PhD Thesis

  
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   Rui Henriques, 2016, Learning from High-Dimensional Data using Local Descriptive Models, PhD Thesis (approved with distinction and honor), Instituto Superior Técnico, Universidade de Lisboa, Lisboa   

Selected Publications in International Journals

  
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   Rui Henriques and Sara C. Madeira, 2021, FleBiC: Learning classifiers from high-dimensional biomedical data using discriminative biclusters with non-constant patterns, Pattern Recognition, Elsevier
[10.1016/j.patcog.2021.107900]
  

  
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   Leonardo Alexandre, Rafael Costa, Lúcio Lara Santos and Rui Henriques, 2021, Mining pre-surgical patterns able to discriminate post-surgical outcomes in the oncological domain, IEEE Journal of Biomedical and Health Informatics, IEEE EMBS
[10.1109/JBHI.2021.3064786]
  

  
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   Francisco Neves, Anna C. Finamore, Sara C. Madeira and Rui Henriques, 2021, Mining actionable patterns of road mobility from heterogeneous traffic data using biclustering, IEEE Transactions on Intelligent Transportation Systems
[10.1109/TITS.2021.3057240]
  

  
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   André Aparício, Rafael Costa, and Rui Henriques, 2021, COVID-19 in Portugal: predictability of hospitalization, ICU and respiratory-assistance needs, Journal of Medical Internet Research (JMIR)
[doi soon available]
  

  
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   David Calhas, Enrique Romero, Rui Henriques, 2020, On the use of Pairwise Distance Learning for Brain Signal Classification with Limited Observations, Artificial Intelligence in Medicine, Elsevier
[10.1016/j.artmed.2020.101852]
  

  
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   João Lobo, Rui Henriques, Sara C. Madeira, 2020, G-Tric: generating three-way synthetic datasets with triclustering solutions, BMC Bioinformatics, BioMed Central Ltd
[10.1186/s12859-020-03925-4]
  

  
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   Rui Henriques and Sara C. Madeira, 2019, Triclustering Algorithms for Three-Dimensional Data Analysis:
A Comprehensive Survey
, ACM Computing Surveys (CSUR), Volume 51, Issue 5, No. 95, pp. 1-43, ACM New York, NY, USA
[10.1145/3195833]
  

  
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   N.D. Mendes*, R. Henriques*, E. Remy, J. Carneiro Jorge, P.T. Monteiro, C. Chaouiya, 2018, Estimating Attractor Reachability in Asynchronous Logical Models, Frontiers in Physiology, Systems Biology, vol.9, pp.1161 (* co-first authoring)
[10.3389/fphys.2018.01161]
  

  
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   Rui Henriques and Sara C. Madeira, 2018, BSig: Evaluating the Statistical Significance of Biclustering Solutions, Data Mining and Knowledge Discovery, Volume 32, Issue 1, pp 124–161
[10.1007/s10618-017-0521-2]
  

  
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   Rui Henriques, Francisco L. Ferreira and Sara C. Madeira, 2017, BicPAMS: Software for Biological Data Analysis with Pattern-based Biclustering, BMC Bioinformatics, 18:82
[10.1186/s12859-017-149]
  

  
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   Rui Henriques and Sara C. Madeira, 2016, BicNET: Flexible module discovery in large-scale biological networks using biclustering, Algorithms for Molecular Biology, 11:1–30
[10.1186/s13015-016-0074-8]
  

  
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   Rui Henriques and Sara C. Madeira, 2016, BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge, Algorithms for Molecular Biology, 11:1–23
[10.1186/s13015-016-0085-5]
  

  
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   Rui Henriques, Cláudia Antunes and Sara C. Madeira, 2015, Generative Modeling of Repositories of Health Records for Predictive Tasks, Data Mining and Knowledge Discovery, 29(4):999-1032, Springer US
[10.1007/s10618-014-0385-7]
  

  
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   Rui Henriques, Cláudia Antunes and Sara C. Madeira, 2015, A Structured View on Pattern Mining-based Biclustering, Pattern Recognition, 48(12):3941-3958, Elsevier
[http://dx.doi.org/10.1016/j.patcog.2015.06.018]
  

  
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   Rui Henriques and Sara C. Madeira, 2015, Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(4):738-752, IEEE/ACM
[10.1109/TCBB.2014.2388206]
  

