Alexandra Sofia Martins de Carvalho

Alexandra Carvalho

Academic position:	Assistant Professor
Joining date:	12-10-2011
Roles in IT:
Thematic Line:	Information and Data Sciences
Group:	Pattern and Image Analysis – Lx

Email: Send Email
Address: IT – Lisboa
Instituto Superior Técnico - Torre Norte - Piso 10
Av. Rovisco Pais, 1
1049 - 001 Lisboa
Tel: +351 21 841 84 54
Fax: +351 21 841 84 72

Alternative Personal Web Page

28-03-2022

Project Snapshot | SmartGlauco – Smart Drug Delivery Devices for Glaucoma Treatment

SmartGlauco offers an unprecedented opportunity to improve the state of art in glaucoma treatment.

Scientific Achievements

Degrees

PhD, Instituto Superior Técnico, 01-01-2011
MSc, Instituto Superior Técnico, 01-01-2004
Licenciatura, Instituto Superior Técnico, 01-01-1998

Affiliations

Instituto Superior Técnico, 01-01-2011,
Instituto Superior Técnico, 01-01-2006,

Expertise Topics

Machine Learning
Algorithmics
Bioinformatics

Academic Activities

43Supervision of MSc theses

As Supervisor

Causal Discovery on Categorical Data with Geometric Complexity, MSc Student, Diogo Sousa Cruz, Concluded 07-2024
Causal graph discovery for explainable insights on marine biotoxin shellfish contamination, MSc Student, Diogo Rafael Esteves Ribeiro, Concluded 12-2023
Comparative analysis of machine learning models for time-series forecasting of Escherichia coli contamination in Portuguese shellfish production areas, MSc Student, Filipe de Jesus Pereira Ferraz, Concluded 12-2023
Clustering Symbolic Temporal Sequences Using Temporal Needleman-Wunsch Algorithm, MSc Student, Matheus de Almeida Orsi e Silva, Concluded 12-2023
Multivariate Time-Series Modeling of Shellfish Contamination with Dynamic Bayesian Networks, MSc Student, Michael Sousa Madeira, Concluded 09-2022
Distinguishing Cause from Effect with Observational Categorical Data, MSc Student, Catarina Oliveira, Concluded 12-2021
Temporal Models for the Prediction of Rheumatic Disease Prescription Outcomes, MSc Student, Jorge Rebelo Albergaria Pacheco, Concluded 12-2021
Sparse Medical Time Series Modeling with Neural Differential Equations, MSc Student, Pedro Miguel Gonçalves Lopes, Concluded 12-2021
Sparse Dynamic Bayesian network estimation using generalized linear models, MSc Student, João Bernardo Almeida Santos, Concluded 11-2021
Survival analysis of transcriptomic high-dimensional oncological data for the identification of cancer biomarkers, MSc Student, Ana Beatriz Rodrigues Correia, Concluded 10-2021
Predicting Ankylosing Spondylitis Treatment Outcome Using Model-based Methods , MSc Student, Alexandre Almeida Abreu, Concluded 07-2021
Dynamic Bayesian networks for clinical decision support on ankylosing spondylitis patients under biological therapies, MSc Student, Ana Rita Lopes Borges Martins, Concluded 07-2021
Cloud-based web application for multivariate time series analysis: A language-agnostic integrative architecture for short- and long-running machine learning algorithms, MSc Student, Vasco de Campos Candeias, Concluded 01-2021
Profiling ALS disease progression through data mining techniques, MSc Student, Tiago Miguel da Silva Leão, Concluded 12-2020
Predictive Medicine using Interpretable Recurrent Neural Networks, MSc Student, André Cristóvão Neves Ferreira, Concluded 11-2020
Longitudinal and survival analysis for rheumatic diseases’ prognosis, MSc Student, Carolina de Seixas Serra Domingos Barata, Concluded 11-2020
