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Sérgio Matos received his PhD in Computer Science in 2007 by the University of Leicester (UK) and the Habilitation in Computer Science in 2024 by the University of Aveiro. He is currently Associate Professor in the Department of Electronics, Telecommunications and Informatics, Universidade de Aveiro and coordinator of the Biomedical Informatics and Technologies group in the Institute of Electronics and Informatics Engineering of Aveiro. He coordinated the creation of the Master's in Data Science at Universidade de Aveiro and has served as director or vice-director since the academic years 2021/22. His main research interests are in natural language processing, machine learning and artificial intelligence, data mining, information retrieval, information extraction, and semantic data annotation. S. Matos has published over 100 papers in international journals and conferences, and has been an active participant in several biomedical and clinical shared tasks and community challenges, including Biocreative, i2b2/n2c2, TREC and BioASQ. He acts as Area Chair for ACL conferences and is a reviewer for several conferences and journals including ACM SIGIR and ECIR. He is currently the Technical Coordinator and Deputy Head of Node of the Portuguese node of ELIXIR – European Life Sciences Infrastructure and participates in two European projects. He coordinates one nationally funded research project, and has previously coordinated one research project, two exploratory projects and four advanced computing projects, all in the areas of NLP and AI. He has supervised over 30 MSc students and 6 PhD theses and is currently supervisor of two PhD students, working in the areas of generative AI, natural language processing, information retrieval and information extraction.
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Identification

Personal identification

Full name
Sérgio Matos

Citation names

  • Matos, Sérgio

Author identifiers

Ciência ID
4F1F-7BD8-AE4E
ORCID iD
0000-0003-1941-3983
Google Scholar ID
qv26xhMAAAAJ
Researcher Id
G-4941-2010
Scopus Author Id
26031510200

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Computer Sciences
  • Exact Sciences - Computer and Information Sciences - Information Science

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Spanish; Castilian Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2024/07/31
Concluded
 AGREGAÇÃO EM INFORMÁTICA (Título de Agregado)
Universidade de Aveiro, Portugal
"Biomedical Natural Language Processing - From Bags of Words to Large Language Models" (THESIS/DISSERTATION)
2007
Concluded
 PhD (Doctor of Philosophy)
University of Leicester, United Kingdom
"Automatic Detection and Analysis of Cough Sounds" (THESIS/DISSERTATION)
 n/a
1999
Concluded
 Engenharia de Sistemas e Computação (Licenciatura)
Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
"Blood Flow Parameters Evaluation Using Wavelet Transforms" (THESIS/DISSERTATION)
 16
Affiliation

Science

Category
Host institution		 Employer
2014/01/01 - Current Researcher (Research) Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
2008/09/01 - 2013/08/31 Auxiliary Researcher (Research) Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
2007/07/16 - 2008/08/15 Researcher (Research) Universidade do Porto Centro de Linguística, Portugal
2001/11/19 - 2006/11/30 Contracted Researcher (Research) University Hospitals of Leicester NHS Trust, United Kingdom

Teaching in Higher Education

Category
Host institution		 Employer
2024/03 - Current Associate Professor (University Teacher) Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2018/06/01 - 2024/03 Assistant Professor (University Teacher) Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal

Positions / Appointments

Category
Host institution		 Employer
2025/09 - Current Director of the Master's in Data Science Universidade de Aveiro, Portugal
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2025/01/01 - Current Member of the Coordinating Committee; Principal Investigator of Biomedical Informatics and Technologies group Universidade de Aveiro, Portugal
Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
2021/06 - 2023/08 Director of the Master's in Data Science Universidade de Aveiro, Portugal
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal

Others

Category
Host institution		 Employer
2001/01/15 - 2001/10/31 Consultant (Informatics) Hospital de Faro, Portugal
Projects

Contract

Designation Funders
2026/01/01 - 2028/12/31 PARCERIA – Plataforma de Assistentes Colaborativos de Inteligência Artificial
CENTRO2030-FEDER-02595400
Principal investigator
Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
 European Union
Ongoing
2024/03/01 - 2027/02/28 EOSC-ENTRUST: A European Network of TRUSTed research environments
101131056
Researcher
BioData.pt, Portugal
 European Union
Ongoing
2022/11/01 - 2026/10/31 GDI - Genomic Data Infrastructure
101081813
Researcher
Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
 European Union
Ongoing
2025/01/01 - 2025/12/31 GLIM-BioData – Gateway for Living Data Management
RE-C05-i08
RI/00138/2024
Other
BioData.pt, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2021/02/01 - 2024/01/31 PandIA - Management of Pandemic Social Isolation Based on City and Social Intelligence
DSAIPA/AI/0088/2020
10.54499/DSAIPA/AI/0088/2020
Researcher
Instituto Politécnico de Bragança, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/11 - 2023/10 EHDEN - Electronic Health Data in a European Network
IMI2 806968
Researcher
Innovative Medicines Initiative
Ongoing
2017/04 - 2020/03 SOCA - Smart Open Campus
CENTRO-01-0145-FEDER-000010
Researcher
European Regional Development Fund
Concluded
2016/07 - 2019/06 Multimodal Information Retrieval in Medical Imaging Repositories
PTDC/EEI-ESS/6815/2014
Researcher
Fundação para a Ciência e a Tecnologia
2016/04 - 2019/03 SCREEN-DR - Image Analysis and Machine Learning Platform for Innovation in Diabetic Retinopathy Screening
CMUP-ERI/TIC/0028/2014
Researcher
Fundação para a Ciência e a Tecnologia
Concluded
2014/01/01 - 2018/12/31 Information extraction and text mining to support literature-based knowledge discovery in biomedicine
IF/01694/2013/CP1162/CT0018
Principal investigator
Concluded
2012/10 - 2016/09 EMIF - European Medical Information Framework
IMI-JU 115372
Researcher
European Commission
2013/01 - 2014/12 NeuroPath - New Strategies Applied to Neuropathological Disorders
CENTRO-07-ST24-FEDER-002034
Researcher
European Regional Development Fund
Concluded
2010/05/01 - 2013/10 Query term expansion methodologies for improved biomedical literature retrieval
info:eu-repo/grantAgreement/FCT/5876-PPCDTI/100541/PT
Principal investigator
Fundação para a Ciência e a Tecnologia
2012/03 - 2012/08 SPotTED - Social web Public healTh Event Detection
n/a
Principal investigator
Servidor de Apontadores Portugueses Online
2008/03/01 - 2012/06 World Search
QREN 11495 WS
Researcher
European Regional Development Fund
Concluded
2008/07 - 2011/06 EU-ADR - Exploring and Understanding Adverse Drug Reactions by Integrative Mining of Clinical Records and Biomedical Knowledge
EU FP7 215847
Researcher
European Commission
Concluded
2007/07 - 2008/06 Corpógrafo
n/a
Research Fellow
Fundacao para a Computacao Cientifica Nacional
Concluded

