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SARA C. MADEIRA is an Associate Professor with tenure at Department of Informatics at Ciências ULisboa (02/2017-now), coordinating Data Science graduation (05/2018 to 01/2022) and teaching graduation courses on Data Science, Machine Learning and Data Mining; and Senior Researcher at LASIGE, coordinating Data and Systems Intelligence and a member of Health and Biomedical Informatics Research Lines of Excellence. She was awarded the Scientific Prize Universidade de Lisboa/Caixa Geral de Depósitos 2021 in the area of Computer Science and Engineering, the Best Runner-Up Outreach Initiative 2020 by LASIGE and Ciências 2022 Productivity Research Award in Computer Science and Engineering by Ciências ULisboa. She received her PhD degree and MSc degrees in Computer Science and Engineering at Instituto Superior Técnico, Universidade Técnica de Lisboa (Técnico Lisboa) in 2008 and 2022, and graduated in Matemática-Informática at Universidade da Beira Interior in 2000. She was a Lecturer at Informatics Department of UBI (11/2002-12/2008), while being a PhD student at Técnico Lisboa, and hired as Assistant Professor after finishing her PhD in 12/2008. She was Assistant Professor at the Computer Science and Engineering department at Técnico ULisboa (06/2009-02/2017), teaching undergraduate courses on algorithms and data structures and programming, and graduate courses on computational biology and integrative bioinformatics; and a Senior Researcher at INESC-ID, receiving the INESC-ID Young Research Award in 2013. She was on sabbatical leave at Biocomputing group - University of Bologna (03/2015 to 07/2016 and 09/2022-07/2023), and an EURIAS Junior Fellow at Istituti di Studi Avanzate in Bologna (09/ 2015-06/2016). She co-chaired the 14th and 15th International Workshops on Data Mining in Bioinformatics (BIOKDD'15 and '16), held in conjunction with ACM SIGKDD '15 and '16. Her research focuses Machine Learning (ML) and applications in Health/Biomedicine, targeting multimodal ML in patient-centred health. In this context, she published 45+ Q1 papers, has 5000+ citations, supervised 5 Phd (+5 ongoing) and 40+ MSc theses (+4 ongoing), and participates/participated in several national and European research projects. In particular, at national level, she was PI of NEUROCLINOMICS - Understanding NEUROdegenerative diseases through CLINical and OMICS data (PTDC/EIA-EIA/111239/2009) and NEUROCLINOMICS2 - Unravelling Prognostic Markers in NEUROdegenerative diseases through CLINical and OMICS data integration (PTDC/EEI-SII/1937/2014); and is now PI of AIpALS - Advanced learnIng models using Patient profiles and disease progression patterns for prognostic prediction in ALS (PTDC/CCI-CIF/4613/2020). At European level, she is now leading FCiencias-ID/LASIGE team in H2020 Project CIRCLES - Controlling mIcRobiomes CircuLations for bEtter food Systems (Grant agreement ID: 818290) and H2020 Project BRAINTEASER - BRinging Artificial INTelligencE home for a better cAre of amyotrophic lateral sclerosis and multiple SclERosis (Grant agreement ID: 101017598). Her 2004 ACM/IEEE TCBB paper Biclustering Algorithms for Biological Data Analysis: a Survey, ESI Hot Paper in Computer Science in 11/2006, has 2500+ citations and is the key reference in the field. Biclustering, triclustering and other ML approaches for biomedical data analysis are her main research topics. She proposed state of the art biclustering algorithms and the first triclustering taxonomy on 2018 ACM Computing Surveys paper Triclustering Algorithms for Three-Dimensional Data Analysis: A Comprehensive survey. She made relevant contributions to prognostic prediction in neurodegenerative diseases, in particular Amyotrophic Lateral Sclerosis and Alzheimer's Disease, using advanced machine learning models, where biclustering and triclustering are used to analyse high-dimensional, heterogeneous and temporal (omics and clinical) data, to unravel key patient profiles and disease progression patterns.
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Identification

Personal identification

Full name
Sara Alexandra Cordeiro Madeira

Citation names

  • Madeira, Sara
  • Sara C. Madeira

Author identifiers

Ciência ID
AF12-AA0D-0C7B
ORCID iD
0000-0002-1459-8096
Google Scholar ID
https://scholar.google.com/citations?user=rpaGL7AAAAAJ&hl=en&oi=ao
Researcher Id
C-5494-2008
Scopus Author Id
6602138051

Knowledge fields

  • Exact Sciences - Computer and Information Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Italian Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Intermediate (B1) Upper intermediate (B2) Intermediate (B1) Upper intermediate (B2) Intermediate (B1)
Education
Degree Classification
2008/12
Concluded
 Engenharia Informática e de Computadores (Doutoramento)
Major in Sem especialidade
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis" (THESIS/DISSERTATION)
2002/09
Concluded
 Engenharia Informática e de Computadores (Mestrado)
Major in Informação e Conhecimento
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Comparison of Target Selection Methods in Direct Marketing" (THESIS/DISSERTATION)
2000/06
Concluded
 Matemática/Informática (Licenciatura)
Major in Não Aplicável
Universidade da Beira Interior, Portugal
Affiliation

Science

Category
Host institution 		Employer
2022/09 - 2023/07 Visiting Researcher (Research) Università degli Studi di Bologna, Italy
2015/03 - 2016/07 Visiting Researcher (Research) Università degli Studi di Bologna, Italy
2014/02 - 2014/02 Visiting Researcher (Research) Centrum Wiskunde en Informatica, Netherlands
2012/09 - 2012/09 Visiting Researcher (Research) Universidade de Vigo, Spain
2012/05 - 2012/05 Visiting Researcher (Research) Universidade de Vigo, Spain
2011/03 - 2011/03 Visiting Researcher (Research) Fundación de la Comunidad Valenciana Centro de Investigación Príncipe Felipe, Spain
2010/09 - 2010/09 Visiting Researcher (Research) Fundación de la Comunidad Valenciana Centro de Investigación Príncipe Felipe, Spain
2010/02 - 2010/02 Visiting Researcher (Research) Katholieke Universiteit Leuven Departement Elektrotechniek, Belgium
2007/02 - 2007/02 Visiting Researcher (Research) Katholieke Universiteit Leuven Departement Elektrotechniek, Belgium
2005/07 - 2005/07 Visiting Researcher (Research) University of California Berkeley Department of Electrical Engineering and Computer Sciences, United States

Teaching in Higher Education

Category
Host institution 		Employer
2017/02 - Current Associate Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2009/06 - 2017/02 Assistant Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
2008/12 - 2009/06 Assistant Professor (University Teacher) Universidade da Beira Interior, Portugal
2002/11 - 2008/12 Assistant (University Teacher) Universidade da Beira Interior, Portugal
2001/09 - 2002/02 Assistant (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal

