Sara C. Madeira

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 47

Top Topics

Disease Progression

Biomedical Data

Mild Cognitive Impairment

Conformal Prediction

Top Venues

CLEF (Working Notes)

J. Biomed. Informatics

Pattern Recognit.

Publications

Giovanni Birolo, Pietro Bosoni, Guglielmo Faggioli, Helena Aidos, Roberto Bergamaschi, Paola Cavalla, Adriano Chiò, Arianna Dagliati, Mamede de Carvalho, Giorgio Maria Di Nunzio, Piero Fariselli, Jose Manuel García Dominguez, Marta Gromicho, Alessandro Guazzo, Enrico Longato, Sara C. Madeira, Umberto Manera, Stefano Marchesin, Laura Menotti, Gianmaria Silvello, Eleonora Tavazzi, Erica Tavazzi, Isotta Trescato, Martina Vettoretti, Barbara Di Camillo, Nicola Ferro
Overview of iDPP@CLEF 2024: The Intelligent Disease Progression Prediction Challenge. CLEF (Working Notes) (2024)
Eduardo N. Castanho, João Lobo, Rui Henriques, Sara C. Madeira
Correction: G-bic: generating synthetic benchmarks for biclustering. BMC Bioinform. 25 (1) (2024)
Eduardo N. Castanho, Helena Aidos, Sara C. Madeira
Biclustering data analysis: a comprehensive survey. Briefings Bioinform. 25 (4) (2024)
Diogo F. Soares, Rui Henriques, Sara C. Madeira
Comprehensive assessment of triclustering algorithms for three-way temporal data analysis. Pattern Recognit. 150 (2024)
Andreia S. Martins, Daniela M. Amaral, Eduardo N. Castanho, Diogo F. Soares, Ruben Branco, Sara C. Madeira, Helena Aidos
Predicting the Functional Rating Scale and Self-Assessment Status of ALS Patients with Sensor Data. CLEF (Working Notes) (2024)
Helena Aidos, Roberto Bergamaschi, Paola Cavalla, Adriano Chiò, Arianna Dagliati, Barbara Di Camillo, Mamede de Carvalho, Nicola Ferro, Piero Fariselli, Jose Manuel García Dominguez, Sara C. Madeira, Eleonora Tavazzi
iDPP@CLEF 2024: The Intelligent Disease Progression Prediction Challenge. ECIR (6) (2024)
Helena Aidos, Roberto Bergamaschi, Paola Cavalla, Adriano Chiò, Arianna Dagliati, Barbara Di Camillo, Mamede de Carvalho, Nicola Ferro, Piero Fariselli, Jose Manuel García Dominguez, Sara C. Madeira, Eleonora Tavazzi
iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge. ECIR (3) (2023)
Erica Tavazzi, Enrico Longato, Martina Vettoretti, Helena Aidos, Isotta Trescato, Chiara Roversi, Andreia S. Martins, Eduardo N. Castanho, Ruben Branco, Diogo F. Soares, Alessandro Guazzo, Giovanni Birolo, Daniele Pala, Pietro Bosoni, Adriano Chiò, Umberto Manera, Mamede de Carvalho, Bruno Miranda, Marta Gromicho, Inês Alves, Riccardo Bellazzi, Arianna Dagliati, Piero Fariselli, Sara C. Madeira, Barbara Di Camillo
Artificial intelligence and statistical methods for stratification and prediction of progression in amyotrophic lateral sclerosis: A systematic review. Artif. Intell. Medicine 142 (2023)
Ruben Branco, Joana Barros Valente, Andreia S. Martins, Diogo F. Soares, Eduardo N. Castanho, Sara C. Madeira, Helena Aidos
Survival Analysis for Multiple Sclerosis: Predicting Risk of Disease Worsening. CLEF (Working Notes) (2023)
Guglielmo Faggioli, Alessandro Guazzo, Stefano Marchesin, Laura Menotti, Isotta Trescato, Helena Aidos, Roberto Bergamaschi, Giovanni Birolo, Paola Cavalla, Adriano Chiò, Arianna Dagliati, Mamede de Carvalho, Giorgio Maria Di Nunzio, Piero Fariselli, Jose Manuel García Dominguez, Marta Gromicho, Enrico Longato, Sara C. Madeira, Umberto Manera, Gianmaria Silvello, Eleonora Tavazzi, Erica Tavazzi, Martina Vettoretti, Barbara Di Camillo, Nicola Ferro
Overview of iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge. CLEF (Working Notes) (2023)
