Academic Qualification
Ph.D. in University of California, Berkeley
Master in Instituto Superior Técnico
Bachelor in Instituto Superior Técnico
Teaching Area
Computer architecture
Electronics for computers
Machine learning
Compilers
Algorithm design
Algorithms and data structures
Introduction to Programming
Decision support systems
Functional genomics and bioinformatics
Biological applications of algorithms
Computational biology
Neuroengineering
Research Area
Algorithms
Machine Learning
Artificial Intelligence
Bioinformatics
CAD
Professional Services
2020 Reviewer of proposals for the Volkswagen Foundation, for the call for projects on Digitalization in Natural Sciences
2018 ~ 2020 Reviewer of projects for the Romanian Executive Agency for Higher Education, Research, Development and Innovation Funding
2020 Reviewer of projects in AI financed by Science Fund of the Republic of Serbia
2018 ~ present Member of the Editorial Board of journal Genes
2017 Reviewer of projects for the European Commission, for call EINFRA-21-2017: Platform-driven e-infrastructure innovation
2015 Reviewer of projects for the Human Brain Project initiative
2014 Reviewer of projects for the Netherlands Organization for Scientific Research
2006 ~ 2008 Coordinator of the evaluation of the countrywide program for PhD and postdoctoral fellowships, in Computer Science, granted by the Portuguese funding agency, FCT (http://alfa.fct.mctes.pt/apoios/bolsas/).
2006 ~ 2008 Coordinator of the evaluation of national research projects, in Computer Science, financed by the Portuguese funding agency, FCT (http://www.fct.mctes.pt/pt/apoios/projectos/)
2005 ~ 2006 Evaluator of project proposals in the sixth framework program of the European Commission
2005 ~ 2006 Reviewer of projects financed by the sixth framework program of theEuropean Commission
2005 ~ 2008 Evaluator of undergraduate and graduate degrees proposals by Portuguese universities in the area of Computer Science and Informatics, nominated by the Portuguese Ministry for Science and Technology
Member of the Technical Program Committee of the Conferences (amongst others)
ECML: European Conference on Machine Learning (2005, 2006, 2007, 2008,2009,2010)
RECOMB: International Conference on Research in Computational Molecular Biology (2010,3013,2014)
PKDD: Principles and Practice of Knowledge Discovery in Databases (2005, 2006, 2007, 2008,2009,2010)
ICGI: International Colloquium on Grammatical Inference (2000, 2002, 2004, 2006, 2008,2010)
ECIR: European Conference on Information Retrieval (2007, 2008)
ESANN: European Symposium on Artificial Neural Networks (2004, 2005, 2006, 2007, 2008,2009,2010)
DATE: Design, Automation and Test in Europe (2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008)
CIKM: Conference on Information and Knowledge Management (2007, 2008, 2009, 2010, 2011, 2012, 2013)
DAWAK: International Conference on Data Warehousing and Knowledge Discovery (2006, 2007)
ADMA: International Conference on Advanced Data Mining and Applications (2005, 2006)
APBC: Asia Pacific Bioinformatics Conference (2014, 2015, 2016, 2017, 2018)
SPIRE: Symposium on String Processing and Information Retrieval (1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007)
GIW: International Conference on Genome Informatics (2016)
Editor of a special issue on String Processing and Information Retrieval of the Journal of Discrete Algorithms.
Reviewer for the journals:
Artificial Intelligence in Medicine
Drug Safety
IEEE Transactions on Computational Biology and Bioinformatics, IEEE Press.
Bioinformatics, Oxford Journals.
Nucleic Acids Research, Oxford Journals.
BMC Bioinformatics, BioMed Central.
International Journal of Applied Mathematics and Computer Science
Journal of Combinatorial Optimization, Springer.
Computers and Graphics, Elsevier.
Journal of Machine Learning Research, International Consortium for the Advancement of Academic Pub.
In Silico Biology, IOS Press.
Theoretical Computer Science, Elsevier.
The Computer Journal, British Computer Society
Grammars, Springer.
Machine Learning, Kluwer Academic Publishers.
Neural Computation, MIT Press.
Operations Research, Institute for Operations Research and the Management Sciences.
EURASIP Journal on Bioinformatics and Systems Biology, Hindawi Publishing Corporation.
IEEE Transactions on Knowledge Discovery and Data Engineering, IEEE
IEEE Transactions on Computers, IEEE
IEEE Transactions on Computer Aided Design, IEEE
IEEE Transactions on VLSI Systems, IEEE
IEEE Journal of Solid-State Circuits, IEEE
IEEE Transactions on Neural Networks, IEEE
IEEE Transactions on Circuits and Systems, IEEE
IEEE Transactions on Systems, Man and Cybernetics, IEEE
Pattern Recognition Letters, Elsevier.
IEEE Intelligent Systems, IEEE
IEE Proceedings on Computers and Digital Techniques, IEE
ACM Transactions on Design Automation of Electronic Systems, ACM Press.
Information Processing Letters, Elsevier
Journal of Combinatorial Optimization, Springer
Computational Statistics and Data Analysis, Elsevier
Journal of Bioinformatics and Computational Biology, Imperial College Press
Working Experience
2005 ~ present, Distinguished (Full) Professor, Instituto Superior Técnico (IST), University of Lisbon
2021 ~ present, President, INESC
2020 ~ present, Member, Board of Caixa Geral de Depositos
1995 ~ present, Senior Researcher, INESC-ID
2020 ~ present, Founder and Principal Investigador, Machine Learning and Knowledge Discovery group of INESC-ID
2022, Visiting Researcher, Tokyo University
2022, Visiting Professor, MIT
2012 ~ 2019, President, Instituto Superior Tecnico
2009 ~ 2011, Vice-President for Administrative and Financial Affairs, Instituto Superior Tecnico
2002 ~ 2014, Member and co-founder of the Knowledge Discovery and Bioinformatics (KDBIO) research group
2012 ~ 2014, Member, Board of Directors (non-executive) of Taguspark S.A.