  
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   Rui Henriques and Sara C. Madeira, 2014, BicPAM: Pattern-based biclustering for biomedical data analysis, Algorithms for Molecular Biology, 9(1):27-, BioMed Central Ltd
[10.1186/s13015-014-0027-z]
  

  
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   Rui Henriques, Sara C. Madeira and Cláudia Antunes, 2015, Multi-period Classification: Learning Sequent Classes from Temporal Domains, Data Mining and Knowledge Discovery, 29(3):792-819, Springer US
[http://dx.doi.org/10.1007/s10618-014-0376-8]
  

  
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   Rui Henriques and Sara C. Madeira, 2014, BicSPAM: Flexible Biclustering using Sequential Patterns, BMC Bioinformatics, 15:130, BioMed Central Ltd
[doi:10.1186/1471-2105-15-130]
  

Selected Articles in International Conferences

  
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   Leonor P. Silva, Vasco Manquinho, Rui Henriques, 2021, UNIANO: robust and efficient anomaly consensus in time series sensitive to cross-correlated anomaly profiles, In SIAM International Conference on Data Mining (SDM21)
[doi soon available]
  

  
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   David Calhas, Rui Henriques, 2021, fMRI Multiple Missing Values Imputation Regularized by a Recurrent Denoiser, In Artificial Intelligence in Medicine (AIME)
[doi soon available]
  

  
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   Francisco Neves, Anna Finamore, Rui Henriques, 2020, Efficient discovery of emerging patterns in heterogeneous spatiotemporal data from mobile sensors, In 17th EAI International Conference on Mobile and Ubiquitous Systems: Computing, Networking and Services (MobiQuitous)
[doi soon available]
  

  
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   Ricardo Sousa, Conceição Amado, Rui Henriques, 2020, AutoMTS: fully autonomous processing of multivariate time series data from heterogeneous sensor networks, In 16th EAI International Conference on Heterogeneous Networking for Quality, Reliability, Security and Robustness (QShine)
[doi soon available]
  

  
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   Diogo Soares, Rui Henriques, Marta Gromicho, Susana Pinto, Mamede de Carvalho, Sara C. Madeira, 2020, Towards Triclustering-Based Classification of Three-Way Clinical Data: A Case Study on Predicting Non-invasive Ventilation in ALS, In IC on Practical Applications of Computational Biology & Bioinformatics (PACBB), 112-122
[10.1007/978-3-030-54568-0_12]
  

  
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   Pavlo Kovalchuk, Diogo Proença, José Borbinha, Rui Henriques, 2020, Moving from formal towards coherent concept analysis: why, when and how, In The 42nd European Conference on Information Retrieval (ECIR2020)
[10.1007/978-3-030-45439-5_19]
  

  
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   Sofia Cerqueira, Elisabete Arsénio, Rui Henriques, 2020, Integrative analysis of traffic and situational context data to support urban mobility planning, In European Transport Conference (ETC), Milan, Italy   

  
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   Carlos Lemonde, Elisabete Arsénio, Rui Henriques, 2020, Exploring multimodal mobility patterns with big data in the city of Lisbon, In European Transport Conference (ETC), Milan, Italy   

  
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   Inês Leite, Anna Carolina Finamore, Rui Henriques, 2020, Context-sensitive modeling of public transport data, In Transport Research Arena (TRA2020), Helsinki   

  
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   Rui Henriques, Anna Carolina Finamore, Marco Antonio Casanova , 2019, On the Discovery of Educational Patterns using Biclustering, In 15th International Conference on Intelligent Tutoring Systems (ITS), Jamaica
[10.1007/978-3-030-22244-4_17]
  

  
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   Pavlo Kovalchuk, Diogo Proença, José Borbinha, Rui Henriques, 2019, An unsupervised method for concept association analysis in text collections, In 23rd International Conference on Theory and Practice of Digital Libraries (TPDL), Oslo, Norway
[10.1007/978-3-030-30760-8_2]
  

  
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   Rui Henriques, Alexandre P. Francisco, Luís Russo and Hideo Bannai , 2018, Order-preserving Pattern Matching Indeterminate Strings, In 29th Annual Symposium on Combinatorial Pattern Matching (CPM), Qingdao, China
[10.4230/LIPIcs.CPM.2018.2]
  

