André Lamúrias

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.