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Arlindo Limede de Oliveira. Concluiu o(a) Licenciatura em Engenharia Electrotécnica e de Computadores em 1986/07/15 pelo(a) Universidade de Lisboa Instituto Superior Técnico e Doctor of Philosophy em Electrical and Computer Engineering em 1994/12/20 pelo(a) University of California, Berkeley. Publicou 101 artigos em revistas especializadas. Possui 1 capítulo(s) de livros e 3 livro(s). No seu currículo Ciência Vitae os termos mais frequentes na contextualização da produção científica, tecnológica e artístico-cultural são: Previsão de Tráfego com Contexto Situacional; Análise Integrativa de Dados Urbanos Heterogéneos; Aprendizagem Profunda por Reforço; Optimização da Mobilidade Urbana; Redução de Modelos; Simulação do Cérebro; Controlo Temporal da Simulação; Computação Paralela; Medicina de Precisão; Tecnologias da saúde; Oncologia; Imunidade; Conectividade Funcional no Cérebro; Análise de Redes de Elevada Complexidade; fMRI por Campos de Elevada Intensidade; fMRI em repouso; análise de dados de interacções; Biologia Computacional; Computação Social; Big Data; redes complexas; dinâmica de/em redes complexas; padrões em redes complexas; algoritmia; Neurodegenerative Diseases; Clinical and Omics Data Integration; Knowledge Discovery; Systems Medicine; Arquitectura Heterogénea com Múltiplos Núcleos; Análise de Sequências Biológicas; Tecnologias de Sequenciação de Elevado Débito; Algoritmos Paralelos; Novas Tecnologias de Sequenciação; Sequenciação de DNA e RNA; Algoritmos de Indexação para Alinhamento; Estruturas de dados distribuidas; Algoritmos ; Bioinformática; Redes de regulação genética; MicroRNA; Sistemas dinâmicos; inferência de haplotipos; satisfação proposicional; parcimónia pura; dados reais; Redes de regulação transcricional; Respostas a drogas; Transportadores de multiplas drogas; Genómica Funcional e Bioinformática; Saccharomyces cerevisiae; Respostas a drogas/stresse químico ; recuperação de informação; bibliotecas digitais; organização de documentos; partilha de informação; Gestão de Informação Pessoal; Recuperação de Informação; Interfaces com o Utilizador; Computação Ubíqua; engenharia de ontologias; aprendizagem de ontologias; Análise de risco; Semantic Web; Genómica; Redes de regulação; Sistema de informação; .
Identification

Personal identification

Full name
Arlindo Limede de Oliveira

Citation names

  • Oliveira, Arlindo

Author identifiers

Ciência ID
E718-A5FB-4F7D
ORCID iD
0000-0001-8638-5594
Education
Degree Classification
1989/08/16 - 1994/12/20
Concluded
Electrical and Computer Engineering (Doctor of Philosophy)
University of California, Berkeley, United States
"Inductive learning by selection of minimal complexity representations" (THESIS/DISSERTATION)
1987/09/01 - 1989/07/30
Concluded
Engenharia Electrotécnica e de Computadores (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"A simulação concorrente de faltas em circuitos integrados usando modelos ao nível de interruptor " (THESIS/DISSERTATION)
1981/01/02 - 1986/07/15
Concluded
Engenharia Electrotécnica e de Computadores (Licenciatura)
Major in Sistemas e Computadores
Universidade de Lisboa Instituto Superior Técnico, Portugal
19
Affiliation

Teaching in Higher Education

Category
Host institution
Employer
2016 - 2018 Full Professor (University Teacher) Universidade de Lisboa, Portugal
2013 - 2016 Full Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal

Positions / Appointments

Category
Host institution
Employer
2017 - 2018 Conselho geral ou orgão correspondente Universidade de Lisboa, Portugal
2016 - 2018 Conselho de gestão ou orgão correspondente Universidade de Lisboa, Portugal
2016 - 2018 Diretor ou presidente da unidade orgânica Universidade de Lisboa, Portugal
2013 - 2016 Diretor ou presidente da unidade orgânica Universidade de Lisboa Instituto Superior Técnico, Portugal
Projects