2007 ~ 2008, Chair of the Department of Computer Science and Engineering, Instituto Superior Tecnico
2009 ~ 2020, Member, Board of Directors of INESC
2014 ~ 2019, Member, Board of Directors of CESAER, the Conference of European Schools for Advanced Engineering Education and Research
2004 ~ 2009, President, INESC-ID
2004 ~ 2005, President, Portuguese Association for Artificial Intelligence (APPIA)
2000 ~ 2003, Member, Executive Board of INESC-ID
2000 ~ 2005, Associate Professor, Instituto Superior Tecnico
2015 ~ 2018, Head, Portuguese Node of ELIXIR Europe
1995 ~ 2000, Assistant Professor, Instituto Superior Tecnico
1986 ~ 1994, Teaching Assistant, Instituto Superior Tecnico
1996 ~ 2009, Research Associate, Cadence Research Laboratories, Berkeley, CA
1995 ~ 1999, Senior Researcher, INESC
1989 ~ 1994, Researcher, Electronics Research Laboratory of UC Berkeley
1986, Junior Researcher, CERN
Academic Publication (selected)
Books
1. Arlindo L. Oliveira, The Digital Mind, MIT Press (https://mitpress.mit.edu/books/digital-mind), 2017
2. Arlindo L. Oliveira, Mentes Digitais (Portuguese edition of The Digital Mind), IST Press
(http://istpress.tecnico.ulisboa.pt/node/464), 2018
3. Arlindo L. Oliveira, 数字思维 阿林多奥利维拉 著 智能未来 思维智能 人类社会变革 中信出版社图书 (Chinese edition of The Digital Mind), CITIC Press, (https://item.jd.com/65401942612.html), 2020
4. Guilherme S. Arroz, José C. Monteiro, Arlindo L. Oliveira, Arquitectura de computadores: dos Sistemas Digitais aos Microprocessadores, IST Press ( http://istpress.ist.utl.pt/larquitecturacomp.htm), 2007
5. Guilherme S. Arroz, José C. Monteiro, Arlindo L. Oliveira , Digital Systems to Microprocessors, World Scientific (https://www.worldscientific.com/worldscibooks/10.1142/10940), 2018
6. Inteligência Artificial, Fundação Francisco Manuel dos Santos (https://www.ffms.pt/publicacoes/detalhe/2878/inteligencia-artificial ), 2019
7. Mário Nascimento and Edleno S. Moura and Arlindo L. Oliveira, editors, String Processing and Information Retrieval (10th SPIRE), Lecture Notes in Computer Science 2857, Oct. 2003, Springer
8. Alberto Laender and Arlindo L. Oliveira, editors, String Processing and Information Retrieval (9th SPIRE), Lecture Notes in Computer Science 2476, Sep. 2002, Springer
9. Arlindo L. Oliveira, editor, Grammatical Inference : Algorithms and Applications (5th ICGI), Lecture Notes in Computer Science 1891, Sep. 2000, Springer
Journal Article
1. Beatriz Valente Silva, João Marques, Miguel Nobre Menezes, Arlindo L. Oliveira, Fausto J. Pinto, Artificial intelligence-based diagnosis of acute pulmonary embolism: Development of a machine learning model using 12-lead electrocardiogram, Revista Portuguesa de Cardiologia, 2023.
2. Miguel Menezes, João Silva, Beatriz Silva, Tiago Rodrigues, Cláudio Guerreiro, João Guedes, Manuel Santos, Arlindo L. Oliveira, Fausto J. Pinto, Coronary X-ray angiography segmentation using Artificial Intelligence: a multicentric validation study of a deep learning model, The International Journal of Cardiovascular Imaging, 2023.
3. Arlindo L. Oliveira, A blueprint for conscious machines, Proceedings of the National Academy of Sciences 119 (23), 2022.
4. Mário Cardoso, André Cavalheiro, Alexandre Borges, Ana F Duarte, Amílcar Soares, Maria João Pereira, Nuno Jardim Nunes, Leonardo Azevedo, Arlindo L 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.
5. Miguel Nobre Menezes, João Lourenço-Silva, Beatriz Silva, Oliveira Rodrigues, Ana Rita G Francisco, Pedro Carrilho Ferreira, Arlindo L Oliveira, Fausto J Pinto, Development of deep learning segmentation models for coronary X-ray angiography: Quality assessment by a new global segmentation score and comparison with human performance, Revista Portuguesa de Cardiologia, 2022.
6. Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo Lopez, Severine Duvaud, Heinz Stockinger, Bengt Persson, Radka Svobodová Vařeková, Tomáš Raček, Jiří Vondrášek, Hedi Peterson, Ahto Salumets, Inge Jonassen, Rob Hooft, Tommi Nyrönen, Alfonso Valencia, Salvador Capella, Josep Gelpí, Federico Zambelli, Babis Savakis, Brane Leskošek, Kristoffer Rapacki, Christophe Blanchet, Rafael Jimenez, Arlindo L. Oliveira, Gert Vriend, Olivier Collin, Jacques van Helden, Peter Løngreen & Søren Brunak, The bio.tools registry of software tools and data resources for the life sciences, Genome Biology, vol. 20, 164, Aug. 2019.
7. Arlindo L. Oliveira, Biotechnology, Big Data and Artificial Intelligence, Biotechnology Journal, vol. 14, 1800613, 2019.
8. Stefan Winzeck, Arsany Hakim, Richard McKinley, José Pinto, Victor Alves, Carlos Silva, Maxim Pisov, Egor Krivov, Mikhail Belyaev, Miguel Monteiro, Arlindo L. Oliveira, Youngwon Choi, Myunghee Cho Paik, Yongchan Kwon, Hanbyul Lee, Beom Joon Kim, Joong-Ho Won, Mobarakol Islam, Hongliang Ren, David Robben, Paul Suetens, Enhao Gong, Yilin Niu, Junshen Xu, John M Pauly, Christian Lucas, Mattias P Heinrich, Luis C Rivera, Laura S Castillo, Laura A Daza, Andrew L Beers, Pablo Arbelaezs, Oskar Maier, Ken Chang, James M Brown, Jayashree Kalpathy-Cramer, Greg Zaharchuk, Roland Wiest, Mauricio Reyes, ISLES 2016 and 2017-benchmarking ischemic stroke lesion outcome prediction based on multispectral MRI, Frontiers in Neurology vol. 9, 679, Sep. 2018.
9. Miguel Monteiro and Ana Catarina Fonseca and Ana T. Freitas and Teresa Pinho e Melo and A. P. Francisco and José M. Ferro and Arlindo L. Oliveira, Using Machine Learning to Improve the Prediction of Functional Outcome in Ischemic Stroke Patients, article in ACM/IEEE Transactions on Computational Biology and Bioinformatics vol. 15 (6) pp. 1953-1959, Mar. 2018.
10. André Veríssimo and Arlindo L. Oliveira and Marie-France Sagot and Susana Vinga, DegreeCox–a network-based regularization method for survival analysis, BMC Binformatics, 17(16), 449,Dec 2016.
11. Miguel Teixeira and Pedro T. Monteiro and Joana Guerreiro and Joana Gonçalves and Nuno Mira and Sandra dos Santos and Tânia Cabrito and Margarida Palma and Catarina Costa and A. P. Francisco and Sara C. Madeira and Arlindo L. Oliveira and Ana T. Freitas and Isabel Sá-Correia, The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae, Nucleic Acids Research, Jan 2014.
12. Orlando Anunciação and Susana Vinga and Arlindo L. Oliveira, Using Information Interaction to Discover Epistatic Effects in Complex Diseases, PLoS ONE, 8(10), pp. , Oct. 2013.
