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Rui Henriques is an Assistant Professor at Instituto Superior Técnico (IST), University of Lisbon, where he lectures in the domains of Artificial Intelligence and Health Systems, and Integrated Researcher at INESC-ID, where he coordinates large-scale multidisciplinary R&D projects. His research contributions cross advances in Machine Learning with real-world applications in Biomedical and Urban domains. Rui received a wide-exposure to real projects in different sectors as a business analyst at McKinsey and as the head of the AI area at Tekever. Rui has been ascribed two scientific career awards in 2020 and 2022. Curriculum vitae: http://web.ist.utl.pt/rmch/upload/ExtendedRuiCV.pdf Personal page: http://web.ist.utl.pt/rmch Google scholar: https://scholar.google.pt/citations?user=l8llniYAAAAJ&hl === Research (synthesis) === 1. Selected institutional and scientific roles • Coordinator of MSc Data Science and Eng. @ Técnico • Coordinator of IDSS Lab @ INESC-ID • Scientific evaluation committee of both nat. and int. R&D projects (e.g. ANI, FWF, GACR) • Mobility Coordinator @ DEI, Técnico • Executive Coord. of AI Scientific Area @ DEI, Técnico • Scientific evaluation committee (excluding presidencies) of >10 PhDs and >70 MSc theses • Elder consultant @ NEIIST • Electoral Committee @ INESC-ID 2. Scientific production • +50 papers in top-tier Q1 SJR/ISI journals (+40 since 2022), including Pattern Recognition, ACM CSUR, IEEE T-ITS, DAMI, J-BHI, JMIR, BMC Bioinf., JMIR, KBS, EPB, AI in Medicine • +40 papers in high-visibility conferences (SIAM SDM, SIGKDD, ECML-PKDD, ECIR, ITS, HICSS, HRI, WABI, BPM, AAMAS) 3. Supervision: +30 MSc/PhD theses successfully concluded; +10 PhD students (http://web.ist.utl.pt/rmch/research/supervision) 4. Knowledge transfer • 39 open-source software packages (http://web.ist.utl.pt/rmch/research/software) • mass media press (Público, DN, SIC) • lecturing activity: entrusted by Técnico with the creation, coordination, lecturing of pivotal courses, including Machine Learning, Data Science, Health Informatics, and massive online courses on Epigenetics and Multi-Omics 5. Fund attraction as PI (including the premiered ILU project DSAIPA/DS/0111/2018) and partner coordinator/task responsible (including FRAIL, WISDOM, Neuroclinomics2, ADMIRAL, Data2Help) 6. Research interests – Learning from Complex Data Structures – AI in Neurology and Psychiatry – Statistical Foundations of Pattern Discovery – Multi-Omic Data Analysis for Novel Therapeutics === Previous positions === • Head of the AI area @ Tekever [2017-18] • R&D fellowship grants (selected) at FPU/NTNU (1018P.05576) [2021], Kyushu Univ., Japan (690941 RISE-BIRDS) [2017], Inst. Gulbenkian de Ciência (IF/01333/2013/CP1204/CT0001) [2016-17], IST-ID (SFRH/BD/75924/2011) [2012-15] • Analyst @ McKinsey & Company [2010–11] • Analyst @ Dep. Studies and Strategy, Millennium BCP [2008] • President @ NEIIST (Núcleo Est. Eng. Informática, IST) [2009-10] • Director @ GCE (Grupo de Contacto com Empresas, IST) [2007-09] • Students Delegate @ DEI [2006–08] === Distinctions === • 2022: Best Senior Researcher award ascribed by INESC-ID • 2022: TRA VISIONS Prize, EU • 2022: IJCAI Distinguished PC Member • 2020: Best Young Researcher award ascribed by INESC-ID • 2020-22: Supervisee distinctions, including 3 Best Thesis awards (F.Neves, J.Aparício, A.Patrício) • 2018-19: Awarded scientific publications (ACM CSUR, DAMI) • 2016: Best PhD Research award ascribed by INESC-ID • 2016: Doctoral research with Distinction and Honor by IST, UL • 2012–14: Research articles nominated as Best Papers in HICSS, ICIS and PhyCS • 2010: Pluim Award by TU Delft • 2005-10: Several distinctions for academic achievements by UL and CGD
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Identification

Personal identification

Full name
Rui Henriques

Citation names

  • Henriques, Rui

Author identifiers

Ciência ID
3D1F-D220-28D1
ORCID iD
0000-0002-3993-0171

Addresses

  • INESC-ID (Room 433), R. Alves Redol 9, 1000-029, Lisboa, Lisboa, Portugal (Professional)

Knowledge fields

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

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Spanish; Castilian Intermediate (B1) Advanced (C1) Intermediate (B1) Intermediate (B1)
Education
Degree Classification
2016
Concluded
 Phd Program in Information Systems and Computer Engineering (Doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Learning from High-Dimensional Data using Local Descriptive Models" (THESIS/DISSERTATION)
 Distinction and Honour (Distinção e Louvor)
2010
Concluded
 Master Degree (MSc) in Information Systems and Computer Engineering (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Object-centered Process Modeling: Principles to Model Data-intensive Systems" (THESIS/DISSERTATION)
 17,4
2008
Concluded
 Degree (BSc) in Information Systems and Computer Engineering (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
 18,0
Affiliation

Science

Category
Host institution 		Employer
2018/02/01 - Current Principal Investigator (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2021/01 - 2021/09 Visiting Researcher (Research) Junta de Andalucia Consejería de Salud y Familias Fundación Progreso y Salud, Spain
2017/06/01 - 2017/08/01 Postdoc (Research) Kyushu Daigaku, Japan
2011/11/01 - 2017/07/01 Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2016/03/01 - 2016/08/31 Postdoc (Research) Instituto Gulbenkian de Ciência, Portugal
2009/01/01 - 2010/10/01 Researcher (Research) INOV INESC INOVAÇÃO - Instituto de Novas Tecnologias, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2018/02/01 - Current Assistant Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
2011/09/01 - 2015/08/01 Invited Assistant (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
2009/09/01 - 2010/08/01 Tutor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal

Positions / Appointments

Category
Host institution 		Employer
2024 - Current Coordinator of MSc in Data Science and Engineering Universidade de Lisboa Instituto Superior Técnico, Portugal
2023/01 - 2025/02 Mobility Coordinator at Dep. Computer Science and Eng. Universidade de Lisboa Instituto Superior Técnico, Portugal
2017/08/01 - 2018/02/10 Organic Unit Director TEKEVER IT, Portugal
2009/10/01 - 2010/10/01 President Núcleo Estudantil de Informática, Instituto Superior Técnico (NEIIST), Portugal
2007/09/01 - 2009/11/01 Organic Unit Director Grupo Contacto com Empresas, Instituto Superior Técnico, Portugal

Others

Category
Host institution 		Employer
2010/08/01 - 2011/10/01 Business Analyst McKinsey and Company Portugal, Portugal
2010/07/01 - 2010/09/01 Certificate Tuck’s Online Business Bridge Program Dartmouth College Tuck School of Business, United States
2009/01/01 - 2009/07/01 Events' Organizer in International Contexts Technische Universiteit Delft, Netherlands
2008/06/01 - 2008/09/01 Analyst in the Department for Studies and Strategy (Corporative Center) Millennium bcp, Portugal
Projects