Contract

Designation Funders
2022/10/01 - Current Center for Responsible Artificial Intelligence
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Ongoing
2022/01/01 - 2024/12/30 Precise and Efficient Learning using Attention Mechanisms (PRELUNA)
Principal investigator
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2021/12/31 iLU: Aprendizagem Avançada em Dados Urbanos com Contexto Situacional para Optimização da Mobilidade nas Cidades
DSAIPA/DS/0111/2018
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Camara Municipal de Lisboa, Portugal

Laboratório Nacional de Engenharia Civil, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/10/01 - 2021/09/30 Algoritmos para Redução de Modelos e Simulação Eficiente de Redes Neuronais Realistas
PTDC/EEI-EEE/31140/2017
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2020/07/01 - 2021/05/31 INTAKE: INtegrating mobility daTa into spAtial risK modEls
Principal investigator
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016/12/01 - 2020/11/30 Promoção do avanço significativo do conhecimento na área de medicina de precisão e sua translação para benefício da sociedade
SAICTPAC/0021/2015
Instituto de Medicina Molecular João Lobo Antunes, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2013/07/01 - 2016/07/03 Tratamento de Dados em Larga-escala em Ambientes Nuvem
EXCL/EEI-ESS/0257/2012
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Fundacao para a Computacao Cientifica Nacional, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade de Lisboa Instituto Superior de Agronomia, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2013/07/01 - 2015/12/31 HIFI-MRI: Análise de Conectividade Funcional no Cérebro usando fMRI por Campos de Elevada Intensidade
PTDC/EEI-ELC/3246/2012
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2012/01/01 - 2014/06/30 NetDyn: Análise de redes reais de grande dimensão, da estrutura à dinâmica
PTDC/EIA-CCO/118533/2010
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2011/03/01 - 2014/02/28 NEUROCLINOMICS - Compreendendo as doenças neurodegenerativas através da integração de dados clínicos e genómicos
PTDC/EIA-EIA/111239/2009
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2013/12/31 HELIX: Arquitectura heterogénea com múltiplos núcleos para análise de sequências biológicas
PTDC/EEA-ELC/113999/2009
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2013/12/31 TAGS : O poder do pequeno - Ferramentas e algoritmos para as novas aplicações de sequenciação
PTDC/EIA-EIA/112283/2009
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2008/01/01 - 2010/12/31 ARN - Algoritmos para a identificação de redes de regulação genética
PTDC/EIA/67722/2006
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2008/01/01 - 2010/12/31 Dyablo: Modelos para o Comportamento Dinâmico de Redes Biológicas
PTDC/EIA/71587/2006
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2008/01/01 - 2010/12/31 SHIPs: Inferência de Haplotipos por Parcimónia Pura baseada em Satisfação Proposicional
PTDC/EIA/64164/2006
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2007/09/12 - 2010/11/10 Caracterização e modelação de uma rede de regulação transcricional específica envolvida na resistência a múltiplas drogas em levedura
PTDC/BIO/72063/2006
Universidade de Lisboa Instituto Superior Técnico, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2005/04/01 - 2008/06/30 IBRID - Informação Biográfica para Recuperação Interactiva de Documentos
POSC/EIA/59022/2004
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2005/06/01 - 2008/06/01 Um Ambiente Integrado para Investigação e Ensino de Tecnologias de Recuperação de Informação
