Alexandra M. Carvalho

Research interests | Publications | Software | Teaching | Short CV

Journal Papers

• Carolina Barata, Ana Rodrigues, Helena Canhão, Susana Vinga, Alexandra M. Carvalho, Predicting biologic therapy outcome in spondyloarthritis' patients using joint models for longitudinal and survival analysis, JMIR Medical Informatics 9(7):e26823 (2021).

• Cláudia Constantino, Alexandra M. Carvalho, Susana Vinga, Coupling sparse Cox models with clustering of longitudinal transcriptomics data for trauma prognosis, BioData Mining 14, 25 (2021).

• Tiago Leão, Sara C. Madeira, Marta Gromicho, Mamede de Carvalho and Alexandra M. Carvalho, Learning dynamic Bayesian networks from time-dependent and time-independent data: Unraveling disease progression in Amyotrophic Lateral Sclerosis, Journal of Biomedical Informatics 117 (2021). [sdtDBN@GitHub] [sdtDBNsGUI@GitHub]

• Jorge L. Serras, Susana Vinga and Alexandra M. Carvalho, Outlier detection for multivariate time series using dynamic Bayesian networks, Applied Sciences 11(4):1955 (2021). [pdf] [METEOR@GitHub]

• Mariano Lemus, João P. Beirão, Nikola Paunkovic, Alexandra M. Carvalho and Paulo Mateus, Information-Theoretical Criteria for Characterizing the Earliness of Time-Series Data, Entropy 22(1):49 (2020). [pdf] [MCEC@GitHub]

• Kishan Rama, Helena Canhão, Alexandra M. Carvalho and Susana Vinga, AliClu - Temporal sequence alignment for clustering longitudinal clinical data, BMC Medical Informatics and Decision Making 19(1):289 (2019). [pdf] [AliClu@GitHub]

• Hugo Loureiro, Eunice Carrasquinha, Irina Alho, Arlindo R. Ferreira, Luís Costa, Alexandra M. Carvalho and Susana Vinga, Modelling cancer outcomes of bone metastatic patients: combining survival data with N-Telopeptide of type I collagen (NTX) dynamics through joint models, BMC Medical Informatics and Decision Making 19(1):13 (2019). [pdf]

• Margarida Sousa and Alexandra M. Carvalho, Polynomial-Time Algorithm for Learning Optimal BFS-Consistent Dynamic Bayesian Networks, Entropy 20(4):274 (2018). [pdf] [bcDBN@GitHub]

• Rui P. Guerra, Alexandra M. Carvalho and Paulo Mateus, Model selection for clustering of pharmacokinetic responses, Computer Methods and Programs in Biomedicine 162:11-18 (2018). [pdf] [PKClusteringMDL@GitHub]

• Elson Tomás, Susana Vinga and Alexandra M. Carvalho, Unsupervised learning of pharmacokinetic responses, Computational Statistics 32(2):409-428 (2017). [pdf]

• Alexandra M. Carvalho, Pedro Adão and Paulo Mateus, Hybrid learning of Bayesian multinets for binary classification, Pattern Recognition 47(10):3438-3450 (2014). [pdf]

• Alexandra M. Carvalho, Pedro Adão and Paulo Mateus, Efficient approximation of the conditional relative entropy with applications to discriminative learning of Bayesian network classifiers, Entropy 15(7):2716-2735 (2013). [pdf]

• Susana Vinga, Alexandra M. Carvalho, Alexandre P. Francisco, Luís M. S. Russo and Jonas S. Almeida, Pattern matching through Chaos Game Representation: Bridging numerical and discrete data structures for biological sequence analysis, Algorithms for Molecular Biology 7:10 (2012). [pdf] [cgrsuffix]

• Alexandra M. Carvalho, Teemu Roos, Arlindo L. Oliveira and Petri Myllymäki, Discriminative learning of Bayesian networks via factorized conditional log-likelihood, Journal of Machine Learning Research 12(Jul):2181-2210 (2011). [pdf] [fCLL]

• Alexandra M. Carvalho and Arlindo L. Oliveira, GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge, Algorithms for Molecular Biology 6:13 (2011). [pdf] [GRISOTTO]