Others

Category
Host institution 		Employer
2017/03 - Current Investigadora/Researcher Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
2018/06 - 2022/01 Coordenação do Mestrado em Ciência de Dados/MSC in Data Science Coordination Universidade de Lisboa Faculdade de Ciências, Portugal
2018/06 - 2021/11 Representante de Ciências ULisboa no Comitê de Coordenação do Laboratório de Dados Urbanos de Lisboa (LxDataLab) Universidade de Lisboa Faculdade de Ciências, Portugal
2009/06 - 2017/12 Investigadora/Researcher Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2002/09 - 2008/12 Investigadora Junior/Junior Researcher Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Projects

Contract

Designation Funders
2021/03/01 - Current AIpALS - Advanced learnIng models using Patient profiles and disease progression patterns for prognostic prediction
PTDC/CCI-CIF/4613/2020
Principal investigator
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
 FCT - Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - Current BRAINTEASER - BRinging Artificial INTelligencE home for a better cAre of amyotrophic lateral sclerosis and multiple SclERosis
Grant agreement ID: 101017598
Researcher
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
 Horizon 2020
Ongoing
2018/11 - Current CIRCLES - Controlling mIcRobiomes CircuLations for bEtterfood Systems
Grant agreement ID: 818290
Researcher
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
Horizon 2020
Ongoing
2020/01/01 - 2023/06/30 LAIfeBlood - Artificial Intelligence for Blood Management
DSAIPA/AI/0033/2019
Researcher
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
FCT - Fundação para a Ciência e a Tecnologia
Concluded
2019/01/01 - 2021/12/31 PREDICT - Personalized therapy for RhEumatic DIseases via machine learning
PTDC/CCI-CIF/29877/2017
Researcher
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
FCT - Fundação para a Ciência e a Tecnologia
Concluded
2018/06/01 - 2021/05/31 iCare4U - Decision support system for personalized medicine in ICUs
PTDC/EME-SIS/31474/2017
Researcher
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
FCT - Fundação para a Ciência e a Tecnologia
Concluded
2016/07/01 - 2020/03/31 NEUROCLINOMICS2 - Unravelling Prognostic Markers in NEUROdegenerative diseases through CLINical and OMICS data integration
PTDC/EEI-SII/1937/2014
Principal investigator
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
FCT - Fundação para a Ciência e a Tecnologia
Concluded
2013/07/01 - 2016/06/30 DataStorm - Large-Scale Data Management in Cloud Environments
EXCL/EEI-ESS/0257/2012
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 FCT - Fundação para a Ciência e a Tecnologia
Concluded
2012/01/01 - 2014/08/31 NetDyn - Understanding real large networks, from structure to dynamics
PTDC/EIA-EIA/118533/2010
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 FCT - Fundação para a Ciência e a Tecnologia
Concluded
2012/01 - 2014/05 NEUROCLINOMICS - Understanding NEUROdegenerative diseases through CLINical and OMICS data integration
PTDC/EIA-EIA/111239/2009
Principal investigator
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 FCT - Fundação para a Ciência e a Tecnologia
Concluded
2010/04 - 2013/03 PneumoSyS - A systems biology approach to the role of pneumococcal carbon metabolism in colonization and invasive disease
PTDC/SAU-MII/100964/2008
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 FCT - Fundação para a Ciência e a Tecnologia
Concluded
2008/01/01 - 2010/12/31 ARN - Algorithms for the identification of genetic Regulatory Networks
PTDC/EIA/67722/2006
Researcher
FCT - Fundação para a Ciência e a Tecnologia
Concluded
2005/01/01 - 2008/12/31 DBYeast - Infrastructure and algorithms for analysis and identification of gene regulatory networks
POSI/EIA/57398/2004
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 FCT - Fundação para a Ciência e a Tecnologia
Concluded
2004/01/15 - 2007/06/30 BioGrid - Parallel Algorithms for Gene Annotation
POSI/SRI/47778/2002
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 FCT - Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Aidos, Helena; Bergamaschi, Roberto; Cavalla, Paola; Chiò, Adriano; Dagliati, Arianna; Di Camillo, Barbara; de Carvalho, Mamede Alves; et al. "iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge". In Lecture Notes in Computer Science, 491-498. Springer Nature Switzerland, 2023.
    Published • 10.1007/978-3-031-28241-6_57
  2. Guazzo, Alessandro; Trescato, Isotta; Longato, Enrico; Hazizaj, Enidia; Dosso, Dennis; Faggioli, Guglielmo; Di Nunzio, Giorgio Maria; et al. "Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2022". In Experimental IR Meets Multilinguality, Multimodality, and Interaction, 395-422. Springer International Publishing, 2022.
    Published • 10.1007/978-3-031-13643-6_25
  3. André Ferreira; Sara C. Madeira; Marta Gromicho; Mamede de Carvalho; Susana Vinga; Alexandra M. Carvalho. "Predictive Medicine Using Interpretable Recurrent Neural Networks". 2021.
    10.1007/978-3-030-68763-2_14
  4. Pires, Sofia; Gromicho, Marta; Pinto, Susana; de Carvalho, Mamede; Madeira, Sara C.. "Patient Stratification Using Clinical and Patient Profiles: Targeting Personalized Prognostic Prediction in ALS". In Bioinformatics and Biomedical Engineering, 529-541. Springer International Publishing, 2020.
    10.1007/978-3-030-45385-5_47
  5. Joana Matos; Sofia Pires; Helena Aidos; Marta Gromicho; Susana Pinto; Mamede de Carvalho; Sara C. Madeira. "Unravelling Disease Presentation Patterns in ALS Using Biclustering for Discriminative Meta-Features Discovery". 517-528. Springer International Publishing, 2020.
    10.1007/978-3-030-45385-5_46
  6. Soares, Diogo; Henriques, Rui; Gromicho, Marta; Pinto, Susana; de Carvalho, Mamede; Madeira, Sara C.. "Towards Triclustering-Based Classification of Three-Way Clinical Data: A Case Study on Predicting Non-invasive Ventilation in ALS". In Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020), 112-122. Springer International Publishing, 2020.
    10.1007/978-3-030-54568-0_12
  7. Henriques, R.; Antunes, C.; Madeira, S.C.. "Methods for the efficient discovery of large item-indexable sequential patterns". 2014.
    10.1007/978-3-319-08407-7_7
  8. Nunes, C.; Silva, D.; Guerreiro, M.; De Mendonça, A.; Carvalho, A.M.; Madeira, S.C.. "Class imbalance in the prediction of dementia from neuropsychological data". 2013.
    10.1007/978-3-642-40669-0_13
  9. López-Fernández, H.; Reboiro-Jato, M.; Madeira, S.C.; López-Cortés, R.; Nunes-Miranda, J.D.; Santos, H.M.; Fdez-Riverola, F.; Glez-Peña, D.. "A Workflow for the Application of Biclustering to Mass Spectrometry Data". 2013.
    10.1007/978-3-319-00578-2_19
  10. Carreiro, A.V.; Ferreira, A.J.; Figueiredo, M.A.T.; Madeira, S.C.. "Prognostic prediction using clinical expression time series: Towards a supervised learning approach based on meta-biclusters". 2012.
    10.1007/978-3-642-28839-5_2
  11. Cristóvão, F.; Madeira, S.C.. "Parallel e-CCC-biclustering: Mining approximate temporal patterns in gene expression time series using parallel biclustering". 2012.
    10.1007/978-3-642-28839-5_3
  12. Aires, R.S.; Carriço, J.A.; Francisco, A.P.; Madeira, S.C.. "Baiacu: A tool for the visual analysis of the Saccharomyces Cerevisiae regulatory network". 2011.
    10.1007/978-3-642-19914-1_7
  13. Moura, P.; Rocha, R.; Madeira, S.C.. "High level thread-based competitive or-parallelism in logtalk". 2009.
    10.1007/978-3-540-92995-6_8
  14. Madeira, S.C.; Oliveira, A.L.. "Efficient biclustering algorithms for time series gene expression data analysis". 2009.
    10.1007/978-3-642-02481-8_154
  15. Moura, P.; Rocha, R.; Madeira, S.C.. "Thread-based competitive or-parallelism". 2008.
    10.1007/978-3-540-89982-2_63
  16. Madeira, S.C.; Oliveira, A.L.. "A linear time biclustering algorithm for time series gene expression data". 2005.
    10.1007/11557067_4
  17. Gael Dias; Sara C. Madeira; Gabriel Pereira Lopes. "Extracting Concepts from dynamic legislative text collections". In Meaningful Texts: The Extraction of Semantic Information from Monolingual and Multilingual Corpora, 5-16. Continuum International Publishing Group, 2005.
    Published
  18. Madeira, Sara C.; Oliveira, Arlindo L.; Conceição, Catarina S.. "A Data Mining Approach to Credit Risk Evaluation and Behaviour Scoring". In Progress in Artificial Intelligence, 184-188. Springer Berlin Heidelberg, 2003.
    10.1007/978-3-540-24580-3_25
Conference paper
  1. Branco, Ruben; Diogo F. Soares; Andreia S. Martins; Barros Valente, Joana; Eduardo N. Castanho; Sara C. Madeira; Aidos, Helena. Corresponding author: Branco, Ruben. "Investigating the impact of environmental data on als prognosis with survival analysis". Paper presented in CLEF, Thessaloniki, 2023.
    In press
  2. Branco, Ruben; Barros Valente, Joana; Andreia S. Martins; Diogo F. Soares; Eduardo N. Castanho; Sara C. Madeira; Aidos, Helena. Corresponding author: Branco, Ruben. "Survival analysis for multiple sclerosis: Predicting risk of disease worsening". Paper presented in CLEF, Thessaloniki, 2023.
    In press
  3. Branco, Ruben; Diogo F. Soares; Andreia S. Martins; Auletta, Eleonora; Eduardo N. Castanho; Susana Nunes; Filipa Serrano; et al. Corresponding author: Branco, Ruben. "Hierarchical Modelling for ALS Prognosis: Predicting the Progression Towards Critical Events". Paper presented in iDPP@CLEF 2022, Bologna, 2022.
    Accepted
  4. Susana Nunes; Rita Sousa; Filipa Serrano; Branco, Ruben; Diogo F. Soares; Andreia S. Martins; Auletta, Eleonora; et al. Corresponding author: Susana Nunes. "Explaining Artificial Intelligence Predictions of Disease Progression with Semantic Similarity". Paper presented in iDPP@CLEF 2022, Bologna, 2022.
    Accepted
  5. Andreia S. Martins; Aidos, Helena; Marta Gromicho; de Carvalho, Mamede; Sara C. Madeira. "Specialized prognostic models based on disease progression patterns: predicting non-invasive ventilation in ALS patients stratified by progression rate". Paper presented in 17th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2021), 2021.
  6. Pereira, Telma; Pires, Sofia; de carvalho, Mamede; Sara C. Madeira. "Predicting assisted ventilation in Amyotrophic Lateral Sclerosis using a mixture of experts and conformal predictors". Paper presented in KDD 2019 Workshop on Applied Data Science for Healthcare, 2019.