POSC/EIA/58194/2004
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2005/04/01 - 2008/03/31 Onto-SeaWeb - Engenharia de Ontologias para a Semantic Web
POSC/EIA/58210/2004
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2006/01/02 - 2008/01/01 Elucidação das complexas redes de regulação que actuam na levedura sujeita a drogas/stresse químico: abordagens de expressão genómica e de bioinformática
PDCT/BIO/56838/2004
Universidade de Lisboa Instituto Superior Técnico, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2005/01/01 - 2007/12/31 DBYeast: Infraestruturas e algoritmos para análise e identificação de redes de regulação genética
POSC/EIA/57398/2004
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Oliveira, Arlindo. Ciência, Tecnologia e Sociedade. Lisboa, Portugal: Guerra e Paz. 2023.
    Published
  2. Oliveira, Arlindo. Inteligência Artificial. Lisboa, Portugal: Fundação Francisco Manuel dos Santos. 2019.
    Published
  3. Oliveira, Arlindo. Computer Architecture. 2018.
    10.1142/10940
  4. Oliveira, A.. The digital mind: How science is redefining humanity. Boston, United States: MIT Press. 2017.
    Published
Book chapter
  1. Oliveira, Arlindo; Mário A. T. Figueiredo. "Artificial Intelligence: Historical Context and State of the Art". In Multidisciplinary Perspectives on Artificial Intelligence and the Law. Springer Nature, 2024.
    Published
  2. L. Oliveira, A.. "COVID-19 Contact Tracing Applications in Portugal: Effectiveness and Privacy Issues". 109-114. 2022.
    10.1007/978-3-031-09823-9_8
  3. Oliveira, A.L.. "Artificial intelligence applications in stroke". 261-273. 2021.
  4. Pais, H.C.; McMillan, K.L.; Sentovich, E.M.; Freitas, A.T.; Oliveira, A.L.. "Improved model checking techniques for state space analysis of gene regulatory networks". 386-404. 2009.
Conference paper
  1. Goulão, M.; Oliveira, A.L.. "Pretraining the Vision Transformer using self-supervised methods for vision based Deep Reinforcement Learning". Paper presented in European Conference on Artificial intelligence, Krakow, 2023.
    10.48550/arXiv.2209.10901
  2. André V. Duarte; Arlindo L. Oliveira. "Improving Address Matching Using Siamese Transformer Networks". Paper presented in EPIA Conference on Artificial Intelligence, Lisboa, 2023.
    10.1007/978-3-031-49011-8_33
  3. Pedro Van Stralen; Dinis L. Rodrigues; Arlindo L. Oliveira; Miguel N. Menezes; Fausto J. Pinto. "Stenosis Detection in X-ray Coronary Angiography with Deep Neural Networks Leveraged by Attention Mechanisms". 2022.
    10.1145/3569192.3569212
  4. Vieira, A.B.; Fonseca, A.C.; Ferro, J.; Oliveira, A.L.. "Using a Siamese Network to Accurately Detect Ischemic Stroke in Computed Tomography Scans". Paper presented in EPIA Conference on Artificial Intelligence, 2022.
    10.1007/978-3-031-16474-3_14
  5. Oliveira, T.G.; Oliveira, A.L.. "Assessing Policy, Loss and Planning Combinations in Reinforcement Learning Using a New Modular Architecture". Paper presented in EPIA Conference on Artificial Intelligence, 2022.
    10.1007/978-3-031-16474-3_35
  6. Pedro, R.; Oliveira, A.L.. "Assessing the Impact of Attention and Self-Attention Mechanisms on the Classification of Skin Lesions". 2022.
    10.1109/IJCNN55064.2022.9892274
  7. Lourenço-Silva, João; Arlindo L. Oliveira. "Using Soft Labels to Model Uncertainty in Medical Image Segmentation". Paper presented in MICCAI Brain Lesion workshop, Virtual, 2021.
    In press
  8. Oliveira, Arlindo. "Efficient and Accurate Haplotype Inference by Combining Parsimony and Pedigree Information". Paper presented in Algebraic and Numeric Biology, 2012.