• Pedro Tiago Monteiro, Nuno Mendes, Miguel Teixeira, Sofia d'Orey, Sandra Tenreiro, Nuno Mira, Hélio Pais, Alexandre Francisco, Alexandra M. Carvalho, Artur Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira and Ana T. Freitas, YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae, Nucleic Acids Research 36(Database-Issue): 132-136 (2008). [pdf] [YEASTRACT-DISCOVERER]

• Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira and Marie-France Sagot, An efficient algorithm for the identification of structured motifs in DNA promoter sequences, IEEE/ACM Transactions on Computational Biology and Bioinformatics 3(2):126-140 (2006). [pdf] [RISO] [RISO@YEASTRACT-DISCOVERER]

Serial Papers

• Joana Godinho, Alexandra M. Carvalho and Susana Vinga, Latent variable modelling and variational inference for scRNA-seq differential expression analysis, Proceedings of the 10th International Conference on Computational Advances in Bio and medical Sciences (ICCABS'20), 2020 (accepted). [biorxiv] [SIENA@GitHub] [ext-ZINBayes@GitHub]

• André Ferreira, Sara C. Madeira, Marta Gormicho, Mamede de Carvalho, Susana Vinga and Alexandra M. Carvalho, Predictive Medicine Using Interpretable Recurrent Neural Networks, In Del Bimbo A. et al. (eds), Pattern Recognition. ICPR International Workshops and Challenges (ICPR'21). Lecture Notes in Computer Science, vol 12661 (2021). Springer, Cham, pages 187-202.

• Cláudia Constantino, Alexandra M. Carvalho and Susana Vinga, Sparse consensus classification for discovering novel biomarkers in rheumatoid arthritis, In Nicosia G. et al. (eds), Proceedings of the 6th International Conference on Machine Learning, Optimization, and Data Science (LOD'20), Lecture Notes in Computer Science, vol 12565 (2020). Springer, Cham, pages 125-136. Revised Selected Papers, 2020. [pdf]

• Manuel Anacleto, Susana Vinga and Alexandra M. Carvalho, MSAX: Multivariate symbolic aggregate approximation for time series classification. In Cazzaniga P., Besozzi D., Merelli I., Manzoni L., editors, Proceedings of the 16th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB'19), Lecture Notes in Computer Science, vol 12313 (2020). Springer, Cham, pages 90-97. Revised Selected Papers, 2020. [pdf]

• Pedro Ferreira, Alexandra M. Carvalho and Susana Vinga, Variational inference in probabilistic single-cell RNA-seq models, In: M. Raposo, P. Ribeiro, S. Sério, A. Staiano, A. Ciaramella A., editors, Proceedings of the 15th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB'18), Lecture Notes in Computer Science, vol 11925. Springer, Cham, pages 11-18. Revised Selected Papers, 2020. [pdf] [biorxiv] [ZINBayes@GitHub]

• João Villa-Brito, Marta B. Lopes, Alexandra M. Carvalho and Susana Vinga, Unravelling breast and prostate common gene signatures by Bayesian network learning, In: M. Raposo, P. Ribeiro, S. Sério, A. Staiano, A. Ciaramella A., editors, Proceedings of the 15th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB'18), volume 11925 of Lecture Notes in Computer Science, pages 285-292. Revised Selected Papers, Springer, Cham, 2020. [pdf]

• Margarida Sousa and Alexandra M. Carvalho, Learning consistent tree-augmented dynamic Bayesian networks, In G. Nicosia et al., editors, Proceedings of the 4th International Conference on Machine Learning, Optimization, and Data Science (LOD'18), volume 11331 of Lecture Notes in Computer Science, pages 1-12. Revised Selected Papers, Springer, Cham, 2018. [pdf] [cDBN@GitHub]

• João Diogo Pinto, Alexandra M. Carvalho and Susana Vinga, Outlier detection in Cox proportional hazard models based on the concordance c-index, In G. Nicosia and P. Pardalos, editors, Proceedings of the 1st International Workshop on Machine Learning, Optimization, and Big Data (MOD'15), volume 9432 of Lecture Notes in Computer Science, pages 252-256. Revised Selected Papers, Springer, Cham, 2015. [pdf] [survBootOutliers@CRAN]

