André Lamúrias

Research

My research work is mainly focused on information extraction applied to biomedical data, such as scientific papers, electronic health records and genomics. I work with machine learning algorithms and integrate the extracted information with domain ontologies.

On my GitHub page you can find past projects and projects I'm currently working on. My publications can be found on Google Scholar and Research Gate.

MSc Thesis Supervisions

On-going

Cláudio Guerra - Information Extraction from Biomedical Documents in Low-Resource Scenarios, Co-supervised with Diana Sousa (2025)
Tomás Carvalho - Information Extraction from Biomedical Documents in Low-Resource Scenarios, Co-supervised with Diana Sousa (2025)
Guilherme Poças - Levering cell embeddings for improved cell type classification, Co-supervised with Muhammad Asif (2025)

Completed

José Barata - Recovering genomes from microbial communities with unsupervised learning (2025)
Tiago Gomes - Exploring Graph Neural Networks for Metagenomics Assembly Graphs (2025)
Diogo Ramos - Multi-domain document retrieval for database curation (2024)
Rodrigo Gonçalves - Entity recognition and linking for biomedical documents (2024)
Miguel Vieira - Development of a Corpus for User-based Scientific Question Answering, Co-supervised with Francisco Couto(2021)
André Neves - Applying Deep Learning Extreme Multi-Label Classification to the Biomedical and Multilingual Panoramas,Co-supervised with Francisco Couto (2020)

Teaching

Bioinformatics (MSc in Computer Science and Engineering @FCT NOVA) 2025/26
Algorithms and Data Structures for Biology (MSc in Computational Biology and Bioinformatics @FCT NOVA) 2024/2025, 2025/26
Artificial Intelligence Techniques for Biology (MSc in Computational Biology and Bioinformatics @FCT NOVA) 2023/24, 2024/2025, 2025/26
Databases (2nd year BSc in Computer Science and Engineering @FCT NOVA - 2022/23, 2023/24, 2024/25, 2025/26
Artificial Intelligence (3rd year BSc in Computer Science and Engineering @FCT NOVA) - 2023/24, 2024/25

Publications

Chapters

A. Lamurias and F. Couto, “Text mining for bioinformatics using biomedical literature,” in Encyclopedia of Bioinformatics and Computational Biology (S. Ranganathan, K. Nakai, C. Schönbach, and M. Gribskov, eds.), vol. 1, pp. 602–611, Oxford: Elsevier, 2019.
F. Couto and A. Lamurias, “Semantic similarity definition,” in Encyclopedia of Bioinformatics and Computational Biology (S. Ranganathan, K. Nakai, C. Schönbach, and M. Gribskov, eds.), vol. 1, pp. 870–876, Oxford: Elsevier, 2019.

Journal

A. Lamurias, M. Sereika, M. Albertsen, K. Hose, & T.D. Nielsen, "Metagenomic binning with assembly graph embeddings". bioRxiv, 2022 (preprint).
A. Lamurias, S. Jesus, V. Neveu, R. Salek, and F. Couto, “Information retrieval using machine learning for biomarker curation in the exposome-explorer,” Frontiers in Research Metrics and Analytics, vol. 6, no. 55, pp. 1--10, 2021.
P. Ruas, A. Lamurias, and F. Couto, “Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature,” Journal of Cheminformatics, vol. 12, no. 57, pp. 1--15, 2020.
D. Sousa, A. Lamurias, and F. Couto, “A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing,” Database: The Journal of Biological Databases and Curation, vol. 2020, no. baaa104, pp. 1--15, 2020.
A. Lamurias, D. Sousa, F.M. Couto, "Generating biomedical question answering corpora from q&a forums." IEEE Access, 8, 161042-161051, 2020
A. Lamurias, P. Ruas, and F. Couto, “PPR-SSM: personalized pagerank and semantic similarity measures for entity linking,” BMC Bioinformatics, vol. 20, no. 534, pp. 1--12, 2019
A. Lamurias, D. Sousa, L. Clarke, and F. Couto, “BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies,” BMC Bioinformatics, vol. 20, no. 10, pp. 1–12, 2019.
F. Couto and A. Lamurias, “MER: a shell script and annotation server for minimal named entity recognition and linking,” Journal of Cheminformatics, vol. 10, no. 58, pp. 1–10, 2018.
A. Lamurias, J. Ferreira, L. Clarke, and F. Couto, “Generating a tolerogenic cell therapy knowledge graph from literature,” Frontiers in Immunology, vol. 8, no. 1656, pp. 1–23, 2017.
M. Lobo, A. Lamurias, and F. Couto, “Identifying human phenotype terms by combining machine learning and validation rules,” BioMed Research International, vol. 2017, pp. 1–14, 2017.
A. Lamurias, L. Clarke, and F. Couto, “Extracting microRNA-gene relations from biomedical literature using distant supervision,” PLoS ONE, vol. 12, no. 3, pp. 1–20, 2017.
A. Lamurias, J. Ferreira, and F. Couto, “Improving chemical entity recognition through h-index based semantic similarity,” Journal of Cheminformatics, vol. 7, no. Suppl 1, pp. S13, 1–20, 2015.
A. Lamurias, J. Ferreira, and F. Couto, “Identifying interactions between chemical entities in biomedical text,” Journal of Integrative Bioinformatics, vol. 11, no. 3, pp. 1–16, 2014.