Other

Designation Funders
2023/04 - Current BioData.pt
POCI-01-0145-FEDER-022231
ELIXIR PT Node Technical Coordinator
2021/01/01 - Current Intelligent Systems Associate Laboratory (LASI)
10.54499/LA/P/0104/2020
Researcher
Universidade Nova de Lisboa Centro de Tecnologias e Sistemas, Portugal

Universidade de Aveiro Centro de Tecnologia Mecânica e Automação, Portugal

Instituto Politécnico do Porto Centro de Investigação em Sistemas Computacionais Embebidos e de Tempo-Real, Portugal

Universidade do Minho, Portugal

Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Centro de Matemática, Portugal

Universidade do Porto Laboratório de Inteligência Artificial e Ciência de Computadores, Portugal

Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal

Universidade de Aveiro, Portugal

Universidade do Minho Instituto de Polímeros e Compósitos, Portugal

Universidade do Minho Centro ALGORITMI, Portugal

Universidade Nova de Lisboa Unidade de Investigação e Desenvolvimento em Engenharia Mecânica e Industrial, Portugal

Instituto Politécnico do Porto Instituto Superior de Engenharia do Porto, Portugal

Universidade de Coimbra, Portugal

Universidade de Coimbra Centro de Informatica e Sistemas, Portugal

Instituto Politécnico do Porto Grupo de Investigação em Engenharia e Computação Inteligente para a Inovação e o Desenvolvimento, Portugal

Instituto Politécnico do Cávado e do Ave, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal

Universidade NOVA de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2002 - Current Leicester Cough Monitor
n/a
Principal investigator
University Hospitals of Leicester NHS Trust, United Kingdom

King's College Hospital, United Kingdom
Ongoing
2013/10 - 2017/10 KEYSTONE - Semantic keyword-based search on structured data sources
COST IC1302
Other
European Cooperation in Science and Technology
Concluded
Outputs