Contract

Designation Funders
2023 - Current ADMIRAL: Empowering Sustainable Logistics by AI-Driven Solutions
HORIZON-CL5-2022-D6-02-01
Researcher
Horizon Europe
Ongoing
2020 - Current MONET: Multi-omic networks in gliomas
PTDC/CCI-BIO/4180/2020
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2020 - Current InnoCyPES: Innovative Tools for Cyber-Physical Energy Systems
H2020-MSCA-ITN-2020
Researcher
Horizon Europe
Ongoing
2020 - 2023 MATISSE: A machine learning based forecasting system for shellfish safety
DSAIPA/DS/0026/2019
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
2019 - 2023 LAIfeBlood: Artificial Intelligence for Blood Management
DSAIPA/AI/0033/2019
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
2019/01/02 - 2022/09 ILU: Integrative Learning from Urban Data and Situational Context for City Mobility Optimization
DSAIPA/DS/0111/2018
Principal investigator
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2019/01/01 - 2022/07 Data2Help: Data Science for Optimization of Emergency Medical Services
DSAIPA/AI/0044/2018
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
2019/01/01 - 2022/07 WISDOM: Water Intelligence System Data
DSAIPA/DS/0089/2018
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
2018 - 2022 iCare4U: Decision Support System for Personalized Medicine in ICUs
LISBOA-01-0145-FEDER-031474
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
2016 - 2020 Neuroclinomics2: Unravelling prognostic markers in neurodegenerative diseases through clinical and omics data integration
PTDC/EEI-SII/1937/2014
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Henriques, Rui; Madeira, Sara C.. "Towards Robust Performance Guarantees for Models Learned from High-Dimensional Data". In Big Data in Complex Systems, 71-104. Springer International Publishing, 2015.
    10.1007/978-3-319-11056-1_3
  2. Henriques, Rui; Ana Paiva. "Learning Effective Models of Emotions from Physiological Signals: The Seven Principles". edited by da Silva, Hugo Pl\'acido; Holzinger, Andreas; Fairclough, Stephen; Majoe, Dennis, 137-155. Springer Berlin Heidelberg, 2014.
    10.1007/978-3-662-45686-6_9
  3. Henriques, Rui; Ana Paiva. "On the Need of New Methods to Mine Electrodermal Activity in Emotion-Centered Studies". edited by Cao, Longbing; Zeng, Yifeng; Symeonidis, AndreasL.; Gorodetsky, VladimirI.; Yu, PhilipS.; Singh, MunindarP, 203-215. Springer Berlin Heidelberg, 2013.
    10.1007/978-3-642-36288-0_18
  4. Henriques, Rui; Cláudia M. Antunes. "On the Need of New Approaches for the Novel Problem of Long-Term Prediction over Multi-dimensional Data". In Computer and Information Science, edited by Lee, Roger, 121-138. Springer Berlin Heidelberg, 2012.
    10.1007/978-3-642-30454-5_9
  5. João Zambujal Oliveira; Miguel Henriques; Henriques, Rui. "Carbon Markets and Investments: EcoSecurities Investment Case Analysis". In Advanced Analytics for Green and Sustainable Economic Development, 15-33. IGI Global, 2012.
    10.4018/978-1-61350-156-6.ch002
Conference paper
  1. Dauphinet, Miguel; Henriques, Rui; Pedro Tiago Monteiro. Corresponding author: Henriques, Rui. "Context-Aware Deep Forecasting: Principles for the Nation-Wide Management of Blood Products". 2024.
    10.1007/978-3-031-73503-5_29
  2. Machado, Eduardo; Henriques, Rui. Corresponding author: Henriques, Rui. "Chatbot Decision Support with Intent-Rich Structures in the Hospitality Industry". 2024.
    10.1007/978-3-031-73503-5_27
  3. Shao, Han; Henriques, Rui; Morais, Hugo; Tedeschi, Elisabetta. "Comparing Deep Neural Networks for 1D Multi-Label Power Quality Disturbance Classification: ResNet, MobileNet, and DenseNet". 2024.
    10.1109/iecon55916.2024.10905211
  4. Cerqueira, Sofia; Aparicio, Joao Tiago; Elisabete Arsenio; Henriques, Rui. "Advancing Green and Digital Logistics through Spatio-Temporal Data Integration". Paper presented in European Transport Conference (ETC), 2024.
  5. Shao, Han; Henriques, Rui; Morais, Hugo; Tedeschi, Elisabetta. "Automatic Power Quality Disturbance Feature Extraction Using Fast Iterative Filtering". 2024.
    10.1109/ichqp61174.2024.10768829
  6. Joao Tiago Aparicio; Elisabete Arsenio; Henriques, Rui. "tex2net: A Package for Storytelling Using Network Models". Paper presented in SIGDOC: Proceedings of the 41st ACM Int. Conf. on Design of Communication, Orlando, 2023.
    10.1145/3615335.3623022
  7. David Calhas; Henriques, Rui. "EEG to fMRI Synthesis Benefits from Attentional Graphs of Electrode Relationships". Paper presented in MLHC 2023: Machine Learning for Healthcare (Proceedings of Machine Learning Research), New York, 2023.
    Published
  8. David Calhas; Henriques, Rui. "EEG To FMRI Synthesis: Is Deep Learning a Candidate?". Paper presented in ISD: Information Systems Development, Organizational Aspects and Societal Trends, 2023.
    Published
  9. Sofia Cerqueira; Elisabete Arsénio; José Barateiro; Henriques, Rui. "Data Analytics to Advance the Inference of Origin-Destination Trips in Public Transport Systems: Tracing Network Vulnerabilities and Age-sensitive Trip Purposes". Paper presented in European Transport Conference (ETC), Milan, 2023.
    Published
  10. Daniel Mateus Gonçalves; Rafael S. Costa; Henriques, Rui. "Context-situated visualization of biclusters to aid decisions: going beyond subspaces with parallel coordinates". Paper presented in IC on Advanced Visual Interfaces (AVI), Roma, 2022.
    10.1145/3531073.3531124
  11. Tiam-Lee, T.J.; Henriques, R.; Costa, J.; Manquinho, V.; Galhardas, H.. "Consolidation of massive medical emergency events with heterogeneous situational context data sources". Paper presented in DARLIAP, 2022.
    Published
  12. Elisabete Arsénio; Henriques, Rui. "Data-driven and user-centric tools for a more resilient and inclusive public transport". Paper presented in CITTA: In 14th Conference on Planning Research - Safe, Equitable and Just Communities, 2022.
    Published
  13. Sofia Cerqueira; Elisabete Arsénio; Henriques, Rui. "Inference of Origin-Destination Matrices for Assessing the Spatio-temporal Attractiveness of Public Transport in relation to Car Travel: a case study in the city of Lisbon". Paper presented in European Transport Conference (ETC), Milan, 2022.
    Published
  14. Sofia Cerqueira; Elisabete Arsénio; Henriques, Rui. "Is there any best practice principles to estimate bus alighting passengers from incomplete smart card transactions?". Paper presented in Transport Research Arena (TRA2022), 2022.
