http://www.scopus.com/inward/record.url?eid=2-s2.0-78650681756&partnerID=MN8TOARS.
    10.1021/ci100219f
  39. Marques, J.M.C.; Pereira, F.B.. "An evolutionary algorithm for global minimum search of binary atomic clusters". Chemical Physics Letters 485 1-3 (2010): 211-216. http://www.scopus.com/inward/record.url?eid=2-s2.0-73349112252&partnerID=MN8TOARS.
    10.1016/j.cplett.2009.11.059
  40. Pereira, F.B.; Marques, J.M.C.. "A study on diversity for cluster geometry optimization". Evolutionary Intelligence 2 3 (2009): 121-140. http://www.scopus.com/inward/record.url?eid=2-s2.0-73349099174&partnerID=MN8TOARS.
    10.1007/s12065-009-0020-5
  41. Tavares, J.; Pereira, F.B.; Costa, E.. "Multidimensional Knapsack Problem: A Fitness Landscape Analysis". IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-48849114751&partnerID=MN8TOARS.
    10.1109/TSMCB.2007.915539
  42. Marques, J.M.C.; Pereira, F.B.; Leitão, T.. "On the use of different potential energy functions in rare-gas cluster optimization by genetic algorithms: Application to argon clusters". Journal of Physical Chemistry A 112 27 (2008): 6079-6089. http://www.scopus.com/inward/record.url?eid=2-s2.0-49249101771&partnerID=MN8TOARS.
    10.1021/jp711918t
  43. Marques, J.M.C.; Prudente, F.V.; Pereira, F.B.; Almeida, M.M.; Maniero, A.M.; Fellows, C.E.. "A new genetic algorithm to be used in the direct fit of potential energy curves to ab initio and spectroscopic data". Journal of Physics B: Atomic, Molecular and Optical Physics 41 8 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-42949172421&partnerID=MN8TOARS.
    10.1088/0953-4075/41/8/085103
Journal issue
  1. Pereira, Francisco. "Special Issue from the 4th Portuguese-Brazilian Summer School on Evolutionary Computation". International Journal of Natural Computing Research 4 4 (2014):
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/09 Deep Learning for Computer Vision and Natural Language Processing Seinajoki University of Applied Sciences, Finland
(Finland)
2023/04/03 Machine Learning Tools for Biomedicine PDBEB Courses
Universidade de Coimbra
2023 Machine Learning in Cancer Research Molecular Biology of Cancer Course
Universidade de Coimbra
2022/03/07 Machine Learning meets Cell Biology and Biomedicine PDBEB Courses 2021/2022 - ONE HEALTH and the Metabolism-Disease-Environment Triangle
2021/09 Machine Learning and Biomedicine Summer School: Methodologies for Scientific Research
2021/07 Machine Learning and Biomedicine PhD Course, Ageing: from fundamental biology to societal impact
Universidade de Coimbra, Portugal
2021/06 Machine Learning: A Brief Overview Graduate Program in Physics
Universidade Federal da Bahia, Brasil
2021/06 Machine Learning Basics 55th Annual Scientific Meeting - ESCI Virtual 2021
2021/06 Machine Learning Basics 55th Annual Meeting of the European Society for Clinical Investigation (ESCI-2021)
2021/03 Machine Learning Meets Cell Biology and Biomedicine Ph.D. Programme in Experimental Biology and Biomedicine
Centro de Neurocie^ncias e Biologia Celular, Universidade de Coimbra, Coimbra, Portugal
2020/10 Machine Learning: A Brief Overview Summer School: Methodologies for Scientific Research – Interdisciplinary Research, Development and Innovation in Cell and Molecular Metabolism
(Portugal)
2020/09 Machine Learning for Cell Biology and Biomedicine Summer School: Methodologies for Scientific Research – Interdisciplinary Research, Development and Innovation in Cell and Molecular Metabolism
2020/03 MitoScreening: Computational Data Analysis PhD Programme in Experimental Biology and Biomedicine
(Portugal)
2019 Introdução à Aprendizagem Automática: Sessão Prática Meet.LAB Coimbra
Universidade de Coimbra
2019 Discovering Low-energy Atomic Clusters with Machine Learning 53rd Annual Meeting of the European Society for Clinical Investigation (ESCI-2019)
2019 Mitoscreening – Computational Data Analysis MitoScreening 1st Annual Meeting
CNC
2019 MitoScreening – Computational Data Analysis ITN Treatment School 3
2018 Otimização com Algoritmos Evolutivos Doctoral Program in Information Science and Technology
University of Coimbra
2017 Otimização de Inspiração Biológica
Federal University of Bahia, São Salvador, Brazil
2017 Aprendizagem Automática: Introdução e Casos Práticos
Federal University of Bahia, São Salvador, Brazil
2017 (Bio-inspired) Optimization Methods for Biological and Biomedical Sciences
CNCB-UC, Coimbra
2017 Bio-inspired Optimization Erasmus Programme
University of Catania, Italy
2017 Introduction to Machine Learning
UC-Biotech
2016 Optimization Methods for Biological and Biomedical Sciences CNC / UC-Biotech Seminars, Biotech
2016 (Bio-inspired) Optimization Methods for Biological and Biomedical Sciences 50th Annual Scientific Meeting of the European Society for Clinical Investigation (ESCI-2106)
2016 Designing Ant Algorithms with Grammatical Evolution: A Hyper-Heuristics Case Study Doctoral Program in Information Science and Technology
University of Coimbra
2016 Otimização com Algoritmos Evolutivos Sexta Sixth Escola Luso-Brasileira de Computação Evolutiva (ELBCE)
2015 Designing Ant Algorithms with Grammatical Evolution: A Hyper-Heuristics Case Study Doctoral Program in Information Science and Technology
University of Coimbra
2014 Designing Ant Algorithms with Grammatical Evolution: A Hyper-Heuristics Case Study Doctoral Program in Information Science and Technology
University of Coimbra
2014 Hyper-Heuristics: Automatic Design of Ant Algorithms with Grammatical Evolution 6th World Congress on Nature and Biologically Inspired Computing