13. A. P. Francisco and R. Baeza-Yates and Arlindo L. Oliveira, Mining query log graphs towards a query folksonomy, Concurrency and Computation: Practice and Experience, (1), Dec. 2012.
14. Dário Abdulrehman and Pedro T. Monteiro and Miguel C. Teixeira and Nuno P. Mira and Artur B. Lourenço and Sónia C. dos Santos and Tânia R. Cabrito and A. P. Francisco and Sara C. Madeira and Ricardo Rubén dos Santos Aires and Arlindo L. Oliveira and Isabel Sá-Correia and Ana T. Freitas, YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface, Nucleic Acids Research, 39(1), pp. D136-D140 , Jan. 2011
15. Dulce Calçada and Susana Vinga and Ana T. Freitas and Arlindo L. Oliveira, Quantitative modeling of the Saccharomyces cerevisiae FLR1 Regulatory Network using an S-System Formalism, Journal of Bioinformatics and Computational Biology, 9(5), pp. , Oct. 2011, World Scientific.
16. Luís M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira, Fully-Compressed Suffix Trees, ACM Transactions on Algorithms, 7(4), Sep. 2011, ACM.
17. Pedro T. Monteiro and Paulo J. Dias and Delphine Ropers and Arlindo L. Oliveira and Isabel Sá-Correia and Miguel C. Teixeira and Ana T. Freitas, Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae, IET Systems Biology, 5(5), pp. 308-316, Sep. 2011, IET.
18. Joana P. Gonçalves and A. P. Francisco and Nuno P. Mira and Miguel C. Teixeira and Isabel Sá-Correia and Arlindo L. Oliveira and Sara C. Madeira, TFRank: network-based prioritization of regulatory associations underlying transcriptional responses, Bioinformatics, 27(22), pp. 3149–3157, Nov. 2011, Oxford University Press.
19. Alexandra M. Carvalho and Teemu Roos and Arlindo L. Oliveira and Petri Myllymäki, Discriminative learning of Bayesian networks via factorized conditional log-likelihood, Journal of Machine Learning Research, 12(7), pp. 2181-2210, Jul. 2011.
20. Francisco Fernandes and Paulo G. S. da Fonseca and Luís M. S. Russo and Arlindo L. Oliveira and Ana T. Freitas,Efficient alignment of pyrosequencing reads for resequencing applications, BMC Bioinformatics, 12(163), Jun. 2011, BioMed Central.
21. Alexandra M. Carvalho and Arlindo L. Oliveira, GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge, Algorithms for Molecular Biology, 6(13), Apr. 2011.
22. Ana Sofia Graça and Joao Marques Silva and Inês Lynce and Arlindo L. Oliveira, Haplotype inference with pseudo-Boolean optimization, Annals of Operations Research, 184(1), pp. 137-162, Jan. 2011, Springer.
23. Ana Sofia Graça and Inês Lynce and Joao Marques Silva and Arlindo L. Oliveira, Haplotype Inference by Pure Parsimony: a Survey, Journal of Computational Biology, 17(8), pp. 969–992, Aug. 2010, Mary Ann Liebert, Inc.
24. Miguel C. Teixeira and Paulo J. Dias and Pedro T. Monteiro and Arlindo L. Oliveira and Ana T. Freitas and Isabel Sá-Correia, Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches, Molecular BioSystems, 6(12), pp. 2471-2481, Nov. 2010, RCS Publishing.
25. Sara C. Madeira and Miguel C. Teixeira and Isabel Sá Correia and Arlindo L. Oliveira, Identification of Regulatory Modules in Time Series Gene Expression Data using a Linear Time Biclustering Algorithm, IEEE Transactions on Computational Biology and Bioinformatics, 7(1), pp. 153-165, Jan. 2010, IEEE/ACM.. IEEE/ACM.
26. Luís M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira and Pedro Morales, Approximate String Matching with Compressed Indexes, Algorithms, 2(3), pp. 1105-1136, Sep. 2009.
27. Joana P. Gonçalves and Sara C. Madeira and Arlindo L. Oliveira, BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data, BMC Research Notes, 2(124), pp. , Jul. 2009, BioMed Central.
28. Miguel Bugalho and Arlindo L. Oliveira, Constant Time Clash Detection in Protein Folding, Journal of Bioinformatics and Computational Biology, 7(1), pp. 55-74, Feb. 2009, World Scientific.
29. Sara C. Madeira and Arlindo L. Oliveira, A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series, Algorithms for Molecular Biology, 4(8), pp. , Jun. 2009, BioMed Central.
30. Ana C Casimiro, Susana Vinga, Ana T Freitas and Arlindo L Oliveira, An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance, BMC Bioinformatics, 9(89), Feb. 2008, BMC Bioinformatics, BioMed Central.
31. Luís M. S. Russo and Arlindo L. Oliveira, A Compressed Self-Index using a Ziv-Lempel Dictionary, Information Retrieval, 11(4), pp. 359-388, Aug. 2008. Springer.
32. Duarte Oliveira and Mauro Santos and Catarina Milheiriço and João Carriço and Susana Vinga and Arlindo L. Oliveira and Hermínia de Lencastre, ccrB Typing Tool: An online resource for staphylococci ccrB sequence, Journal of Antimicrobial Chemotherapy, 61(4):959-960, Jan. 2008.
33. André Martins and H. Sofia Pinto and Arlindo L. Oliveira, Using Grammatical Inference Techniques to Learn Ontologies that Describe the Structure of Domain Instances, 22(1/2), pp. 139-167, Applied Artificial Intelligence, Taylor & Francis.
34. Pedro Monteiro and Nuno Mendes and Miguel C. Teixeira and Sofia Orey and Sandra Tenreiro and Nuno Mira and Hélio Pais and Alexandre P. Francisco and Alexandra M. Carvalho and Artur Lourenço and Isabel Sá-Correia and Arlindo L. Oliveira and Ana T. Freitas, YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae, Nucleic Acids Research, Jan. 2008, Oxford University Press.
35. Luís M. S. Russo and Arlindo L. Oliveira, Efficient generation of super condensed neighborhoods, Journal of Discrete Algorithms, 5(3), pp. 501-513, Sep. 2007, Elsevier.
36. Nuno Mendes and Ana Casimiro and Pedro M. Santos and Isabel Sá-Correia and Arlindo L. Oliveira and Ana T. Freitas, MUSA: a parameter free algorithm for the identification of biologically significant motifs, Bioinformatics, 22(24), pp. 2996-3002, Dec. 2006, Oxford Journals.
37. Alexandra M. Carvalho and Ana T. Freitas and Arlindo L. Oliveira and Marie-France Sagot, An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(2), pp. 126-140, Apr. 2006, IEEE.