• Cecília Nunes, Dina Silva, Manuela Guerreiro, Alexandre Mendonça, Alexandra M. Carvalho and Sara C. Madeira, Class imbalance in the prediction of dementia from neuropsychological data, In L. M. Correia, L. Reis and J. M. Cascalho, editors, Proceedings of the 16th Portuguese Conference on Artificial Intelligence (EPIA'13), volume 8154 of the Lecture Notes in Computer Science, pages 138-151. Springer-Verlag, 2013. [pdf]

• Alexandra M. Carvalho, Arlindo L. Oliveira and Marie-France Sagot, Efficient learning of Bayesian network classifiers: An extension to the TAN classifier, In M. A. Orgun and J. Thornton, editors, Proceedings of the 20th Australian Joint Conference on Artificial Intelligence (AI'07), volume 4830 of Lecture Notes in Artificial Intelligence, pages 16-25. Springer-Verlag, 2007. [pdf]

• Nadia Pisanti, Alexandra M. Carvalho, Laurent Marsan and Marie-France Sagot, RISOTTO: Fast extraction of motifs with mismatches, In J. R. Correa, A. Hevia and M. Kiwi, editors, Proceedings of the 7th Latin American Theoretical Informatics Symposium (LATIN'06), volume 3887 of Lecture Notes in Computer Science, pages 757-768. Springer-Verlag, 2006. [pdf] [RISOTTO]

• Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira and Marie-France Sagot, A highly scalable algorithm for the extraction of cis-regulatory regions, In Yi-Ping Phoebe Chen and Limsoon Wong, editors, Proceedings of the 3rd Asia Pacific Bioinformatics Conference (APBC'05), volume 1 of Advances in Bioinformatics and Computational Biology, pages 273-282. Imperial College Press, 2005. [pdf]

• Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira and Marie-France Sagot, Efficient extraction of structured motifs using box-links, In A. Apostolico and M. Melucci, editors, Proceedings of the 11th Symposium on String Processing and Information Retrieval (SPIRE'04), volume 3246 of Lecture Notes in Computer Science, pages 267-268. Springer-Verlag, 2004. [pdf]

International Conference Papers

• José L. Monteiro, Susana Vinga and Alexandra M. Carvalho, Polynomial-time algorithm for learning optimal tree-augmented dynamic Bayesian networks, In Proceedings of the 31st Conference on Uncertainty in Artificial Intelligence (UAI'15), pages 622-631, 2015. [pdf] [tDBN@GitHub]

• João Diogo Pinto, Alexandra M. Carvalho and Susana Vinga, Outlier detection in survival analysis based on the concordance c-index, In Proceedings of the 6th International Conference on BIOINFORMATICS, pages 75-82, 2015. [pdf] [survBootOutliers@CRAN]

• André V. Carreiro, Susana Pinto, Alexandra M. Carvalho, Mamede de Carvalho and Sara C. Madeira, Predicting non-invasive ventilation in ALS patients using time windows, In Proceedings of the 20th ACM SIGKDD Workshop on Healthcare Informatics (HI-KDD 2014), 2014. [pdf]

• Alexandra M. Carvalho and Arlindo L. Oliveira, Learning Bayesian networks consistent with the optimal branching, In Proceedings of the 6th International Conference on Machine Learning and Applications, pages 369-374, 2007. [pdf]

• Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira and Marie-France Sagot, A parallel algorithm for the extraction of structured motifs, In Proceedings of the 19th ACM Symposium on Applied Computing, pages 147-153, 2004. [pdf]

• João Câmara, Alexandra M. Carvalho, Nuno Gama and Fernando Tareco, Inserting persistence mechanisms into object oriented models, using a transformation approach, In Proceedings of the 3rd Workshop Ibero-americano de Engenharia de Requisitos e Ambientes de Software, 2000.

Posters and abstracts

• João Diogo Pinto, Alexandra M. Carvalho and Susana Vinga, Outlier detection in Cox proportional hazard models based on the concordance c-index, Poster in the International Workshop on Machine Learning, Optimization and Big Data (MOD'15), Taormina, Sicily, 2015.