    10.1016/j.trpro.2023.11.780
  15. Marta Bubicz; Elisabete Arsénio; José Barateiro; Henriques, Rui. "Planning for more resilient urban transportation systems: Lessons learned from the Covid-19 pandemic". Paper presented in Transport Research Arena (TRA2022), 2022.
    10.1016/j.trpro.2023.11.780
  16. Leonor Pimenta; Vasco Manquinho; Helena Galhardas; Henriques, Rui. "UNIANO: robust and efficient anomaly consensus in time series sensitive to cross-correlated anomaly profiles". Paper presented in SIAM International Conference on Data Mining (SDM21), 2021.
    10.1137/1.9781611976700.37
  17. Thomas J. Tiam-Lee; Henriques, Rui. "Where are the Passengers? Individual Passenger Route Choice Estimation from Gate Information in Urban Rail Transit Systems". Paper presented in European Transport Conference (ETC), Milan, 2021.
    Published
  18. Sofia Cerqueira; Elisabete Arsenio; Henriques, Rui. "Inference of Dynamic Origin-Destination Matrices with Trip and Transfer Status from Individual Smart Card Data". Paper presented in European Transport Conference (ETC), 2021.
    Published
  19. Calhas, David; Henriques, Rui. "Fitting Regularized Population Dynamics with Neural Differential Equations". Paper presented in The Symbiosis of Deep Learning and Differential Equations (DLDE) Workshop, Neural Information Processing Systems conference (NeurIPS), 2021.
    Published
  20. Lemonde, C.; Arsenio, E.; Henriques, R.. "Public Transportation Multimodality in the City of Lisbon". Paper presented in CIT, Burgos, 2021.
    10.1016/j.trpro.2021.11.011
  21. Aparicio, J.T.; Trinca, M.; Castro, D.; Henriques, R.. "Vehicle Smart Grid Allocation using Multi-Agent Systems sensitive to Irrational Behavior and Unstable Power Supply". Paper presented in 16th Iberian Conference on Information Systems and Technologies (CISTI), Chaves, 2021.
    10.23919/CISTI52073.2021.9476320
  22. Calhas, D.; Henriques, R.; David Calhas; Henriques, Rui. "fMRI Multiple Missing Values Imputation Regularized by a Recurrent Denoiser". Paper presented in AIME 2021: Artificial Intelligence in Medicine, Porto, 2021.
    10.1007/978-3-030-77211-6_3
  23. Francisco Neves; Anna C. Finamore; Henriques, Rui; Neves, F.; Finamore, A.; Henriques, R.. "Efficient discovery of emerging patterns in heterogeneous spatiotemporal data from mobile sensors". Paper presented in 17th EAI International Conference on Mobile and Ubiquitous Systems: Computing, Networking and Services (MobiQuitous), 2020.
    10.1145/3448891.3448949
  24. Ricardo Sousa; Conceição Amado; Henriques, Rui; Sousa, R.; Amado, C.; Henriques, R.. "AutoMTS: fully autonomous processing of multivariate time series data from heterogeneous sensor networks". Paper presented in 16th EAI International Conference on Heterogeneous Networking for Quality, Reliability, Security and Robustness (QShine), 2020.
    10.1007/978-3-030-77569-8_12
  25. Sofia Cerqueira; Elisabete Arsénio; Henriques, Rui. "Integrative analysis of traffic and situational context data to support urban mobility planning". Paper presented in European Transport Conference (ETC), 2020.
    Published
  26. Carlos Lemonde; Elisabete Arsénio; Henriques, Rui. "Exploring multimodal mobility patterns with big data in the city of Lisbon". Paper presented in European Transport Conference (ETC), 2020.
    Published
  27. Inês Leite; Anna C. Finamore; Henriques, Rui. "Context-sensitive modeling of public transport data". Paper presented in Transport Research Arena (TRA2020), 2020.
    Published
  28. Pavlo Kovalchuk; Diogo Proença; José Borbinha; Rui Henriques. "Moving from Formal Towards Coherent Concept Analysis: Why, When and How". Paper presented in ECIR, 2020.
    10.1007/978-3-030-45439-5_19
  29. Diogo Soares; Henriques, Rui; Marta Gromicho; Susana Pinto; Mamede de Carvalho; Sara C. Madeira. "Towards Triclustering-Based Classification of Three-Way Clinical Data: A Case Study on Predicting Non-invasive Ventilation in ALS". Paper presented in IC on Practical Applications of Computational Biology & Bioinformatics (PACBB), 2020.
    10.1007/978-3-030-54568-0_12
  30. Rui Henriques; Anna Carolina Finamore; Marco Antonio Casanova. "On the Discovery of Educational Patterns using Biclustering". Paper presented in ITS: 15th International Conference on Intelligent Tutoring Systems, Kingston, 2019.
    10.1007/978-3-030-22244-4_17
  31. Pavlo Kovalchuk; Diogo Proença; José Borbinha; Henriques, Rui. "An Unsupervised Method for Concept Association Analysis in Text Collections". Paper presented in 23rd Int. Conf. on Theory and Practice of Digital Libraries (TPDL), Oslo, 2019.
    10.1007/978-3-030-30760-8_2
  32. Henriques, Rui; Alexandre Francisco; Luís Russo; Hideo Bannai. "Order-preserving Pattern Matching Indeterminate Strings". Paper presented in 29th Annual Symposium on Combinatorial Pattern Matching (CPM), Qingdao, 2018.
    10.4230/LIPIcs.CPM.2018.2
  33. Rui Duarte; Álvaro Simões; Henriques, Rui; Horácio C. Neto. "FPGA-based OpenCL Accelerator for Discovering Temporal Patterns in Gene Expression Data Using Biclustering". Paper presented in Parallelism in Bioinformatics (PBio'18), 2018.
    10.1145/3235830.3235836
  34. Henriques, Rui; Sara C. Madeira. "BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules". Paper presented in Algorithms in Bioinformatics (WABI), Atlanta, 2015.
    10.1007/978-3-662-48221-6_1
  35. Henriques, Rui; Madeira, S.C.. "Pattern-based biclustering with constraints for gene expression data analysis". Paper presented in EPIA 2015: Progress in Artificial Intelligence, Coimbra, 2015.
    10.1007/978-3-319-23485-4_34
  36. Henriques, Rui; Cláudia M. Antunes. "Learning Predictive Models from Integrated Healthcare Data: Extending Pattern-Based and Generative Models to Capture Temporal and Cross-Attribute Dependencies". Paper presented in Hawai International Conference on System Sciences (HICSS), 2562-2569, IEEE Computer Science, Waikoloa, 2014.
    10.1109/HICSS.2014.322
  37. Henriques, Rui; Ana Paiva. "Seven principles to mine flexible behavior from physiological signals for effective emotion recognition and description in affective interactions". Paper presented in Physiological Computing Systems (PhyCS'14), Lisbon, 2014.
    10.5220/0004666400750082
  38. Henriques, Rui; Antunes, Cláudia. "Generative Modeling of Itemset Sequences derived from Real Databases". Paper presented in IC on Enterprise Information Systems (ICEIS'14), 2014.
    10.5220/0004898302640272