Clustering multivariate time series using dynamic Bayesian networks, MSc Student, José Pedro de Almeida Gabriel Vieira Borges, Concluded 11-2020
Latent variable modelling and variational inference for single-cell RNA-seq differential expression analysis, MSc Student, Joana de Oliveira Mira Godinho, Concluded 12-2019
Time series analysis using restricted Boltzmann machines and dynamic Bayesian networks, MSc Student, João Henrique Fialho Rodrigues, Concluded 12-2019
Analysis of heterogeneous and high-dimensional data of rheumatic diseases patients through clustering methods, MSc Student, Sara Cristina Pontes Vieira, Concluded 12-2019
Latent factors of multi-omics data and clustering, MSc Student, Xia Anbang, Concluded 12-2019
Time series data imputation - Comparison of Dynamic Time Warping with Needleman-Wunsch algorithm, MSc Student, Guilherme Reis de Moura, Concluded 11-2019
MSAX: Multivariate symbolic aggregate approximation for time series classification, MSc Student, Manuel Pereira da Conceição Monteiro Anacleto, Concluded 11-2019
Outlier detection for multivariate time series, MSc Student, Jorge Luís Fuzeta Serras, Concluded 11-2018
Unveiling Interpretable Behaviour in Two-Way High-Dimensional Clinical Data, MSc Student, Luís Bernardo de Brito Mendes Rei, Concluded 11-2018
Network-based Regularisation for Survival Analysis, MSc Student, Pedro Jorge Estrela Martinho, Concluded 11-2018
Probabilistic Modelling of Single-cell Transcriptomics, MSc Student, Pedro Miguel Falé Ferreira, Concluded 11-2018
Model-based Learning in Multivariate Time Series, MSc Student, Samuel David Pelaio Arcadinho, Concluded 11-2018
Unravelling breast and prostate common gene signatures by Bayesian network learning, MSc Student, João Araújo Delgado Vila de Brito, Concluded 07-2018
Temporal sequence alignment and agglomerative clustering for the analysis of medical longitudinal data, MSc Student, Kishan Rameshchandra Rama, Concluded 06-2018
Profiling the Amyotrophic Lateral Sclerosis disease progression through data mining techniques, MSc Student, Orlando Bastos Vaz, Concluded 06-2018
Multivariate Correlations for Early Classification, MSc Student, João Pedro Carriço Beirão, Concluded 05-2018
Genetic programming for time series forecasting, MSc Student, Frederico Borges Costa Coelho Nunes, Concluded 04-2018
Modelling cancer progression through joint models for longitudinal and time-to-event data, MSc Student, Hugo Daniel Paes Loureiro Santos Ambrósio, Concluded 12-2017
Advances in Probabilistic Graphical Models, MSc Student, Margarida Nunes de Almeida Rodrigues de Sousa, Concluded 12-2017
Feature analysis to predict treatment outcome in rheumatoid arthritis, MSc Student, Cátia Sofia Tadeu Botas, Concluded 11-2017
Model Selection for Clustering of Pharmacokinetic Responses with the Minimum Description Length, MSc Student, Rui Pedro Pimentel de Almeida Guerra, Concluded 11-2017
Biclustering-based imputation in longitudinal data, MSc Student, Inês Nolasco, Concluded 05-2015
Analysis of Electronic Medical Records of Rheumatoid Arthritis Patients on Biological Therapies, MSc Student, João Pedro Bento Machado Marques de Freitas, Concluded 05-2015
Outlier Detection in Survival Analysis, MSc Student, João Pinto, Concluded 05-2015
Prognostic prediction in patients with Amyotrophic Lateral Sclerosis using graphical models, MSc Student, José Jorge dos Reis, Concluded 11-2014
Learning from short multivariate time series, MSc Student, José Maria Líbano Monteiro, Concluded 11-2014
Learning from imbalanced data, MSc Student, Cecília Nunes, Concluded 12-2012