  
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   Rui Henriques and Sara C. Madeira, 2015, Pattern-based Biclustering with Constraints for Gene Expression Data Analysis, In Computational Methods in Bioinformatics and Systems Biology (EPIA-CMBSB), 326-339, LNAI Series, vol.9273, Springer, Coimbra, Portugal
[10.1007/978-3-319-23485-4_34]
  

  
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   Rui Henriques and Sara C. Madeira, 2015, BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules, In Algorithms in Bioinformatics, 1-15, LNCS Series, vol.9289, Springer Berlin Heidelberg, Atlanta, GA, US
[10.1007/978-3-662-48221-6_1]
  

  
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   Rui Henriques and Cláudia Antunes, 2014, Learning Predictive Models from Integrated Healthcare Data: Extending Pattern-based and Generative Models to Capture Temporal and Cross-Attribute Dependencies, In Hawai International Conference on System Sciences (HICSS), 2562-2569, IEEE Computer Science, Waikoloa, Hawaii
[doi:10.1109/HICSS.2014.322]
  

  
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   Rui Henriques and Cláudia Antunes, 2014, Generative Modeling of Itemset Sequences derived from Real Databases, In IC on Enterprise Information Systems (ICEIS), 264-272, INSTICC, Lisbon, Portugal
[doi:10.5220/0004898302640272]
  

  
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   Rui Henriques and Ana Paiva, 2014, Seven principles to mine flexible behavior from physiological signals for effective emotion recognition and description in affective interactions, In Physiological Computing Systems (PhyCS’14), 75-82, SCITEPRESS, Lisbon, Portugal
[doi:10.5220/0004666400750082]
  

  
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   Rui Henriques and Ana Paiva, 2014, Descriptive Models of Emotion: Learning Useful Abstractions from Physiological Responses during Affective Interactions, In PhyCS Special Session on Recognition of Affect Signals from PhysiologIcal Data for Social Robots (OASIS’14), 393-400, SCITEPRESS, Lisbon, Portugal
[doi:10.5220/0004902703930400]
  

  
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   Rui Henriques, Silvia Moura Pina and Cláudia Antunes, 2013, Temporal Mining of Integrated Healthcare Data: Methods, Revealings and Implications, In SDM’13, 2nd IW on Data Mining for Medicine and Healthcare, 56-64, SIAM, Austin, US   

  
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   Rui Henriques, Sara C. Madeira and Cláudia Antunes, 2013, F2G: Efficient Discovery of Full-Patterns, In ECML/PKDD IW on New Frontiers to Mine Complex Patterns, Springer-Verlag, Prague, Czech Republic   

  
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   Rui Henriques, Ana Paiva and Cláudia Antunes, 2013, Accessing Emotion Patterns from Affective Interactions using Electrodermal Activity, In Affective Computing and Intelligent Interaction (ACII’13), 43-48, IEEE Computer Society, Geneva, Switzerland
[doi:10.1109/ACII.2013.14]
  

  
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   Rui Henriques, Ana Paiva and Cláudia Antunes, 2012, On the Need of New Methods to Mine Electrodermal Activity in Emotion-centered Studies, In AAMAS’12, 8th IW on Agents and Data Mining Interaction, Springer-Verlag LNAI series, Valência, Spain
[http://dx.doi.org/10.1007/978-3-642-36288-0_18]
  

  
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   Rui Henriques and António Rito Silva, 2010, Object-centered Process Modeling: Principles to Model Data-intensive Systems, In Business Process Management Workshops (EdBPM’10), Volume 66 of Lecture Notes in Business Information Processing, 683-694, Springer Berlin Heidelberg, New York, U.S.
[http://dx.doi.org/10.1007/978-3-642-20511-8_62]
  

Other Selected Scientific Publications

  
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   David Calhas and Rui Henriques, 2020, EEG to fMRI Synthesis: Is Deep Learning a Candidate?, arXiv:2009.14133
[https://arxiv.org/abs/2009.14133]
  

  
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   David Calhas and Rui Henriques, 2020, fMRI Multiple Missing Values Imputation Regularized by a Recurrent Denoiser, arXiv:2009.12602
[https://arxiv.org/abs/2009.12602]
  

  
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   André Patrício, Rafael Costa, Rui Henriques, 2020, COVID-19 in Portugal: predictability ofhospitalization, ICU and respiratory-assistance needs, medRxiv 2020.09.29.20203141
[10.1101/2020.09.29.20203141]
  