  39. Henriques, Rui; Ana Paiva. "Descriptive Models of Emotion: Learning Useful Abstractions from Physiological Responses during Affective Interactions". Paper presented in PhyCS Special Session on Recognition of Affect Signals from PhysiologIcal Data for Social Robots (OASIS'14), 2014.
    10.5220/0004902703930400
  40. Henriques, Rui; Ana Paiva. "Accessing Emotion Patterns from Affective Interactions Using Electrodermal Activity". Paper presented in 2013 Humaine Association Conference on Affective Computing and Intelligent Interaction (ACII), 2013.
    10.1109/ACII.2013.14
  41. Iolanda Leite; Henriques, Rui; Carlos Martinho; Ana Paiva. "Sensors in the wild: Exploring electrodermal activity in child-robot interaction". Paper presented in 2013 8th ACM/IEEE International Conference on Human-Robot Interaction (HRI), Tokyo, 2013.
    10.1109/HRI.2013.6483500
  42. Henriques, Rui; Cláudia M. Antunes. "F2G: Efficient Discovery of Full-Patterns". Paper presented in ECML/PKDD IW on New Frontiers to Mine Complex Patterns, Prague, 2013.
    Published
  43. Henriques, Rui; Cláudia M. Antunes. "IndexSpan: Efficient Discovery of Item-Indexable Sequential Patterns". Paper presented in ECML/PKDD IW on New Frontiers to Mine Complex Patterns, Prague, 2013.
    Published
  44. Henriques, Rui; Silvia Moura Pina; Cláudia M. Antunes. "Temporal Mining of Integrated Healthcare Data: Methods, Revealings and Implications". Paper presented in Data Mining for Medicine and Healthcare, Austin, 2013.
    Published
  45. Henriques, Rui; Cláudia M. Antunes. "An Integrated Approach for Healthcare Planning over Multi-dimensional Data Using Long-Term Prediction". Paper presented in HIS 2012: Health Information Science, Beijing, 2012.
    10.1007/978-3-642-29361-0_6
  46. Henriques, Rui; António Rito Silva. "Object-Centered Process Modeling: Principles to Model Data-Intensive Systems". Paper presented in BPM 2010: Business Process Management, Hoboken, NY, 2010.
    10.1007/978-3-642-20511-8_62
Journal article
  1. Alexandre, Leonardo; Costa, Rafael S.; Henriques, Rui. Corresponding author: Henriques, Rui. "Integrating statistical significance and discriminative power in pattern discovery". Knowledge-Based Systems (2025): 113356. https://doi.org/10.1016/j.knosys.2025.113356.
    10.1016/j.knosys.2025.113356
  2. G. Silva, Miguel; C. Madeira, Sara; Henriques, Rui; Silva, Miguel; Sara C. Madeira; Henriques, Rui. "A Comprehensive Survey on Biclustering-based Collaborative Filtering". ACM Computing Surveys 56 12 (2024): 1-32. https://doi.org/10.1145/3674723.
    Published • 10.1145/3674723
  3. Leonardo Alexandre; Rafael S. Costa; Rui Henriques. "TriSig: Evaluating the statistical significance of triclusters". Pattern Recognition (2024): https://doi.org/10.1016/j.patcog.2023.110231.
    10.1016/j.patcog.2023.110231
  4. 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
  5. Aparicio, Joao Tiago; Elisabete Arsenio; Santos, Francisco C.; Henriques, Rui. "Walkability defined neighborhoods for sustainable cities". Cities 149 (2024): https://doi.org/10.1016/j.cities.2024.104944.
    Published
  6. Joao T. Aparicio; Elisabete Arsenio; Francisco Santos; Rui Henriques. "Using dynamic knowledge graphs to detect emerging communities of knowledge". Knowledge-Based Systems (2024): https://doi.org/10.1016/j.knosys.2024.111671.
    10.1016/j.knosys.2024.111671
  7. Sofia Cerqueira; Elisabete Arsenio; José Barateiro; Henriques, Rui. "Moving from classical towards machine learning stances for bus passengers’ alighting estimation: a comparison of state-of-the-art approaches in the city of Lisbon". Transportation Engineering (2024): https://doi.org/10.1016/j.treng.2024.100239.
    10.1016/j.treng.2024.100239
  8. Palet, João; Manquinho, Vasco; Henriques, Rui. "Multiple-Input Neural Networks for Time Series Forecasting Incorporating Historical and Prospective Context". Data Mining and Knowledge Discovery (DAMI) 38 (2024): 315-341. https://doi.org/10.1007/s10618-023-00984-y.
    10.1007/s10618-023-00984-y
  9. Han Shao; Henriques, Rui; Hugo Morais; Elisabetta Tedeschi. "Power quality monitoring in electric grid integrating offshore wind energy: A review". Renewable and Sustainable Energy Reviews 191 (2024): https://doi.org/10.1016/j.rser.2023.114094.
    Published • 10.1016/j.rser.2023.114094
  10. 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
  11. Joao T. Aparicio; Elisabete Arsenio; Francisco C. Santos; Rui Henriques. "Spatiotemporal trip profiles in public transportation reveal city modular structure". Transportation Research Interdisciplinary Perspectives (2023): https://doi.org/10.1016/j.trip.2023.100840.
    10.1016/j.trip.2023.100840
  12. Diogo F. Soares; Rui Henriques; Marta Gromicho; Mamede de Carvalho; 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): https://doi.org/10.1038%2Fs41598-023-33223-x.
    10.1038/s41598-023-33223-x
  13. Luís Madeira; Guilherme Queiroz; Rui Henriques. "Prepandemic psychotropic drug status in Portugal: a nationwide pharmacoepidemiological profile". Scientific Reports 13 1 (2023): https://doi.org/10.1038%2Fs41598-023-33765-0.
    10.1038/s41598-023-33765-0
  14. Joana Barreto; Rui Henriques; Sílvia Cabral; Bruno Pedro; César Peixoto; António Veloso. "Movement Prototypes in a Complex Teamgym Gymnastics Technique on the Vaulting Table and Their Relationship with Judges’ Scores". Sensors (2023): https://doi.org/10.3390/s23063240.
    10.3390/s23063240
  15. Patricio, Andre; Costa, Rafael S; Henriques, Rui. "On the challenges of predicting treatment response in Hodgkin’s Lymphoma using transcriptomic data". BMC Medical Genomics (2023): https://doi.org/10.1186/s12920-023-01508-9.
    10.1186/s12920-023-01508-9
  16. Daniel M. Gonçalves; Rui Henriques; Rafael S. Costa. "Predicting metabolic fluxes from omics data via machine learning: Moving from knowledge-driven towards data-driven approaches". Computational and Structural Biotechnology Journal (2023): https://doi.org/10.1016/j.csbj.2023.10.002.
    10.1016/j.csbj.2023.10.002
  17. Eduardo N. Castanho; João P. Lobo; Sara C. Madeira; Henriques, Rui. "G-bic: generating synthetic benchmarks for biclustering". BMC Bioinformatics 24 457 (2023): https://doi.org/10.1186/s12859-023-05587-4.
    10.1186/s12859-023-05587-4
  18. 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
  19. André Patrício; Marta B. Lopes; Pedro Reis Costa; Costa, R; Rui Henriques; Susana Vinga. "Time-Lagged Correlation Analysis of Shellfish Toxicity Reveals Predictive Links to Adjacent Areas, Species, and Environmental Conditions". Toxins (2022): https://doi.org/10.3390/toxins14100679.