Ruben Branco, Diogo F. Soares, Andreia S. Martins, Joana Barros Valente, Eduardo N. Castanho, Sara C. Madeira, Helena Aidos
Investigating the Impact of Environmental Data on ALS Prognosis with Survival Analysis. CLEF (Working Notes) (2023)
Guglielmo Faggioli, Alessandro Guazzo, Stefano Marchesin, Laura Menotti, Isotta Trescato, Helena Aidos, Roberto Bergamaschi, Giovanni Birolo, Paola Cavalla, Adriano Chiò, Arianna Dagliati, Mamede de Carvalho, Giorgio Maria Di Nunzio, Piero Fariselli, Jose Manuel García Dominguez, Marta Gromicho, Enrico Longato, Sara C. Madeira, Umberto Manera, Gianmaria Silvello, Eleonora Tavazzi, Erica Tavazzi, Martina Vettoretti, Barbara Di Camillo, Nicola Ferro
Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2023. CLEF (2023)
Eduardo N. Castanho, João Lobo, Rui Henriques, Sara C. Madeira
G-bic: generating synthetic benchmarks for biclustering. BMC Bioinform. 24 (1) (2023)
Eduardo N. Castanho, Helena Aidos, Sara C. Madeira
Biclustering fMRI time series: a comparative study. BMC Bioinform. 23 (1) (2022)
Ruben Branco, Diogo F. Soares, Andreia S. Martins, Eleonora Auletta, Eduardo N. Castanho, Susana Nunes, Filipa Serrano, Rita Torres Sousa, Catia Pesquita, Sara C. Madeira, Helena Aidos
Hierarchical Modelling for ALS Prognosis: Predicting the Progression Towards Critical Events. CLEF (Working Notes) (2022)
Andreia S. Martins, Marta Gromicho, Susana Pinto, Mamede de Carvalho, Sara C. Madeira
Learning Prognostic Models Using Disease Progression Patterns: Predicting the Need for Non-Invasive Ventilation in Amyotrophic Lateral Sclerosis. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (5) (2022)
Francisco Neves, Anna Carolina Finamore, Sara C. Madeira, Rui Henriques
Mining Actionable Patterns of Road Mobility From Heterogeneous Traffic Data Using Biclustering. IEEE Trans. Intell. Transp. Syst. 23 (7) (2022)
Marta D. M. Noronha, Rui Henriques, Sara C. Madeira, Luis Enrique Zárate
Impact of metrics on biclustering solution and quality: A review. Pattern Recognit. 127 (2022)
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. J. Biomed. Informatics 134 (2022)
Alessandro Guazzo, Isotta Trescato, Enrico Longato, Enidia Hazizaj, Dennis Dosso, Guglielmo Faggioli, Giorgio Maria Di Nunzio, Gianmaria Silvello, Martina Vettoretti, Erica Tavazzi, Chiara Roversi, Piero Fariselli, Sara C. Madeira, Mamede de Carvalho, Marta Gromicho, Adriano Chiò, Umberto Manera, Arianna Dagliati, Giovanni Birolo, Helena Aidos, Barbara Di Camillo, Nicola Ferro
Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2022. CLEF (2022)
Susana Nunes, Rita Torres Sousa, Filipa Serrano, Ruben Branco, Diogo F. Soares, Andreia S. Martins, Eleonora Auletta, Eduardo N. Castanho, Sara C. Madeira, Helena Aidos, Catia Pesquita
Explaining Artificial Intelligence Predictions of Disease Progression with Semantic Similarity. CLEF (Working Notes) (2022)
Maria Lua Nunes, Duarte Folgado, Carlos Fujão, Luís Silva, João Rodrigues, Pedro Matias, Marília Barandas, André V. Carreiro, Sara C. Madeira, Hugo Gamboa
Posture Risk Assessment in an Automotive Assembly Line Using Inertial Sensors. IEEE Access 10 (2022)
Alessandro Guazzo, Isotta Trescato, Enrico Longato, Enidia Hazizaj, Dennis Dosso, Guglielmo Faggioli, Giorgio Maria Di Nunzio, Gianmaria Silvello, Martina Vettoretti, Erica Tavazzi, Chiara Roversi, Piero Fariselli, Sara C. Madeira, Mamede de Carvalho, Marta Gromicho, Adriano Chiò, Umberto Manera, Arianna Dagliati, Giovanni Birolo, Helena Aidos, Barbara Di Camillo, Nicola Ferro
Overview of iDPP@CLEF 2022: The Intelligent Disease Progression Prediction Challenge. CLEF (Working Notes) (2022)