2014 Bio-inspired Optimization CNC / UC-Biotech Seminars, Biotech
2013 Hyper-Heuristics: Automatic Design of Ant Algorithms with Grammatical Evolution Erasmus Programme
Brno University of Technology, Czech Republic
2013 Relações entre Híper-Heurísticas e Aprendizado: Passado, Presente e Futuro Quarta Escola Luso-Brasileira de Computação Evolutiva (ELBCE-Coimbra)
2012 Algoritmos Genéticos: Optimização com Inspiração Biológica Terceira Escola Luso-Brasileira de Computação Evolutiva (ELBCE-São Carlos)
2010 CHE: Evolutionary Algorithms for Cluster Geometry Optimization
Instituto de Engenharia de Sistemas e Computadores – Investigação e Desenvolvimento (INNESC-ID)
2010 Bioinformática: À Descoberta dos Genes Hands On @ DEIS
Instituto Superior de Engenharia de Coimbra
2010 Computação Evolucionária: Optimização com Inspiração Biológica Encontro Nacional de Estudantes de Informática (ENEI 2010)
2010 Algoritmos Genéticos: Optimização com Inspiração Biológica Segunda Escola Luso-Brasileira de Computação Evolutiva (ELBCE-Guimarães)
2010 Towards an Effective Evolutionary Approach for Binary Lennard-Jones Clusters IEEE Congress on Evolutionary Computation (CEC-2010), Barcelona, Spain
2009 Analysis of Crossover Operators for Cluster Geometry Optimization International Symposium on Computational Intelligence for Engineering Systems
2008 A Self-Adaptive Evolutionary Algorithm for Cluster Geometry Optimization Eight International Conference on Hybrid Intelligent Systems (HIS 2008), Barcelona, Spain
2007 A Influência da Representação na Resolução de Problemas de Optimização Combinatória Inteligência Artificial e a Investigação nos ISE’s
Instituto Superior de Engenharia do Porto
2006 Analysis of Locality in Hybrid Evolutionary Cluster Optimization IEEE Congress on Evolutionary Computation (CEC-2006), Vancouver, Canada
2004 How to Solve It: Evolutionary Computation Algorithms and Optimisation Problem International Guest Lectures on Computer Science and Related Fields
Hogeschool von Utrecht, Utrecht, The Netherlands
2003 How to Solve It: an Overview of Several Artificial Intelligence Techniques Used in Optimisation Problems First European Computer Science Seminar
Instituto Superior de Engenharia de Coimbra
2003 Golomb Rulers: The Advantage of Evolution Eleventh Portuguese Conference on Artificial Intelligence (EPIA-03), Beja, Portugal
2001 How Learning Improves the Performance of Evolutionary Agents: a Case Study with an Information Retrieval System for a Distributed Environment Third International Symposium on Adaptive Systems: Evolutionary Computation and Probabilistic Graphical Models (ISAS 2001), Havana, Cuba
2001 The Influence of Learning in the Evolution of Busy Beavers First European Workshop on Evolutionary Learning: Fourth European Conference on Genetic Programming (EuroGP-2001), Como, Italy
2001 Understanding the Role of Learning in the Evolution of Busy Beavers: a Comparison Between the Baldwin Effect and a Lamarckian Strategy Genetic and Evolutionary Computation Conference (GECCO-2001), San Francisco, USA.
2000 The Influence of Learning in the Behavior of Information Retrieval Adaptive Agents ACM Symposium on Applied Computing (SAC 2000), Como, Italy
2000 How Adaptive Agents Learn to Deal with Incomplete Queries in Distributed Environments IEEE Conference on Evolutionary Computation (CEC-2000), San Diego, USA
1999 Application of Genetic Algorithms to Optimization Problems Hogeschool von Utrecht, Utrecht, The Netherlands
1999 Busy Beaver: an Evolutionary Approach Second Symposium on Artificial Intelligence (CIMAF-99), Havana, Cuba
1999 Graph-Based Crossover: A Case Study with the Busy Beaver Problem Genetic and Evolutionary Computation Conference (GECCO-99), Orlando, Florida, USA
1998 Interacções entre Evolução e Aprendizagem em Sistemas Evolutivos Artificiais 2nd Workshop on Genetic Algorithms and Artificial Life
Instituto Superior Técnico
1998 An Artificial Life Model for Information Retrieval in a Distributed Environment Thirteenth European Conference on Artificial Intelligence (ECAI-98), Brighton, UK
1997 The Influence of Learning in the Optimization of Royal Road Functions Third International Mendel Conference on Genetic, Optimization Problems, Fuzzy Logic, Neural Networks, Rough Sets (Mendel 97), Brno, Czech Republic
1996/10 Application of Genetic Algorithms to Scheduling Problems Advanced School on Artificial Intelligence (EAIA-96)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023 - Current Criação de Séries Temporais Padronizadas com Modelos Generativos
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2023 - Current Interpretação de Banda Desenhada com Large Language Models
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2023 - Current Transfer Learning for Generative Adversarial Networks
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2022 - Current Estratégias de Aprendizagem por Reforço para Role Playing Games
Co-supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2022 - Current IoT Platform for Personal Healthcare of Elderly People
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2022 - Current Metabolic profiling and reversion of mitochondrial dysfunction in Amyotrophic lateral sclerosis patients: innovative application of human neuronal cells differentiated from urine-derived stem cells
Co-supervisor
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
2021 - Current A deep insight in obesity-associated human adipose tissue dysfunction: identifying new microbial and molecular markers for novel therapeutic approaches
Co-supervisor
Universidade de Coimbra, Portugal