Publications

Book chapter
  1. Richard Adolph Aires Jonker; Roshan Poudel; Olga Fajarda; Sérgio Matos; José Luís Oliveira; Rui Pedro Lopes. "Analyzing the Impact of COVID-19 on Portuguese Social Media". 2024.
    10.1007/978-3-031-75204-9_7
  2. Richard Adolph Aires Jonker; Roshan Poudel; Olga Fajarda; José Luís Oliveira; Rui Pedro Lopes; Sérgio Matos. "DyPrune: Dynamic Pruning Rates for Neural Networks". 2023.
    10.1007/978-3-031-49008-8_12
  3. Jorge Miguel Silva; Diogo Pratas; Sérgio Matos. "Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications". 2023.
    10.1007/978-3-031-36007-7_12
  4. Jorge Miguel Silva; Diogo Pratas; Tânia Caetano; Sérgio Matos. "Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods". 309-320. Springer International Publishing, 2022.
    10.1007/978-3-031-04881-4_25
  5. João Rafael Almeida; João Figueira Silva; Alejandro Pazos Sierra; Sergio Matos; José Luís Oliveira. "Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information". 2021.
    10.1007/978-3-030-72379-8_26
  6. Almeida, João Rafael; Silva, João Figueira; Matos, Sérgio; Pazos, Alejandro; Oliveira, José Luís. "A Recommender System to Help Refining Clinical Research Studies". In Studies in Health Technology and Informatics. IOS Press, 2021.
    10.3233/shti210174
  7. Alina Trifan; Rui Antunes; Sérgio Matos; Jose Luís Oliveira. "Understanding Depression from Psycholinguistic Patterns in Social Media Texts". 402-409. Springer International Publishing, 2020.
    10.1007/978-3-030-45442-5_50
  8. Tiago Almeida; Sérgio Matos. "Calling Attention to Passages for Biomedical Question Answering". 69-77. Springer International Publishing, 2020.
    10.1007/978-3-030-45442-5_9
  9. Matos, Sérgio. "Improving Document Prioritization for Protein-Protein Interaction Extraction Using Shallow Linguistics and Word Embeddings". In 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 43-49. Springer International Publishing, 2017.
    10.1007/978-3-319-60816-7_6
  10. Antunes, Rui; Matos, Sérgio. "Biomedical Word Sense Disambiguation with Word Embeddings". In 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 273-279. Springer International Publishing, 2017.
    10.1007/978-3-319-60816-7_33
  11. Sernadela, P.; Lopes, P.; Campos, D.; Matos, S.; Oliveira, J.L.. "A semantic layer for unifying and exploring biomedical document curation results". In 11th International Conference on Practical Applications of Computational Biology & Bioinformatics. 2015.
  12. Nunes, Tiago; Matos, Sérgio; Oliveira, José Luís. "Extracting Sentences Describing Biomolecular Events from the Biomedical Literature". In Distributed Computing and Artificial Intelligence, 11th International Conference, 417-424. Springer International Publishing, 2014.
    10.1007/978-3-319-07593-8_48
  13. Arrais, J; Pereira, JE; Lopes, P; Matos, S; Oliveira, JL. "Improving Cross Mapping in Biomedical Databases". 69-76. 2010.
    10.1007/978-3-642-13214-8_9
  14. Matos, S; Arrais, JP; Oliveira, JL. "Expanding Gene-Based PubMed Queries". 61-68. 2010.
    10.1007/978-3-642-13214-8_8
Conference paper
  1. Jonker, Richard; Martins, Bárbara; Matos, Sérgio. "BioGraphletQA: Knowledge-Anchored Generation of Complex Question Answering Datasets". Paper presented in ECIR 2026 - 48th European Conference on Information Retrieval, Delft, 2026.
    Accepted
  2. Rubinstein, Beny; Matos, Sérgio. "SynDocDis: A Metadata-Driven Framework for Generating Synthetic Physician Discussions Using Large Language Models". Paper presented in EPIA 2025 - International Conference on Artificial Intelligence, Faro, 2025.
    Published • 10.1007/978-3-032-05176-9_24
  3. Jonker, Richard; Almeida, Tiago; Almeida, João Rafael; Matos, Sérgio. "BIT.UA at BioASQ 13B: Revisiting Evaluation, DPRF-Enhanced Retrieval and Fine-Tuned LLMs". Paper presented in CLEF 2025 - Conference and Labs of the Evaluation Forum, Madrid, 2025.
    Published
  4. Ferreira, Daniel Jorge Bernardo; Almeida, Tiago; Matos, Sérgio. "A Framework for Fine-Grained Complexity Control in Health Answer Generation". Paper presented in ACL 2025 - 63rd Annual Meeting of the Association for Computational Linguistics, Vienna, 2025.
    Published • 10.18653/v1/2025.acl-srw.87
  5. Richard A. A. Jonker; Tiago Almeida; Sérgio Matos. "Analyzing a Decade of Evolution: Trends in Natural Language Processing". 2024.
    Published • 10.1007/978-3-031-68323-7_13
  6. Tiago Almeida; Sérgio Matos. "SPARe: Supercharged Lexical Retrievers on GPU with Sparse Kernels". 2024.
    Published • 10.1007/978-3-031-56063-7_33
  7. Jonker, Richard Adolph Aires; Poudel, Roshan; Fajarda, Olga; Matos, Sérgio; Oliveira, José Luís; Lopes, Rui Pedro. "Portuguese Twitter Dataset on COVID-19". Istanbul, 2022.
    10.1109/asonam55673.2022.10068592
  8. Almeida, Tiago; Antunes, Rui; Silva, João Figueira; Almeida, João Rafael; Matos, Sérgio. "Chemical detection and indexing in PubMed full text articles using deep learning and rule-based methods". Paper presented in BioCreative VII Challenge Evaluation Workshop, Online, 2021.
  9. Antunes, Rui; Almeida, Tiago; Silva, João Figueira; Matos, Sérgio. "Chemical¿protein relation extraction in PubMed abstracts using BERT and neural networks". Paper presented in BioCreative VII Challenge Evaluation Workshop, Online, 2021.
  10. Silva, João Figueira; Almeida, Tiago; Antunes, Rui; Almeida, João Rafael; Matos, Sérgio. "Drug mention recognition in Twitter posts using a deep learning approach". Paper presented in BioCreative VII Challenge Evaluation Workshop, Online, 2021.
  11. Matos, Sérgio. "BioASQ Synergy: A strong and simple baseline rooted in relevance feedback". Paper presented in CLEF 2021 - Conference and Labs of the Evaluation Forum, 2021.
    Published
  12. Almeida, Tiago; Matos, Sérgio. "Universal Passage Weighting Mecanism (UPWM) in BioASQ 9b". Paper presented in CLEF 2021 - Conference and Labs of the Evaluation Forum, 2021.
    Published
  13. Silva, Joao Figueira; Matos, Sergio. "Patient Trajectory Modelling in Longitudinal Data: A Review on Existing Solutions". 2021.
    10.1109/cbms52027.2021.00057
  14. Almeida, Tiago; Matos, Sérgio. "Benchmarking a transformer-{FREE} model for ad-hoc retrieval". Paper presented in 16th Conference of the European Chapter of the Association for Computational Linguistics, 2021.
    Published
  15. Jorge Miguel Ferreira da Silva; Pratas, Diogo; Caetano, Tania; Matos, Sérgio. "Archaea Taxonomic Classification". Paper presented in 27th Portuguese Conference on Pattern Recognition, RecPad 2021, Évora, 2021.
    Published
  16. Almeida, Tiago; Matos, Sérgio. "Frugal neural reranking: evaluation on the Covid-19 literature". 2020.
    10.18653/v1/2020.nlpcovid19-2.3
  17. Almeida, Tiago; Matos, Sérgio. "BIT.UA at BioASQ 8: Lightweight neural document ranking with zero-shot snippet retrieval". 2020.
    Published
  18. Antunes, Rui; Silva, João Figueira; Matos, Sérgio. "Evaluating semantic textual similarity in clinical sentences using deep learning and sentence embeddings". Brno, 2020.
    Published • 10.1145/3341105.3373987
  19. Almeida, João Rafael; Matos, Sérgio. "Rule-based extraction of family history information from clinical notes". Brno, 2020.
    Published • 10.1145/3341105.3374000