    10.1007/978-3-642-28067-2_3
  9. Ferreira, A.; Oliveira, A.; Figueiredo, M.. "On the use of suffix arrays for memory-efficient Lempel-Ziv data compression". 2009.
  10. Russo, L.M.S.; Navarro, G.; Oliveira, A.L.. "Indexed hierarchical approximate string matching". Paper presented in International Symposium on String Processing and Information Retrieval, 2008.
    10.1007/978-3-540-89097-3_15
  11. Francisco, A.P.; Baeza-Yates, R.; Oliveira, A.L.. "Clique analysis of query log graphs". Paper presented in International Symposium on String Processing and Information Retrieval, 2008.
    10.1007/978-3-540-89097-3_19
  12. Trezentos, P.; Oliveira, A.L.. "Metrics for grid applicability: A distributed elliptic curve platform assessment". Paper presented in Parallel Processing and Applied Mathematics, 2004.
    10.1007/978-3-540-24669-5_112
  13. Freitas, A.T.; Oliveira, A.L.. "Implicit resolution of the Chapman-Kolmogorov equations for sequential circuits: An application in power estimation". 2003.
    10.1109/DATE.2003.1253699
  14. Antunes, C.M.; Oliveira, A.L.. "Inference of sequential association rules guided by context-free grammars". 2002.
    10.1007/3-540-45790-9_1
  15. Oliveira, A.L.; Murgai, R.. "An exact gate assignment algorithm for tree circuits under rise and fall delays". 2000.
    10.1109/ICCAD.2000.896513
  16. Oliveira, A.L.; Silva, J.P.M.. "Efficient search techniques for the inference of minimum size finite automata". 1998.
    10.1109/SPIRE.1998.712986
  17. Oliveira, A.L.; Edwards, S.. "Limits of exact algorithms for inference of minimum size finite state machines". Paper presented in Algorithmic Learning Theory, 1996.
    10.1007/3-540-61863-5_34
  18. Oliveira, A.L.; Sangiovanni-Vincentelli, A.. "Inferring Reduced Ordered Decision Graphs of Minimum Description Length". 1995.
  19. Oliveira, A.L.; Sangiovanni-Vincentelli, A.. "Constructive Induction Using a Non-Greedy Strategy for Feature Selection". 1992.
    10.1016/B978-1-55860-247-2.50050-4
  20. Oliveira, A.L.; Sangiovanni-Vincentelli, A.. "Learning Concepts by Synthesizing Minimal Threshold Gate Networks". 1991.
    10.1016/B978-1-55860-200-7.50042-8
Edited book
  1. Oliveira, Arlindo. Multidisciplinary Perspectives on Artificial Intelligence and the Law. Netherlands: Springer. 2024.
    Published • Editor
Journal article
  1. Gonçalo Oliveira; Ana Catarina Fonseca; José Ferro; Arlindo L. Oliveira. "Deep Learning-Based Extraction of Biomarkers for the Prediction of the Functional Outcome of Ischemic Stroke Patients". Diagnostics (2023): https://doi.org/10.3390/diagnostics13243604.
    10.3390/diagnostics13243604
  2. Oliveira, Arlindo. "Segmentation of X-ray coronary angiography with an artificial intelligence deep learning model: Impact in operator visual assessment of coronary stenosis severity". Catheterization and cardiovascular interventions (2023):
    Published
  3. Oliveira, Arlindo. "Potential and Limitations of Computed Tomography Images as Predictors of the Outcome of Ischemic Stroke Events: A Review". Frontiers in Stroke (2023): https://www.frontiersin.org/articles/10.3389/fstro.2023.1242901/full.
  4. Nobre Menezes, M.; Silva, J.L.; Silva, B.; Rodrigues, T.; Guerreiro, C.; Guedes, J.P.; Santos, M.O.; Oliveira, A.L.; Pinto, F.J.. "Coronary X-ray angiography segmentation using Artificial Intelligence: a multicentric validation study of a deep learning model". International Journal of Cardiovascular Imaging (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85152078210&partnerID=MN8TOARS.
    10.1007/s10554-023-02839-5