    Published • https://arxiv.org/abs/1907.13070
  7. Pires, S.; Gromicho, M.; Pinto, S.; Carvalho, M.; Madeira, S.C.. "Predicting non-invasive ventilation in ALS patients using stratified disease progression groups". 2019.
    10.1109/ICDMW.2018.00113
  8. Sousa, Joao M.C.; Vieira, Susana M.; Carvalho, Joao P.; Madeira, Sara C.; Celi, Leo; Finkelstein, Stan N.. "An Architecture Based on Fuzzy Systems for Personalized Medicine in ICUs". 2019.
    10.1109/fuzz-ieee.2019.8858903
  9. Ferreira, F.L.; Cardoso, S.; Silva, D.; de Mendonça, A.; Madeira, S.C.. "Improving prognostic prediction from mild cognitive impairment to Alzheimer's Disease using genetic algorithms". 2017.
    10.1007/978-3-319-60816-7_22
  10. Pereira, T.; Cardoso, S.; Silva, D.; de Mendonça, A.; Guerreiro, M.; Madeira, S.C.. "Towards trustworthy predictions of conversion from mild cognitive impairment to dementia: A conformal prediction approach". 2017.
    10.1007/978-3-319-60816-7_19
  11. Henriques, R.; Madeira, S.C.. "Bicnet: Efficient biclustering of biological networks to unravel non-trivial modules". 2015.
    10.1007/978-3-662-48221-6_1
  12. Henriques, R.; Madeira, S.C.. "Pattern-based biclustering with constraints for gene expression data analysis". 2015.
    10.1007/978-3-319-23485-4_34
  13. Gonçalves, J.P.; Madeira, S.C.. "Heuristic approaches for time-lagged biclustering". 2013.
    10.1145/2500863.2500865
  14. Carreiro, A.V.; Anunciação, O.; Carriço, J.A.; Madeira, S.C.. "Biclustering-based classification of clinical expression time series: A case study in patients with multiple sclerosis". 2011.
    10.1007/978-3-642-19914-1_31
  15. Gonçalves, J.P.; Madeira, S.C.; Moreau, Y.. "Network-based disease candidate gene prioritization: Towards global diffusion in heterogeneous association networks". 2010.
  16. MADEIRA, SARA C.; OLIVEIRA, ARLINDO L.. "AN EFFICIENT BICLUSTERING ALGORITHM FOR FINDING GENES WITH SIMILAR PATTERNS IN TIME-SERIES EXPRESSION DATA". 2007.
    10.1142/9781860947995_0010
  17. Madeira, S.C.; Oliveira, A.L.. "An efficient biclustering algorithm for finding genes with similar patterns in time-series expression data". 2007.
  18. Sousa, J.M.; Madeira, S.; Kaymak, U.. "Modeling charity donations using target selection for revenue maximization". 2003.
    10.1109/fuzz.2003.1209441
  19. Sousa, J.M.; Kaymak, U.; Madeira, S.. "A comparative study of fuzzy target selection methods in direct marketing". 2002.
    10.1109/fuzz.2002.1006683
Conference poster
  1. Diogo F. Soares; Sara C. Madeira. "Learning Prognostic Models Using a Mixture of Biclustering and Triclustering". Paper presented in Symposium on Intelligent Data Analysis, 2021.
Journal article
  1. Soares, Diogo F.; Henriques, Rui; C. Madeira, Sara. "Comprehensive assessment of triclustering algorithms for three-way temporal data analysis". Pattern Recognition 150 (2024): 110303. http://dx.doi.org/10.1016/j.patcog.2024.110303.
    Published • 10.1016/j.patcog.2024.110303
  2. Castanho, Eduardo N.; Lobo, João P.; Henriques, Rui; Madeira, Sara C.. "G-bic: generating synthetic benchmarks for biclustering". BMC Bioinformatics 24 1 (2023): http://dx.doi.org/10.1186/s12859-023-05587-4.
    Open access • Published • 10.1186/s12859-023-05587-4
  3. Miguel G Silva; Sara C Madeira; Rui Henriques. "Actionable descriptors of spatiotemporal urban dynamics from large-scale mobile data: A case study in Lisbon city". Environment and Planning B: Urban Analytics and City Science (2023): https://doi.org/10.1177/23998083231219048.
    10.1177/23998083231219048
  4. Tavazzi, Erica; Longato, Enrico; Vettoretti, Martina; Aidos, Helena; Trescato, Isotta; Roversi, Chiara; Martins, Andreia S.; et al. "Artificial intelligence and statistical methods for stratification and prediction of progression in amyotrophic lateral sclerosis: A systematic review". Artificial Intelligence in Medicine 142 (2023): 102588. http://dx.doi.org/10.1016/j.artmed.2023.102588.
    Open access • Published • 10.1016/j.artmed.2023.102588
  5. Soares, Diogo F.; Henriques, Rui; Gromicho, Marta; de Carvalho, Mamede; Sara C. Madeira. "Triclustering-based classification of longitudinal data for prognostic prediction: targeting relevant clinical endpoints in amyotrophic lateral sclerosis". Scientific Reports 13 1 (2023): http://dx.doi.org/10.1038/s41598-023-33223-x.
    Open access • Published • 10.1038/s41598-023-33223-x
  6. Pinheiro, Marco G.; Madeira, Sara C.; Francisco, Alexandre P.. "Short-term electricity load forecasting—A systematic approach from system level to secondary substations". Applied Energy 332 (2023): 120493. http://dx.doi.org/10.1016/j.apenergy.2022.120493.
    10.1016/j.apenergy.2022.120493
  7. Diogo F. Soares; Rui Henriques; Marta Gromicho; Mamede de Carvalho; Sara C. Madeira. "Learning prognostic models using a mixture of biclustering and triclustering: Predicting the need for non-invasive ventilation in Amyotrophic Lateral Sclerosis". Journal of Biomedical Informatics (2022): https://doi.org/10.1016/j.jbi.2022.104172.
    10.1016/j.jbi.2022.104172
  8. Miguel G. Silva; Sara C. Madeira; Rui Henriques. "Water Consumption Pattern Analysis Using Biclustering: When, Why and How". Water (2022): https://doi.org/10.3390/w14121954.
    10.3390/w14121954
  9. Castanho, Eduardo N.; Aidos, Helena; Madeira, Sara C.. "Biclustering fMRI time series: a comparative study". BMC Bioinformatics 23 1 (2022): http://dx.doi.org/10.1186/s12859-022-04733-8.
    10.1186/s12859-022-04733-8
  10. Gromicho, Marta; Leão, Tiago; Oliveira Santos, Miguel; Pinto, Susana; Carvalho, Alexandra M.; Madeira, Sara C.; De Carvalho, Mamede. "Dynamic Bayesian networks for stratification of disease progression in amyotrophic lateral sclerosis". European Journal of Neurology 29 8 (2022): 2201-2210. http://dx.doi.org/10.1111/ene.15357.
    10.1111/ene.15357
  11. Marco G. Pinheiro; Sara C. Madeira; Alexandre P. Francisco. "Shapelets to Classify Energy Demand Time Series". Energies 15 8 (2022): 2960-2960. https://doi.org/10.3390/en15082960.
    10.3390/en15082960
  12. Marta D.M. Noronha; Rui Henriques; Sara C. Madeira; Luis E. Zárate. "Impact of Metrics on Biclustering Solution and Quality: A Review". Pattern Recognition (2022): 108612-108612. https://doi.org/10.1016/j.patcog.2022.108612.
    10.1016/j.patcog.2022.108612
  13. Maria Lua Nunes; Duarte Folgado; Carlos Fujao; Luis Silva; Joao Rodrigues; Pedro Matias; Marilia Barandas; et al. "Posture Risk Assessment in an Automotive Assembly Line Using Inertial Sensors". IEEE Access 10 (2022): 83221-83235. https://doi.org/10.1109/ACCESS.2022.3196473.
    10.1109/ACCESS.2022.3196473
  14. Henriques, Rui; Madeira, Sara C.. "FleBiC: Learning classifiers from high-dimensional biomedical data using discriminative biclusters with non-constant patterns". Pattern Recognition 115 (2021): 107900. http://dx.doi.org/10.1016/j.patcog.2021.107900.
    10.1016/j.patcog.2021.107900
  15. Leão, Tiago; Madeira, Sara C.; Gromicho, Marta; de Carvalho, Mamede; Carvalho, Alexandra M.. "Learning dynamic Bayesian networks from time-dependent and time-independent data: Unraveling disease progression in Amyotrophic Lateral Sclerosis". Journal of Biomedical Informatics 117 (2021): 103730. http://dx.doi.org/10.1016/j.jbi.2021.103730.
    10.1016/j.jbi.2021.103730
  16. Lobo, João; Henriques, Rui; Madeira, Sara C.. "G-Tric: generating three-way synthetic datasets with triclustering solutions". BMC Bioinformatics 22 1 (2021): http://dx.doi.org/10.1186/s12859-020-03925-4.
    10.1186/s12859-020-03925-4
  17. Neves, Francisco; Finamore, Anna C.; Madeira, Sara C.; Henriques, Rui. "Mining Actionable Patterns of Road Mobility From Heterogeneous Traffic Data Using Biclustering". IEEE Transactions on Intelligent Transportation Systems (2021): 1-16. http://dx.doi.org/10.1109/tits.2021.3057240.
    10.1109/tits.2021.3057240
  18. Martins, Andreia S.; Gromicho, Marta; Pinto, Susana; Carvalho, Mamede de; Madeira, Sara C.. "Learning Prognostic Models using Disease Progression Patterns: Predicting the Need for Non-Invasive Ventilation in Amyotrophic Lateral Sclerosis". IEEE/ACM Transactions on Computational Biology and Bioinformatics (2021): 1-1. http://dx.doi.org/10.1109/tcbb.2021.3078362.
    10.1109/tcbb.2021.3078362
  19. Gromicho, Marta; Figueiral, Manuel; Uysal, Hilmi; Grosskreutz, Julian; Kuzma-Kozakiewicz, Magdalena; Pinto, Susana; Petri, Susanne; et al. "Spreading in ALS: The relative impact of upper and lower motor neuron involvement". Annals of Clinical and Translational Neurology 7 7 (2020): 1181-1192. http://dx.doi.org/10.1002/acn3.51098.
    10.1002/acn3.51098
  20. Pereira, Telma; Cardoso, Sandra; Guerreiro, Manuela; Mendonça, Alexandre; Madeira, Sara C.. "Targeting the uncertainty of predictions at patient-level using an ensemble of classifiers coupled with calibration methods, Venn-ABERS, and Conformal Predictors: A case study in AD". Journal of Biomedical Informatics 101 (2020): 103350. http://dx.doi.org/10.1016/j.jbi.2019.103350.
    10.1016/j.jbi.2019.103350
  21. Henriques, R.; Madeira, S.C.. "BSig: evaluating the statistical significance of biclustering solutions". Data Mining and Knowledge Discovery 32 1 (2018): 124-161. http://www.scopus.com/inward/record.url?eid=2-s2.0-85025088727&partnerID=MN8TOARS.
    10.1007/s10618-017-0521-2
  22. Henriques, R.; Madeira, S.C.. "Triclustering algorithms for three-dimensional data analysis: A comprehensive survey". ACM Computing Surveys 51 5 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85053911694&partnerID=MN8TOARS.
    10.1145/3195833
  23. Pereira, T.; Ferreira, F.L.; Cardoso, S.; Silva, D.; De Mendonça, A.; Guerreiro, M.; Madeira, S.C.. "Neuropsychological predictors of conversion from mild cognitive impairment to Alzheimer's disease: A feature selection ensemble combining stability and predictability". BMC Medical Informatics and Decision Making 18 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85058892569&partnerID=MN8TOARS.
    10.1186/s12911-018-0710-y
  24. Henriques, R.; Ferreira, F.L.; Madeira, S.C.. "BicPAMS: Software for biological data analysis with pattern-based biclustering". BMC Bioinformatics 18 1 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85011343879&partnerID=MN8TOARS.
