Publications

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Book Chapter
Lamurias, A., J. Ferreira, and F. Couto, "Chemical named entity recognition: Improving recall using a comprehensive list of lexical features", 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014): Springer International Publishing, pp. 253–260, 2014.
Conference Paper
Lamurias, A., M.. Lobo, M.. Antunes, L.. Clarke, and F. Couto, "Identifying chemical entities in patents using brown clustering and semantic similarity", 5th BioCreative Challenge Evaluation, 2015.
Lamurias, A., and F. Couto, "Identifying Interactions Between Chemical Entities in Text", Bioinformatics Open Days, University of Braga, 2014.
Lamurias, A., L.. Clarke, and F. Couto, "IICE: web tool for automatic identification of chemical entities and interactions", European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Demo Track, 2015.
Couto, F. M., L. Campos, and A. Lamurias, "MER: a minimal named-entity recognition tagger and annotation server", Proceedings of the BioCreative, Conference: BeCalm challenge evaluation workshop (Biocreative V.5), at Barcelona, Spain, vol. 5, 2017.
Barros, M., A. Lamurias, G. Figueiró, M. Antunes, J. Teixeira, A. Pinheiro, and F. M. Couto, "ULISBOA at SemEval-2016 Task 12: Extraction of temporal expressions, clinical events and relations using IBEnt.", SemEval@ NAACL-HLT, pp. 1263–1267, 2016.
Lamurias, A., D. Sousa, S. Pereira, L. Clarke, and F. M. Couto, "ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events", Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval-2017), pp. 1019–1023, 2017.
Journal Article
Lamurias, A., L. A. Clarke, and F. M. Couto, "BO-LSTM: Classifying relations via long short-term memory networks along biomedical ontologies", bioRxiv: Cold Spring Harbor Laboratory, pp. 336719, 2018.
Krallinger, M.., O.. Rabal, F.. Leitner, M.. Vazquez, D.. Salgado, Z.. Lu, R.. Leaman, Y.. Lu, D.. Ji, D.. Lowe, et al., "The CHEMDNER corpus of chemicals and drugs and its annotation principles", Journal of Cheminformatics, vol. 7, pp. S2, 1-20, 2015.
Lamurias, A., T. Grego, and F. Couto, "Chemical compound and drug name recognition using CRFs and semantic similarity based on ChEBI", BioCreative Challenge Evaluation Workshop, vol. 2, pp. 75, 2013.
Lamurias, A., J. Ferreira, and F. Couto, "Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical", Bioinformatics (Pacbb 2014), vol. 294: Springer, pp. 253, 2014.
Lamurias, A., L. A. Clarke, and F. M. Couto, "Extracting microRNA-gene relations from biomedical literature using distant supervision", PloS one, vol. 12, no. 3: Public Library of Science, pp. e0171929, 2017.
Lamurias, A., M. J. Rodrigues, L. A. Clarke, and F. M. Couto, "Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision", ACL 2016, pp. 88, 2016.
Lamurias, A., J. D. Ferreira, L. A. Clarke, and F. M. Couto, "Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature", Frontiers in Immunology, vol. 8: Frontiers, pp. 1656, 2017.
Lobo, M., A. Lamurias, and F. M. Couto, "Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules", BioMed Research International, vol. 2017: Hindawi, 2017.
Lamurias, A., J. Ferreira, and F. Couto, "Identifying interactions between chemical entities in biomedical text", Journal of integrative bioinformatics, vol. 11, no. 3, pp. 247, 2014.
Lamurias, A., Identifying interactions between chemical entities in text, , 2014.
Lamurias, A., J. Ferreira, and F. Couto, "Improving chemical entity recognition through h-index based semantic similarity", Journal of Cheminformatics, vol. 7, pp. S13, 1-20, 2015.
Rodrigues, M. J., M. Falé, A. Lamurias, and F. M. Couto, "WS4A: a biomedical question and answering system based on public web services and ontologies", arXiv preprint arXiv:1609.08492, 2016.