Publications

14Books Chapters

A. Baião, C. Peixoto, M. Lopes, P. Costa, A. M. Carvalho, S. Vinga, Evaluating the Causal Role of Environmental Data in Shellfish Biotoxin Contamination on the Portuguese Coast, Chapter in, Progress in Artificial Intelligence, Moniz, N., Vale, Z., Cascalho, J., Silva, C., Sebastião, R., Springer, Cham, Cham, 2023
A. M. Carvalho, D. R. Ribeiro, F. F. Ferraz, M. Lopes, S. Rodrigues, P. Costa, S. Vinga, Causal Graph Discovery for Explainable Insights on Marine Biotoxin Shellfish Contamination, Chapter in, Intelligent Data Engineering and Automated Learning, Quaresma, P., Camacho, D., Yin, H., Gonçalves, T., Julian, V., Tallón-Ballesteros, A.J., Springer, Cham, Cham, 2023
A. Ferreira, S. Madeira, M. Gromicho, M. Carvalho, S. Vinga, A. M. Carvalho, Predictive Medicine Using Interpretable Recurrent Neural Networks, Chapter in, Pattern Recognition, ICPR International Workshops and Challenges, Del Bimbo A. et al., Springer, Cham, 2021
J. Brito, M. Lopes, A. M. Carvalho, S. Vinga, Unravelling breast and prostate common gene signatures by Bayesian network learning, Chapter in, Computational Intelligence methods for Bioinformatics and Biostatistics, Springer, Cham, 2020
P. Ferreira, A. M. Carvalho, S. Vinga, Variational inference in probabilistic single-cell RNA-seq models, Chapter in, Computational Intelligence methods for Bioinformatics and Biostatistics, Springer, Cham, 2020
M. Anacleto, S. Vinga, A. M. Carvalho, MSAX: Multivariate symbolic aggregate approximation for time series classification, Chapter in, Computational Intelligence methods for Bioinformatics and Biostatistics, Cazzaniga P., Besozzi D., Merelli I., Manzoni L., Springer, Cham, 2020
A. M. Carvalho, S. Vinga, Sparse Consensus Classification for Discovering Novel Biomarkers in Rheumatoid Arthritis, Chapter in, Machine Learning, Optimization, and Data Science, Giuseppe NicosiaVarun OjhaEmanuele La MalfaGiorgio JansenVincenzo SciaccaPanos PardalosGiovanni GiuffridaRenato Umeton, Springer, Cham, 2020
M. Sousa, A. M. Carvalho, Learning consistent tree-augmented dynamic Bayesian networks, Chapter in, The 4th International Conference on Machine Learning, Optimization and Data Science, Giuseppe Nicosia, Panos Pardalos, Giovanni Giuffrida, Renato Umeton, Vincenzo Sciacca, Springer, Cham, 2018
J. D. Pinto, A. M. Carvalho, S. Vinga, Outlier Detection in Cox Proportional Hazards Models Based on the Concordance c-Index, Chapter in, Machine Learning, Optimization, and Big Data - Revised Selected Papers, pages 252-256, Springer International Publishing, Cham, 2015
C. Nunes, D. Silva, M. Guerreiro, A. de Mendonça, A. M. Carvalho, S. Madeira, Class imbalance in the prediction of dementia from neuropsychological data, Chapter in, Portuguese Conference on Artificial Intelligence, volume 8154 of Lecture Notes in Computer Science, pages 138-151, Luis Miguel Correia, Luís Paulo Reis and José Manuel Cascalho, Springer, Angra do Heroísmo, Açores, 2014
A. M. Carvalho, A. L. Oliveira, M.-F. Sagot Sagot, Efficient learning of Bayesian network classifiers: An extension to the TAN classifier, Chapter in, Australian Joint Conference on Artificial Intelligence, volume 4830 of Lecture Notes in Artificial Intelligence, pages 16-25, M. A. Orgun and J. Thornton, Springer, Gold Coast, Australia, 2007
N. Pisanti, A. M. Carvalho, L. Marsan, M.-F. Sagot Sagot, RISOTTO: Fast extraction of motifs with mismatches, Chapter in, Latin American Theoretical Informatics Symposium, volume 3887 of Lecture Notes in Computer Science, pages 757-768, J. R. Correa, A. Hevia and M. Kiwi, Springer, Valdivia, Chile, 2006
A. M. Carvalho, A. L. Oliveira, M.-F. Sagot Sagot, A highly scalable algorithm for the extraction of cis-regulatory regions, Chapter in, Asia Pacific Bioinformatics Conference, volume 1 of Advances in Bioinformatics and Computational Biology, pages 273-282, Yi-Ping Phoebe Chen and Limsoon Wong, Singapore, 2005
A. M. Carvalho, A. L. Oliveira, M.-F. Sagot Sagot, Efficient extraction of structured motifs using box-links, Chapter in, Symposium on String Processing and Information Retrieval, volume 3246 of Lecture Notes in Computer Science, pages 267-268, A. Apostolico and M. Melucci, Springer, Padova, Italy, 2004