    10.1186/s12859-017-1493-3
  25. Pereira, T.; Lemos, L.; Cardoso, S.; Silva, D.; Rodrigues, A.; Santana, I.; De Mendonça, A.; et al. "Predicting progression of mild cognitive impairment to dementia using neuropsychological data: A supervised learning approach using time windows". BMC Medical Informatics and Decision Making 17 1 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85024856259&partnerID=MN8TOARS.
    10.1186/s12911-017-0497-2
  26. Henriques, R.; Madeira, S.C.. "BicNET: Flexible module discovery in large-scale biological networks using biclustering". Algorithms for Molecular Biology 11 1 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84974628457&partnerID=MN8TOARS.
    10.1186/s13015-016-0074-8
  27. Henriques, R.; Madeira, S.C.. "BiC2PAM: Constraint-guided biclustering for biological data analysis with domain knowledge". Algorithms for Molecular Biology 11 1 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84987738939&partnerID=MN8TOARS.
    10.1186/s13015-016-0085-5
  28. Maruta, C.; Pereira, T.; Madeira, S.C.; De Mendonça, A.; Guerreiro, M.. "Classification of primary progressive aphasia: Do unsupervised data mining methods support a logopenic variant?". Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration 16 3-4 (2015): 147-159. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929744594&partnerID=MN8TOARS.
    10.3109/21678421.2015.1026266
  29. Carreiro, A.V.; Amaral, P.M.T.; Pinto, S.; Tomás, P.; de Carvalho, M.; Madeira, S.C.. "Prognostic models based on patient snapshots and time windows: Predicting disease progression to assisted ventilation in Amyotrophic Lateral Sclerosis". Journal of Biomedical Informatics 58 (2015): 133-144. http://www.scopus.com/inward/record.url?eid=2-s2.0-84947905778&partnerID=MN8TOARS.
    10.1016/j.jbi.2015.09.021
  30. Henriques, R.; Madeira, S.C.; Antunes, C.. "Multi-period classification: Learning sequent classes from temporal domains". Data Mining and Knowledge Discovery 29 3 (2015): 792-819. http://www.scopus.com/inward/record.url?eid=2-s2.0-84938322142&partnerID=MN8TOARS.
    10.1007/s10618-014-0376-8
  31. Henriques, R.; Madeira, S.C.. "Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes". IEEE/ACM Transactions on Computational Biology and Bioinformatics 12 4 (2015): 738-752. http://www.scopus.com/inward/record.url?eid=2-s2.0-84939200062&partnerID=MN8TOARS.
    10.1109/TCBB.2014.2388206
  32. Henriques, R.; Antunes, C.; Madeira, S.C.. "A structured view on pattern mining-based biclustering". Pattern Recognition 48 12 (2015): 3941-3958. http://www.scopus.com/inward/record.url?eid=2-s2.0-84941418114&partnerID=MN8TOARS.
    10.1016/j.patcog.2015.06.018
  33. Henriques, R.; Antunes, C.; Madeira, S.C.. "Generative modeling of repositories of health records for predictive tasks". Data Mining and Knowledge Discovery 29 4 (2015): 999-1032. http://www.scopus.com/inward/record.url?eid=2-s2.0-84930485460&partnerID=MN8TOARS.
    10.1007/s10618-014-0385-7
  34. Carreiro, A.V.; Mendonça, A.; de Carvalho, M.; Madeira, S.C.. "Integrative biomarker discovery in neurodegenerative diseases". Wiley Interdisciplinary Reviews: Systems Biology and Medicine (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84935104844&partnerID=MN8TOARS.
    10.1002/wsbm.1310
  35. Henriques, Rui; Sara C. Madeira. "BicPAM: Pattern-based biclustering for biomedical data analysis". Algorithms for Molecular Biology (2014): http://www.almob.org/content/9/1/27.
    10.1186/s13015-014-0027-z
  36. Gonc¸alves, J.P.; Madeira, S.C.. "LateBiclustering: Efficient heuristic algorithm for time-lagged bicluster identification". IEEE/ACM Transactions on Computational Biology and Bioinformatics 11 5 (2014): 801-813. http://www.scopus.com/inward/record.url?eid=2-s2.0-84907971489&partnerID=MN8TOARS.
    10.1109/TCBB.2014.2312007
  37. Henriques, R.; Madeira, S.C.. "BicSPAM: Flexible biclustering using sequential patterns". BMC Bioinformatics 15 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84903272533&partnerID=MN8TOARS.
    10.1186/1471-2105-15-130
  38. Teixeira, M.C.; Monteiro, P.T.; Guerreiro, J.F.; Gonçalves, J.P.; Mira, N.P.; Dos Santos, S.C.; Cabrito, T.R.; et al. "The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae". Nucleic Acids Research 42 D1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84891806965&partnerID=MN8TOARS.
    10.1093/nar/gkt1015
  39. Carreiro, A.V.; Ferreira, A.J.; Figueiredo, M.A.; Madeira, S.C.. "Towards a classification approach using meta-biclustering: impact of discretization in the analysis of expression time series.". Journal of integrative bioinformatics 9 3 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84875027675&partnerID=MN8TOARS.
  40. Gonçalves, J.P.; Francisco, A.P.; Moreau, Y.; Madeira, S.C.. "Interactogeneous: Disease Gene Prioritization Using Heterogeneous Networks and Full Topology Scores". PLoS ONE 7 11 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84869744645&partnerID=MN8TOARS.
    10.1371/journal.pone.0049634
  41. Palma, M.; Madeira, S.C.; Mendes-Ferreira, A.; Sá-Correia, I.. "Impact of assimilable nitrogen availability in glucose uptake kinetics in Saccharomyces cerevisiae during alcoholic fermentation". Microbial Cell Factories 11 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84864371726&partnerID=MN8TOARS.
    10.1186/1475-2859-11-99
  42. Gonçalves, J.P.; Moreau, Y.; Madeira, S.C.. "Alibimotif: Integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences". International Journal of Data Mining and Bioinformatics 6 2 (2012): 196-215. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864564175&partnerID=MN8TOARS.
    10.1504/IJDMB.2012.048198
  43. Gonçalves, J.P.; Aires, R.S.; Francisco, A.P.; Madeira, S.C.. "Regulatory snapshots: Integrative mining of regulatory modules from expression time series and regulatory networks". PLoS ONE 7 5 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84871185628&partnerID=MN8TOARS.
    10.1371/journal.pone.0035977
  44. 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
  45. 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
  46. Carreiro, A.V.; Anunciação, O.; Carriço, J.A.; Madeira, S.C.. "Prognostic prediction through biclustering-based classification of clinical gene expression time series.". Journal of integrative bioinformatics 8 3 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-84855529005&partnerID=MN8TOARS.
  47. Nitsch, D.; Tranchevent, L.-C.; Gonalves, J.P.; Vogt, J.K.; Madeira, S.C.; Moreau, Y.. "PINTA: A web server for network-based gene prioritization from expression data". Nucleic Acids Research 39 SUPPL. 2 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79959922954&partnerID=MN8TOARS.
    10.1093/nar/gkr289
  48. Madeira, S.C.; Teixeira, M.C.; Sá-Correia, I.; Oliveira, A.L.. "Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm". IEEE/ACM Transactions on Computational Biology and Bioinformatics 7 1 (2010): 153-165. http://www.scopus.com/inward/record.url?eid=2-s2.0-76849109141&partnerID=MN8TOARS.
    10.1109/TCBB.2008.34
  49. Medina, I.; Carbonell, J.; Pulido, L.; Madeira, S.C.; Goetz, S.; Conesa, A.; Tárraga, J.; et al. "Babelomics: An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling". Nucleic Acids Research 38 SUPPL. 2 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77954339096&partnerID=MN8TOARS.
    10.1093/nar/gkq388
  50. Gonçalves, J.P.; Madeira, S.C.; Oliveira, A.L.. "BiGGEsTS: Integrated environment for biclustering analysis of time series gene expression data". BMC Research Notes 2 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-75649124958&partnerID=MN8TOARS.
    10.1186/1756-0500-2-124
  51. Madeira, S.C.; Oliveira, A.L.. "A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series". Algorithms for Molecular Biology 4 1 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-67651018681&partnerID=MN8TOARS.
    10.1186/1748-7188-4-8
  52. Madeira, S.C.; Oliveira, A.L.. "Biclustering algorithms for biological data analysis: A survey". IEEE/ACM Transactions on Computational Biology and Bioinformatics 1 1 (2004): 24-45. http://www.scopus.com/inward/record.url?eid=2-s2.0-3142768191&partnerID=MN8TOARS.
    10.1109/TCBB.2004.2
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2019 Predicting disease progression in Amyotrophic Lateral Sclerosis using Machine Learning: Lear- ning from longitudinal data using time windows and progression patterns 53rd Annual Scientific Meeting of the ESCI (European Society for Clinical Investigation) - ESCI-2019
2018 High Dimensional Data Analysis in a Nutshell 19th Bologna Winter School: Big Data and Bioinformatics
(Italy)
2018 Biclustering in Biomedical Data Analysis: Algorithms and Applications 19th Bologna Winter School: Big Data and Bioinformatics
(Italy)
2017 Novel time window based data mining approaches Encontro do European Alzheimer’s Disease Consortium (EADC)
2017 Identification of Regulatory Modules in Time Series Gene Expression Data using Biclustering Algorithms KULeuven Seminars on Bioinformatics
KULeuven (Belgium)
2016 Biclustering Algorithms for Biomedical Data Analysis 16th Bologna Winter School: In Silico Markers for Precision Medicine
(Italy)
2015 Biclustering Algorithms for Biomedical Data Analysis Università degli studi di Verona
(Italy)
2011 (Clustering and) Biclustering Gene Expression Data VII International Course of MASSIVE Data Analysis (MDA 2011)
Centro di Investigation Principe Felipe (Spain)
2010 Biclustering Gene Expression Time Series: Algorithms and Applications Workshop on biclustering methods for microarray data
Hasselt University (Belgium)
2010 Clustering Gene Expression Data VI International Course of MASSIVE Data Analysis (MDA 2010)
Centro de Investigacion Principe Felipe (CIPF) (Spain)
2010 Efficient Biclustering Algorithms for Biological Data Analysis KULeuven Seminars on Bioinformatics
KULeuven (Belgium)
2006 Discovering Modules in Time Series Gene Expression Data using Biclustering International Fede- ration of Classification Societies 2006 Conference: Data Science and Classification (IFCS 2006)
(Slovenia)
2006 CCC-Biclustering and CCC-Biclustering with Errors BAOBAB Research Group, INRIA Rhone- Alpes, Universita Claude Bernard, Lyon