2018 - 2023 MitoBone: Mitochondrial Performance on Osteoclast Differentiation and Function during E2 Deprivation - Finding new targets for osteoporosis treatment
Co-supervisor
Universidade de Coimbra, Portugal
2021 - 2022 SYNTHETIC DATA AUGMENTATION FOR BIOLOGICAL DATASETS
Co-supervisor
Universidade de Coimbra, Portugal
2020 - 2021 TILS: um me´todo de engenharia de features baseado em algoritmos de pesquisa local
Co-supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2016 - 2021 NEURONAL MITOCHONDRIAL METABOLISM AND DYNAMIC PROFILING UNDER PHYSIOLOGICAL AND PATHOLOGICAL CONDITIONS USING BIOLOGICAL-BASED MACHINE LEARNING APPROACHES
Co-supervisor
Universidade de Coimbra, Portugal
2019 - 2020 Optimization by Learning
Co-supervisor
Universidade de Coimbra, Portugal
2018 - 2019 Ensemble SGE
Co-supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2018 - 2019 Métodos baseados em Árvores para Meta-Aprendizagem
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2017 - 2018 JiTT.travel Web Platform
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2011 - 2018 Self-Adaptation in Ant Colony Optimization
Co-supervisor
Universidade de Coimbra, Portugal
2016 - 2017 Waldo, the Virtual & Intelligent Cyber Analyst
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2016 - 2017 Prediction of Mitochondrial Toxicity Indexes for Pharmacological Compounds.
Co-supervisor
Universidade de Coimbra, Portugal
2015 - 2016 Automação de Espaços – Sauter
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2011 - 2016 Enhancing Grammar-Based Approaches for the Automatic Design of Algorithms
Co-supervisor
Universidade de Coimbra, Portugal
2014 - 2015 Previsão da Estrutura de Proteínas com Modelos HP
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2010 - 2011 Swarm Intelligence Algorithms for Cluster Geometry Optimization.
Co-supervisor
Universidade de Coimbra, Portugal
2009 - 2010 Framework Cnoti3D
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2009 - 2009 Desenvolvimento de Software para o projecto AirMonitor
Supervisor
Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2004 - 2007 Evolvability in Optimization Problems: the Role of Representations and Heuristics
Co-supervisor
2003 - 2003 An Evolutionary Approach to the Vehicle Routing Problem, Master in Informatics Engineering
Co-supervisor
Universidade de Coimbra, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2022/06/08 - 2022/06/10 Bioinformatics and Computational Biology for Biomedicine (BCB-Biomed): a symposium from the 56th Annual Scientific Meeting of the European Society for Clinical Investigation (ESCI-2022), Bari, Italy (2022/06/08 - 2022/06/10)
Symposium (Co-organisor)
2021/06 - 2021/06 Bioinformatics and Computational Biology for Biomedicine (BCB-Biomed): a symposium from the 55th Annual Scientific Meeting of the European Society for Clinical Investigation (ESCI-2021 Virtual Meeting) (2021/06 - 2021/06)
Symposium (Member of the Organising Committee)
2020/09 - 2020/09 Bioinformatics and Computational Biology for Biomedicine (BCB-Biomed): a symposium from the 54th Annual Scientific Meeting of the European Society for Clinical Investigation (ESCI-2020) (2020/09 - 2020/09)
2019/05 - 2019/05 Bioinformatics and Machine in Biomedicine Symposium at the 53rd Annual Meeting of the European Society for Clinical Investigation (ESCI-2019) (2019/05 - 2019/05)
Symposium (Co-organisor)
 European Society for Clinical Investigation, Netherlands
2019/01 - 2019/01 Encontro sobre Estratégias Inteligentes para Química Computacional (2019/01 - 2019/01)
Workshop
 Universidade de Coimbra, Portugal
2015/09 - 2015/09 17th Portuguese Conference on Artificial Intelligence (EPIA-2015) (2015/09 - 2015/09)
Congress (Co-organisor)
2015/07 - 2015/07 Evolutionary Combinatorial Optimization and Metaheuristics (ECOM) at the Genetic and Evolutionary Computation Conference (GECCO-2015) (2015/07 - 2015/07)
Symposium (Co-organisor)
2013/09 - 2013/09 Artificial Life and Evolutionary Algorithms (ALEA@EPIA 2013): workshop from the 16th Portuguese Conference on Artificial Intelligence (EPIA-2013) (2013/09 - 2013/09)
Symposium (Co-organisor)
2013/07 - 2013/07 4th Portuguese-Brazilian Summer School on Evolutionary Computation (ELBCE-Coimbra 2013) (2013/07 - 2013/07)
Meeting (President of the Organising Committee)
2011/10 - 2011/10 Artificial Life and Evolutionary Algorithms (ALEA@EPIA 2011): workshop from the 15th Portuguese Conference on Artificial Intelligence (EPIA-2013) (2011/10 - 2011/10)
Symposium (Co-organisor)
2007/09 - 2007/09 Analysis of Genetic Representations and Operators (AGRO-07): special track of the IEEE Congress on Evolutionary Computation (CEC-2007) (2007/09 - 2007/09)
Symposium (Co-organisor)
2006/05 - 2006/05 Evolutionary Optimization (EvoOpt-2006): special track of the 19th International FLAIRS (Florida Artificial Research Society) Conference (2006/05 - 2006/05)
Symposium (Co-organisor)
2004/06 - 2004/06 Application of Hybrid Evolutionary Algorithms to Complex Optimization Problems (EvoHybrid-04): workshop from the Genetic and Evolutionary Conference (GECCO-2004). (2004/06 - 2004/06)
Workshop (Co-organisor)
2003/10 - 2003/10 First Portuguese Workshop on Artificial Life and Evolutionary Algorithms (ALEA-03): workshop from the 11th Portuguese Conference on Artificial Intelligence (EPIA-03) (2003/10 - 2003/10)
Symposium (Co-organisor)
2003/07 - 2003/07 Application of Hybrid Evolutionary Algorithms to NP-complete Problems (EvoHybridNP-03): workshop from the Genetic and Evolutionary Conference (GECCO-2003) (2003/07 - 2003/07)
Workshop (Co-organisor)