• João Diogo Pinto, Alexandra M. Carvalho and Susana Vinga, Outlier detection in Cox proportional hazard models based on the concordance c-index, Poster in Ascona Workshop 2015, Ascona, Switzerland, 2015.

• Elson Tomás, Alexandra M. Carvalho, Paulo Mateus and Susana Vinga, Unsupervised classification of pharmacokinetic responses using non-linear mixed effects models, Poster in the 13th European Conference on Computational Biology (ECCB'14), Strasbourg, France, 2014.

• Pedro Brazão-Faria, Alexandra M. Carvalho, Susana Vinga and Nuno L. Barbosa-Morais, Analyses of alternative splicing landscapes in clear cell renal cell carcinomas reveal putative novel prognosis factors, Poster in the 13th European Conference on Computational Biology (ECCB'14), Strasbourg, France, 2014.

• Alexandra M. Carvalho and Arlindo L. Oliveira, Graphical models for transcription factor binding sites, Poster and Extended abstract in Jornadas de Bioinformática, Lisboa, Portugal, 2009.

• Miguel Cacho Teixeira, Pedro Monteiro, Sandra Tenreiro, N. P. Mira, A. B. Lourenço, Alexandra M. Carvalho, Nuno Mendes, Sofia d'Orey, Hélio Pais, Ana T. Freitas, Arlindo L. Oliveira and Isabel Sá Correia, Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database, Extended abstract in 3rd Conference on Physiology of Yeasts and Filamentous Fungi, S245:52, Helsinki, Finland, 2007.

• Pedro Monteiro, Nuno Mendes, Miguel Cacho Teixeira, Sofia d'Orey, Sandra Tenreiro, N. P. Mira, Hélio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, A. B. Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira and Ana T. Freitas, Analysis of new and known DNA-binding site motifs in Saccharomyces cerevisiae using the YEASTRACT-DISCOVERER tools, Poster and Extended abstract in Congresso Nacional de MICRO'07-BIOTEC'07-XXXIII, Lisboa, Portugal, 2007.
  Sartorius award - Inovation in Microbiology/Biotecnology

• Miguel Cacho Teixeira, Pedro Monteiro, Sandra Tenreiro, Alexandra M. Carvalho, Nuno Mendes, Ana Casimiro, Carlos Filipe Almeida de Oliveira, Christian Sá Nogueira , Ana T. Freitas, Arlindo L. Oliveira and Isabel Sá Correia, Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database, Poster at the Yeast Genetics and Molecular Biology Meeting, Book of Abstracts 529A, Princeton, USA, 2006.

• Miguel Cacho Teixeira, Pedro Monteiro, Sandra Tenreiro, Alexandra M. Carvalho, Nuno Mendes, Ana Casimiro, Carlos Filipe Almeida de Oliveira, Christian Sá Nogueira , Ana T. Freitas, Arlindo L. Oliveira and Isabel Sá Correia, Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database, Poster at the 2nd FEMS Congress of European Microbiologists, Book of Abstracts W12.4-P.COM.3, Madrid, Spain, 2006.

Dissertations

• Alexandra M. Carvalho, Motif representation and discovery, PhD thesis, IST, Universidade Técnica de Lisboa, 2011. Supervised by Arlindo L. Oliveira and Marie-France Sagot.

• Alexandra M. Carvalho, Efficient algorithms for structured motif extraction in DNA sequences, Master's thesis, IST, Universidade Técnica de Lisboa, 2004. Supervised by Arlindo L. Oliveira and Ana T. Freitas.

• Alexandra M. Carvalho, Category theory in COQ, Diploma thesis, IST, Universidade Técnica de Lisboa, 1998. Supervised by Amílcar Sernadas.

Technical Reports

• Alexandra M. Carvalho, Scoring functions for learning Bayesian networks, INESC-ID Tec. Rep. 54/2009, Apr 2009.

• Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira and Marie-France Sagot, A parallel algorithm for the extraction of structured motifs, INESC-ID Tec. Rep. 49/2003, Dec 2003.

• Alexandra M. Carvalho, Primes in P: an exposition of the AKS algorithm, INESC-ID Tec. Rep. 1/2003, Mar 2003.

Research interests | Publications | Software | Teaching | Short CV