@phdthesis{antunes2023a,
  author    = {Antunes, Rui},
  month     = mar,
  school    = {University of Aveiro},
  title     = {Biomedical information extraction with natural language processing and machine learning methods},
  url       = {https://github.com/ruiantunes/ua-thesis},
  year      = {2023},
}

@article{leaman2023a,
  author    = {Leaman, Robert and Islamaj, Rezarta and Adams, Virginia and Alliheedi, Mohammed A. and Almeida, Jo{\~a}o Rafael and Antunes, Rui and Bevan, Robert and Chang, Yung-Chun and Erdengasileng, Arslan and Hodgskiss, Matthew and Ida, Ryuki and Kim, Hyunjae and Li, Keqiao and Mercer, Robert E. and Mertov{\'a}, Lukr{\'e}cia and Mobasher, Ghadeer and Shin, Hoo-Chang and Sung, Mujeen and Tsujimura, Tomoki and Yeh, Wen-Chao and Lu, Zhiyong},
  journal   = {Database},
  month     = mar,
  note      = {Oxford University Press},
  pages     = {baad005},
  title     = {Chemical identification and indexing in full-text articles: an overview of the {{NLM-Chem}} track at {{BioCreative VII}}},
  url       = {https://doi.org/10.1093/database/baad005},
  volume    = {2023},
  year      = {2023},
}

@article{almeida2022a,
  author    = {Almeida, Tiago and Antunes, Rui and Silva, Jo{\~a}o F. and Almeida, Jo{\~a}o R. and Matos, S{\'e}rgio},
  journal   = {Database},
  month     = jul,
  note      = {Oxford University Press},
  number    = {baac047},
  title     = {Chemical identification and indexing in {{PubMed}} full-text articles using deep learning and heuristics},
  url       = {https://doi.org/10.1093/database/baac047},
  volume    = {2022},
  year      = {2022},
}

@inproceedings{silva2021b,
  address   = {Online},
  author    = {Silva, Jo{\~a}o Figueira and Almeida, Tiago and Antunes, Rui and Almeida, Jo{\~a}o Rafael and Matos, S{\'e}rgio},
  booktitle = {{{BioCreative VII Challenge Evaluation Workshop}}},
  month     = nov,
  pages     = {210--213},
  title     = {Drug mention recognition in {{Twitter}} posts using a deep learning approach},
  url       = {https://biocreative.bioinformatics.udel.edu/resources/publications/bc-vii-workshop-proceedings/},
  year      = {2021},
}

@inproceedings{almeida2021a,
  address   = {Online},
  author    = {Almeida, Tiago and Antunes, Rui and Silva, Jo{\~a}o Figueira and Almeida, Jo{\~a}o Rafael and Matos, S{\'e}rgio},
  booktitle = {{{BioCreative VII Challenge Evaluation Workshop}}},
  month     = nov,
  pages     = {119--123},
  title     = {Chemical detection and indexing in {{PubMed}} full text articles using deep learning and rule-based methods},
  url       = {https://biocreative.bioinformatics.udel.edu/resources/publications/bc-vii-workshop-proceedings/},
  year      = {2021},
}

@inproceedings{antunes2021a,
  address   = {Online},
  author    = {Antunes, Rui and Almeida, Tiago and Silva, Jo{\~a}o Figueira and Matos, S{\'e}rgio},
  booktitle = {{{BioCreative VII Challenge Evaluation Workshop}}},
  month     = nov,
  pages     = {76--79},
  title     = {Chemical--protein relation extraction in {{PubMed}} abstracts using {{BERT}} and neural networks},
  url       = {https://biocreative.bioinformatics.udel.edu/resources/publications/bc-vii-workshop-proceedings/},
  year      = {2021},
}