Miguel G. Silva, Rui Henriques, Sara C. Madeira
User-Specific Bicluster-based Collaborative Filtering: Handling Preference Locality, Sparsity and Subjectivity. CoRR (2022)
João Lobo, Rui Henriques, Sara C. Madeira
G-Tric: generating three-way synthetic datasets with triclustering solutions. BMC Bioinform. 22 (1) (2021)
Tiago Leão, Sara C. Madeira, Marta Gromicho, Mamede de Carvalho, Alexandra M. Carvalho
Learning dynamic Bayesian networks from time-dependent and time-independent data: Unraveling disease progression in Amyotrophic Lateral Sclerosis. J. Biomed. Informatics 117 (2021)
Rui Henriques, Sara C. Madeira
FleBiC: Learning classifiers from high-dimensional biomedical data using discriminative biclusters with non-constant patterns. Pattern Recognit. 115 (2021)
Sofia Pires, Marta Gromicho, Susana Pinto, Mamede de Carvalho, Sara C. Madeira
Patient Stratification Using Clinical and Patient Profiles: Targeting Personalized Prognostic Prediction in ALS. IWBBIO (2020)
André Ferreira, Sara C. Madeira, Marta Gromicho, Mamede de Carvalho, Susana Vinga, Alexandra M. Carvalho
Predictive Medicine Using Interpretable Recurrent Neural Networks. ICPR Workshops (1) (2020)
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. IWBBIO (2020)
Telma Pereira, Sandra Cardoso, Manuela Guerreiro, Alexandre de Mendonça, Sara C. Madeira, Alzheimer's Disease Neuroimaging Initiative
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. J. Biomed. Informatics 101 (2020)
Diogo Soares, Rui Henriques, 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. PACBB (2020)
Telma Pereira, Sofia Pires, Marta Gromicho, Susana Pinto, Mamede de Carvalho, Sara C. Madeira
Predicting assisted ventilation in Amyotrophic Lateral Sclerosis using a mixture of experts and conformal predictors. CoRR (2019)
Rui Henriques, Sara C. Madeira
Triclustering Algorithms for Three-Dimensional Data Analysis: A Comprehensive Survey. ACM Comput. Surv. 51 (5) (2019)
João M. C. Sousa, Susana M. Vieira, João P. Carvalho, Sara C. Madeira, Leo A. Celi, Stan N. Finkelstein
An Architecture Based on Fuzzy Systems for Personalized Medicine in ICUs. FUZZ-IEEE (2019)
Telma Pereira, Sandra Cardoso, Dina Silva, Manuela Guerreiro, Alexandre de Mendonça, Sara C. Madeira
Ensemble learning with Conformal Predictors: Targeting credible predictions of conversion from Mild Cognitive Impairment to Alzheimer's Disease. CoRR (2018)
Sofia Pires, Marta Gromicho, Susana Pinto, Mamede de Carvalho, Sara C. Madeira
Predicting Non-invasive Ventilation in ALS Patients Using Stratified Disease Progression Groups. ICDM Workshops (2018)
Telma Pereira, Francisco L. Ferreira, Sandra Cardoso, Dina Silva, Alexandre de Mendonça, Manuela Guerreiro, Sara C. Madeira
Neuropsychological predictors of conversion from mild cognitive impairment to Alzheimer's disease: a feature selection ensemble combining stability and predictability. BMC Medical Informatics Decis. Mak. 18 (1) (2018)
Rui Henriques, Sara C. Madeira
BSig: evaluating the statistical significance of biclustering solutions. Data Min. Knowl. Discov. 32 (1) (2018)
Rui Henriques, Francisco L. Ferreira, Sara C. Madeira
Erratum to: BicPAMS: software for biological data analysis with pattern-based biclustering. BMC Bioinform. 18 (1) (2017)
Telma Pereira, Luís Lemos, Sandra Cardoso, Dina Silva, Ana Rodrigues, Isabel Santana, Alexandre de Mendonça, Manuela Guerreiro, Sara C. Madeira
Predicting progression of mild cognitive impairment to dementia using neuropsychological data: a supervised learning approach using time windows. BMC Medical Informatics Decis. Mak. 17 (1) (2017)