  20. Matos, Sérgio. "Clinical concept normalization on medical records using word embeddings and heuristics". 2020.
    10.3233/SHTI200129
  21. Jorge Miguel Ferreira da Silva; Pratas, Diogo; Matos, Sérgio. "Comparison and Evaluation of Information-based Measures in Images.". Paper presented in 26th Portuguese Conference on Pattern Recognition, RecPad 2020, Évora, 2020.
    Published
  22. Antunes, Rui; Silva, João; Pereira, Arnaldo; Matos, Sérgio. "Rule-based and Machine Learning Hybrid System for Patient Cohort Selection". Prague, 2019.
    Published • 10.5220/0007349300590067
  23. Jorge Miguel Ferreira da Silva; Pratas, Diogo; Matos, Sérgio. "Evaluation of Statistical Complexity in Viral Genome Sequences". Paper presented in 25th Portuguese Conference on Pattern Recognition, RecPad 2019, Porto, Porto, 2019.
    Published
  24. Matos, Pedro; Matos, Sérgio. "Recognition of genetic mutations in text using deep learning". 2018.
    10.1145/3279996.3280020
  25. Pereira, Vitor; Matos, Sérgio; Oliveira, José Luís. "Automated ICD-9-CM medical coding of diabetic patient's clinical reports". 2018.
    10.1145/3279996.3280019
  26. Silva, Joao Figueira; Silva, Jorge Miguel; Guerra, Antonio; Matos, Sergio; Costa, Carlos. "Ejection Fraction Classification in Transthoracic Echocardiography Using a Deep Learning Approach". 2018.
    10.1109/cbms.2018.00029
  27. Matos, Sérgio. "Ejection fraction classification in transthoracic echocardiography using a deep learning approach". 2018.
    10.1109/CBMS.2018.00029
  28. Antunes, Rui; Matos, Sérgio. "Evaluation of word embedding vector averaging functions for biomedical word sense disambiguation". Paper presented in 9th INForum ¿ Informatics Symposium, Aveiro, 2017.
  29. Matos, Sérgio; Antunes, Rui. "Identifying relevant literature for precision medicine using deep neural networks". Paper presented in BioCreative VI Workshop, Bethesda, Maryland, 2017.
  30. Antunes, Rui; Matos, Sérgio. "Machine learning with word embeddings applied to biomedical concept disambiguation". Paper presented in 22nd Portuguese Conference on Pattern Recognition, Aveiro, 2016.
  31. Santos, A.; Matos, S.; Campos, D.; Oliveira, J.L.. "A curation pipeline and web-services for PDF documents". 2016.
  32. Monteiro, E.; Sernadela, P.; Matos, S.; Costa, C.; Oliveira, J.L.. "Semantic knowledge base construction from radiology reports". 2016.
  33. Viana-Ferreira, C.; Matos, S.; Costa, C.. "Incremental learning versus batch learning for classification of user's behaviour in medical imaging". 2015.
  34. Sernadela, P.; Matos, S.; Oliveira, J.L.. "Ann2RDF: Moving annotations to semantic web". 2015.
    10.1145/2837185.2837253
  35. Ruano, A.E.; Ferreira, P.M.; Cabrita, C.; Matos, S.. "Training neural networks and neuro-fuzzy systems: A unified view". 2002.
Journal article
  1. Beny Rubinstein; Sergio Matos. "Value Creation for Healthcare Ecosystems through Artificial Intelligence Applied to Physician-to-Physician Communication: A Systematic Review". Neural Processing Letters (2025): https://doi.org/10.1007/s11063-025-11725-1.
    10.1007/s11063-025-11725-1
  2. Richard A A Jonker; Tiago Almeida; Rui Antunes; João R Almeida; Sérgio Matos. "Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes". Database (2024): https://doi.org/10.1093/database/baae068.
    10.1093/database/baae068
  3. Tiago Almeida; Richard A A Jonker; Rui Antunes; João R Almeida; Sérgio Matos. "Towards discovery: an end-to-end system for uncovering novel biomedical relations". Database (2024): https://doi.org/10.1093/database/baae057.
    10.1093/database/baae057
  4. Sara Duarte-Pereira; Sérgio Matos; José Luís Oliveira; Raquel M. Silva. "Study of NAD-interacting proteins highlights the extent of NAD regulatory roles in the cell and its potential as a therapeutic target". Journal of Integrative Bioinformatics (2023): https://doi.org/10.1515/jib-2022-0049.
    10.1515/jib-2022-0049
  5. João Figueira Silva; Sérgio Matos. "Modelling patient trajectories using multimodal information". Journal of Biomedical Informatics (2022): https://doi.org/10.1016/j.jbi.2022.104195.
    10.1016/j.jbi.2022.104195
  6. Jorge Miguel Silva; Diogo Pratas; Tânia Caetano; Sérgio Matos. "The complexity landscape of viral genomes". GigaScience (2022): https://doi.org/10.1093/gigascience/giac079.
    10.1093/gigascience/giac079
  7. Tiago Almeida; Rui Antunes; João F. Silva; João R Almeida; Sérgio Matos. "Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics". Database (2022): https://doi.org/10.1093/database/baac047.
    10.1093/database/baac047
  8. Sara Duarte-Pereira; Olga Fajarda; Sérgio Matos; José Luís Oliveira; Raquel Monteiro Silva. "NAPRT Expression Regulation Mechanisms: Novel Functions Predicted by a Bioinformatics Approach". Genes (2021): https://doi.org/10.3390/genes12122022.
    10.3390/genes12122022
  9. Almeida, João Rafael; Silva, João Figueira; Matos, Sérgio; Oliveira, José Luís. "A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases". Journal of Biomedical Informatics 120 (2021): 103849. http://dx.doi.org/10.1016/j.jbi.2021.103849.
    10.1016/j.jbi.2021.103849
  10. Silva, Jorge Miguel; Pratas, Diogo; Antunes, Rui; Matos, Sérgio; Pinho, Armando J.. "Automatic analysis of artistic paintings using information-based measures". Pattern Recognition 114 (2021): 107864. http://dx.doi.org/10.1016/j.patcog.2021.107864.
    10.1016/j.patcog.2021.107864
  11. João Figueira Silva; João Rafael Almeida; Sérgio Matos. "Extraction of Family History Information From Clinical Notes: Deep Learning and Heuristics Approach". JMIR Medical Informatics (2020): https://doi.org/10.2196/22898.
    10.2196/22898
  12. Jorge Miguel Silva; Eduardo Pinho; Sérgio Matos; D. Pratas. "Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model". Entropy (2020): https://www.mdpi.com/1099-4300/22/1/105.
    10.3390/e22010105
  13. Antunes, Rui; Matos, Sérgio. "Extraction of chemical–protein interactions from the literature using neural networks and narrow instance representation". Database (2019): http://dx.doi.org/10.1093/database/baz095.
    10.1093/database/baz095
  14. Islamaj Dogan, Rezarta; Kim, Sun; Chatr-aryamontri, Andrew; Wei, Chih-Hsuan; Comeau, Donald C; Antunes, Rui; Matos, Sérgio; et al. "Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine". Database 2019 (2019): http://dx.doi.org/10.1093/database/bay147.
    10.1093/database/bay147
  15. Sérgio Matos. "Configurable web-services for biomedical document annotation". Journal of Cheminformatics 10 1 (2018): https://doi.org/10.1186/s13321-018-0317-4.
    10.1186/s13321-018-0317-4
  16. Pedrosa, Micael; Silva, Jorge Miguel; Silva, João Figueira; Matos, Sérgio; Costa, Carlos. "SCREEN-DR: Collaborative platform for diabetic retinopathy". International Journal of Medical Informatics 120 (2018): 137-146. http://dx.doi.org/10.1016/j.ijmedinf.2018.10.005.
    10.1016/j.ijmedinf.2018.10.005
  17. Turner, R. D.; Birring, S. S.; Darmalingam, M.; Hooper, R. L.; Kunst, H.; Matos, S.; Bothamley, G. H.. "Daily cough frequency in tuberculosis and association with household infection". The International Journal of Tuberculosis and Lung Disease 22 8 (2018): 863-870. http://dx.doi.org/10.5588/ijtld.17.0652.
    10.5588/ijtld.17.0652