38. Miguel C. Teixeira and Pedro Monteiro and Pooja Jain and Sandra Tenreiro and Alexandra R. Fernandes and Nuno P. Mira and Marta Alenquer and Ana T. Freitas and Arlindo L. Oliveira and Isabel Sá-Correia, The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae, Nucleic Acids Research, 34(), pp. D446-D451, Jan. 2006, Oxford Journals.
39. Miguel Bugalho and Arlindo L. Oliveira, Inference of regular languages using state merging algorithms with search, Pattern Recognition, 38(9), pp. 1457-1467, Sep. 2005, Elsevier.
40. Sara C. Madeira and Arlindo L. Oliveira, Biclustering algorithms for biological data analysis: a survey, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1(1), pp. 24-45, Jan. 2004, IEEE/ACM.
41. Arlindo L. Oliveira and Rajeev Murgai, On the Problem of Gate Assignment Under Different Rise and Fall Delays, IEEE Transactions on Computer Aided Design, 22(11), pp. 807--814, Jun. 2003, IEEE.
42. J. Monteiro and Arlindo L. Oliveira, Implicit FSM Decomposition Applied To Low Power Design, IEEE Transactions on Very Large Scale Integration Systems, 10(5), pp. 560-565, Oct. 2002, IEEE.
43. Arlindo L. Oliveira, Techniques For The Creation Of Digital Watermarks In Sequential Circuit Designs, IEEE Transactions on Computer Aided Design, 20(9), pp. 1101-1117, Sep. 2001. IEEE.
44. Arlindo L. Oliveira and João Marques Silva, Efficient Algorithms For The Inference Of Minimum Size DFAs, Machine Learning, 44(1), pp. 93-119, Jul. 2001, Kluwer Academic Publishers. J. G. Pena and Arlindo L. Oliveira, A new algorithm for exact reduction of incompletely specified finite state machines, IEEE Transactions on Computer Aided Design, 18(11), pp. 1619--1632, Nov. 1999, IEEE.
45. Arlindo L. Oliveira and Luca Carloni and Tiziano Villa and Alberto Sangiovanni-Vincentelli, Exact Minimization of Binary Decision Diagrams Using Implicit Techniques, IEEE Transactions on Computers, 47(11), pp. 1282-1296, Nov. 1998, IEEE.
46. Arlindo L. Oliveira and A. Sangiovanni-Vincentelli, Using the minimum description length principle to infer reduced ordered decision graphs, Machine Learning, 25(1), pp. 23--50, Jan. 1996, Kluwer.
Conference Papers and Book Chapters
1. Arlindo L. Oliveira, COVID-19 Contact Tracing Applications in Portugal: Effectiveness and Privacy Issues, in Towards Trustworthy Artificial Intelligent Systems, pp. 109-114, Springer, 2022
2. Manuel Goulão and Arlindo L. Oliveira, Pretraining the Vision Transformer using self-supervised methods for vision based Deep Reinforcement Learning, NeurIPS Deep Reinforcemente Learning Workshop, 2022
3. Ana Beatriz Vieira, Ana Catarina Fonseca, José Ferro and Arlindo Oliveira, Using a Siamese Network to Accurately Detect Ischemic Stroke in Computed Tomography Scans, 21st EPIA Conference on Artificial Intelligence, LNCS, 2022.
4. Tiago Oliveira and Arlindo Oliveira, Assessing Policy, Loss and Planning Combinations in Reinforcement Learning using a New Modular Architecture, 21st EPIA Conference on Artificial Intelligence, LNCS, 2022.
5. Rafael Pedro, Arlindo L. Oliveira , Assessing the Impact of Attention and Self-Attention Mechanisms on the Classification of Skin Lesions, International Joint Conference on Neural Networks, 2022.
6. João Lourenço-Silva, Arlindo L. Oliveira, Using Soft Labels to Model Uncertainty in Medical Image Segmentation, International MICCAI Brainlesion Workshop, 585-596, LNCS, 2022.
7. João Lourenço-Silva, Miguel Nobre Menezes, Tiago Rodrigues, Beatriz Silva, Fausto J. Pinto and Arlindo L. Oliveira. Encoder-Decoder Architectures for Clinically Relevant Coronary Artery Segmentation, 11th International Conference on Computational Advances in Bio and Medical Sciences, Springer LNCS, 2021.
8. Arlindo L. Oliveira, Artificial Intelligence Applications in Stroke, in Precision Medicine in Stroke, Springer, 2021.
9. Alexandre Borges, Arlindo L. Oliveira, Combining Off and On-Policy Training in Model-Based Reinforcement Learning, Adaptive and Learning Agents AAMAS workshop, 2021.
10. João Rico, José Barateiro, Arlindo L. Oliveira, Graph Neural Networks for Traffic Forecasting, presented at 17th International Operations and Maintenance Conference in the Arab Countries (OIMANTEC) 2019.
11. Miguel Monteiro, Mário A. T. Figueiredo, Arlindo L. Oliveira, Conditional Random Fields as Recurrent Neural Networks for 3D Medical Imaging Segmentation, Medical Imaging meets NeurIPS Workshop, Dec. 2018
12. Miguel Monteiro, Arlindo L. Oliveira, Fully Convolutional Neural Network for 3D Stroke Lesion Segmentation, presented at Ischemic Stroke Lesion Segmentation Challenge (ISLES), International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2017.
13. André Veríssimo, Eunice Carrasquinha, Marta Lopes, Arlindo L. Oliveira, Marie-France Sagot, Susana Vinga, Network-based sparse modeling of breast invasive carcinoma survival data, presented at Signal Processing with Adaptive Sparse Structured Representations (SPARS) 2017.
14. Miguel Monteiro, Ana C. Fonseca, Ana T. Freitas, Teresa P. Melo, Alexandre P. Francisco, José M. Ferro, Improving the Prediction of Functional Outcome in Ischemic Stroke Patients, presented at the International Workshop on Data Mining in Bioinformatics (BIOKDD) 2017.
15. André Veríssimo, Eunice Carrasquinha, Marta Lopes, Arlindo L. Oliveira, Marie-France Sagot, Susana Vinga, Random Sample Consensus (RANSAC) for the robust identification of outliers in transcriptomic data, ISMB/ECCB 2017.
16. André Veríssimo, Arlindo L. Oliveira, Susana Vinga, DegreeCox: a network-based regularization method for survival analysis, Tenth International Workshop on Machine Learning in Systems Biology (MLSB) 2016.
17. Nelson Silveira, Thiago Elias, Susana Vinga, Arlindo L. Oliveira, Selection of biomarkers and drug target in HNSCC based on meta and structural analysis, SolBio International Conference and Computational Biology for Innovative Genomics (SoiBIO) 2016.