22Papers in Journals

B. L. Leitão, A. Veríssimo, A. M. Carvalho, S. Vinga, Enhancing Prognostic Signatures in Glioblastoma with Feature Selection and Regularised Cox Regression, Genes, Vol. 16, No. 5, pp. 473 - 473, April, 2025 | BibTex
L. Costa, J. Colaço, A. M. Carvalho, S. Vinga, A. Teixeira, Using Markov chains and temporal alignment to identify clinical patterns in Dementia, Journal of Biomedical Informatics, Vol. 140, No. 1, pp. 104328 - 104328, April, 2023 | BibTex
D. Azevedo, A. Rodrigues, H. Canhão, A. M. Carvalho, A. Souto, Zgli: A Pipeline for Clustering by Compression with Application to Patient Stratification in Spondyloarthritis, Sensors, Vol. 23, No. 3, pp. 1219 - 1219, January, 2023 | BibTex
B. Mera, P. Mateus, A. M. Carvalho, Model complexity in statistical manifolds: the role of curvature, IEEE Transactions on Information Theory, Vol. 68, No. 9, pp. 5619 - 5636, September, 2022 | BibTex
M. Gromicho, T. Leão, M. Santos, S. Pinto, A. M. Carvalho, S. Madeira, M. Carvalho, Dynamic Bayesian networks for stratification of disease progression in amyotrophic lateral sclerosis, European Journal of Neurology, Vol. 2022, No. 1, pp. 1 - 10, April, 2022 | BibTex
C. Barata, H. Canhão, A. Rodrigues, S. Vinga, A. M. Carvalho, Predicting Biologic Therapy Outcome of Patients With Spondyloarthritis: Joint Models for Longitudinal and Survival Analysis, JMIR Medical Informatics, Vol. 9, No. 7, pp. e26823 - e26823, July, 2021 | BibTex
T. Leão, S. Madeira, M. Gromicho, M. Carvalho, A. M. Carvalho, Learning dynamic Bayesian networks from time-dependent and time-independent data: Unraveling disease progression in Amyotrophic Lateral Sclerosis, Journal of Biomedical Informatics, Vol. 117, No. 1, pp. 103730 - 103730, April, 2021 | BibTex
C. Constantino, A. M. Carvalho, S. Vinga, Coupling sparse Cox models with clustering of longitudinal transcriptomics data for trauma prognosis, BioData Mining, Vol. 14, No. 1, pp. 25 - 25, April, 2021 | BibTex
J. Serras, S. Vinga, A. M. Carvalho, Outlier Detection for Multivariate Time Series Using Dynamic Bayesian Networks, Applied Sciences, Vol. 11, No. 4, pp. 1955 - 1955, February, 2021 | BibTex
M. Lemus, J. Beirão, N. Paunkovic, A. M. Carvalho, P. Mateus, Information-Theoretical Criteria for Characterizing the Earliness of Time-Series Data, Entropy, Vol. 22, No. 1, pp. 49 - 49, January, 2020 | BibTex
K. Rama, H. Canhão, A. M. Carvalho, S. Vinga, AliClu - Temporal sequence alignment for clustering longitudinal clinical data, BMC Medical Informatics and Decision Making, Vol. 19, No. 1, pp. 1 - 11, December, 2019 | BibTex
H. Loureiro, E. Carrasquinha, I. Alho, A. Ferreira, L. Costa, A. M. Carvalho, S. 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, Vol. 19, No. 13, pp. 1 - 12, January, 2019 | BibTex
R. Guerra, A. M. Carvalho, P. Mateus, Model Selection for Clustering of Pharmacokinetic Responses, Computer Methods and Programs in Biomedicine, Vol. 162, No. 2018, pp. 11 - 18, August, 2018 | BibTex
M. Sousa, A. M. Carvalho, Polynomial-Time Algorithm for Learning Optimal BFS-Consistent Dynamic Bayesian Networks, Entropy, Vol. 20, No. 4, pp. 274 - 274, April, 2018 | BibTex
E. Tomás, S. Vinga, A. M. Carvalho, Unsupervised learning of pharmacokinetic responses, Computational Statistics, Vol. 32, No. 2, pp. 409 - 428, June, 2017 | BibTex
A. M. Carvalho, P. Adão, P. Mateus, Hybrid learning of Bayesian multinets for binary classification, Pattern Recognition, Vol. 47, No. 10, pp. 3438 - 3450, April, 2014 | BibTex
A. M. Carvalho, P. Adão, P. Mateus, Efficient Approximation of the Conditional Relative Entropy with Applications to Discriminative Learning of Bayesian Network Classifiers, Entropy, Vol. 15, No. 7, pp. 2716 - 2735, July, 2013 | BibTex
S. Vinga, A. M. Carvalho, A. P. Francisco, L. M. S. Russo, J. S. Almeida, Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis, Algorithms for Molecular Biology, Vol. 7, No. 10, pp. 1 - 12, May, 2012 | BibTex
A. M. Carvalho, T. Roos, A. L. Oliveira, P. Myllymäki, Discriminative learning of Bayesian networks via factorized conditional log-likelihood, Journal of Machine Learning Research, Vol. 12, No. Jul, pp. 2181 - 2210, July, 2011 | BibTex
A. M. Carvalho, A. L. Oliveira, GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge, Algorithms for Molecular Biology, Vol. 6, No. 13, pp. 0 - 0, April, 2011 | BibTex
P. T. Monteiro, N. D. Mendes, M. C. Teixeira, S. Orey, S. Tenreiro, N. Mira, A. P. Francisco, A. M. Carvalho, A. B. Lourenço, I. Sá-Correia, YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae, Nucleic Acids Research, Vol. 36, No. Database-Issue, pp. 132 - 136, October, 2008 | BibTex
A. M. Carvalho, A. L. Oliveira, M.-F. Sagot Sagot, An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 3, No. 2, pp. 126 - 140, April, 2006 | BibTex