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2021/07 AutomAted evolution for design
Thesis Member
 Tiago Filipe dos Santos Martins (Doutoramento) (PhD)
Universidade de Coimbra, Portugal
2021/02 Escalonamento Inteligente com Recurso à Aprendizagem por Reforço
(Thesis) Arguer
 Bruno Cunha (PhD)
Universidade de Trás-os-Montes e Alto Douro Escola de Ciências e Tecnologia, Portugal
2020/04 Populações Baseadas em Multisets para Algoritmos Evolutivos
(Thesis) Arguer
 António Manso (PhD)
Universidade de Lisboa, Portugal
2018 Self-Adaptation in Ant Colony Optimization
Supervisor
 Leonor Melo (PhD)
Universidade de Coimbra, Portugal
2016 Enhancing Grammar-Based Approaches for the Automatic Design of Algorithms
Supervisor
 Nuno Lourenço (PhD)
Universidade de Coimbra, Portugal
2014 Sistema Inteligente para Escalonamento Assistido por Aprendizagem
(Thesis) Arguer
 Ivo Pereira (PhD)
Universidade de Trás-os-Montes e Alto Douro, Portugal
2013 Incorporation of Preferences, Adaptive Operators and Hybridization in Multi-Objective Evolutionary Algorithms
Thesis Member
 Eunice Oliveira (PhD)
Universidade de Coimbra, Portugal
2009 Representações Redundantes para Procura Evolutiva
(Thesis) Arguer
 Marisol Correia (PhD)
Universidade do Algarve, Portugal
2009 Substructural Local Search in Discrete Estimation of Distribution Algorithms
(Thesis) Arguer
 Cláudio Lima (PhD)
Universidade do Algarve - Campus de Gambelas, Portugal
2009 Evolutionary Computational Intelligence for Multi-Agent Simulations
Thesis Member
 Telmo Menezes (PhD)
Universidade de Coimbra, Portugal
2008 Controlling Bloat: Individual and Population Based Approaches in Genetic Programming
Thesis Member
 Sara Silva (PhD)
Universidade de Coimbra, Portugal
2007 Evolvability in Optimization Problems: the Role of Representations and Heuristics.
Supervisor
 Jorge Tavares (PhD)
Universidade de Coimbra, Portugal
2007 Inteligência Artificial e Arte
Thesis Member
 Fernando Penousal Machado (PhD)
Universidade de Coimbra, Portugal

