Sara C. Madeira

Orcid: 0000-0002-1459-8096

Affiliations:
  • University of Lisbon, Instituto Superior Técnico, Portugal


According to our database1, Sara C. Madeira authored at least 82 papers between 2002 and 2024.

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Bibliography

2024
Correction: G-bic: generating synthetic benchmarks for biclustering.
BMC Bioinform., December, 2024

2023
G-bic: generating synthetic benchmarks for biclustering.
BMC Bioinform., December, 2023

Artificial intelligence and statistical methods for stratification and prediction of progression in amyotrophic lateral sclerosis: A systematic review.
Artif. Intell. Medicine, August, 2023

iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge.
Proceedings of the Advances in Information Retrieval, 2023



Survival Analysis for Multiple Sclerosis: Predicting Risk of Disease Worsening.
Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2023), 2023

Investigating the Impact of Environmental Data on ALS Prognosis with Survival Analysis.
Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2023), 2023

2022
Mining Actionable Patterns of Road Mobility From Heterogeneous Traffic Data Using Biclustering.
IEEE Trans. Intell. Transp. Syst., 2022

Learning Prognostic Models Using Disease Progression Patterns: Predicting the Need for Non-Invasive Ventilation in Amyotrophic Lateral Sclerosis.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Impact of metrics on biclustering solution and quality: A review.
Pattern Recognit., 2022

Learning prognostic models using a mixture of biclustering and triclustering: Predicting the need for non-invasive ventilation in Amyotrophic Lateral Sclerosis.
J. Biomed. Informatics, 2022

User-Specific Bicluster-based Collaborative Filtering: Handling Preference Locality, Sparsity and Subjectivity.
CoRR, 2022

Biclustering fMRI time series: a comparative study.
BMC Bioinform., 2022

Posture Risk Assessment in an Automotive Assembly Line Using Inertial Sensors.
IEEE Access, 2022

Explaining Artificial Intelligence Predictions of Disease Progression with Semantic Similarity.
Proceedings of the Working Notes of CLEF 2022 - Conference and Labs of the Evaluation Forum, Bologna, Italy, September 5th - to, 2022


Overview of iDPP@CLEF 2022: The Intelligent Disease Progression Prediction Challenge.
Proceedings of the Working Notes of CLEF 2022 - Conference and Labs of the Evaluation Forum, Bologna, Italy, September 5th - to, 2022

Hierarchical Modelling for ALS Prognosis: Predicting the Progression Towards Critical Events.
Proceedings of the Working Notes of CLEF 2022 - Conference and Labs of the Evaluation Forum, Bologna, Italy, September 5th - to, 2022

2021
FleBiC: Learning classifiers from high-dimensional biomedical data using discriminative biclusters with non-constant patterns.
Pattern Recognit., 2021

Learning dynamic Bayesian networks from time-dependent and time-independent data: Unraveling disease progression in Amyotrophic Lateral Sclerosis.
J. Biomed. Informatics, 2021

G-Tric: generating three-way synthetic datasets with triclustering solutions.
BMC Bioinform., 2021

2020
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, 2020

Towards Triclustering-Based Classification of Three-Way Clinical Data: A Case Study on Predicting Non-invasive Ventilation in ALS.
Proceedings of the Practical Applications of Computational Biology & Bioinformatics, 2020

Patient Stratification Using Clinical and Patient Profiles: Targeting Personalized Prognostic Prediction in ALS.
Proceedings of the Bioinformatics and Biomedical Engineering, 2020

Unravelling Disease Presentation Patterns in ALS Using Biclustering for Discriminative Meta-Features Discovery.
Proceedings of the Bioinformatics and Biomedical Engineering, 2020

Predictive Medicine Using Interpretable Recurrent Neural Networks.
Proceedings of the Pattern Recognition. ICPR International Workshops and Challenges, 2020

2019
Triclustering Algorithms for Three-Dimensional Data Analysis: A Comprehensive Survey.
ACM Comput. Surv., 2019

Predicting assisted ventilation in Amyotrophic Lateral Sclerosis using a mixture of experts and conformal predictors.
CoRR, 2019

An Architecture Based on Fuzzy Systems for Personalized Medicine in ICUs.
Proceedings of the 2019 IEEE International Conference on Fuzzy Systems, 2019

2018
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., 2018

BSig: evaluating the statistical significance of biclustering solutions.
Data Min. Knowl. Discov., 2018

Ensemble learning with Conformal Predictors: Targeting credible predictions of conversion from Mild Cognitive Impairment to Alzheimer's Disease.
CoRR, 2018

Predicting Non-invasive Ventilation in ALS Patients Using Stratified Disease Progression Groups.
Proceedings of the 2018 IEEE International Conference on Data Mining Workshops, 2018

2017
Predicting progression of mild cognitive impairment to dementia using neuropsychological data: a supervised learning approach using time windows.
BMC Medical Informatics Decis. Mak., 2017

Erratum to: BicPAMS: software for biological data analysis with pattern-based biclustering.
BMC Bioinform., 2017

BicPAMS: software for biological data analysis with pattern-based biclustering.
BMC Bioinform., 2017