    10.3390/toxins14100679
  20. Pedro Rodrigues; Rafael S. Costa; Rui Henriques; Rodrigues, P.; Costa, R.S.; Henriques, R.. "Enrichment analysis on regulatory subspaces: A novel direction for the superior description of cellular responses to SARS-CoV-2". Computers in Biology and Medicine (2022): https://doi.org/10.1016/j.compbiomed.2022.105443.
    10.1016/j.compbiomed.2022.105443
  21. Joao Tiago Aparicio; Elisabete Arsenio; Francisco C. Santos; Rui Henriques. "LINES: muLtImodal traNsportation rEsilience analySis". Sustainability (2022): https://doi.org/10.3390/su14137891.
    10.3390/su14137891
  22. Thomas James Tiam-Lee; Rui Henriques; Vasco Manquinho. "Associative Analysis of Inefficiencies and Station Activity Levels in Emergency Response". ISPRS International Journal of Geo-Information (2022): https://doi.org/10.3390/ijgi11070356.
    10.3390/ijgi11070356
  23. 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
  24. Hugo Mochão; Daniel Gonçalves; Leonardo Alexandre; Carolina Castro; Duarte Valério; Pedro Barahona; Daniel Moreira-Gonçalves; et al. "IPOscore: An interactive web-based platform for postoperative surgical complications analysis and prediction in the oncology domain". Computer Methods and Programs in Biomedicine 219 (2022): 106754-106754. https://doi.org/10.1016/j.cmpb.2022.106754.
    10.1016/j.cmpb.2022.106754
  25. Mariana Carrasco; António Rito Silva; Henriques, Rui. "Detecting Fraudulent Student Communication in a Multiple Choice Online Test Environment". IEEE Transactions on Computational Social Systems (2022): https://doi.org/10.1109/TCSS.2023.3254504.
    10.1109/TCSS.2023.3254504
  26. Marta D.M. Noronha; Rui Henriques; Sara C. Madeira; Luis E. Zárate. "Impact of metrics on biclustering solution and quality: A review". Pattern Recognition 127 (2022): 108612-108612. https://doi.org/10.1016%2Fj.patcog.2022.108612.
    10.1016/j.patcog.2022.108612
  27. Tiam-Lee, T.J.; Henriques, R.. "Route choice estimation in rail transit systems using smart card data: handling vehicle schedule and walking time uncertainties". European Transport Research Review 14 1 (2022): https://doi.org/10.1186/s12544-022-00558-x.
    10.1186/s12544-022-00558-x
  28. Russo, L.M.S.; Costa, D.; Henriques, R.; Bannai, H.; Francisco, A.P.. "Order-preserving pattern matching indeterminate strings". Information and Computation (2022): https://doi.org/10.1016/j.ic.2022.104924.
    10.1016/j.ic.2022.104924
  29. Aparicio, J.T.; Arsenio, E.; Henriques, R.; Joao T. Aparicio; Elisabete Arsenio; Henriques, Rui. "Assessing robustness in multimodal transportation systems: a case study in Lisbon". European Transport Research Review 14 1 (2022): https://doi.org/10.1186/s12544-022-00552-3.
    10.1186/s12544-022-00552-3
  30. Alexandre, Leonardo; Costa, Rafael S; Henriques, Rui; Alexandre, L.; Costa, R.S.; Henriques, R.. "DISA tool: Discriminative and informative subspace assessment with categorical and numerical outcomes". PLoS ONE 17 10 (2022): https://doi.org/10.1371/journal.pone.0276253.
    10.1371/journal.pone.0276253
  31. Sofia Cerqueira; Elisabete Arsenio; Rui Henriques. "On how to incorporate public sources of situational context in descriptive and predictive models of traffic data". European Transport Research Review 13 1 (2021): https://doi.org/10.1186%2Fs12544-021-00519-w.
    10.1186/s12544-021-00519-w
  32. Susana C. Gomes; Susana Vinga; Rui Henriques. "Spatiotemporal Correlation Feature Spaces to Support Anomaly Detection in Water Distribution Networks". Water (2021): https://doi.org/10.3390/w13182551.
    10.3390/w13182551
  33. Leonardo Alexandre; Rafael S. Costa; Rui Henriques; Alexandre, L.; Costa, R.S.; Henriques, R.. "DI2: prior-free and multi-item discretization of biological data and its applications". BMC Bioinformatics 22 1 (2021): https://doi.org/10.1186%2Fs12859-021-04329-8.
    10.1186/s12859-021-04329-8
  34. Joao T. Aparicio; Elisabete Arsenio; Rui Henriques. "Understanding the Impacts of the COVID-19 Pandemic on Public Transportation Travel Patterns in the City of Lisbon". Sustainability 13 15 (2021): 8342-8342. https://doi.org/10.3390/su13158342.
    10.3390/su13158342
  35. Daniel M. Gonçalves; Rui Henriques; Rafael S. Costa. "Predicting Postoperative Complications in Cancer Patients: A Survey Bridging Classical and Machine Learning Contributions to Postsurgical Risk Analysis". Cancers 13 13 (2021): 3217-3217. https://doi.org/10.3390/cancers13133217.
    10.3390/cancers13133217
  36. Gonçalves D; Henriques R; Santos LL; Costa RS. "On the predictability of postoperative complications for cancer patients: a Portuguese cohort study.". BMC medical informatics and decision making (2021): https://doi.org/10.1186/s12911-021-01562-2.
    10.1186/s12911-021-01562-2
  37. André Patrício; Rafael S Costa; Rui Henriques. "Predictability of COVID-19 Hospitalizations, Intensive Care Unit Admissions, and Respiratory Assistance in Portugal: Longitudinal Cohort Study". Journal of Medical Internet Research (2021): https://doi.org/10.2196/26075.
    10.2196/26075
  38. Henriques, Rui; Sara C. Madeira. "FleBiC: Learning classifiers from high-dimensional biomedical data using discriminative biclusters with non-constant patterns". Pattern Recognition, Elsevier (2021): https://doi.org/10.1016/j.patcog.2021.107900.
    10.1016/j.patcog.2021.107900
  39. Francisco Neves; Anna C. Finamore; Sara C. Madeira; Rui Henriques. "Mining Actionable Patterns of Road Mobility From Heterogeneous Traffic Data Using Biclustering". IEEE Transactions on Intelligent Transportation Systems (2021): https://doi.org/10.1109/TITS.2021.3057240.
    10.1109/TITS.2021.3057240
  40. Alexandre, Leonardo; Costa, Rafael S; Santos, Lucio Lara; Henriques, Rui. "Mining pre-surgical patterns able to discriminate post-surgical outcomes in the oncological domain". IEEE Journal of Biomedical and Health Informatics (2021): 1-1. http://dx.doi.org/10.1109/jbhi.2021.3064786.
    10.1109/jbhi.2021.3064786
  41. Carlos Lemonde; Elisabete Arsenio; Rui Henriques. "Integrative analysis of multimodal traffic data: addressing open challenges using big data analytics in the city of Lisbon". European Transport Research Review 13 1 (2021): https://doi.org/10.1186%2Fs12544-021-00520-3.
    10.1186/s12544-021-00520-3