@article{silva2021a,
  author    = {Silva, Jorge Miguel and Pratas, Diogo and Antunes, Rui and Matos, S{\'e}rgio and Pinho, Armando J.},
  journal   = {Pattern Recognition},
  month     = jun,
  note      = {Elsevier},
  pages     = {107864},
  title     = {Automatic analysis of artistic paintings using information-based measures},
  url       = {https://doi.org/10.1016/j.patcog.2021.107864},
  volume    = {114},
  year      = {2021},
}

@inproceedings{trifan2020b,
  address   = {Online},
  author    = {Trifan, Alina and Antunes, Rui and Oliveira, Jos{\'e} Lu{\'i}s},
  booktitle = {14th {{International Conference}} on {{Practical Applications}} of {{Computational Biology}} \& {{Bioinformatics}}},
  month     = oct,
  pages     = {102--111},
  publisher = {Springer Nature},
  title     = {Machine learning for depression screening in online communities},
  url       = {https://doi.org/10.1007/978-3-030-54568-0_11},
  year      = {2020},
}

@inproceedings{silva2020a,
  address   = {Canceled},
  author    = {Silva, Jo{\~a}o Figueira and Antunes, Rui and Almeida, Jo{\~a}o Rafael and Matos, S{\'e}rgio},
  booktitle = {30th {{Medical Informatics Europe Conference}}},
  month     = apr,
  pages     = {93--97},
  publisher = {IOS Press},
  title     = {Clinical concept normalization on medical records using word embeddings and heuristics},
  url       = {http://hdl.handle.net/10773/29190},
  year      = {2020},
}

@inproceedings{trifan2020a,
  address   = {Online},
  author    = {Trifan, Alina and Antunes, Rui and Matos, S{\'e}rgio and Oliveira, Jose Lu{\'i}s},
  booktitle = {42nd {{European Conference}} on {{Information Retrieval}}},
  month     = apr,
  pages     = {402--409},
  publisher = {Springer Nature},
  title     = {Understanding depression from psycholinguistic patterns in social media texts},
  url       = {https://doi.org/10.1007/978-3-030-45442-5_50},
  year      = {2020},
}

@inproceedings{antunes2020a,
  address   = {Online},
  author    = {Antunes, Rui and Silva, Jo{\~a}o Figueira and Matos, S{\'e}rgio},
  booktitle = {35th {{Annual ACM Symposium}} on {{Applied Computing}}},
  month     = mar,
  pages     = {662--669},
  publisher = {ACM},
  title     = {Evaluating semantic textual similarity in clinical sentences using deep learning and sentence embeddings},
  url       = {http://hdl.handle.net/10773/31473},
  year      = {2020},
}

@article{antunes2019b,
  author    = {Antunes, Rui and Matos, S{\'e}rgio},
  journal   = {Database},
  month     = oct,
  note      = {Oxford University Press},
  number    = {baz095},
  title     = {Extraction of chemical--protein interactions from the literature using neural networks and narrow instance representation},
  url       = {https://doi.org/10.1093/database/baz095},
  volume    = {2019},
  year      = {2019},
}

@inproceedings{antunes2019a,
  address   = {Prague, Czech Republic},
  author    = {Antunes, Rui and Silva, Jo{\~a}o Figueira and Pereira, Arnaldo and Matos, S{\'e}rgio},
  booktitle = {12th {{International Joint Conference}} on {{Biomedical Engineering Systems}} and {{Technologies}}},
  month     = feb,
  pages     = {59--67},
  publisher = {SciTePress},
  title     = {Rule-based and machine learning hybrid system for patient cohort selection},
  url       = {https://doi.org/10.5220/0007349300590067},
  year      = {2019},
}