(France)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023/09 - Current Learning Temporal Associative Classifiers using discriminative triclusters for Biomedical data analysis
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/09 - Current Predicting clinically relevant endpoints in ALS using machine learning
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/09 - Current Multiple Sclerosis Patient Stratification through Triclustering
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/09 - Current Stratified survival analysis based on phrenic nerve in ALS patients
Supervisor
 Engenharia Biomédica e Biofísica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - Current Biclustering Heterogeneous Data
Supervisor of Eduardo Castanho
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - Current Pattern-centric Descriptive and Predictive Models of Urban Dynamics using Spatiotemporal Data from Sensor Networks
Supervisor of Miguel Garção Silva
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - Current Data-driven patient stratification for prognostic prediction in ALS
Supervisor of Eleonora Auletta
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - Current Large-scale Clinical Data Generation with Generative Models
Supervisor of Ruben Branco
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - Current Efficient Algorithms for Temporal Triclustering: Targeting the Challenges of Temporality for Effective Solutions in Biomedical Applications
Supervisor of Diogo Soares
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Short-Term Electric Load Forecasting
Supervisor of Marco Pinheiro
 Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - 2023 Relapse Prediction in Multiple Sclerosis: a Supervised Learning Approach
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Deep Learning for Predicting Disease Progression of Clinical Endpoints in ALS
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Modelo preditivo para a aquisição do produto Solar da EDP Comercial
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 Better Science Through an Enhanced User Interface with the ALMA Archive
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 Prognostic prediction models using Self-Attention for ICU patients developing acute kidney injury
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 Towards Reinforcement Learning based N­Clustering
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 Characterization of Behavioural Patterns of Portuguese Blood Donors using Supervised and Unsupervised Learning
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 Plataforma de apoio a utentes e profissionais de desporto e nutrição
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Aprendizagem automática para classificar a cobertura do solo em espaços verdes urbanos através de dados de satélite
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Quantifying the ergonomic risk and biomechanical exposure in automotive assembly lines
Supervisor
 Ciências da Engenharia - Engenharia Biomédica e Biofísica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Unravelling Patterns from a Blood Donation Data Set using Machine Learning Approaches
Supervisor
 Ciências de Engenharia - Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2021 Data-Driven Approaches for ALS Patient Stratification using Clinical Profiles
Supervisor
 Ciências de Engenharia - Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2021 Learning models using disease progression patterns for prognostic prediction in ALS
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Characterization of Behavioural Patterns of Portuguese Blood Donors using Supervised and Unsupervised Learning
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Aprendizagem Automática para classificar a cobertura do solo em Espaços Verdes Urbanos através de dados de satélite
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Quantifying the Ergonomic Risk and Biomechanical Exposure in Automotive Assembly Lines
Supervisor
 Engenharia Biomédica e Biofísica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Learning models using disease progression patterns for prognostic prediction in ALS
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Learning Predictive Models from Temporal Three-way Data using Triclustering: Applications in Clinical Data Analysis
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Profiling ALS disease progression through data mining techniques
Co-supervisor
 Ciências de Engenharia - Engenharia Electrotécnica e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - 2020 G-Tric: enhancing triclustering evaluation using three-way synthetic datasets with ground truths
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Biclustering fMRI Time Series
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 User-Specific Bicluster-based Collaborative Filtering
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Predicting post-surgical length of stay using machine learning
Supervisor
 Ciências da Engenharia - Engenharia Biomédica e Biofísica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Biclustering FMRI Time Series
Supervisor of Eduardo Castanho
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 G-Tric: enhancing triclustering evaluation using three-way synthetic datasets with ground truth
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 User-Specific Bicluster-based collaborative Filtering
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Learning Predictive Models From Temporal Three-way Data Using Triclustering: Applications in Clinical Data Analysis
Supervisor of Diogo Soares
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Predicting post-surgical length of stay using machine learning
Supervisor
 Engenharia Biomédica e Biofísica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Understanding ALS Patients using Semantic Similarity
Co-supervisor
 Bioinformatica e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Modelling the head and neck region for microwave imaging of cervical lymph nodes
Co-supervisor
 mestrado integrado em engenharia biomédica e biofísica (Master)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2019 - 2019 Biclustering electronic health records to unravel disease presentation patterns
Supervisor
 Mestrado em Ciência de Dados (Master)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2019 - 2019 Biclustering electronic health records to unravel disease presentation patterns
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Prognostic models targeting time to conversion, stable predictors, and reliability at patient-level: Predicting progression from mild cognitive impairment to dementia
Supervisor
 Engenharia Biomédica (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2016 An integrative mining approach to unravel prognostic markers in neurodegenerative diseases
Supervisor
 Programa Doutoral em Engenharia Biomédica (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2016 An Integrative mining approach for prognostic prediction in neurodegenerative diseases
Supervisor
 Engenharia Biomédica (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2016 Predicting conversion from mild cognitive impairment to Alzheimer´s Disease using ensemble learning
Supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 - 2016 Predicting conversion from mild cognitive impairment to Alzheimer´s Disease using a temporal mining approach: An exploratory study in real data approach
Supervisor
 Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2015 Learning from High-Dimensional Data using Local Descriptive Models
Supervisor
 Engenharia Informática e de Computadores (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2015 A temporal mining approach for prognostic prediction in Alzheimer´s disease using heterogeneous clinical data
Supervisor
 Engenharia Biomédica (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2015 Predicting the conversion from Mild Cognitive Impairment to Alzheimer´s disease using disease staging: A case study in ADNI data
Supervisor
 Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2015 Towards the identification of biomarker-genes for the diagnosis of invasive candidemia caused by Candida glabrata
Co-supervisor
 Engenharia Biológica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2015 Effect of alterations in non-coding regions in genomic expression reprogramming of two Candida glabrata clinical isolates
Co-supervisor
 Microbiologia (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2014 - 2014 Mining Coherent Evolution Patterns in Education through Biclustering
Co-supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2014 - 2014 Predicting the Conversion from Mild Cognitive Impairment to Alzheimer´s Disease using Evolution Patterns
Supervisor
 Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2013 - 2013 A data mining approach to study disease presentation patterns in Primary Progressive Aphasia
Supervisor
 Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2012 - 2012 A data mining approach to predict conversion from mild cognitive impairment to Alzheimer´s Disease
Supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2012 - 2012 Prognostic prediction in patients with Amyotrophic Lateral Sclerosis using data mining techniques
Supervisor
 Engenharia Informática e de Computadores (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2012 - 2012 Integration of Genomics and Transcriptomics: Analysis of Streptococcus pneumoniae wild-type and DeltaccpA Strains
Co-supervisor
 Biotecnologia (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2012 - 2012 Unravelling regulatory modules in Amyotrophic Lateral Sclerosis
Supervisor
 Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2012 - 2012 A study on gene-disease relations in the context of neurodegenerative diseases
Supervisor
 Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2010 - 2010 Classification of clinical expression time series: A case study in patients with Multiple Sclerosis
Supervisor
 Engenharia Biomédica (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2007 - 2007 Integrative Mining of Gene Regulation and its Perturbations
Supervisor
 Engenharia Informática e de Computadores (PhD)