  42. David Calhas; Enrique Romero; Henriques, Rui; Calhas, D.; Romero, E.; Henriques, R.. "On the use of Pairwise Distance Learning for Brain Signal Classification with Limited Observations". Artificial Intelligence in Medicine, Elsevier (2020): https://doi.org/10.1016/j.artmed.2020.101852.
    Published • 10.1016/j.artmed.2020.101852
  43. João Lobo; Henriques, Rui; Sara C. Madeira. "G-Tric: generating three-way synthetic datasets with triclustering solutions". BMC Bioinformatics (2020): https://doi.org/10.1186/s12859-020-03925-4.
    10.1186/s12859-020-03925-4
  44. Henriques, Rui; Sara C. Madeira. "Triclustering Algorithms for Three-Dimensional Data Analysis: A Comprehensive Survey". ACM Computing Surveys (CSUR) 51 5 (2018): 95:1-95:43. https://dl.acm.org/doi/10.1145/3195833.
    10.1145/3195833
  45. Mendes, N.D.; Henriques, R.; Remy, E.; Carneiro, J.; Monteiro, P.T.; Chaouiya, C.. "Estimating attractor reachability in asynchronous logical models". Frontiers in Psychology 9 SEP (2018): https://doi.org/10.3389/fphys.2018.01161.
    10.3389/fpsyg.2018.01681
  46. Henriques, Rui; Sara C. Madeira. "BSig: Evaluating the Statistical Significance of Biclustering Solutions, Data Mining and Knowledge Discovery". Data Mining and Knowledge Discovery (2017): https://doi.org/10.1007/s10618-017-0521-2.
    10.1007/s10618-017-0521-2
  47. Henriques, Rui; Ferreira, F.L.; Madeira, S.C.. "BicPAMS: Software for biological data analysis with pattern-based biclustering". BMC Bioinformatics 18 1 (2017): https://doi.org/10.1186/s12859-017-1493-3.
    10.1186/s12859-017-1493-3
  48. Henriques, Rui; Sara C. Madeira. "BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge". Algorithms for Molecular Biology 11 1 (2016): 23-23. https://almob.biomedcentral.com/articles/10.1186/s13015-016-0085-5.
    10.1186/s13015-016-0085-5
  49. Henriques, Rui; Sara C. Madeira. "BicNET: Flexible module discovery in large-scale biological networks using biclustering". Algorithms for Molecular Biology 11 1 (2016): 1-30. http://almob.biomedcentral.com/articles/10.1186/s13015-016-0074-8.
    10.1186/s13015-016-0074-8
  50. Henriques, Rui; Cláudia M. Antunes; Sara C. Madeira. "A structured view on pattern mining-based biclustering". Pattern Recognition 48 12 (2015): 3941-3958. http://www.sciencedirect.com/science/article/pii/S003132031500240X.
    10.1016/j.patcog.2015.06.018
  51. 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. https://dl.acm.org/doi/10.1109/TCBB.2014.2388206.
    10.1109/TCBB.2014.2388206
  52. 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
  53. Henriques, Rui; Cláudia M. Antunes; Sara C. Madeira. "Generative modeling of repositories of health records for predictive tasks". Data Mining and Knowledge Discovery (2014): 1-34. http://dx.doi.org/10.1007/s10618-014-0385-7.
    10.1007/s10618-014-0385-7
  54. Henriques, Rui. "Multi-period classification: learning sequent classes from temporal domains". Data Mining and Knowledge Discovery (2014): 1-28. http://dx.doi.org/10.1007/s10618-014-0376-8.
    10.1007/s10618-014-0376-8
  55. Henriques, Rui; Cláudia M. Antunes. "Methods for the Efficient Discovery of Large Item-Indexable Sequential Patterns". ECML/PKDD New Frontiers to Mine Complex Patterns 8399 (2014): 94-108. https://link.springer.com/chapter/10.1007/978-3-319-08407-7_7.
    10.1007/978-3-319-08407-7_7
  56. Henriques, Rui; Sara C. Madeira. "BicSPAM: Flexible Biclustering using Sequential Patterns". BMC Bioinformatics 15 (2014): 130-130. http://www.biomedcentral.com/1471-2105/15/130.
    10.1186/1471-2105-15-130
Preprint
  1. David Belchior; Luís Madeira; Henriques, Rui. "Psychopharmacoepidemiological trends in the Portuguese territory during the pandemic and post-pandemic periods (2019–2022)". 2024. https://doi.org/10.1101/2024.05.26.24307948.
    10.1101/2024.05.26.24307948
  2. David Calhas; Rui Henriques. "EEG to fMRI Synthesis for Medical Decision Support: A Case Study on Schizophrenia Diagnosis". 2023. https://doi.org/10.1101/2023.08.07.23293748.
    10.1101/2023.08.07.23293748
  3. André Patrício; Rafael S. Costa; Rui Henriques. "Pattern-centric transformation of omics-data sources grounded on multi-wise gene associations aids predictive tasks in TCGA while ensuring interpretability". 2023. https://doi.org/10.1101/2023.05.28.542574.
    10.1101/2023.05.28.542574
  4. Alexandre, Leonardo; Costa, Rafaela S.; Henriques, Rui. "Scaling pattern mining through non-overlapping variable partitioning". 2023. https://doi.org/10.48550/arXiv.2212.05340.
    10.48550/arXiv.2212.05340
  5. Luís Madeira; Guilherme Queiroz; Rui Henriques. "Psychotropic drugs in Portugal from 2016 to 2019: a nationwide pharmacoepidemiological profile". 2022. https://doi.org/10.1101/2022.09.14.22279819.
    10.1101/2022.09.14.22279819
  6. Vasco Silva; Anna C. Finamore; Henriques, Rui; Silva, V.; Finamore, A.; Henriques, R.. "On the Role of Multi-Objective Optimization to the Transit Network Design Problem". 2022. https://doi.org/10.48550/arXiv.2201.11616.
    10.48550/arXiv.2201.11616
  7. Miguel Silva; Henriques, Rui; Sara C. Madeira. "User-Specific Bicluster-based Collaborative Filtering: Handling Preference Locality, Sparsity and Subjectivity". 2022. https://doi.org/10.48550/arXiv.2211.08366.
    10.48550/arXiv.2211.08366
  8. Marta Bubicz; Elisabete Arsénio; Barateiro, José; Henriques, Rui; Bubicz, M.; Arsenio, E.; Henriques, R.; Barateiro, J.. "Sustainable Urban Mobility Measures in Response to Covid-19 a Systematic Literature Review and Emerging Policy Challenges". 2022. https://dx.doi.org/10.2139/ssrn.4055178.
    10.2139/ssrn.4055178
  9. Sardinha, C.; Finamore, A.C.; Henriques, R.. "Context-aware demand prediction in bike sharing systems: Incorporating spatial, meteorological and calendrical context". 2021. https://doi.org/10.48550/arXiv.2105.01125.
    10.48550/arXiv.2105.01125
  10. Henriques, Rui; Inês Lynce; Vasco Manquinho. "On When and How to use SAT to Mine Frequent Itemsets". 2012. https://doi.org/10.48550/arXiv.1207.6253.
    10.48550/arXiv.1207.6253
Thesis / Dissertation
  1. Henriques, Rui. "Learning from High-Dimensional Data using Local Descriptive Models". PhD, Universidade de Lisboa Instituto Superior Técnico, 2016. http://web.ist.utl.pt/rmch/research/publications/phd.
  2. Henriques, Rui. "Object-centered Process Modeling: Towards a Modeling Approach for Data-Intensive Systems". Master, Universidade de Lisboa Instituto Superior Técnico, 2010. http://web.ist.utl.pt/~rmch/upload/publications/Object-centered%20Process%20Modeling%20-%20Master%20Thesis%20(Rui%20Henriques).pdf.