Telma Pereira, Sandra Cardoso, Dina Silva, Alexandre de Mendonça, Manuela Guerreiro, Sara C. Madeira
Towards Trustworthy Predictions of Conversion from Mild Cognitive Impairment to Dementia: A Conformal Prediction Approach. PACBB (2017)
Rui Henriques, Francisco L. Ferreira, Sara C. Madeira
BicPAMS: software for biological data analysis with pattern-based biclustering. BMC Bioinform. 18 (1) (2017)
Telma Pereira, Alexandre de Mendonça, Francisco L. Ferreira, Sara C. Madeira, Manuela Guerreiro
Towards a reliable prediction of conversion from Mild Cognitive Impairment to Alzheimer's Disease: stepwise learning using time windows. MIH@KDD (2017)
Francisco L. Ferreira, Sandra Cardoso, Dina Silva, Manuela Guerreiro, Alexandre de Mendonça, Sara C. Madeira
Improving Prognostic Prediction from Mild Cognitive Impairment to Alzheimer's Disease Using Genetic Algorithms. PACBB (2017)
Rui Henriques, Sara C. Madeira
BicNET: Flexible module discovery in large-scale biological networks using biclustering. Algorithms Mol. Biol. 11 (2016)
Rui Henriques, Sara C. Madeira
BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge. Algorithms Mol. Biol. 11 (2016)
André Valério Carreiro, Pedro M. T. Amaral, Susana Pinto, Pedro Tomás, Mamede de Carvalho, Sara C. Madeira
Prognostic models based on patient snapshots and time windows: Predicting disease progression to assisted ventilation in Amyotrophic Lateral Sclerosis. J. Biomed. Informatics 58 (2015)
Rui Henriques, Sara C. Madeira
Pattern-Based Biclustering with Constraints for Gene Expression Data Analysis. EPIA (2015)
Rui Henriques, Cláudia Antunes, Sara C. Madeira
Generative modeling of repositories of health records for predictive tasks. Data Min. Knowl. Discov. 29 (4) (2015)
Rui Henriques, Sara C. Madeira, Cláudia Antunes
Multi-period classification: learning sequent classes from temporal domains. Data Min. Knowl. Discov. 29 (3) (2015)
Rui Henriques, Cláudia Antunes, Sara C. Madeira
A structured view on pattern mining-based biclustering. Pattern Recognit. 48 (12) (2015)
Rui Henriques, Sara C. Madeira
Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (4) (2015)
Rui Henriques, Sara C. Madeira
BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules. WABI (2015)
Rui Henriques, Sara C. Madeira
BicPAM: Pattern-based biclustering for biomedical data analysis. Algorithms Mol. Biol. 9 (2014)
André Vale, Sara C. Madeira, Cláudia Antunes
Mining coherent evolution patterns in education through biclustering. EDM (2014)
Rui Henriques, Sara C. Madeira
BicSPAM: flexible biclustering using sequential patterns. BMC Bioinform. 15 (2014)
Joana P. Gonçalves, Sara C. Madeira
LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (5) (2014)
Joana P. Gonçalves, Sara C. Madeira
Heuristic approaches for time-lagged biclustering. BIOKDD (2013)
Hugo López-Fernández, Miguel Reboiro-Jato, Sara C. Madeira, Rubén López-Cortés, J. D. Nunes-Miranda, Hugo Miguel Santos, Florentino Fdez-Riverola, Daniel Glez-Peña
A Workflow for the Application of Biclustering to Mass Spectrometry Data. PACBB (2013)
Cecília Nunes, Dina Silva, Manuela Guerreiro, Alexandre de Mendonça, Alexandra M. Carvalho, Sara C. Madeira
Class Imbalance in the Prediction of Dementia from Neuropsychological Data. EPIA (2013)
Rui Henriques, Cláudia Antunes, Sara C. Madeira
Methods for the Efficient Discovery of Large Item-Indexable Sequential Patterns. NFMCP (2013)
André Valério Carreiro, Artur J. Ferreira, Mário A. T. Figueiredo, Sara C. Madeira
Prognostic Prediction Using Clinical Expression Time Series: Towards a Supervised Learning Approach Based on Meta-biclusters. PACBB (2012)