18. André Leitão, A. P. Francisco, Arlindo L. Oliveira, Rodolfo Abreu, Sandro Nunes, Juliana Rodrigues, Patrícia Figueiredo, Lawrence L. Wald, Marta Bianciardi and L. Miguel Silveira, Voxel-Based Analysis of Functional Connectivity Networks from Ultra-High Resolution fMRI, Organization for Human Brain Mapping Annual Conference, Jun. 2015
19. Francisco Fernandes, Paulo Fonseca, Luís M. S. Russo, Arlindo L. Oliveira and Ana T. Freitas, An efficient data representation for large scale genome re-sequencing, presented at 13tth International Meeting on Human Genome Variation and Complex Genome Analysis (HGV2012), Sep. 2012
20. Luís M. S. Russo, Ana T. Freitas and Arlindo L. Oliveira, Transparent Hidden Markov Models, presented at the Learning Workshop, Mar. 2012.
21. Francisco Fernandes, Paulo Fonseca, Luís M. S. Russo, Arlindo L. Oliveira and Ana T. Freitas, TAPYR: An efficient high-throughput sequence aligner for re-sequencing applications, presented at 7th International Conference of the Brazilian Association for Bioinformatics and Computational Biology, Oct. 2011.
22. Paulo J. Dias, Pedro T. Monteiro, Arlindo L. Oliveira, Ana T. Freitas, Isabel Sá-Correia and Miguel C. Teixeira, Insights into the transcription regulatory network controlling the multidrug resistance gene FLR1: a systems biology approach, presented at 25th International Conference on Yeast Genetics and Molecular biology, Jul. 2011.
23. Dulce Calçada, Susana Vinga, Ana T. Freitas and Arlindo L. Oliveira, Quantitative modeling the Saccharomyces cerevisiae FLR1 Regulatory Network using an S-System Formalism, presented at IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology, Jul. 2011.
24. Alexandre P. Francisco, Sophie Schbath, Ana T. Freitas and Arlindo L. Oliveira, Using Graph Modularity Analysis to Identify Transcription Factor Binding Sites, presented at International Workshop on Graph Theoretic Analysis of Biological Networks at the IEEE International Conference on Bioinformatics and Biomedicine (BIBM10), Dec. 2010.
25. Alexandre P. Francisco, Arlindo L. Oliveira, Fully generalized graph cores, presented at Complex Networks, Oct. 2010.
26. Alexandre P. Francisco, Ricardo Baeza-Yates and Arlindo L. Oliveira, Mining large query induced graphs towards a hierarchical query folksonomy, presented at String Processing and Information Retrieval (SPIRE), Oct. 2010.
27. Alexandre and Arlindo L. Oliveira, On community detection in very large networks, presented at Complex Networks, Oct. 2010 [bibTex]
28. Paulo Trezentos, Inês Lynce and Arlindo L. Oliveira, Apt-pbo: Solving the Software Dependency Problem using Pseudo-Boolean Optimization, presented at 25th IEEE/ACM International Conference on Automated Software Engineering, Sep. 2010.
29. Pedro T. Monteiro, Paulo J. Dias, Delphine Ropers, Arlindo L. Oliveira, Isabel Sá-Correia, Miguel C. Teixeira and Ana T. Freitas, Computational Modeling and Analysis of the Yeast FLR1 Regulatory Network in Mancozeb-challenged Cells, presented at Eleven International Conference on Systems Biology, Sep. 2010.
30. Alexandre P. Francisco, Arlindo L. Oliveira and Ana T. Freitas, A graph based approach to motif clustering, presented at Fourteenth International Conference on Research in Computational Molecular Biology (RECOMB), Aug. 2010.
31. Dulce Calçada, Susana Vinga and Arlindo L. Oliveira, An S-System Model of the Saccharomyces cerevisiae FLR1 Regulatory Network, presented at 14th International Conference on Research in Computational Molecular Biology (RECOMB), Aug. 2010.
32. Ana Sofia Graça, Inês Lynce, João Marques Silva and Arlindo L. Oliveira, Efficient and Accurate Haplotype Inference by Combining Parsimony and Pedigree Information, presented at Algebraic and Numeric Biology (ANB10), Aug. 2010.
33. Orlando Anunciação, Bruno Gomes, Susana Vinga, Jorge Gaspar, Arlindo L. Oliveira and José Rueff, A Data Mining Approach for the detection of High-Risk Breast Cancer Groups, presented at 3rd International Workshop on Practical Applications of Computational Biology and Bioinformatics, Jun. 2010.
34. Luís M. S. Russo, Gonzalo Navarro and Arlindo L. Oliveira, Parallel and Distributed Compressed Indexes, presented at Proc. 21st Annual Symposium on Combinatorial Pattern Matching (CPM), Jun. 2010.
35. Alexandre P. Francisco, Joana P. Gonçalves, Sara C. Madeira and Arlindo L. Oliveira, Using personalized ranking to unravel relevant regulations in the Saccharomyces cerevisiae regulatory network, presented at Jornadas de Bioinformatica, Nov. 2009.
36. Ana Sofia Graça, Inês Lynce, João Marques Silva and Arlindo L. Oliveira, Haplotype Inference Combining Pedigrees and Unrelated Individuals, presented at CP Workshop on Constraint Based Methods for Bioinformatics (WCB), Sep. 2009.
37. Sara C. Madeira and Arlindo L. Oliveira, Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis, presented at 3rd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 09), IWANN 2009, Jun. 2009.
38. Artur Ferreira and Arlindo L. Oliveira and Mário Figueiredo, On the Use of Suffix Arrays for Memory-Efficient Lempel-Ziv Data Compression, presented at IEEE Data Compression Conference (DCC), Mar. 2009.
39. Alexandre P. Francisco and Arlindo L. Oliveira, Improved Algorithm and Data Structures for Modularity Analysis of Large Networks, presented at NIPS Workshop on Analyzing Graphs, Dec. 2008.
40. Alexandre P. Francisco, Ricardo Baeza-Yates and Arlindo L. Oliveira, Clique Analysis of Query Log Graphs, presented at String Processing and Information Retrieval, Nov. 2008.
41. Inês Lynce, Ana Sofia Graça, João and Arlindo L. Oliveira, Haplotype Inference with Boolean Constraint Solving: an Overview, presented at 20th IEEE International Conference on Tools with Artificial Intelligence (ICTAI), Nov. 2008.
42. Luís M. S. Russo, Gonzalo Navarro and Arlindo L. Oliveira, Indexed Hierarchical Approximate String Matching, String Processing and Information Retrieval (SPIRE), Nov. 2008.
43. Miguel Bugalho and Arlindo L. Oliveira, An Evaluation of the Impact of Side Chain Positioning on the Accuracy of Discrete Models of Protein Structures, presented at Brasilian Symposium on Bioinformatics, Aug. 2008.