  
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   Rui Henriques, Inês Lynce and Vasco Manquinho, 2012, On When and How to use SAT to Mine Frequent Itemsets, IST/INESC-ID, CoRR journal, abs/1207.6253, Cornell University Library
[http://arxiv.org/abs/1207.6253]
  

Selected Chapters in Scientific Books

(first author)

  
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   Rui Henriques and Sara C. Madeira, 2015, Towards Robust Performance Guarantees for Models Learned from High-Dimensional Data, Chapter 3, Big Data in Complex Systems: Challenges and Opportunities, Vol. 9 of Studies in Big Data Series, 71-104, Springer International Publishing
[http://dx.doi.org/10.1007/978-3-319-11056-1_3]
  

  
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   Rui Henriques, Cláudia Antunes and Sara C. Madeira, 2014, Methods for the Efficient Discovery of Large Item-Indexable Sequential Patterns, Lecture Notes in Computer Science, 100-116, Springer International Publishing
[10.1007/978-3-319-08407-7_7]

  
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   Rui Henriques and Ana Paiva, 2014, Learning Effective Models of Emotions from Physiological Signals: The Seven Principles, Physiological Computing Systems, Lecture Notes in Computer Science, pp.137-155, Springer Berlin Heidelberg
[10.1007/978-3-662-45686-6_9]

  
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   Rui Henriques and Cláudia Antunes, 2012, On the Need of New Approaches for the Novel Problem of Long-term Prediction over Multi-Dimensional Data, In Computer and Information Science 2012, Volume 429 of Studies in Computational Intelligence, 121-138, Springer Berlin Heidelberg, Shangai, China
[http://dx.doi.org/10.1007/978-3-642-30454-5_9]
  

Additional Scientific Publications

  
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   Rui P. Duarte, Álvaro Simões, Rui Henriques, and Horácio C. Neto, 2018, FPGA-based OpenCL Accelerator for Discovering Temporal Patterns in Gene Expression Data Using Biclustering, In 6th IW on Parallelism in Bioinformatics (PBio’18), pp. 53-62, ACM
[10.1145/3235830.3235836]
  

  
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   Rui Henriques and Sara C. Madeira, 2014, BiP: Effective Discovery of Overlapping Biclusters using
Flexible Plaid Models
, In 13th IW of Data Mining in Bioinformatics (BIOKDD’14), ACM, New York, US
  

  
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   Iolanda Leite, Rui Henriques and Ana Paiva, 2013, Sensors in the Wild: Exploring
Electrodermal Activity in Child-Robot Interaction
, In Human-Robot Interaction (HRI’13), ACM Digital Library, Tokyo, Japan
[10.1109/HRI.2013.6483500]
  

  
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   Rui Henriques, Sara C. Madeira and Cláudia Antunes, 2013, IndexSpan: Efficient Discovery of Item-Indexable Sequential Patterns, In ECML/PKDD IW on New Frontiers to Mine Complex Patterns, Springer-Verlag, Prague, Czech Republic   

  
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   Rui Henriques and Cláudia Antunes, 2012, An Integrated Approach for Healthcare Planning over Multi-Dimensional Data using Long-term Prediction, In Health Information Science, Volume 7231 of Lecture Notes in Computer Science, 36-48, Springer Berlin / Heidelberg, Beijing, China
[http://dx.doi.org/10.1007/978-3-642-29361-0_6]
  

  
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   João Z. Oliveira, Miguel Henriques, and Rui Henriques, 2012, Carbon Markets and Investments: EcoSecurities Investment Case Analysis, In Advanced Analytics for Green and Sustainable Economic Development: Supply Chain Models and Financial Technologies, 15-33, IGI Global
[doi:10.4018/978-1-61350-156-6.ch002]
  

  
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   Rui Henriques, 2010, Object-centered Process Modeling: Towards a Modeling Approach for Data-Intensive Systems, Lisboa, MSc dissertation [full, summary]   

  
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   Rui Henriques, Miguel Henriques and João Z. Oliveira, 2010, Analysis of an Investment Decision in the Carbon Market: The EcoSecurities’ VAM Project, In IASK’10 proceedings, Oviedo, Spain   

  
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   Rui Henriques, Miguel Henriques and Phil Hunte, 2009, Meta-heuristic Approaches Consolidation for the Edge-Weighted K-Cardinality Tree Problem, Technical Report (IN4082), Technical University of Delft   

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