Other

Software
  1. Henriques, Rui. "38 publicly available software packages provided under GNU Public Licenses". http://web.ist.utl.pt/rmch/research/software. 2023.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/12 Advances on Explainable AI: from Description to Prediction COMPAMA
NTNU (Norway)
2024/07 Intelligent Health Systems: Breakthroughs at INESC-ID Encontro Ciência
(Porto, Portugal)
2024/06 Inteligência Artificial, Saúde e Pegada Ecológica Celebrações do Dia do Médico, Aula Magna, Universidade de Lisboa
ULS Santa Maria / FMUL (Portugal)
2023/06 Meeting some of the AI Potentials for Human Health: A Journey grounded on the Captivating Experiences of a Data Sciences Fraunhofer Open Sessions, Lisbon/WEB
2023/04 Machine Learning in Bioinformatics: New Discoveries and Challenges VIII Semana da Bioengenharia
2022/11 AI in Psychiatry: Prospects for Prodormal Psychosis XV National Congress of Psychiatry, Palácio de Congressos do Algarve
2022/09 Impactos Societais – Serviços Digitais à Dociedade Jornadas da Assembleia de Escola 2022, Instituto Superior Técnico
2021/11 Omics and Psychiatry: Data Science redefining Mental Health XV National Congress of Psychiatry, Lisbon
2021/07 Predicting Tissue-specific Regulatory Activity: Myths and Opportunities Fundacion Progreso y Salud (FPS), Seville, Spain
2020/02 Mining Temporal Data: A Systemic View DELIX 2020
2020/01 Context-situated Descriptive, Predictive and Prescriptive Urban Data Analytics Fundação para a Ciência e Tecnologia (FCT), Lisbon
2019/11 Trustwhorthy Descriptors and Predictors: Statistically Assessing Decisions IPO, Porto
2019/03 Context-aware Learning in Biomedical and Urban Data Domains RISE-SICS, Sweeden
2018/10 Integrative Learning from Urban Data to Support Sustainable City Mobility Decisions Encontro com Ministros, Instituto Nacional de Estatística (INE)
2017/08 Classification Decisions with Guarantees of Statistical Significance Kyushu University, Fukuoka, Japan
2015/04 Learning from High-Dimensional Data: Myths and Pitfalls Rensselaer Polytechnic Institute, Troy, United States
2014 Selected conference talks: - HICSS @ Waikoloa, Hawaii, 1/2014 - Intelligent Tutoring Systems @ Kingston, Jamaica, 6/2019 - EAI MobiQuitous @ Japan/WEB, 12/2020 Diverse conferences
2013/04 Mining Patterns in Repositories of Health Records: Methods, Revelations and Implications University of Texas at Austin, Austin US
2012/09 On How to Learn from Electrodermal Activity Data to Decode Emotions in HRI University of Valencia, Valencia, Spain
2010/09 Object-centered Process Modeling: Principles to Model Data-intensive Systems Stevens Institute of Technology, Hoboken, NY, United States

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2022 - Current Multi-omics pattern discovery in systems oncology
Supervisor of André Patrício
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022 - Current Real-time analytics on high fidelity synchronized measurements
Co-supervisor of Han Shao
Norges teknisk-naturvitenskapelige universitet, Norway
2021 - Current Glycoproteogenomics in colorectal cancer using deep learning approaches
Supervisor of Daniel Gonçalves
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - Current Descriptive and predictive pattern-centric markers from annotated tensor data
Supervisor of Leonardo Alexandre
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - Current Modeling actionable spatiotemporal dynamics from heterogeneous urban data
Supervisor of Miguel Garção Silva
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - Current Knowledge acquisition from dynamic multi-layered networks
Supervisor of João Aparício
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - Current Spatiotemporal Pattern Analysis of Big Data in Engineering Systems
Supervisor of Sofia Cerqueira
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - Current Anomoulous and emerging pattern discovery from spatiotemporal data
Supervisor of Leonor Pimenta
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - 2025 High-throughput in-silico characterization of 3D astrocyte-neuron cell cultures
Supervisor of Maria Beatriz Fernandes
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - 2024 Chatbot decision support in adaptive, domain-guided, and sentiment-rich settings
Supervisor of Eduardo Machado
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - 2024 Predicting Transcriptional Signatures in the Brain from Molecular Screens Of Peripheral Tissues
Supervisor of Alexandra Pestana Rodrigues
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - 2024 Mapping the Spatial Distribution of Neurotransmission Markers using Postmortem Cohorts
Supervisor of Miguel Moreira
2022 - 2024 Context-aware forecasting of blood donation and demand for efficient nationwide management of blood products
Supervisor of Miguel Dauphinet Barros
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022 - 2024 Psychopharmacoepidemiological trends in Portugal
Supervisor of David Belchior
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2024 Triclustering three-way temporal and heterogeneous data : targeting predictive and descriptive tasks for biomedical applications
Supervisor of Diogo Soares
 Doutoramento em Eng. Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2023 Context-based predictive models for medical emergencies
Supervisor of João Palet
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022 - 2023 Modeling of blood activity in Portugal to support sourcing and campaign decisions
Supervisor of José Diogo Castro
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022 - 2023 Chatbot decision support in adaptive, domain-guided, and sentiment-rich settings
Supervisor of Eduardo Machado
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2023 Spatiotemporal patterns of emergency prevalence and response in Portugal
Supervisor of Francisco Barata
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - 2023 EEG to fMRI Synthesis
Supervisor of David Calhas
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2023 EEG to fMRI Synthesis
Supervisor of David Calhas (80980)
 Doutoramento em Eng. Informática
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022 Detecting student collusion in online test environments from answer agreement
Supervisor of Mariana Carrasco
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022 Optimizing bus networks from multimodal travel flows
Supervisor of Vasco Silva
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022 Fraud detection in multiple choice exams from question answer times
Supervisor of Pedro Caldeira
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022 Local transcriptomic patterns of regulatory response to infection by SARS-CoV-2
Supervisor of Pedro Rodrigues
Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - 2022 Exploring and forecasting nation-wide blood donations and demand
Supervisor of Mariana Brejo
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - 2021 Autonomous time series data processing on historical and real-time settings
Supervisor of Ricardo Sousa
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - 2021 Are national hospitals suitably funded according to activity, quality, access and expenses?
Co-supervisor of Rodrigo Graça
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - 2021 Neuroimage consolidation from a grid of hospitals to externally validate predictors
Supervisor of Rui Nóbrega
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - 2021 Modeling and assessing resilience in multimodal transportation systems
Supervisor of João Aparício
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - 2021 Differential regulatory response of Hodgkin’s Lymphoma according to PET result
Supervisor of André Patrício
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2020 Discovery of actionable patterns in road traffic
Supervisor of Francisco Neves
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2020 Clinical prognosis and risk prediction of postoperative complications in cancer patients
Supervisor of Daniel Gonçalves
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2020 Unsupervised anomaly detection in water systems using recurrent neural networks
Supervisor of Margarida Costa
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2020 Describing and predicting demand in Lisbon’s public Bike sharing system
Supervisor of Cláudio Sardinha
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2020 Drone Mission Review in Virtual Reality
Co-supervisor of Ricardo Mota
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2020 Multimodal analysis of transport in the city of Lisbon
Supervisor of Carlos Lemonde Macedo
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2020 Modeling of water distribution network dynamics using multivariate time series data
Supervisor of Susana Gomes
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2020 Discriminative pattern mining in oncological data to understand surgical risk factors
Supervisor of Leonardo Alexandre
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2020 End-to-end traffic flow analysis of public transport data in the city of Lisbon
Supervisor of Sofia Cerqueira
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - 2019 Contextual outlier detection in traffic data
Supervisor of Inês Leite
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2019 Learning from heterogeneous data with block-wise missings to aid psychiatric diagnoses
Supervisor of Pedro Lindeza
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2019 Schizophrenia diagnosis from electroencephalography with contrastive learning
Supervisor of David Calhas
Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - 2019 Unsupervised concept analysis in legal documents
Supervisor of Pavlo Kovalchuck
2018 - 2019 Mining temporal patterns from multivariate time series data to aid dementia diagnosis
Supervisor of José Mota
Universidade de Lisboa Instituto Superior Técnico, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2019 - 2019 Oceans of Energy Innovation School (international summer school promoted by EIT InnoEnergy) (2019 - 2019) KIC InnoEnergy SE, Netherlands
2018 - 2018 KIC IE bootcamp (international summer school promoted by EIT InnoEnergy) (2018 - 2018) KIC InnoEnergy SE, Netherlands