44. Artur J. Ferreira, Arlindo L. Oliveira and Mário T. Figueiredo, On the Suitability of Suffix Arrays for Lempel-Ziv Data Compression, presented at 5th International Conference on e-Business and Telecommunications, Jul. 2008.
45. Artur J. Ferreira, Arlindo L. Oliveira and Mário A. T. Figueiredo, Suffix Arrays: a competitive choice for fast Lempel-Ziv Compression, presented at International Conference on Signal Processing and Multimedia Applications (SIGMAP), Jul. 2008.
46. Luís M. S. Russo, Gonzalo Navarro and Arlindo L. Oliveira, Dynamic Fully-Compressed Suffix Trees, presented at Combinatorial Pattern Matching (CPM), Jun. 2008.
47. Ana Sofia Graça, João Marques Silva, Inês Lynce and Arlindo L. Oliveira, Efficient Haplotype Inference with Combined CP and OR Techniques, presented at Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems, May. 2008.
48. Ana Sofia Graça, Inês Lynce, João Marques Silva and Arlindo L. Oliveira, Generic ILP vs Specialized 0-1ILP for Haplotype Inference, presented at Workshop on Constraint Based Methods for Bioinformatics, May. 2008.
49. Alexandre P. Francisco, Arlindo L. Oliveira and Ana T. Freitas, Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-occurrence Graph, presented at International Symposium on Bioinformatics Research and Applications, May. 2008.
50. Luís M. S. Russo, Gonzalo Navarro and Arlindo L. Oliveira, Fully-Compressed Suffix Trees, presented at 8th Latin American Symposium on Theoretical Informatics (LATIN), Apr. 2008.
51. Luís M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira, Dynamic Fully-Compressed Suffix Trees, Combinatorial Pattern Matching (CPM), Jun. 2008, pp. 191-203 , Springer.
52. Xiaoshu Wang and Jonas S. Almeida and Arlindo L. Oliveira, Ontology Design Principles and Normalization Techniques in the Web, Data Integration in the Life Sciences, Jun. 2008 , pp. 28-43 , Springer.
53. Luís M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira, Fully-Compressed Suffix Trees, 8th Latin American Symposium on Theoretical Informatics (LATIN), Apr. 2008 , pp. 362-373 , Springer.
54. João Marques Silva and Inês Lynce and Ana Graça and Arlindo L. Oliveira, Efficient and Tight Upper Bounds for Haplotype Inference by Pure Parsimony, 13th Portuguese Conference on Artificial Intelligence (EPIA 07), Dec. 2007, pp. 621-632 , Springer.
55. Alexandra M. Carvalho and Arlindo L. Oliveira and Marie-France Sagot, Efficient learning of Bayesian network classifiers: An extension to the TAN classifier, Proceedings of the 20th Australian Joint Conference on Artificial Intelligence, Dec. 2007, pp. 16-25 , Springer.
56. Alexandra M. Carvalho and Arlindo L. Oliveira, Learning Bayesian networks consistent with the optimal branching, Proceedings of the 6th International Conference on Machine Learning and Applications (ICMLA), Dec. 2007.
57. Luís M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira, Approximate String Matching with Lempel-Ziv Compressed Indexes, String Processing and Information Retrieval (SPIRE), Oct. 2007, pp. 264-275, Springer.
58. Ana Graça and João Marques Silva and Inês Lynce and Arlindo L. Oliveira, Efficient Haplotype Inference with Pseudo-Boolean Optimization, Algebraic Biology, Jul. 2007, pp. 125-139 , Springer.
59. Ana Cardoso-Cachopo and Arlindo L. Oliveira, Semi-supervised Single-label Text Categorization using Centroid-based Classifiers, ACM SAC 22nd Annual ACM Symposium on Applied Computing, Special Track n Information Access and Retrieval (IAR), Mar. 2007, pp. 844-851 , ACM.
60. Sara C. Madeira and Arlindo L. Oliveira, An Efficient Biclustering Algorithm for finding Genes with Similar Patterns in Time-Series Expression Data, Asia Pacific Bioinformatics Conference (APBC), Jan. 2007, pp. 67-80.
61. Luís M. S. Russo and Arlindo L. Oliveira, A Compressed Self-index Using a Ziv-Lempel Dictionary String Processing and Information Retrieval (SPIRE), Oct. 2006 , pp. 163-180 , Springer.
62. Luis Coelho and Arlindo L. Oliveira, Dotted Suffix Trees: A Structure for Approximate Text Indexing, String Processing and Information Retrieval (SPIRE), Oct. 2006 , pp. 329-336 , Springer.
63. Luís M. S. Russo and Arlindo L. Oliveira, Faster Generation of Super Condensed Neighbourhoods Using Finite Automata, String Processing and Information Retrieval (SPIRE), Nov. 2005 , pp. 246-255 , Springer.
64. Sara C. Madeira and Arlindo L. Oliveira, A Linear Time Biclustering Algorithm for Time Series Gene Expression Data, 5th Workshop on Algorithms in Bioinformatics (WABI), Oct. 2005 , pp. 39-52 , Springer.
65. Luís M. S. Russo and Arlindo L. Oliveira, An Efficient Algorithm for Generating Super Condensed Neighborhoods, Combinatorial Pattern Matching: 16th Annual Symposium (CPM), Jun. 2005 , pp. 104-115 , Springer.
66. Alexandra M. Carvalho and Ana T. Freitas and Arlindo L. Oliveira and Marie-France Sagot, A highly scalable algorithm for the extraction of cis-regulatory regions, Proceedings of the 3rd Asia Pacific Bioinformatics Conference (APBC), Jan. 2005 , pp. 273-282 , Imperial College Press.
67. J. Poveda and Arlindo L. Oliveira and M. Gould, A new quick point location algorithm, First Workshopon Conceptual Modeling for GIS, Nov. 2004 , pp. 184-196 , Springer.
68. Alexandra M. Carvalho and Ana T. Freitas and Arlindo L. Oliveira and Marie-France Sagot, Efficient extraction of structured motifs using box links, Eleventh Symposium on String Processing and Information Retrieval (SPIRE), Nov. 2004 , pp. 267-268 , Springer.
69. Cláudia Martins Antunes and Arlindo L. Oliveira, Constraint Relaxations for Discovering Unknown Sequential Patterns, KDID 2004, Knowledge Discovery in Inductive Databases, Revised Selected and Invited Papers, Sep. 2004 , pp. 11-32 , Springer.
70. Paulo Trezentos and Arlindo L. Oliveira, Metrics for Grid Applicability: A Distributed Elliptic Curve Platform Assessment, 5th Parallel Processing and Applied Mathematics Conference, Apr. 2004 , pp. 864-871 , Springer.