  5. Barbulescu, R.; Mestre, G.; Oliveira, A.L.; Silveira, L.M.. "Learning the dynamics of realistic models of C. elegans nervous system with recurrent neural networks". Scientific Reports 13 1 (2023): http://www.scopus.com/inward/record.url?eid=2-s2.0-85146105516&partnerID=MN8TOARS.
    10.1038/s41598-022-25421-w
  6. Mário Cardoso; André Cavalheiro; Alexandre Borges; Ana Filipa Duarte; Amílcar Soares; Maria João Pereira; Nuno Jardim Nunes; Leonardo Azevedo; Arlindo Oliveira. "Modeling the Geospatial Evolution of COVID-19 using Spatio-temporal Convolutional Sequence-to-sequence Neural Networks". ACM Transactions on Spatial Algorithms and Systems (2022): https://doi.org/10.1145/3550272.
    10.1145/3550272
  7. Arlindo L. Oliveira. "A blueprint for conscious machines". Proceedings of the National Academy of Sciences (2022): https://doi.org/10.1073/pnas.2205971119.
    10.1073/pnas.2205971119
  8. Oliveira, Arlindo. "The bio.tools registry of software tools and data resources for the life sciences". Genome Biology (2019): http://dx.doi.org/10.1186/s13059-019-1772-6.
    10.1186/s13059-019-1772-6
  9. Oliveira, Arlindo. "Biotechnology, Big Data and Artificial Intelligence". Biotechnology Journal (2019): http://dx.doi.org/10.1002/biot.201800613.
    10.1002/biot.201800613
  10. Miguel Monteiro; Ana Catarina Fonseca; Ana Teresa Freitas; Teresa Pinho e Melo; Alexandre P. Francisco; Jose M. Ferro; Arlindo L. Oliveira. "Using Machine Learning to Improve the Prediction of Functional Outcome in Ischemic Stroke Patients". IEEE/ACM Transactions on Computational Biology and Bioinformatics 15 6 (2018): 1953-1959. https://doi.org/10.1109/TCBB.2018.2811471.
    10.1109/TCBB.2018.2811471
  11. Oliveira, Arlindo. "ISLES 2016 and 2017-Benchmarking Ischemic Stroke Lesion Outcome Prediction Based on Multispectral MRI". Frontiers in Neurology (2018): http://dx.doi.org/10.3389/fneur.2018.00679.
    10.3389/fneur.2018.00679
  12. Oliveira, Arlindo. "Computational Approach to the Discovery of Phytochemical Molecules with Therapeutic Potential Targets to the PKCZ protein". Letters in Drug Design & Discovery (2018): http://dx.doi.org/10.2174/1570180814666170810120150.
    10.2174/1570180814666170810120150
  13. Oliveira, Arlindo. "DegreeCox – a network-based regularization method for survival analysis". BMC Bioinformatics (2016): http://dx.doi.org/10.1186/s12859-016-1310-4.
    10.1186/s12859-016-1310-4
  14. Niklas Blomberg; Arlindo Oliveira; Barend Mons; Bengt Persson; Inge Jonassen. "The ELIXIR channel in F1000Research [version 2; referees: not peer reviewed]". (2016): http://f1000research.com/articles/4-1471/v2.
    10.12688/f1000research.7587.2
  15. Oliveira, Arlindo. "The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation inSaccharomyces cerevisiae". Nucleic Acids Research (2014): http://dx.doi.org/10.1093/nar/gkt1015.
    10.1093/nar/gkt1015
  16. Oliveira, Arlindo. "Using Information Interaction to Discover Epistatic Effects in Complex Diseases". PLoS ONE (2013): http://dx.doi.org/10.1371/journal.pone.0076300.
    10.1371/journal.pone.0076300
  17. Oliveira, Arlindo. "Mining query log graphs towards a query folksonomy". Concurrency and Computation: Practice and Experience (2012): http://dx.doi.org/10.1002/cpe.1773.
    10.1002/cpe.1773
  18. Oliveira, Arlindo. "GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge". Algorithms for Molecular Biology (2011): http://dx.doi.org/10.1186/1748-7188-6-13.
    10.1186/1748-7188-6-13
  19. Oliveira, Arlindo. "QUANTITATIVE MODELING OF THE SACCHAROMYCES CEREVISIAE FLR1 REGULATORY NETWORK USING AN S-SYSTEM FORMALISM". Journal of Bioinformatics and Computational Biology (2011): http://dx.doi.org/10.1142/s0219720011005690.