Committee member

Activity description
Role 		Institution / Organization
2021 - Current Coordenador do Mestrado em Engenharia Informática
Coordinator
 Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal
2015 - 2019 Direção da Associação Portuguesa para a Inteligência Artificial (APPIA)
Member
2014 - 2018 Presidente da Comissão Científica da Área Científica de Engenharia Informática e Sistemas do Instituto Superior de Engenharia de Coimbra
President / Vice-president
 Instituto Politécnico de Coimbra Instituto Superior de Engenharia de Coimbra, Portugal

Conference scientific committee

Conference name Conference host
2015 - Current Artificial Evolution (EA)
2006 - Current IEEE Congress on Evolutionary Computation (CEC)
2003 - Current • European Conference on Evolutionary Computation in Combinatorial Optimisation (EvoCOP)
2003 - Current Workshop on Artificial Life and Evolutionary Algorithms (ALEA)
2002 - Current Genetic and Evolutionary Computation Conference (GECCO)

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2012 - Current Perito da Agência de Avaliação e Acreditação do Ensino Superior (A3ES): avaliação de licenciaturas e mestrados da área da informática do ensino superior politécnico.
Evaluator

Interview (tv / radio show)

Program Topic
2020/10 - 2020/10 17ª Semana de Ciência e Tecnologia da Universidade Estadual Feira de Santana, Brasil Mesa de Debate - Machine Learning: A Brief Overview
Distinctions

Award

2012 Best Paper Award: Fifteenth European Conference on Genetic Programming (EuroGP-2012) with the paper "Automatic Design of Ant Algorithms with Grammatical Evolution"
2001 Best paper award: First European Workshop on Evolutionary Learning (EvoLearn-01) with the paper "The Influence of Learning in the Evolution of Busy Beavers".
1999 Best paper award: Second European Conference on Genetic Programming (EuroGP-99) with the paper "Busy Beaver: the Influence of Representation".