@article{dogan2019a,
  author    = {Do{\u g}an, Rezarta Islamaj and Kim, Sun and {Chatr-aryamontri}, Andrew and Wei, Chih-Hsuan and Comeau, Donald C. and Antunes, Rui and Matos, S{\'e}rgio and Chen, Qingyu and Elangovan, Aparna and Panyam, Nagesh C. and Verspoor, Karin and Liu, Hongfang and Wang, Yanshan and Liu, Zhuang and Alt{\i}nel, Berna and H{\"u}s{\"u}nbeyi, Zehra Melce and {\"O}zg{\"u}r, Arzucan and Fergadis, Aris and Wang, Chen-Kai and Dai, Hong-Jie and Tran, Tung and Kavuluru, Ramakanth and Luo, Ling and Steppi, Albert and Zhang, Jinfeng and Qu, Jinchan and Lu, Zhiyong},
  journal   = {Database},
  month     = jan,
  note      = {Oxford University Press},
  number    = {bay147},
  title     = {Overview of the {{BioCreative VI Precision Medicine Track}}: mining protein interactions and mutations for precision medicine},
  url       = {https://doi.org/10.1093/database/bay147},
  volume    = {2019},
  year      = {2019},
}

@article{matos2017b,
  author    = {Matos, S{\'e}rgio and Antunes, Rui},
  journal   = {Journal of Integrative Bioinformatics},
  month     = dec,
  note      = {De Gruyter},
  number    = {4},
  title     = {Protein--protein interaction article classification using a convolutional recurrent neural network with pre-trained word embeddings},
  url       = {https://doi.org/10.1515/jib-2017-0055},
  volume    = {14},
  year      = {2017},
}

@article{antunes2017c,
  author    = {Antunes, Rui and Matos, S{\'e}rgio},
  journal   = {Journal of Integrative Bioinformatics},
  month     = dec,
  note      = {De Gruyter},
  number    = {4},
  title     = {Supervised learning and knowledge-based approaches applied to biomedical word sense disambiguation},
  url       = {https://doi.org/10.1515/jib-2017-0051},
  volume    = {14},
  year      = {2017},
}

@inproceedings{matos2017a,
  address   = {Bethesda, Maryland, USA},
  author    = {Matos, S{\'e}rgio and Antunes, Rui},
  booktitle = {{{BioCreative VI Workshop}}},
  month     = oct,
  pages     = {99--101},
  title     = {Identifying relevant literature for precision medicine using deep neural networks},
  url       = {https://biocreative.bioinformatics.udel.edu/events/biocreative-vi/workshop/},
  year      = {2017},
}

@inproceedings{antunes2017b,
  address   = {Aveiro, Portugal},
  author    = {Antunes, Rui and Matos, S{\'e}rgio},
  booktitle = {9th {{INForum}} --- {{Informatics Symposium}}},
  month     = oct,
  pages     = {25--30},
  publisher = {University of Aveiro},
  title     = {Evaluation of word embedding vector averaging functions for biomedical word sense disambiguation},
  url       = {http://hdl.handle.net/10773/25119},
  year      = {2017},
}

@inproceedings{antunes2017a,
  address   = {Porto, Portugal},
  author    = {Antunes, Rui and Matos, S{\'e}rgio},
  booktitle = {11th {{International Conference}} on {{Practical Applications}} of {{Computational Biology}} \& {{Bioinformatics}}},
  month     = jun,
  pages     = {273--279},
  publisher = {Springer Nature},
  title     = {Biomedical word sense disambiguation with word embeddings},
  url       = {http://hdl.handle.net/10773/25112},
  year      = {2017},
}

@inproceedings{antunes2016a,
  address   = {Aveiro, Portugal},
  author    = {Antunes, Rui and Matos, S{\'e}rgio},
  booktitle = {22nd {{Portuguese Conference}} on {{Pattern Recognition}}},
  month     = oct,
  pages     = {77--78},
  publisher = {University of Aveiro},
  title     = {Machine learning with word embeddings applied to biomedical concept disambiguation},
  url       = {http://hdl.handle.net/10773/25118},
  year      = {2016},
}

@mastersthesis{antunes2015a,
  author    = {Antunes, Rui},
  month     = jul,
  school    = {University of Aveiro},
  title     = {Genomics music},
  url       = {http://hdl.handle.net/10773/18866},
  year      = {2015},
}