    10.1142/s0219720011005690
  20. Oliveira, Arlindo. "Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae". IET Systems Biology (2011): http://dx.doi.org/10.1049/iet-syb.2011.0001.
    10.1049/iet-syb.2011.0001
  21. Oliveira, Arlindo. "Efficient alignment of pyrosequencing reads for re-sequencing applications". BMC Bioinformatics (2011): http://dx.doi.org/10.1186/1471-2105-12-163.
    10.1186/1471-2105-12-163
  22. CalÇada, D.; Vinga, S.; Freitas, A.T.; Oliveira, A.L.. "Quantitative modeling of the saccharomyces cerevisiae FLR1 regulatory network using an s-system formalism". Journal of Bioinformatics and Computational Biology 9 5 (2011): 613-630. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053654755&partnerID=MN8TOARS.
    10.1142/S0219720011005690
  23. Dias, P.J.; Costa, C.P.; Sá-Correia, I.; Teixeira, M.C.; Monteiro, P.T.; Oliveira, A.L.; Freitas, A.T.. "Using systems biology approaches to study a multidrug resistance network". 1st Portuguese Meeting in Biomedical Engineering, ENBENG 2011 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80053956931&partnerID=MN8TOARS.
    10.1109/ENBENG.2011.6026073
  24. Gonçalves, J.P.; Francisco, A.P.; Mira, N.P.; Teixeira, M.C.; Sá-Correia, I.; Oliveira, A.L.; Madeira, S.C.. "TFRank: Network-based prioritization of regulatory associations underlying transcriptional responses". Bioinformatics 27 22 (2011): 3149-3157. http://www.scopus.com/inward/record.url?eid=2-s2.0-80755171153&partnerID=MN8TOARS.
    10.1093/bioinformatics/btr546
  25. Francisco, A.P.; Oliveira, A.L.. "Fully generalized graph cores". Communications in Computer and Information Science 116 CCIS (2011): 22-34. http://www.scopus.com/inward/record.url?eid=2-s2.0-81755166860&partnerID=MN8TOARS.
    10.1007/978-3-642-25501-4_3
  26. Francisco, A.P.; Oliveira, A.L.. "On community detection in very large networks". Communications in Computer and Information Science 116 CCIS (2011): 208-216. http://www.scopus.com/inward/record.url?eid=2-s2.0-81755166850&partnerID=MN8TOARS.
    10.1007/978-3-642-25501-4_21
  27. Abdulrehman, D.; Monteiro, P.T.; Teixeira, M.C.; Mira, N.P.; Lourenço, A.B.; Dos Santos, S.C.; Cabrito, T.R.; et al. "YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface". Nucleic Acids Research 39 SUPPL. 1 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-78651272522&partnerID=MN8TOARS.
    10.1093/nar/gkq964
  28. Graça, A.; Marques-Silva, J.; Lynce, I.; Oliveira, A.L.. "Haplotype inference with pseudo-Boolean optimization". Annals of Operations Research 184 1 (2011): 137-162. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952281186&partnerID=MN8TOARS.
    10.1007/s10479-009-0675-4
  29. Ferreira, A.; Oliveira, A.; Figueiredo, M.. "Sliding window update using suffix arrays". Data Compression Conference Proceedings (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79955740041&partnerID=MN8TOARS.
    10.1109/DCC.2011.60
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    10.1145/368434.368678
  97. Oliveira, Arlindo L.. "Robust techniques for watermarking sequential circuit designs". Proceedings - Design Automation Conference (1999): 837-842. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032638553&partnerID=MN8TOARS.
    10.1145/309847.310082
  98. Pena, J.M.; Oliveira, A.L.. "A new algorithm for exact reduction of incompletely specified finite state machines". IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 18 11 (1999): 1619-1632. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033322750&partnerID=MN8TOARS.
    10.1109/43.806807