Filipe Cristóvão, Sara C. Madeira
Parallel e-CCC-Biclustering: Mining Approximate Temporal Patterns in Gene Expression Time Series Using Parallel Biclustering. PACBB (2012)
Joana P. Gonçalves, Yves Moreau, Sara C. Madeira
AliBiMotif: Integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences. Int. J. Data Min. Bioinform. 6 (2) (2012)
André Valério Carreiro, Orlando Anunciação, João A. Carriço, Sara C. Madeira
Biclustering-Based Classification of Clinical Expression Time Series: A Case Study in Patients with Multiple Sclerosis. PACBB (2011)
Dário Abdulrehman, Pedro T. Monteiro, Miguel C. Teixeira, Nuno P. Mira, Artur B. Lourenço, Sandra Costa dos Santos, Tânia Rodrigues Cabrito, Alexandre P. Francisco, Sara C. Madeira, Ricardo Santos Aires, Arlindo L. Oliveira, Isabel Sá-Correia, Ana T. Freitas
through a web services interface. Nucleic Acids Res. 39 (Database-Issue) (2011)
Ricardo Santos Aires, João A. Carriço, Alexandre P. Francisco, Sara C. Madeira
Regulatory Network. PACBB (2011)
Joana P. Gonçalves, Alexandre P. Francisco, Nuno P. Mira, Miguel C. Teixeira, Isabel Sá-Correia, Arlindo L. Oliveira, Sara C. Madeira
TFRank: network-based prioritization of regulatory associations underlying transcriptional responses. Bioinform. 27 (22) (2011)
Daniela Nitsch, Léon-Charles Tranchevent, Joana P. Gonçalves, Josef Korbinian Vogt, Sara C. Madeira, Yves Moreau
PINTA: a web server for network-based gene prioritization from expression data. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Sara C. Madeira, Miguel C. Teixeira, Isabel Sá-Correia, Arlindo L. Oliveira
Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (1) (2010)
Joana P. Gonçalves, Sara C. Madeira, Yves Moreau
Network-Based Disease Candidate Gene Prioritization: Towards Global Diffusion in Heterogeneous Association Networks. NyNaK (2010)
Joana P. Gonçalves, Sara C. Madeira
-BiMotif: Combining Sequence Alignment and Biclustering to Unravel Structured Motifs. IWPACBB (2010)
Ignacio Medina, José Carbonell, Luis Pulido, Sara C. Madeira, Stefan Götz, Ana Conesa, Joaquín Tárraga, Alberto D. Pascual-Montano, Rubén Nogales-Cadenas, Javier Santoyo, Francisco García-García, Martina Marbà, David Montaner, Joaquín Dopazo
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Sara C. Madeira, Arlindo L. Oliveira
A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series. Algorithms Mol. Biol. 4 (2009)
Paulo Moura, Ricardo Rocha, Sara C. Madeira
High Level Thread-Based Competitive Or-Parallelism in Logtalk. PADL (2009)
Sara C. Madeira, Arlindo L. Oliveira
Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis. IWANN (2) (2009)
Paulo Moura, Ricardo Rocha, Sara C. Madeira
Thread-Based Competitive Or-Parallelism. ICLP (2008)
Sara C. Madeira, Arlindo L. Oliveira
An Efficient Biclustering Algorithm for Finding Genes with Similar Patterns in Time-series Expression Data. APBC (2007)
Sara C. Madeira, Arlindo L. Oliveira
A Linear Time Biclustering Algorithm for Time Series Gene Expression Data. WABI (2005)
Sara C. Madeira, Arlindo L. Oliveira
Biclustering Algorithms for Biological Data Analysis: A Survey. IEEE ACM Trans. Comput. Biol. Bioinform. 1 (1) (2004)
Sara C. Madeira, Arlindo L. Oliveira, Catarina S. Conceição
A Data Mining Approach to Credit Risk Evaluation and Behaviour Scoring. EPIA (2003)
João M. C. Sousa, Sara C. Madeira, Uzay Kaymak
Modeling charity donations using target selection for revenue maximization. FUZZ-IEEE (2003)
João M. C. Sousa, Uzay Kaymak, Sara C. Madeira
A comparative study of fuzzy target selection methods in direct marketing. FUZZ-IEEE (2002)