Ad Hoc journal article review

Journal title (ISSN) Publisher
2016 - Current Periodic Reviewer for >20 Computer Science Q1 journals, including: Pattern Recognition, ACM TOMM, Knowledge-based Systems, DAMI, Constraints, Interaction Studies, Soft Computing, Frontiers in Big Data, IEEE Access, IEEE T-ITS, AIHC, Journal of Big Data, etc. https://www.webofscience.com/wos/author/record/1511268
2016 - Current Periodic Reviewer for >10 Biomedical Q1 journals, including: Scientific Reports (Nature), Bioinformatics (Oxford), BMC Bioinf., Archives of Gerontology and Geriatrics, Briefings in Bioinf. (Oxford), Comput. Biology and Chemistry, IEEE TCBM, Frontiers in Genetic, etc. https://www.webofscience.com/wos/author/record/1511268

Committee member

Activity description
Role 		Institution / Organization
2024 - Current Executive Coordinator of the AI Scientific Area at Dep. Computer Science and Eng. (strategic and operational planning of lecturing activity at a departmental level)
Coordinator
 Universidade de Lisboa Instituto Superior Técnico, Portugal
2024 - Current Executive Coordinator of IDSS Research Group
Coordinator
 Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2021 - Current Coordinator of Information Systems specialization area @ MEIC, DEI
Coordinator
 Universidade de Lisboa Instituto Superior Técnico, Portugal
2019 - Current Yearly member of the program committee of the International Joint Conference on Artificial Intelligence (+20 revised manuscripts), including IJCAI 2019 (28th Ed.); IJCAI 2020 (29th Ed.); IJCAI 2021 (30th Ed.); IJCAI 2022 (31st Ed.); IJCAI 2023 (32nd Ed.) International Joint Conferences on Artificial Intelligence, United States
2019 - Current Regular reviewer (PC) for key conferences, including ICMLA, ICDS, WACV, PACIS, and CPAIOR
2019 - Current Electoral Committee of INESC-ID in 2019, 2021 and 2023 Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Consulting

Activity description Institution / Organization
2023 - Current Technical advisor (first opinion) to GED Ventures

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2022 - Current DASH: Unsupervised Data Analysis (Responsible/Coordinator): 2022, 2023 and 2024 editions Técnico+ Universidade de Lisboa Instituto Superior Técnico, Portugal
2021 - Current Machine Learning (Responsible/Coordinator): 2021/22, 2022/23, 2023/24 editions BSc in Computer Science and Eng., MSc in Biomedical Eng., IST Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - Current Information Processing and Retrieval (Responsible): 2022/2023, 2021/2022, 2020/2021 editions MSc in Computer Science and Eng., MSc in Data Science and Eng. Universidade de Lisboa Instituto Superior Técnico, Portugal
2020 - Current Large-audience MOOCs on Epigenetics and Multi-Omics (Responsible/Creator) since 2020 Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - Current Data Science (Proponent): 2018/19 (1st edition) and 2019/20 (2nd edition) MSc in Information Systems and Computer Engineering Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - Current Autonomous Agents and Multi-Agent Systems (Responsible/Coordinator): 2019/20, 2018/19, 2017/18 editions MSc in Computer Science and Eng., MSc in Data Science and Eng. Universidade de Lisboa Instituto Superior Técnico, Portugal
2017 - Current Health Informatics (Responsible): 2018/19 and 2017/18 editions MSc in Computer Science and Eng., MSc in Biomedical Eng. Universidade de Lisboa Instituto Superior Técnico, Portugal
2009 - 2017 Analysis and Synthesis of Algorithms (2016-2017) Programming Foundations (2016-2017) Software Architectures (2011-2015) Independent Studies II (2011/12) Software Engineering (2009-2010) IT Project Management (2009-2010) Information Systems and Computer Engineering (BSc and MSc levels) Universidade de Lisboa Instituto Superior Técnico, Portugal

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2023 - Current Evaluation Committees for BSc and MSc Degree Recognitions @ DEI and Reitoria Universidade de Lisboa Universidade de Lisboa Instituto Superior Técnico, Portugal
2018 - Current Scientific evaluator of national R&D projects for Agência Nacional de Inovação (ANI)
Evaluator
 Agência Nacional de Inovação SA, Portugal
2018 - Current Scientific evaluator of international R&D project grants, including Austrian Science Fund (FWF) and Czech Science Foundation (GACR), among others
2016 - Current Scientific Evaluation Committee (CAT) for >10 PhDs (presidency in 6), including: Francisco Raposo, Ricardo Rei, Kenny Maia, Rui Maia, Guilherme Varela, João Rico, Ramona Merhej, Mariana Abreu, Zygimantas Jasiunas, Luís Sá-Couto, Bernardo Neves
Evaluator
 Universidade de Lisboa Instituto Superior Técnico, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2016 - Current Scientific Evaluation Committee of +70 MSc theses (listings available at Universidade de Lisboa) Universidade de Lisboa Instituto Superior Técnico, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
Distinctions

Award

2022 Best Senior Researcher Award (Research Excellence)
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2022 IJCAI Distinguished PC Member
International Joint Conferences on Artificial Intelligence, United States
2020 Best Young Researcher Award (Research Excellence)
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2019 Best 2019 Paper
LASIGE Laboratório de Sistemas Informáticos de Grande Escala, Portugal
2016 Research Excellence (best PhD research)
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2014 Three Research Articles elected as Best Papers (2012-2014)
2010 Best Student Award
Caixa Geral de Depositos, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

Other distinction

2022 ULisboa-RedeMov Awards (Best Thesis for Supervisees Francisco Neves in 2021 and João Aparício in 2022)
Universidade de Lisboa, Portugal
2016 Merit Distinction and Honors (PhD excellence)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2010 Pluim Award (Revolutionary ICT-Infrastructures)
Technische Universiteit Delft, Netherlands
2009 Merit Distinction (academic achievements)
Universidade de Lisboa, Portugal
2008 Merit Distinction (academic achievements)
Universidade de Lisboa, Portugal
2007 Merit Distinction (academic achievements)
Universidade de Lisboa, Portugal
2005 Merit Distinction
Escola Secundária Madeira de Torres, Portugal