  99. Monteiro, Jose C.; Oliveira, Arlindo L.. "Finite state machine decomposition for low power". Proceedings - Design Automation Conference (1998): 758-763. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031630266&partnerID=MN8TOARS.
    10.1145/277044.277235
  100. Oliveira, A.L.; Carloni, L.P.; Villa, T.; Sangiovanni-Vincentelli, A.L.. "Exact minimization of binary decision diagrams using implicit techniques". IEEE Transactions on Computers 47 11 (1998): 1282-1296. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032202219&partnerID=MN8TOARS.
    10.1109/12.736442
  101. Pena, Jorge M.; Oliveira, Arlindo L.. "New algorithm for the reduction of incompletely specified finite state machines". IEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers (1998): 482-489. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032317583&partnerID=MN8TOARS.
  102. Mota, Antonio; Monteiro, Jose; Oliveira, Arlindo. "Power optimization of combinational modules using self-timed precomputation". Proceedings - IEEE International Symposium on Circuits and Systems 2 (1998): 17-20. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031623452&partnerID=MN8TOARS.
  103. Murgai, Rajeev; Fujita, Masahiro; Oliveira, Arlindo. "Using complementation and resequencing to minimize transitions". Proceedings - Design Automation Conference (1998): 694-697. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031624020&partnerID=MN8TOARS.
  104. Oliveira, A.L.; Carloni, L.P.; Villa, T.; Sangiovanni-Vincentelli, A.L.. "Exact minimization of binary decision diagrams using implicit techniques". IEEE Transactions on Computers 47 11 (1998): 1282-1296. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032202219&partnerID=MN8TOARS.
  105. Manquinho, Vasco M.; Flores, Paulo F.; Silva, Joao P.Marques; Oliveira, Arlindo L.. "Prime implicant computation using satisfiability algorithms". Proceedings of the International Conference on Tools with Artificial Intelligence (1997): 232-239. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031334557&partnerID=MN8TOARS.
  106. Oliveira, A.L.; Sangiovanni-Vincentelli, A.. "Using the minimum description length principle to infer reduced ordered decision graphs". Machine Learning 25 1 (1996): 23-50. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030263540&partnerID=MN8TOARS.
  107. Oliveira, Arlindo L.; Sangiovanni-Vincentelli, Alberto. "LSAT--An algorithm for the synthesis of two level threshold gate networks". 1991 IEEE International Conference on Computer-Aided Design Digest of Technical Papers (1992): 130-133. http://www.scopus.com/inward/record.url?eid=2-s2.0-0027091099&partnerID=MN8TOARS.
  108. Gracio, J.A.; Bicudo, P.A.; Rua, N.N.; Oliveira, A.M.; Almeida, C.F.B.; Teixeira, J.P.. "Bottom-up methodology for test preparation and refinement". Proceedings - IEEE International Symposium on Circuits and Systems 2 (1989): 949-952. http://www.scopus.com/inward/record.url?eid=2-s2.0-0024946663&partnerID=MN8TOARS.
  109. Gracio, J.A.; Bicudo, P.A.; Rua, N.N.; Oliveira, A.M.; Almeida, C.F.B.; Teixeira, J.P.. "Test preparation and fault analysis using a bottom-up methodology". (1989): 168-174. http://www.scopus.com/inward/record.url?eid=2-s2.0-0024866858&partnerID=MN8TOARS.
Online resource
  1. Dinis L. Rodrigues; Miguel Nobre Menezes; Fausto J. Pinto; Oliveira, Arlindo. Automated Detection of Coronary Artery Stenosis in X-ray Angiography using Deep Neural Networks. 2021. https://arxiv.org/abs/2103.02969.
  2. Alexandre Borges; Oliveira, Arlindo; Borges, A.; Oliveira, A.L.. Combining Off and On-Policy Training in Model-Based Reinforcement Learning. 2021. https://arxiv.org/abs/2102.12194.