5Papers in Conferences

J. L. Monteiro, S. Vinga, A. M. Carvalho, Polynomial-time algorithm for learning optimal tree-augmented dynamic Bayesian networks, Conference on Uncertainty in Artificial Intelligence, Amsterdam, Netherlands, Vol. 31, pp. 622 - 631, July, 2015 | BibTex
J. D. Pinto, A. M. Carvalho, S. Vinga, Outlier detection in survival analysis based on the concordance c-index, BIOINFORMATICS, Lisbon, Portugal, Vol. 6, pp. 75 - 82, January, 2015 | BibTex
A.V.C. Carreiro, S. Pinto, A. M. Carvalho, M. Carvalho, S. Madeira, Predicting non-invasive ventilation in ALS patients using time windows, ACM SIGKDD Workshop on Healthcare Informatics HI-KDD, New York, United States, Vol. 20, pp. 1 - 8, August, 2014 | BibTex
A. M. Carvalho, A. L. Oliveira, Learning Bayesian networks consistent with the optimal branching, International Conf. on Machine Learning and Applications - ICMLA, Ohio, United States, Vol., pp. 369 - 374, December, 2007 | BibTex
A. M. Carvalho, A. L. Oliveira, M.-F. Sagot Sagot, A parallel algorithm for the extraction of structured motifs, ACM Symp. on Appl. Computing, Nicosia, Cyprus, Vol., pp. 147 - 153, March, 2004 | BibTex

Projects

Closed Projects9

Acronym	Name	Funding Agency	Start date	Ending date
CancerSys	Multiscale modeling for personalized therapy of bone metastasis	FCT	01-04-2014	01-10-2015
LAY(RF)^2	Ready-to-Fabricate RF and mmWave Integrated Circuit Layouts	IT	01-02-2020	31-01-2022
MATISSE	A machine learning-based forecasting system for shellfish safety	FCT	01-04-2020	31-03-2023
MONET	Multi-omic networks in gliomas	FCT	01-03-2021	29-02-2024
NEUROCLINOMICS2	Unravelling Prognostic Markers in NEUROdegenerative diseases through CLINical and OMICS data integration	FCT	01-07-2016	31-03-2020
PERSEIDS	Personalizing cancer therapy through integrated modeling and decision	FCT	17-06-2016	16-12-2019
PREDICT	oPtical fibeR sEnsors for aDvanced applICaTions	FCT, IT/LA	01-01-2018	31-03-2023
PREDICT	Personalized therapy for RhEumatic DIseases via machine learning methods	FCT	01-01-2019	31-12-2021
SmartGlauco	Smart Drug Delivery Device for Glaucoma Treatment	FCT	01-03-2021	29-02-2024

Other Scientific Achievements

4Awards

S. Vinga, A. M. Carvalho, A. P. Francisco, L. M. S. Russo, J. S. Almeida, Highly accessed article, for the paper, Pattern matching through Chaos Game Representation: Bridging numerical and discrete data structures for biological sequence analysis, by BioMed Central, 01-01-2012
A. M. Carvalho, A. L. Oliveira, Highly accessed article, for the paper GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge, by BioMed Central, 01-11-2011
N. D. Mendes, M. C. Teixeira, S. Orey, S. Tenreiro, N. Mira, H. Pais, A. P. Francisco, A. M. Carvalho, A. B. Lourenço, Sartorius award, Inovation in Microbiology/Biotecnology, for the work that lead to the article YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae, at Micro-Biotec 2007, 01-01-2007
A. M. Carvalho, Diploma Thesis award, PRODEP program 5/5.2/207/011/PRODEP/98, 01-02-1998

1Short Courses and Seminars

A. M. Carvalho, Complete MDL for Bayesian networks, Portugal, Lisbon, 07-2013

Other Contributions

3Conference Committees

Machine Learning, Optimization, and Data Science LOD, Technical Programme Committee, 2018
Portuguese Conf. on Artificial Intelligence - EPIA, Technical Programme Committee, 2013
European Conf. on Machine Learning - ECML, Technical Programme Committee, 2012

5Refereeing Journals