Conference

D. Sousa, A. Lamurias, and F. Couto, “A silver standard corpus of human phenotype-gene relations,” in Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL 2019), vol. N19-1152, p. 1487–1492, 2019.
A. Lamurias, L. Clarke, and F. Couto, “IICE: web tool for automatic identification of chemical entities and interactions,” in European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Demo Track, pp. 285–288, 2015.
A. Lamurias, V. Pedro, L. Clarke, and F. Couto, “Annotating biomedical terms in electronic health records using crowd-sourcing,” in International Conference on Biomedical Ontologies (ICBO), Early Career, 2015.
A. Lamurias, J. Ferreira, and F. Couto, “Chemical named entity recognition: Improving recall using a comprehensive list of lexical features,” in Practical Applications of Computational Biology and Bioinformatics (PACBB), vol. 294, pp. 253–260, Lecture Notes in Computer Science, 2014.

Workshop

A. Lamurias and F. Couto, “LasigeBioTM at MEDIQA 2019: Biomedical question answering using bidirectional transformers and named entity recognition,” in 18th ACL Workshop on Biomedical Natural Language Processing (BioNLP 2019), 2019.
L. Campos, A. Lamurias, and F. Couto, “Can the wisdom of the crowd be used to improve the creation of gold-standard for text mining applications?,” in INForum – Simpósio de Informática, 2017.
F. Couto, L. Campos, and A. Lamurias, “MER: a minimal named-entity recognition tagger and annotation server,” in BioCreative V.5 Challenge Evaluation, 2017.
A. Lamurias, L. Campos, and F. Couto, “IBEnt: Chemical entity mentions in patents using ChEBI,” in BioCreative V.5 Challenge Evaluation, 2017.
A. Lamurias, D. Sousa, S. Pereira, L. Clarke, and F. Couto, “ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events,” in 10th International Workshop on Semantic Evaluation (SemEval), 2017.
M. Barros, A. Lamurias, G. Figueiro, M. Antunes, J. Teixeira, A. Pinheiro, and F. Couto, “ULISBOA at SemEval-2016 task 12: Extraction of temporal expressions, clinical events and relations using IBEnt,” in 9th International Workshop on Semantic Evaluation (SemEval), 2016.
A. Lamurias, M. Lobo, M. Antunes, L. Clarke, and F. Couto, “Identifying chemical entities in patents using brown clustering and semantic similarity,” in 5th BioCreative Challenge Evaluation, 2015.
A. Lamurias, T. Grego, and F. Couto, “Chemical compound and drug name recognition using CRFs and semantic similarity based on ChEBI,” in 4th BioCreative Challenge Evaluation, 2013.

Presentations

2023/08/29 - ICML Workshop on Computational Biology, Honolulu, Hawaii, USA (Poster presentation): Graph Neural Networks for Metagenomic Binning
2023/08/27 - ICML, Honolulu, Hawaii, USA (Poster presentation): Metagenomic Binning using Connectivity-constrained Variational Autoencoders
2023/04/26 - NOVA Lincs seminar: Making sense of biological sequences: biomedical text mining and microbial genome recovery
2021/11/16 - Hands-on metagenomics using Oxford Nanopore DNA sequencing (PhD course), Aalborg University, Aalborg, Denmark: Metagenomic Binning
2021/11/11 - AI for the People Conference and Networking (Poster presentation)
2021/06/22 - Fundamentals of Clinical Data Science (PhD course), Aalborg University Hospital, Aalborg, Denmark: Lecture on Extraction of information from unstructured data using NLP
2020/10/23 - Seminar for Bioinformatics MSc Students, FCUL, Lisbon, Portugal: Text mining approaches for health and life sciences
2019/11/28 - 8th DeST Meeting, FCUL, Lisbon, Portugal: Python packaging tutorial
2019/10/04 - Seminar for Data Science MSc Students, FCUL, Lisbon, Portugal: Text mining approaches for bioinformatics
2019/06/03 - NAACL, Minneapolis, Minnesota, USA (Poster presentation): A Silver Standard Corpus of Human Phenotype-Gene Relations
2019/05/29 - Cool Tools for Science, Champalimaud Foundation, Lisboa, Portugal
2019/04/12 - IV Ciclo Conferências de Ciências Biomédicas à Tarde, UBI Covilha, Portugal: Text Mining Approaches for Bioinformatics
2019/02/22 - The role of text mining in curation workflows, GREEKC Workshop, Málaga, Spain: Extracting microRNA-gene relations from biomedical literature using distant supervision

PhD Defense

2018/12/19 - 2nd DeST Meeting, FCUL, Lisbon, Portugal: Development of Text Mining Approach to Disease Network Discovery (first draft of PhD defense)
2018/12/03 - Seminar for Bioinformatics MSc Students, FCUL, Lisbon, Portugal: Text mining approaches for bioinformatics
2017/10/12 - INforum, Aveiro, Portugal: the Wisdom of the Crowd Be Used to Improve the Creation of Gold-standard for Text Mining applications?
2017/02/22 - Text mining workshop, Bioinformatics Open Days, Braga, Portugal,
2016/07/23 - Instituto de Higiene Medicina Tropical, Lisboa, Portugal; Big Data, Desenvolvimento Sustentável e a Ciência Aberta
2015/07/30 - ICBO, Early Careers track, Lisbon, Portugal: Annotating biomedical ontology terms in electronic health records using crowd-sourcing
2015/09/08 - ECML PKDD demo track, Porto, Portugal: IICE: web tool for automatic identification of chemical entities and interactions
2014/09/26 - Master's thesis defense, FCUL, Lisbon, Portugal: Identifying Interactions Between Chemical Entities in Text