Towards Trustworthy Predictions of Conversion from Mild Cognitive Impairment to Dementia: A Conformal Prediction Approach.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

Improving Prognostic Prediction from Mild Cognitive Impairment to Alzheimer's Disease Using Genetic Algorithms.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

Towards a reliable prediction of conversion from Mild Cognitive Impairment to Alzheimer's Disease: stepwise learning using time windows.
Proceedings of the 1st ACM Workshop on Medical Informatics and Healthcare, 2017

2016
BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge.
Algorithms Mol. Biol., 2016

BicNET: Flexible module discovery in large-scale biological networks using biclustering.
Algorithms Mol. Biol., 2016

2015
Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

A structured view on pattern mining-based biclustering.
Pattern Recognit., 2015

Prognostic models based on patient snapshots and time windows: Predicting disease progression to assisted ventilation in Amyotrophic Lateral Sclerosis.
J. Biomed. Informatics, 2015

Multi-period classification: learning sequent classes from temporal domains.
Data Min. Knowl. Discov., 2015

Generative modeling of repositories of health records for predictive tasks.
Data Min. Knowl. Discov., 2015

BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules.
Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

Pattern-Based Biclustering with Constraints for Gene Expression Data Analysis.
Proceedings of the Progress in Artificial Intelligence, 2015

2014
LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in <i>Saccharomyces cerevisiae</i>.
Nucleic Acids Res., 2014

BicSPAM: flexible biclustering using sequential patterns.
BMC Bioinform., 2014

BicPAM: Pattern-based biclustering for biomedical data analysis.
Algorithms Mol. Biol., 2014

Mining coherent evolution patterns in education through biclustering.
Proceedings of the 7th International Conference on Educational Data Mining, 2014

2013
Methods for the Efficient Discovery of Large Item-Indexable Sequential Patterns.
Proceedings of the New Frontiers in Mining Complex Patterns, 2013

A Workflow for the Application of Biclustering to Mass Spectrometry Data.
Proceedings of the 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2013

Heuristic approaches for time-lagged biclustering.
Proceedings of the 12th International Workshop on Data Mining in Bioinformatics, 2013

Class Imbalance in the Prediction of Dementia from Neuropsychological Data.
Proceedings of the Progress in Artificial Intelligence, 2013

2012
Towards a Classification Approach using Meta-Biclustering: Impact of Discretization in the Analysis of Expression Time Series.
J. Integr. Bioinform., 2012

AliBiMotif: Integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences.
Int. J. Data Min. Bioinform., 2012

Parallel e-CCC-Biclustering: Mining Approximate Temporal Patterns in Gene Expression Time Series Using Parallel Biclustering.
Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2012

Prognostic Prediction Using Clinical Expression Time Series: Towards a Supervised Learning Approach Based on Meta-biclusters.
Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2012

2011
PINTA: a web server for network-based gene prioritization from expression data.
Nucleic Acids Res., 2011

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in <i>Saccharomyces cerevisiae</i> through a web services interface.
Nucleic Acids Res., 2011

Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series.
J. Integr. Bioinform., 2011

TFRank: network-based prioritization of regulatory associations underlying transcriptional responses.
Bioinform., 2011

Biclustering-Based Classification of Clinical Expression Time Series: A Case Study in Patients with Multiple Sclerosis.
Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2011

Baiacu: A Tool for the Visual Analysis of the <i>Saccharomyces Cerevisiae</i> Regulatory Network.
Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2011

2010
Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.
Nucleic Acids Res., 2010

Network-Based Disease Candidate Gene Prioritization: Towards Global Diffusion in Heterogeneous Association Networks.
Proceedings of the 1st Workshop on Dynamic Networks and Knowledge Discovery, 2010

<i>e</i>-BiMotif: Combining Sequence Alignment and Biclustering to Unravel Structured Motifs.
Proceedings of the Advances in Bioinformatics, 2010

2009
A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series.
Algorithms Mol. Biol., 2009

High Level Thread-Based Competitive Or-Parallelism in Logtalk.
Proceedings of the Practical Aspects of Declarative Languages, 2009

Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis.
Proceedings of the Distributed Computing, 2009

2008
Thread-Based Competitive Or-Parallelism.
Proceedings of the Logic Programming, 24th International Conference, 2008

2007
An Efficient Biclustering Algorithm for Finding Genes with Similar Patterns in Time-series Expression Data.
Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2005
A Linear Time Biclustering Algorithm for Time Series Gene Expression Data.
Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

2004
Biclustering Algorithms for Biological Data Analysis: A Survey.
IEEE ACM Trans. Comput. Biol. Bioinform., 2004

2003
Modeling charity donations using target selection for revenue maximization.
Proceedings of the 12th IEEE International Conference on Fuzzy Systems, 2003

A Data Mining Approach to Credit Risk Evaluation and Behaviour Scoring.
Proceedings of the Progress in Artificial Intelligence, 2003

2002
A comparative study of fuzzy target selection methods in direct marketing.
Proceedings of the 2002 IEEE International Conference on Fuzzy Systems, 2002


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