71. Alexandra M. Carvalho and Ana T. Freitas and Arlindo L. Oliveira and Marie-France Sagot, A parallel algorithm for the extraction of structured motifs, 19th ACM Symposium on Applied Computing, Mar. 2004 , pp. 147-153 , ACM.
72. Joel Phillips and João Afonso and Arlindo L. Oliveira and Luis Miguel Silveira, Analog Macromodeling using Kernel Methods, IEEE International Conference on Computer Aided Design (ICCAD), Nov. 2003 , pp. 446-453 , IEEE.
73. Ana Cardoso-Cachopo and Arlindo L. Oliveira, An Empirical Comparison of Text Categorization Methods, SPIRE 2003 - Tenth Symposium on String Processing and Information Retrieval (SPIRE), Oct. 2003 , pp. 183-196 , Springer.
74. Cláudia Martins Antunes and Arlindo L. Oliveira, Generalization of pattern-growth methods for sequential pattern mining with gap constraints, International Conference on Machine Learning and Data Mining, Jul. 2003 , pp. 239--251 , Springer.
75. Ana T. Freitas and Arlindo L. Oliveira, Implicit Resolution of the Chapman-Kolmogorov Equations in Sequential Circuits: An Application in Power Estimation, Design Automation and Test in Europe (DATE), Mar. 2003 , pp. 764-769 , IEEE Press.
76. Cláudia Martins Antunes and Arlindo L. Oliveira, Inference of Sequential Association Rules Guided by Context-Free Grammars, Sixth International Colloquium on Grammatical Inference (ICGI), Sep. 2002 , pp. 1-13 , Springer.
77. Ana T. Freitas and Arlindo L. Oliveira, Circuit partitioning techniques for power estimation using the full set of input correlations, Proceedings of the IEEE International Conference on Circuits and Systems (ISCAS), Sep. 2001 , pp. 903-907 , IEEE Press. (Best Paper Award).
78. Arlindo L. Oliveira and R. Murgai, An exact gate assignment algorithm for tree circuits under rise and fall delays, ACM/IEEE International Conference on Computer Aided Design, Nov. 2000 , pp. 451-457 , IEEE.
79. J. Monteiro and Arlindo L. Oliveira, FSM Decomposition by Direct Circuit Manipulation Applied to Low Power Design, IEEE/ACM Asian and South Pacific Design Automation Conference, Jan. 2000 , pp. 351-358 .
80. A. S. Mota and N. M. Ferreira and Arlindo L. Oliveira and J. Monteiro, Integrating Dynamic Power Management in the Design Flow, X IFIP Conference on VLSI, Dec. 1999 , pp. 233--244 .
81. Ana T. Freitas and Arlindo L. Oliveira and J. Monteiro and Horácio Claúdio Campos Neto, Exact Power Estimation Using Word Level Transition Probabilities, IEEE International Workshop on Power and Timing Modelling, Optimization and Simulation, Oct. 1999 , pp. 355-364 .
82. P. J. Ramos and Arlindo L. Oliveira, Low overhead encodings for reduced activity in data and address buses, Fourth International Symposium on Signals, Circuits and Systems, Jul. 1999 , pp. 21-24 .
83. Arlindo L. Oliveira, Robust techniques for watermarking sequential circuit designs, ACM/IEEE Design Automation Conference, Jun. 1999 , pp. 837--842 , IEEE.
84. J. G. Pena and Arlindo L. Oliveira, A new algorithm for the reduction of incompletely specified finite state machines, ACM/IEEE International Conference on Computer Aided Design, Nov. 1998 , pp. 482--489 , ACM.
85. Arlindo L. Oliveira and João Marques Silva, Efficient search techniques for the inference of minimum size finite automata, Fifth String Processing and Information Retrieval Symposium, Sep. 1998 , pp. 81--89 , IEEE.
86. Vasco Manquinho and Arlindo L. Oliveira and João Marques Silva, Models and algorithms for computing minimum size prime implicants, International Workshop on Boolean Problems, Sep. 1998 , pp. 83--92 .
87. J. Monteiro and Arlindo L. Oliveira, Finite State Machine Decomposition for Low Power, ACM/IEEE Design Automation Conference, Jun. 1998 , pp. 758--763 , ACM.
88. Vasco Manquinho and João Marques Silva and Arlindo L. Oliveira and K. Sakallah, Satisfiability-based algorithms for 0-1 integer programming, International Workshop on Logic Synthesis, Jun. 1998 , pp. 25--34 .
89. R. Murgai and M. Fujita and Arlindo L. Oliveira, Using complementation and resequencing to minimize transitions, ACM/IEEE Design Automation Conference, Jun. 1998 , pp. 694--697 , ACM.
90. A. S. Mota and J. Monteiro and Arlindo L. Oliveira, Power Optimization of Combinational Modules using Self-timed Precomputation, IEEE International Symposium on Circuits and Systems, May. 1998 , pp. II.17-II.20 , IEEE.
91. Vasco Manquinho and Paulo Flores and João Marques Silva and Arlindo L. Oliveira, Prime implicant computation using satisfiability algorithms, 9th IEEE International Conference on Tools with Artificial Intelligence, Nov. 1997 , pp. 232--239 , IEEE.
92. Arlindo L. Oliveira and L. Carloni and T. Villa and A. Sangiovanni-Vincentelli, An implicit formulation for exact BDD minimization of incompletely specified functions, VLSI: Integrated Systems on Silicon, Aug. 1997 , pp. 315--326 , Chapman-Hall.
93. Arlindo L. Oliveira and S. Edwards, Limits of exact algorithms for inference of minimum size finite state machines, Seventh Workshop on Algorithmic Learning Theory, Oct. 1996 , pp. 59--66 , Springer.
94. Arlindo L. Oliveira and A. Sangiovanni-Vincentelli, Inferring reduced ordered decision graphs of minimum description length, Twelfth International Conference in Machine Learning, Jul. 1995 , pp. 421--429 , Morgan Kaufmann.
95. Arlindo L. Oliveira and A. Sangiovanni-Vincentelli, Learning complex Boolean functions : Algorithms and applications, Advances in Neural Information Processing Systems 6, Nov. 1993 , pp. 911--918 , Morgan Kaufmann.
96. Arlindo L. Oliveira and A. Sangiovanni-Vincentelli, Constructive induction using a non-greedy strategy for feature selection, Ninth International Conference in Machine Learning, Jul. 1992 , pp. 355--360 , Morgan Kaufmann.
97. Arlindo L. Oliveira and A. Sangiovanni-Vincentelli, LSAT - an algorithm for the synthesis of two level threshold gate networks, ACM/IEEE International Conference on Computer Aided Design, Nov. 1991 , pp. 130--133 , IEEE.
98. Arlindo L. Oliveira and A. Sangiovanni-Vincentelli, Learning concepts by synthesizing minimal threshold gate networks, Eigth International Workshop in Machine Learning, Jun. 1991 , pp. 193--197 , Morgan Kaufmann.