  18. Antunes, Rui; Matos, Sérgio. "Supervised Learning and Knowledge-Based Approaches Applied to Biomedical Word Sense Disambiguation". Journal of Integrative Bioinformatics 14 4 (2017): http://dx.doi.org/10.1515/jib-2017-0051.
    10.1515/jib-2017-0051
  19. Matos, Sérgio; Antunes, Rui. "Protein-Protein Interaction Article Classification Using a Convolutional Recurrent Neural Network with Pre-trained Word Embeddings". Journal of Integrative Bioinformatics 14 4 (2017): http://dx.doi.org/10.1515/jib-2017-0055.
    10.1515/jib-2017-0055
  20. Spinou, A.; Lee, K.K.; Sinha, A.; Elston, C.; Loebinger, M.R.; Wilson, R.; Chung, K.F.; et al. "The Objective Assessment of Cough Frequency in Bronchiectasis". Lung 195 5 (2017): 575-585. http://www.scopus.com/inward/record.url?eid=2-s2.0-85023773419&partnerID=MN8TOARS.
    10.1007/s00408-017-0038-x
  21. Viana-Ferreira, C.; Guerra, A.; Silva, J.F.; Matos, S.; Costa, C.. "An Intelligent Cloud Storage Gateway for Medical Imaging". Journal of Medical Systems 41 9 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85027055714&partnerID=MN8TOARS.
    10.1007/s10916-017-0790-8
  22. Lee, K.K.; Matos, S.; Ward, K.; Rafferty, G.F.; Moxham, J.; Evans, D.H.; Birring, S.S.. "Sound: A non-invasive measure of cough intensity". BMJ Open Respiratory Research 4 1 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85019456990&partnerID=MN8TOARS.
    10.1136/bmjresp-2017-000178
  23. Kim, Sun; Dogan, Rezarta Islamaj; Chatr-Aryamontri, Andrew; Chang, Christie S.; Oughtred, Rose; Rust, Jennifer; Batista-Navarro, Riza; et al. "BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID". Database-the Journal of Biological Databases and Curation (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000383834200001&KeyUID=WOS:000383834200001.
    10.1093/database/baw121
  24. Wang, Q.; Abdul, S.S.; Almeida, L.; Ananiadou, S.; Balderas-Martínez, Y.I.; Batista-Navarro, R.; Campos, D.; et al. "Overview of the interactive task in BioCreative V". Database 2016 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-85009926974&partnerID=MN8TOARS.
    10.1093/database/baw119
  25. Matos, Sergio; Campos, David; Pinho, Renato; Silva, Raquel M.; Mort, Matthew; Cooper, David N.; Oliveira, Jose Luis. "Mining clinical attributes of genomic variants through assisted literature curation in Egas". Database-the Journal of Biological Databases and Curation (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000381519300001&KeyUID=WOS:000381519300001.
    10.1093/database/baw096
  26. Viana-Ferreira, C.; Ribeiro, L.; Matos, S.; Costa, C.. "Pattern recognition for cache management in distributed medical imaging environments". International Journal of Computer Assisted Radiology and Surgery (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84938651646&partnerID=MN8TOARS.
    10.1007/s11548-015-1272-4
  27. Vanegas, J. A.; Matos, S.; Gonzalez, F.; Oliveira, J. L.. "An Overview of Biomolecular Event Extraction from Scientific Documents". Computational and Mathematical Methods in Medicine (2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000364704100001&KeyUID=WOS:000364704100001.
    10.1155/2015/571381
  28. Viana-Ferreira, Carlos; Matos, Sergio; Costa, Carlos. "Long-term prefetching for cloud medical imaging repositories.". Studies in health technology and informatics 210 (2015): 1028-30. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:25991361&KeyUID=MEDLINE:25991361.
  29. Krallinger, Martin; Rabal, Obdulia; Leitner, Florian; Vazquez, Miguel; Salgado, David; Lu, Zhiyong; Leaman, Robert; et al. "The CHEMDNER corpus of chemicals and drugs and its annotation principles.". Journal of cheminformatics 7 Suppl 1 Te (2015): S2-S2. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:25810773&KeyUID=MEDLINE:25810773.
    10.1186/1758-2946-7-S1-S2
  30. Campos, David; Matos, Sergio; Oliveira, Jose L. "A document processing pipeline for annotating chemical entities in scientific documents.". Journal of cheminformatics 7 Suppl 1 Te (2015): S7-S7. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:25810778&KeyUID=MEDLINE:25810778.
    10.1186/1758-2946-7-S1-S7
  31. Coelho, E.D.; Arrais, J.P.; Matos, S.; Pereira, C.; Rosa, N.; Correia, M.J.; Barros, M.; Oliveira, J.L.. "Computational prediction of the human-microbial oral interactome". BMC Systems Biology 8 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84897570043&partnerID=MN8TOARS.
    10.1186/1752-0509-8-24
  32. Prieto, V.M.; Matos, S.; Álvarez, M.; Cacheda, F.; Oliveira, J.L.. "Twitter: A good place to detect health conditions". PLoS ONE 9 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84900419026&partnerID=MN8TOARS.
    10.1371/journal.pone.0086191
  33. Campos, D.; Bui, Q.-C.; Matos, S.; Oliveira, J.L.. "TrigNER: Automatically optimized biomedical event trigger recognition on scientific documents". Source Code for Biology and Medicine 9 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84892661802&partnerID=MN8TOARS.
    10.1186/1751-0473-9-1
  34. Santos, J.C.; Matos, S.. "Analysing Twitter and web queries for flu trend prediction". Theoretical Biology and Medical Modelling 11 SUPPL.1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84900339672&partnerID=MN8TOARS.
    10.1186/1742-4682-11-S1-S6
  35. Campos, D.; Lourenço, J.; Matos, S.; Oliveira, J.L.. "Egas: a collaborative and interactive document curation platform.". Database : the journal of biological databases and curation 2014 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84906539811&partnerID=MN8TOARS.
  36. Campos, D.; Matos, S.; Oliveira, J.L.. "A modular framework for biomedical concept recognition". BMC Bioinformatics 14 1 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84884469671&partnerID=MN8TOARS.
    10.1186/1471-2105-14-281
  37. Yousaf, N.; Monteiro, W.; Matos, S.; Birring, S.S.; Pavord, I.D.. "Cough frequency in health and disease". European Respiratory Journal 41 1 (2013): 241-243. http://www.scopus.com/inward/record.url?eid=2-s2.0-84872173633&partnerID=MN8TOARS.
    10.1183/09031936.00089312
  38. Lee, K.K.; Matos, S.; Evans, D.H.; White, P.; Pavord, I.D.; Birring, S.S.. "A longitudinal assessment of acute cough". American Journal of Respiratory and Critical Care Medicine 187 9 (2013): 991-997. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877111516&partnerID=MN8TOARS.
    10.1164/rccm.201209-1686OC
  39. Campos, D.; Matos, S.; Oliveira, J.L.. "Gimli: Open source and high-performance biomedical name recognition". BMC Bioinformatics 14 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84873744177&partnerID=MN8TOARS.
    10.1186/1471-2105-14-54
  40. Nunes, T.; Campos, D.; Matos, S.; Oliveira, J.L.. "BeCAS: Biomedical concept recognition services and visualization". Bioinformatics 29 15 (2013): 1915-1916. http://www.scopus.com/inward/record.url?eid=2-s2.0-84880552535&partnerID=MN8TOARS.
    10.1093/bioinformatics/btt317
  41. Prieto, V.M.; Matos, S.; Álvarez, M.; Cacheda, F.; Oliveira, J.L.. "Analysing Relevant Diseases from Iberian Tweets". Advances in Intelligent Systems and Computing 222 (2013): 69-76. http://www.scopus.com/inward/record.url?eid=2-s2.0-84880375780&partnerID=MN8TOARS.
    10.1007/978-3-319-00578-2_10