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2021 - Current 19th Symposium on Intelligent Data Analysis (IDA 2021) (2021/04)
Conference (Co-organisor)
2022 - 2024 Intelligent Disease Progression Prediction at CLEF (2022 - 2024)
Conference (Co-organisor)
2016 - 2016 15th International Workshop on Data Mining in Bioinformatics (BIOKDD'16) (2016/08)
Workshop (Co-organisor)
2016 - 2016 Thematic Track Bioinformatics, INForum 2016 (Simpósio de Informática) (2016)
Symposium (Co-organisor)
2015 - 2015 14th International Workshop on Data Mining in Bioinformatics (BIOKDD'15) (2015/08)
Workshop (Co-organisor)
2015 - 2015 Thematic track Computational Methods in Bioinformatics and Systems Biology, XVII Portuguese Conference in Artificial Intelligence (EPIA 2015) (2015 - 2015)
Conference (Co-organisor)
2013 - 2013 Thematic track Computational Methods in Bioinformatics and Systems Biology, XVI Portuguese Conference in Artificial Intelligence (EPIA 2013) (2013/09)
Conference (Co-organisor)
2013 - 2013 Thematic Track Bioinformatics, INForum 2013 (Simpósio de Informática) (2013)
Symposium (Co-organisor)
2011 - 2011 Thematic Track Bioinformatics, INForum 2011 (Simpósio de Informática) (2011/09)
Symposium (Co-organisor)
2010 - 2010 14th International Conference in Research in Computational biology (RECOMB’10). (2010/08)
Conference (Co-organisor)