Pre-prints and reports
1. Gonçalo Mestre, Ruxandra Barbulescu, Arlindo L Oliveira, L Miguel Silveira, Modelling Neuronal Behaviour with Time Series Regression: Recurrent Neural Networks on C. Elegans Data, arXiv preprint arXiv:2107.06762
2. Dinis L Rodrigues, Miguel Nobre Menezes, Fausto J Pinto, Arlindo L Oliveira, Automated Detection of Coronary Artery Stenosis in X-ray Angiography using Deep Neural Networks, arXiv preprint arXiv:2103.02969
Research Grants
2022 -- 2025 Center for Responsible Artificial Intelligence, funded by PRR (78M€), coordinator of the participation of IST and participant though INESC-ID
2021 -- 2024 PRELUNA: Precise and Efficient Learning using Attention Mechanisms, funded by FCT (249K€)
2020 -- 2020 INTAKE: INtegrating mobility daTa into spAtial risK modEls, funded by FCT (38K €)
2015 -- 2019 ELIXIR-EXCELERATE: fast-track ELIXIR implementation and drive early user exploitation, funded by the European Commission (20M €) across the life sciences.
Biodata, Portuguese Biological Data Network, funded by FCT (2M €)
2019 -- 2021 iLU: Integrative Learning from Urban Data, funded by FCT (299K €)
2018 -- 2021 Algorithms for Model Reduction and Efficient Simulation of realistic neuronal networks, funded by FCT (238K €)
2016 -- 2020 PRECISE: Accelerating progress toward the new era of precision medicine, funded by FCT (2500K €)
2013 -- 2015 HIFI-MRI: Whole Brain Functional Connectivity Analysis of Ultra-High Field fMRI, funded by FCT (127K €)
2012 -- 2014 NetDyn: Understanding real large networks, from structure to dynamics, funded by FCT (75K €)
2021 -- 2014 NEUROCLINOMICS - Understanding NEUROdegenerative diseases throught CLINical and OMICS data integration, funded by FCT (130K €)
2011 -- 2013 TAGS, The power of the short - Tools and Algorithms for next Generation Sequencing applications, funded by FCT (100K €)
2011 -- 2013 HELIX, Heterogeneous Multi-Core Architecture for Biological Sequence Analysls, funded by FCT (120K €)
2007 -- 2009 DYABLO, Models for the Dynamic Behavior of Biological Networks, funded by FCT (120K €)
2007 -- 2009 ARN, Algorithms for the identification of genetic Regulatory Networks, funded by FCT (120K €) (principal investigator: Ana Teresa Freitas)
2005 -- 2007 DBYeast: A Framework for the development and application of algorithms to the analysis and identification of gene regulatory networks, funded by FCT (90K €)
2007 -- 2009 SHIPs: SAT-based haplotype inference by pure parsimony, funded by FCT (92K €) (principal investigator: Inês Lynce)
1995 -- 2007 Cadence Labs: Machine Learning and Data Mining Techniques in CAD, 1995-2007, funded by Cadence Design Systems (1.1M USD)
2004 -- 2007 BioGrid - Parallel Algorithms for Gene Annotation, funded by FCT (134K €)
2005 -- 2007 Insights into the complex regulatory networks acting in yeast cells changed with drugs/chemical stresses: genome wide expressions approaches supported by bioinformatics, funded by FCT (40K €) (principal investigator: Isabel Sá-Correia)
1999 -- 2000 PCBIT - Low-Power ISDN Interface for Portable PCs, funded by the EC (90K €)
1999 -- 2002 TGV - Techniques for Global Functional Verification of Complex Digital Systems, funded by FCT (120K €)
1999 -- 2001 COOLCHIPS: An Environment for the Design and Analysis of Power Efficient Systems, funded by FCT (97K €) (principal investigator: José Monteiro)
1999 -- 2001 LowPower - Design techniques for low power circuits, funded by FCT (90K €)
Professional Certification and Awards
Distinguished professor of Instituto Superior Técnico, awarded in 2020.
Municipal Medal of Merit, granted by the Loures Municipality, for scientific and technical contributions, in 2017.
Prize Barca Aldegalega, granted by the Montijo Municipality, for contributions to society, in 2016.
UTL/Santander Prize for Excellence in Research in 2009.
Prize Sartorius for Innovation in Biotechnology, at Micro-Biotec 2007, for the work that lead to the Yeastract information system and the article YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae published in NAR. in 2008 (with a number of co-authors, see publication list).
Best paper award for the 2001 ICECS article Circuit partitioning techniques for power estimation using the full set of input correlations (with Ana Teresa Freitas).
Fulbright fellowship to pursue PhD studies at the University of California, Berkeley in 1989.
Best student in Electrical Engineering and Computer Science, granted by the Portuguese chapter of IEEE, in 1986
Professional Society Membership
Senior Member of the Institute for Electrical and Electronics Engineers (IEEE)
Member of the Association for Computing Machinery (ACM)
Member of the Portuguese Academy of Engineering
Member of Ordem dos Engenheiros
Member of the International Advisory Board (IAB) of the European Parliament Science and Technology Options Assessment (STOA) Panel
Member of the National Council for Science, Technology and Innovation (CNCTI)
Member of the Risks Committee of Caixa Geral de Depositos (CDG)
Chair of the Nomination and Remuneration Committee of Caixa Geral de Depositos (CGD)
Member of the General Council of the Portuguese Association for the Development of Information Systems - (APDSI)
Member of the Strategic Council for Innovation of Vieira de Almeida, Sociedade de Advogados
Member of the Advisory Board of the Portuguese Association for Artificial Intelligence (APPIA)
Member of the Strategic Council for Digital Economy of Confederacao Empresarial de Portugal (CIP)
Member of the Lisbon Regional Innovation Council (CRI) of CCDR-LVT
Member of the Strategic Advisory Board of the Armilar Technology Transfer Fund
Member of the Nomination and Remuneration Committee of Caixa Geral de Depositos (CGD)
Member of the Advisory Board of Indico Capital Partners
Member of the Digital Advisory Board of Caixa Geral de Depositos (CGD)
Member of the Scientific Council of Taguspark S.A.
Member of the Consulting Council of Agencia Nacional de Inovacao (ANI)
Member of the Board of Directors of Taguspark S.A.
Member of the Board of Directors of Associacao para o Desenvolvimento do Centro Academico de Medicina de Lisboa (ADCAML)
Member of the Strategic Council for Digital Economy of Confederacao Empresarial de Portugal (CIP)
President of Associacao do Instituto Superior Tecnico para a Investigacao e Desenvolvimento (IST-ID)
President of Associacao para o Desenvolvimento do Instituto Superior Tecnico (ADIST)
Member of the Advisory Board of Heartgenetics S.A.
