Sara Alexandra Cordeiro Madeira (AF12-AA0D-0C7B)

Curriculum Vitae

Sara Alexandra Cordeiro Madeira

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	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 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 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 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 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 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 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 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 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 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 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 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 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 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 Moura, P.; Rocha, R.; Madeira, S.C.. "Thread-based competitive or-parallelism". 2008. 10.1007/978-3-540-89982-2_63 Madeira, S.C.; Oliveira, A.L.. "A linear time biclustering algorithm for time series gene expression data". 2005. 10.1007/11557067_4 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 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	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 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 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 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 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. 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 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 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 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 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 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 Henriques, R.; Madeira, S.C.. "Pattern-based biclustering with constraints for gene expression data analysis". 2015. 10.1007/978-3-319-23485-4_34 Gonçalves, J.P.; Madeira, S.C.. "Heuristic approaches for time-lagged biclustering". 2013. 10.1145/2500863.2500865 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 Gonçalves, J.P.; Madeira, S.C.; Moreau, Y.. "Network-based disease candidate gene prioritization: Towards global diffusion in heterogeneous association networks". 2010. 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 Madeira, S.C.; Oliveira, A.L.. "An efficient biclustering algorithm for finding genes with similar patterns in time-series expression data". 2007. Sousa, J.M.; Madeira, S.; Kaymak, U.. "Modeling charity donations using target selection for revenue maximization". 2003. 10.1109/fuzz.2003.1209441 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	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	Miguel G. Silva; Sara C. Madeira; Rui Henriques. "A Comprehensive Survey on Biclustering-based Collaborative Filtering". ACM Computing Surveys (2024): https://doi.org/10.1145/3674723. 10.1145/3674723 Daniela M. Amaral; Diogo F. Soares; Marta Gromicho; Mamede de Carvalho; Sara C. Madeira; Pedro Tomás; Helena Aidos. "Temporal stratification of amyotrophic lateral sclerosis patients using disease progression patterns". Nature Communications (2024): https://doi.org/10.1038/s41467-024-49954-y. 10.1038/s41467-024-49954-y 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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. 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 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 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 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 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 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 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. 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 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 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 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 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 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

Other

Other output

Biclustering Data Analysis: A Comprehensive Survey. 2024. Eduardo Castanho; Helena Aidos; Sara Madeira. https://doi.org/10.1093/bib/bbae342.
10.1093/bib/bbae342

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
2020/10 - 2024/09	Triclustering Three-way Temporal and Heterogeneous Data: Targeting Predictive and Descriptive Tasks for 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 Multivariate 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).