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023 Exploiting Machine Learning in Complex Biological Systems: Insights into Protein Stability Prediction and Mutational Signatures Analysis Corrado Pancotti (PhD)
Università degli Studi di Torino, Italy
2022 Towards a Differentially-Private Co-Clustering
(Thesis) Arguer
 Elena Battaglia (PhD)
Università degli Studi di Torino, Italy
2021 Computational Resources for Structural and Metagenomic Characterization of Functions in Bacteria and Bacterial Communities. Antimicrobial Resistance, Pathways for Xenobiotic Degradation and Relationship between Gut Microbiome and Ageing
(Thesis) Arguer
 Teresa Tavella (PhD)
Università degli Studi di Bologna, Italy
2020 Biclustering Algorithms and Interactive Tools for the Exploration of Multiva- riate and Functional Data
(Thesis) Arguer
 Jacopo di Iorio (PhD)
Politecnico di Milano, Italy
2020 Identificando padrões de longevidade baseada na transformação de dados e seleção de caracteríticas por meio de biclusterização
(Thesis) Main arguer
 Marta Noronha (Master)
Pontifícia Universidade Católica de Minas Gerais, Brazil
2019 Mining complex data and biclustering using formal concept analysis
(Thesis) Main arguer
 Nyoman Juniarta (PhD)
Université de Lorraine, France
2018 Un’Indagine su Larga Scala dell’Interazione Enhancer – Promotore Mediata da Fattori di Transcrizione
(Thesis) Arguer
 Francesco Aggazio (PhD)
Università degli Studi di Bologna, Italy
2017 Graphical Model approaches for Biclustering
(Thesis) Main arguer
 Matteo Denitto (PhD)
2017 Ranking to Learn and Learning to Rank: On the Role of Ranking in Pattern Recognition Application
(Thesis) Main arguer
 Giorgio Roffo (PhD)
Università degli Studi di Verona, Italy
2016 Understanding disease mechanisms with statistical models of signaling pathway activities
(Thesis) Main arguer
 Patricia Sebastian Leon (PhD)
Universitat de València, Spain
2013 Methodological Advances in the Functional Profiling of Genomic Studies
(Thesis) Arguer
 David Montaner (PhD)
Universitat de València, Spain
2012 Evolutionary Framework for DNA Microarray Cluster Analysis
(Thesis) Main arguer
 Jose Antonio Castellanos (PhD)
Universidad de Valladolid, Spain
2011 Inferring gene networks by means of regression
(Thesis) Main arguer
 Isabel Nepomuceno-Chamorro (PhD)
Universidad Pablo de Olavide, Spain
2010 Visual analysis of gene expression data by means of biclustering
(Thesis) Main arguer
 Rodrigo Santamaria (PhD)
Universidad de Salamanca, Spain