  42. Matos, S.; Araújo, H.; Oliveira, J.L.. "Structuring and exploring the biomedical literature using latent semantics". Advances in Intelligent Systems and Computing 217 (2013): 609-616. http://www.scopus.com/inward/record.url?eid=2-s2.0-84891135595&partnerID=MN8TOARS.
    10.1007/978-3-319-00551-5_72
  43. Carlos, Jose; Matos, Sergio; Ortuno, F; Rojas, I. "Predicting Flu Incidence from Portuguese Tweets". Proceedings Iwbbio 2013: International Work-Conference on Bioinformatics and Biomedical Engineering (2013): 11-18.
  44. Correia, Maria; Coelho, Edgar D; Arrais, Joel P.; Matos, Sérgio; Rosa, Nuno; Barros, Marlene; Oliveira, José Luís. "Computational Approach to Predict Inter-Species Oral Protein-Protein Interactions". PROCEEDINGS IWBBIO 2013: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING 2013 (2013): 193-194.
    Published
  45. Campos, D.; Matos, S.; Lewin, I.; Oliveira, J.L.; Rebholz-Schuhmann, D.. "Harmonization of gene/protein annotations: Towards a gold standard medline". Bioinformatics 28 9 (2012): 1253-1261. http://www.scopus.com/inward/record.url?eid=2-s2.0-84860473173&partnerID=MN8TOARS.
    10.1093/bioinformatics/bts125
  46. Lee, K.K.; Savani, A.; Matos, S.; Evans, D.H.; Pavord, I.D.; Birring, S.S.. "Four-hour cough frequency monitoring in chronic cough". Chest 142 5 (2012): 1237-1243. http://www.scopus.com/inward/record.url?eid=2-s2.0-84868611639&partnerID=MN8TOARS.
    10.1378/chest.11-3309
  47. Matos, S.; Oliveira, J.L.. "Prioritizing literature search results using a training set of classified documents". Advances in Intelligent and Soft Computing 93 (2011): 381-388. http://www.scopus.com/inward/record.url?eid=2-s2.0-80052949641&partnerID=MN8TOARS.
    10.1007/978-3-642-19914-1_49
  48. Lu, Z.; Kao, H.-Y.; Wei, C.-H.; Huang, M.; Liu, J.; Kuo, C.-J.; Hsu, C.-N.; et al. "The gene normalization task in BioCreative III". BMC Bioinformatics 12 SUPPL. 8 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80052774027&partnerID=MN8TOARS.
    10.1186/1471-2105-12-S8-S2
  49. Krallinger, M.; Vazquez, M.; Leitner, F.; Salgado, D.; Chatr-aryamontri, A.; Winter, A.; Perfetto, L.; et al. "The Protein-Protein Interaction tasks of BioCreative III: Classification/ranking of articles and linking bio-ontology concepts to full text". BMC Bioinformatics 12 SUPPL. 8 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80053423937&partnerID=MN8TOARS.
    10.1186/1471-2105-12-S8-S3
  50. Lee, K. K.; Matos, S.; Evans, D. H.; Pavord, I. D.; Birring, S. S.. "ACUTE COUGH: A LONGITUDINAL OBSERVATIONAL STUDY". Thorax 66 (2011): A65-A66.
    10.1136/thoraxjnl-2011-201054b.144
  51. Lee, K. K.; Matos, S.; Evans, D. H.; Pavord, I. D.; Birring, S. S.. "PREDICTORS OF 24-H COUGH FREQUENCY IN ACUTE COUGH". Thorax 66 (2011): A64-A64.
    10.1136/thoraxjnl-2011-201054b.140
  52. Matos, S.; Oliveira, J.L.. "Classification methods for finding articles describing protein-protein interactions in PubMed.". Journal of integrative bioinformatics 8 3 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-84855546021&partnerID=MN8TOARS.
  53. Campos, D.; Matos, S.; Oliveira, J.L.. "Recognition of gene/protein names using conditional random fields". KDIR 2010 - Proceedings of the International Conference on Knowledge Discovery and Information Retrieval (2010): 275-280. http://www.scopus.com/inward/record.url?eid=2-s2.0-78651435591&partnerID=MN8TOARS.
  54. Yousaf, N.; Monteiro, W.; Parker, D.; Matos, S.; Birring, S.; Pavord, I.D.. "Long-term low-dose erythromycin in patients with unexplained chronic cough: A double-blind placebo controlled trial". Thorax 65 12 (2010): 1107-1110. http://www.scopus.com/inward/record.url?eid=2-s2.0-78649636793&partnerID=MN8TOARS.
    10.1136/thx.2010.142711
  55. Lee, K. K.; Savani, A.; Matos, S.; Woods, C.; Pavord, I. D.; Birring, S. S.. "4 H COUGH FREQUENCY MONITORING WITH THE LEICESTER COUGH MONITOR". Thorax 65 (2010): A54-A54.
    10.1136/thx.2010.150946.18
  56. Matos, S.; Arrais, J.P.; Maia-Rodrigues, J.; Oliveira, J.L.. "Concept-based query expansion for retrieving gene related publications from MEDLINE". BMC Bioinformatics 11 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77951569837&partnerID=MN8TOARS.
    10.1186/1471-2105-11-212
  57. Matos, S.; Barreiro, A.; Oliveira, J.L.. "Syntactic parsing for bio-molecular event detection from scientific literature". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 5816 LNAI (2009): 79-85. http://www.scopus.com/inward/record.url?eid=2-s2.0-71049149316&partnerID=MN8TOARS.
    10.1007/978-3-642-04686-5_7
  58. Yousaf, N; Matos, S; Birring, SS; Pavord, ID. "FACTORS AFFECTING COUGH FREQUENCY IN A MIXED POPULATION". Thorax 64 (2009): A151-A151.
    10.1136/thx.2009.127183t
  59. Birring, S.S.; Mann, V.M.; Matos, S.; Yousaf, N.; Wood, C.; Fleming, T.; Evans, D.H.; Morice, A.H.; Pavord, I.D.. "The Leicester cough monitor: A semi-automated, semi-validated cough detection system? (European Respiratory Journal (2008) 32, (530-531))". European Respiratory Journal 33 1 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-58849144267&partnerID=MN8TOARS.
    10.1183/09031936.50060808
  60. Birring, S.S.; Fleming, T.; Matos, S.; Raj, A.A.; Evans, D.H.; Pavord, I.D.. "The Leicester Cough Monitor: Preliminary validation of an automated cough detection system in chronic cough". European Respiratory Journal 31 5 (2008): 1013-1018. http://www.scopus.com/inward/record.url?eid=2-s2.0-47049099230&partnerID=MN8TOARS.
    10.1183/09031936.00057407
  61. Birring, S.S.; Mann, V.M.; Matos, S.; Yousaf, N.; Wood, C.; Fleming, T.; Evans, D.H.; Morice, A.H.; Pavord, I.D.. "From the authors". European Respiratory Journal 32 2 (2008): 530-531. http://www.scopus.com/inward/record.url?eid=2-s2.0-58849131973&partnerID=MN8TOARS.
    10.1183/09031936.00060808
  62. Matos, S.; Birring, S.S.; Pavord, I.D.; Evans, D.H.. "An automated system for 24-h monitoring of cough frequency: The Leicester cough monitor". IEEE Transactions on Biomedical Engineering 54 8 (2007): 1472-1479. http://www.scopus.com/inward/record.url?eid=2-s2.0-34447509649&partnerID=MN8TOARS.
    10.1109/TBME.2007.900811
  63. Birring, S.S.; Ing, A.J.; Chan, K.; Cossa, G.; Matos, S.; Morgan, M.D.L.; Pavord, I.D.. "Obstructive sleep apnoea: A cause of chronic cough". Cough 3 1 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-34547183940&partnerID=MN8TOARS.
    10.1186/1745-9974-3-7
  64. Birring, S.S.; Matos, S.; Patel, R.B.; Prudon, B.; Evans, D.H.; Pavord, I.D.. "Cough frequency, cough sensitivity and health status in patients with chronic cough". Respiratory Medicine 100 6 (2006): 1105-1109. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646029390&partnerID=MN8TOARS.
    10.1016/j.rmed.2005.09.023
  65. Matos, S.; Birring, S.S.; Pavord, I.D.; Evans, D.H.. "Detection of cough signals in continuous audio recordings using hidden Markov models". IEEE Transactions on Biomedical Engineering 53 6 (2006): 1078-1083. http://www.scopus.com/inward/record.url?eid=2-s2.0-33744988731&partnerID=MN8TOARS.
    10.1109/TBME.2006.873548
  66. Matos, S.; Ruano, M.G.; Ruano, A.E.; Evans, D.H.. "Neural network classification of cerebral embolic signals". Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings 2 (2001): 1761-1764. http://www.scopus.com/inward/record.url?eid=2-s2.0-61549098434&partnerID=MN8TOARS.
    10.1109/IEMBS.2001.1020560