Other

Other output
  1. Connecting metrics for shape-texture knowledge in computer vision. 2023. Oliveira, T.; Marques, T.; Oliveira, A.L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85147409275&partnerID=MN8TOARS.
    10.48550/arXiv.2301.10608
  2. Biomedical image analysis competitions: The state of current participation practice. 2022. Eisenmann, M.; Reinke, A.; Weru, V.; Tizabi, M.D.; Isensee, F.; Adler, T.J.; Godau, P.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85144875054&partnerID=MN8TOARS.
    10.48550/arXiv.2212.08568
  3. Assessing Policy, Loss and Planning Combinations in Reinforcement Learning using a New Modular Architecture. 2022. Oliveira, T.G.; Oliveira, A.L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85123254317&partnerID=MN8TOARS.
  4. Assessing the Impact of Attention and Self-Attention Mechanisms on the Classification of Skin Lesions. 2021. Pedro, R.; Oliveira, A.L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85122052969&partnerID=MN8TOARS.
  5. Graph neural networks for traffic forecasting. 2021. Rico, J.; Barateiro, J.; Oliveira, A.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85106396946&partnerID=MN8TOARS.
  6. Automated detection of coronary artery stenosis in X-ray angiography using deep neural networks. 2021. Rodrigues, D.L.; Menezes, M.N.; Pinto, F.J.; Oliveira, A.L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85102815592&partnerID=MN8TOARS.
  7. Using soft labels to model uncertainty in medical image segmentation. 2021. Silva, J.L.; Oliveira, A.L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85116784765&partnerID=MN8TOARS.
  8. Modelling neuronal behaviour with time series regression: Recurrent neural networks on C. elegans data. 2021. Mestre, G.; Barbulescu, R.; Oliveira, A.L.; Miguel Silveira, L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85110846569&partnerID=MN8TOARS.
  9. Encoder-decoder architectures for clinically relevant coronary artery segmentation. Proceedings of the 11th International Conference on Computational Advances in Bio and medical Sciences. 2021. Silva, J.L.; Menezes, M.N.; Rodrigues, T.; Silva, B.; Pinto, F.J.; Oliveira, A.L.; Lourenço-Silva, João; Arlindo L. Oliveira. http://www.scopus.com/inward/record.url?eid=2-s2.0-85109607505&partnerID=MN8TOARS.
  10. Modeling the geospatial evolution of COVID-19 using spatio-temporal convolutional sequence-to-sequence neural networks. 2021. Cardoso, M.; Duarte, A.F.; Nunes, N.J.; Cavalheiro, A.; Soares, A.; Azevedo, L.; Borges, A.; Pereira, M.J.; Oliveira, A.L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85108017340&partnerID=MN8TOARS.
  11. Sparse network-based regularization for the analysis of patientomics high-dimensional survival data. 2018. André Veríssimo; Eunice Carrasquinha; Marta B. Lopes; Arlindo L. Oliveira; Marie-France Sagot; Susana Vinga. https://doi.org/10.1101/403402.
    10.1101/403402
  12. Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge. 2018. Bakas, S.; Reyes, M.; Jakab, A.; Bauer, S.; Rempfler, M.; Crimi, A.; Shinohara, R.T.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85094531334&partnerID=MN8TOARS.
  13. Conditional random fields as recurrent neural networks for 3D medical imaging segmentation. 2018. Monteiro, M.; Figueiredo, M.A.T.; Oliveira, A.L.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85093217375&partnerID=MN8TOARS.
Activities

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2021/01/01 - 2025/07/30 Attention Mechanisms in Computer Vision
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019/01/01 - 2025/07/30 Optimization of traffic flow using data mining techniques
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019/01/01 - 2023/07/30 Machine Learning Techniques for Processing Electrophysiological Signals in Brain-Computer Interfaces
Co-supervisor
Engenharia Informática
Universidade de Lisboa Faculdade de Ciências, Portugal
2015/01/01 - 2021/02/23 Network-based sparse regularization for the identification of disease signatures
Co-supervisor of André Veríssimo
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2010/01/01 - 2014/11/30 Application of data mining techniques to identify disease susceptibility from genotype data
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2008/01/01 - 2012/11/30 Variability in Biological Systems: Modeling Consequences and Applications
Co-supervisor of Filipe Grácio
Engenharia Biológica (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2007/01/01 - 2011/07/30 Techniques for the resolution of dependencies in the installation process of software components
Supervisor of Paulo Trezentos
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2007/01/01 - 2011/07/01 Motif representation and discovery
Supervisor of Alexandre Carvalho
Engenharia Electrotécnica e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2007/01/01 - 2011/01/30 Satisfiability-based Algorithms for Haplotype Inference,
Co-supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2006/01/01 - 2010/11/30 Search Based Methods for Proteín Structure Prediction
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2006/01/01 - 2010/05/30 Analyzing graph structure: algorithms and applications
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2004/01/01 - 2008/12/20 Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis
Supervisor
Universidade de Lisboa Instituto Superior Técnico, Portugal
2004/01 - 2008/03/30 Uma Metodologia para a Determinação de Observabilidade e Controlabilidade em Circuitos Digitais
Supervisor of José Ramirez Colaço
Engenharia Electrotécnica e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2003/01/01 - 2007/10/30 Improving Methods for Single-label Text Categorization
Supervisor
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2002/01/01 - 2005/01/30 Pattern Mining over Nominal Event Sequences using Constraint Relaxations
Supervisor of Cláudia Antunes
Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
1998/01/01 - 2002/11/30 Estimação de potência em circuitos digitais utilizando técnicas de enumeração implícita,
Supervisor of Ana Teresa Freitas
Engenharia Electrotécnica e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
Distinctions

Award

2009 Prémio Científico UTL/Santander Totta
Universidade de Lisboa, Portugal