Committee member

Activity description
Role 		Institution / Organization
2024 - 2024 European Conference on Artificial Intelligence (ECAI)

Conference scientific committee

Conference name Conference host
2024 - 2024 European Conference on Artificial Intelligence (ECAI)
2021 - 2021 Symposium on Intelligent Data Analysis (IDA)
2021 - 2021 International Joint Conferences on Artificial Intelligence (IJCAI)
2021 - 2021 International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB)
2019 - 2019 European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD)
2019 - 2019 IEEE International Conference on Data Mining (ICDM)
2015 - 2016 ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD)
2011 - 2016 International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB)
2012 - 2014 Ibero-American Society of Artificial Intelligence (IBERAMIA)

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2017 - 2022 Machine Learning (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2022 Data Mining (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2009 - 2014 Bioinformatics and Computacional Biology (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal

Journal scientific committee

Journal title (ISSN) Publisher
2023 - Current Artificial Intelligence in Medicine
2021 - Current Computer Methods and Programs in Biomedicine
2021 - Current Journal of Machine Learning Research
2015 - Current Journal of Biomedical Informatics
2015 - Current Pattern Recognition
2015 - Current Knowledge Discovery and Data Mining
2015 - Current IEEE Journal of Biomedical and Health Informatics
2015 - Current IEEE Transactions on Knowledge and Data Engineering
2015 - Current Briefings in Bioinformatics
2009 - Current Algorithms for Molecular Biology
2004 - Current IEEE/ACM Transactions on Computational Biology and Bioinformatics
2004 - Current Bioinformatics
2004 - Current BMC Bioinformatics
Distinctions

Award

2022 Ciências 2022 Productivity Research Award in Computer Science and Engineering
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 Prémio Científico ULisboa/Caixa Geral de Depósitos 2021 na área de Ciências da Computação e Engenharia Informática
Caixa Geral de Depositos, Portugal
2020 Menção Honrosa no Prémio Científico ULisboa/Caixa Geral de Depósitos 2020 na área de Ciências da Computação e Engenharia Informática
Caixa Geral de Depositos, Portugal
2019 Best Student Paper Award - "Predicting assisted ventilation in Amyotrophic Lateral Sclerosis using a mixture of experts and conformal predictors", KDD 2019 Workshop on Applied Data Science, Alasca, USA.
2016 Menção Honrosa no Prémio Científico ULisboa/Caixa Geral de Depósitos 2016 na área de Ciências da Computação e Engenharia Informática
Caixa Geral de Depositos, Portugal
2013 INESC-ID Award - Young Researcher 2013
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2011 Menção Honrosa no Prémio Jovens Investigadores UTL/Caixa Geral de Depósitos 2011 na área Engenharia Electrotécnica, Engenharia Informática, Ciências da Computação e Engenharia Aeroespacial (Aviónica)
Caixa Geral de Depositos, Portugal
2010 Menção Honrosa nos Prémios Jovens Investigadores UTL/Caixa Geral de Depósitos 2010 na área Engenharia Electrotécnica, Engenharia Informática, Ciências da Computação e Engenharia Aeroespacial (Aviónica)
Caixa Geral de Depositos, Portugal
2000 Best Student Award in Computer Science
Universidade da Beira Interior, Portugal
1998 Merit Grant - degree in Computer Science
Universidade da Beira Interior, Portugal

Other distinction

2012 Diploma de Excelência Pedagógica
Universidade de Lisboa Instituto Superior Técnico, Portugal
2009 Highly Accessed Article, "A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series", Algorithms for Molecular Biology
2006 Hot Paper in Computer Science (Biclustering Algorithms for Biological Data Analysis: a Survey, ACM/IEEE TCBB).