Other

Other output
  1. End-to-End Extraction of Family History Information from Clinical Notes Using Deep Learning and Heuristics (Preprint). 2020. João Figueira Silva; João Rafael Almeida; Sérgio Matos. https://doi.org/10.2196/preprints.22898.
    10.2196/preprints.22898
  2. Corpógrafo and NooJ: using linguistic resources to obtain aligned concordances from corpora. In this presentation we will describe the integration of NooJ within the Corpógrafo environment. We will demonstrate how the NooJ corpus processing engine and linguistic resources are used in Corpógrafo for extracting lexical bundles and for obtaining simple concordances from corpora and aligned concordances from parallel corpora, and how we are implementing the search for "parallel" concordances. 2008. Matos, Sérgio; Barreiro, Anabela; Maia, Belinda. http://hdl.handle.net/10400.26/127.
Activities

Supervision

Thesis Title
Role		 Degree Subject (Type)
Institution / Organization
2023/09 - Current Domain knowledge enhanced generative question answering using Transformers and Knowledge Graphs
Supervisor
 Engenharia Informática (PhD)
Universidade de Aveiro, Portugal
2022/10 - Current Value creation for healthcare ecosystems through artificial intelligence applied to physician-to-physician communication
Supervisor
 Inovação em Empresas (PhD)
Universidade de Aveiro, Portugal
2024/09 - 2025/07/15 Answering consumer health questions with non-expert language
Supervisor
 Engenharia Informática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2020/09/01 - 2025/01/13 Biomedical question answering: from retrieval to answer generation
Supervisor
 Engenharia Informática (PhD)
Universidade de Aveiro, Portugal
2023/09 - 2024/12/18 Streamlining the analysis of phishing emails using Artificial Intelligence
Co-supervisor
 Engenharia Informática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2023/09 - 2024/07/10 Models for outcome prediciton and sports betting optimization
Supervisor
 Data Science (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2023/09 - 2024/07/05 Scientific landscape construction using large language models
Supervisor
 Data Science (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2023/09 - 2024/04/12 Content analysis and semantic enrichment of financial news
Supervisor
 Data Science (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2022/09 - 2023/12/11 Integrating an electric vehicle route planner into a microservices architecture: design and implementation
Co-supervisor
 Engenharia Informática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2022/09/01 - 2023/07/14 Database for human heritability values: a help to geneticists
Co-supervisor
 Master in Clinical Bioinformatics (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2022/09 - 2023/07/14 Exploring transformers for aspect based sentiment analysis
Supervisor
 Data Science (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2022/09 - 2023/07/13 Connected HVAC systems behaviour analysis: data mining on error codes using DS/ML techniques
Co-supervisor
 Data Science (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2022/09 - 2023/07/13 Machine learning algorithms for fuel consumption prediction: a comparative study
Co-supervisor
 Data Science (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2022/09 - 2023/07/03 Improving the performance of water demand forecasting: drift detection with machine learning model’s retraining
Supervisor
 Data Science (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2022/09 - 2023/03/28 Dynamic neural network architecture tuning during training
Supervisor
 Ciência de Dados (Master)
Universidade de Aveiro, Portugal
2015 - 2023/03/07 Biomedical information extraction with natural language processing and machine learning methods
Supervisor
 Engenharia Informática (PhD)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2018 - 2023 Algorithmic information approximations in data analysis
Supervisor
 Engenharia Informática (PhD)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2021/09 - 2022/12/13 Analysing the impact of multimorbidity on health outcomes among stomach cancer hospitalizations
Co-supervisor
 Master in Biomedical Engineering (Master)
Universidade de Aveiro Departamento de Ciências Médicas, Portugal
2021/10 - 2022/12 Dense and hybrid models for information retrieval
Supervisor
 Engenharia Informática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2021/01 - 2022/07 Collection, extraction and classification of opinions on playful applications for health and well-being
Supervisor
 Mestrado em Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2018 - 2022/06 Multimodal Content Fusion For Modelling Patient Trajectories
Supervisor
 Engenharia Informática (PhD)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2020/10 - 2021/12 Collaborative annotation and mapping tool for clinical concepts
Supervisor
 Mestrado em Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2020/10 - 2021/12 @Twitter: tracking reactions to political news
Supervisor
 Mestrado em Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2019/09/01 - 2021/02/17 Biomedical knowledge discovery through graph embeddings
Supervisor
 Mestrado Integrado em Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2019/10 - 2020/07 Using structured data to answer consumers health-related questions
Supervisor
 Mestrado em Engenharia Informática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2019 - 2019 Predicting the behaviour of water distribution networks with machine learning methods
Supervisor
 Engenharia Informática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2019 - 2019 Neural Information Retrieval for Biomedical Question-Answering
Supervisor
 Engenharia Informática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2018 - 2018 Web-based tool for searching table contents
Supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2018 - 2018 Sentiment analysis in web comments
Supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2018 - 2018 Recognition of textual mentions of genetic variants using deep learning
Supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2018 - 2018 Information extraction from diabetes clinical reports
Co-supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2017 - 2017 Deep learning for identification of pathogenic genetic mutations
Supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2016 - 2016 Automatic and interactive annotation of PDF documents
Supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2016 - 2016 Automatic knowledge base construction from unstructured text
Supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2015 - 2015 Graph-based methods for biomedical concept disambiguation
Supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2010 - 2015 Feature Selection for Enhanced Extraction of Information
Co-supervisor
 Engenharia Informática (PhD)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2014 - 2014 Aplicação e Serviços Web para Análise da Tosse em Pacientes Crónicos
Supervisor
 Sistemas de Informação (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2014 - 2014 Biomedical literature web annotation and curation
Co-supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2014 - 2014 Identification of health concepts in social networks
Co-supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2009 - 2014 Mining biomedical information from scientific literature
Co-supervisor
 Engenharia Informática (PhD)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2013 - 2013 A phrase-based information retrieval system for biomedical corpora
Co-supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2013 - 2013 Platform for chronic respiratory disease patient management
Co-supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2012 - 2012 Exploring biomedical literature using latent semantic indexing
Co-supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
2012 - 2012 Identification of term co-occurrence in scientific texts
Co-supervisor
 Engenharia de Computadores e Telemática (Master)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal

Event organisation

Event name
Type of event (Role)		 Institution / Organization
2020/12/01 - 2021/06/30 34th IEEE International Symposium on Computer-Based Medical Systems (IEEE CBMS2021) (2021/06/07 - 2021/06/09)
Conference (Member of the Organising Committee)
 Universidade de Aveiro, Portugal

Event participation

Activity description
Type of event		 Event name
Institution / Organization
2017/10/18 - 2017/10/20 BioCreative is a community-wide effort for evaluating text mining and information extraction systems applied to the biomedical domain. The BioCreative workshops bring together stakeholders from the biocuration community with researchers from text mining and natural language processing applied to the biomedical literature.
Workshop
 BioCreative VI
2017/04/26 - 2017/04/27 BioCreative is a community-wide effort for evaluating text mining and information extraction systems applied to the biomedical domain. The BioCreative workshops bring together stakeholders from the biocuration community with researchers from text mining and natural language processing applied to the biomedical literature.
Workshop
 BioCreative V.5
2015/09/09 - 2015/09/11 BioCreative is a community-wide effort for evaluating text mining and information extraction systems applied to the biomedical domain. The BioCreative workshops bring together stakeholders from the biocuration community with researchers from text mining and natural language processing applied to the biomedical literature.
Workshop
 BioCreative V
2013/10/07 - 2013/10/09 BioCreative is a community-wide effort for evaluating text mining and information extraction systems applied to the biomedical domain. The BioCreative workshops bring together stakeholders from the biocuration community with researchers from text mining and natural language processing applied to the biomedical literature.
Workshop
 BioCreative IV
2012/07/19 - 2012/07/25 Escola de verão em Machine Learning, participação como monitor
Other
 2nd Lisbon Machine Learning School
2012/05/02 - 2012/05/05 International School on Semantic Web Applications and Technologies for the Life Sciences
Workshop
 SWAT4LS 2012
2011/09/19 - 2011/09/20 OpenPHACTS/GEN2PHEN Workshop "Solving Bottlenecks in Data Sharing in the Life Sciences"
Workshop
2011/07/20 - 2011/07/25 Escola de verão em Machine Learning, participação como monitor
Other
 1st Lisbon Machine Learning School
2010/09/13 - 2010/09/15 BioCreative is a community-wide effort for evaluating text mining and information extraction systems applied to the biomedical domain. The BioCreative workshops bring together stakeholders from the biocuration community with researchers from text mining and natural language processing applied to the biomedical literature.
Workshop
 BioCreative III
2009/10/07 - 2009/10/09 BioCreative is a community-wide effort for evaluating text mining and information extraction systems applied to the biomedical domain. The BioCreative workshops bring together stakeholders from the biocuration community with researchers from text mining and natural language processing applied to the biomedical literature.
Workshop
 BioCreative II.5

Ad Hoc journal article review

Journal title (ISSN) Publisher
2023 - Current JMIR AI (2817-1705) JMIR
2022 - Current JMIR AI JMIR
2019 - Current Scientific Reports (2045-2322) Nature
2018 - Current International Journal of Medical Informatics (1872-8243) Elsevier
2018 - Current Applied Sciences (2076-3417) MDPI
2018 - Current IEEE Journal of Biomedical and Health Informatics IEEE
2017 - Current Computer Methods and Programs in Biomedicine (1872-7565) Elsevier
2017 - Current Artificial Intelligence in Medicine (1873-2860) Elsevier
2017 - Current Briefings in Bioinformatics (1477-4054) Oxford Academic
2016 - Current Information Sciences (1872-6291) Elsevier
2016 - Current IEEE Access IEEE
2016 - Current Journal of Cheminformatics (1758-2946) BMC
2015 - Current Bioinformatics (1367-4811) Oxford Academic
2015 - Current Database (1758-0463) Oxford Academic
2014 - Current IEEE Transactions on Biomedical Engineering IEEE
2014 - Current Journal of Biomedical Semantics (2041-1480) BMC
2014 - Current BMC Bioinformatics (1471-2105) BMC
2013 - Current PLoS ONE (1932-6203) PLOS
2023 - 2023 Scientific Data (2052-4463) Nature
2020 - 2020 JMIR Medical Informatics (2291-9694) JMIR
2019 - 2020 Applied Sciences MDPI
2018 - 2020 Sensors (1424-8220) MDPI
2018 - 2018 Computational Biology and Chemistry (1476-928X) Elsevier
2018 - 2018 Annals of Biomedical Engineering (1573-9686) Springer
2017 - 2017 PeerJ PeerJ
2017 - 2017 Computational and Mathematical Methods in Medicine Hindawi
2017 - 2017 Computers & Geosciences (1873-7803) Elsevier
2016 - 2016 Computer Speech & Language (1095-8363) Elsevier
2015 - 2016 Computers and Electronics in Agriculture (1872-7107) Elsevier
2015 - 2015 Biosystems (1872-8324) Elsevier
2015 - 2015 Software: Practice and Experience Wiley
2014 - 2014 Frontiers of Information Technology & Electronic Engineering (2095-9230) Springer
2014 - 2014 BioMed Research International Hindawi
2013 - 2013 Information Retrieval Journal (2948-2984) Springer
2007 - 2008 Computers and Electronics in Agriculture (1872-7107) Elsevier

Committee member

Activity description
Role		 Institution / Organization
2025/09/01 - 2026/08/31 Member of the Scientific Advisory Board, project TRExt (UK Research and Innovation)
Advisor / Consultant

Conference scientific committee

Conference name Conference host
2023 - Current ACL - Annual Meeting of the Association for Computational Linguistics
2023 - Current SIGIR - International ACM SIGIR Conference on Research and Development in Information Retrieval
2023 - Current EMNLP - Conference on Empirical Methods in Natural Language Processing
2020 - Current ECIR - European Conference on Information Retrieval
2025/10/22 - 2025/10/24 JBI2025 - XV Symposium on Bioinformatics

Evaluation committee

Activity description
Role		 Institution / Organization Funding entity
2025 - 2025 Horizon Europe Expert Evaluator
Evaluator
Distinctions

Award

1998 Merit Scholarship
Universidade do Algarve, Portugal

Other distinction

2013 Bolsa Investigador FCT
Fundação para a Ciência e a Tecnologia, Portugal