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PEDRO SIMÕES RUAS. Concluiu o Mestrado em Bioinformática e Biologia Computacional em 2019 pela Universidade de Lisboa-Faculdade de Ciências, a Licenciatura em Bioquímica em 2014 pela Universidade do Porto-Faculdade de Ciências e Instituto de Ciências Biomédicas Abel Salazar. Frequenta o Doutoramento em Informática pela Universidade de Lisboa-Faculdade de Ciências desde 2020/10. É bolseiro de doutoramento e encontra-se associado à Universidade de Lisboa-Laboratório de Sistemas Informáticos de Grande Escala (LASIGE). Atua nas áreas de Ciências Exatas com ênfase em Ciências da Computação e da Informação e em Bioinformática.
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Identification

Personal identification

Full name
PEDRO SIMÕES RUAS

Citation names

  • RUAS, PEDRO

Author identifiers

Ciência ID
5A15-C96E-F9E1
ORCID iD
0000-0002-1293-4199

Email addresses

  • psruas@fc.ul.pt (Professional)

Websites

Knowledge fields

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

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Elementary (A2) Upper intermediate (B2) Elementary (A2) Upper intermediate (B2)
Education
Degree Classification
2020/10 - 2024/10
Ongoing
 Informática (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal

Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
2017/09 - 2019/07/26
Concluded
 Bioinformática e Biologia Computacional (Mestrado)
Major in Sem especialização
Universidade de Lisboa Faculdade de Ciências, Portugal
"Exploring Biomedical Ontologies, Personalized PageRank and Semantic Similarity in the Entity Linking task " (THESIS/DISSERTATION)
 18/20
2014/10 - 2017/04/05
Concluded
 Parasitologia Médica (Mestrado)
Major in Sem especialização
Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical, Portugal
"Association of efflux pump inhibitors with antileishmanial drugs as na alternative treatment for leishmaniasis." (THESIS/DISSERTATION)
 17/20
2011/09 - 2014/07
Concluded
 Bioquímica (Licenciatura)
Universidade do Porto Faculdade de Ciências, Portugal

Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
15/20
Affiliation

Science

Category
Host institution 		Employer
2019/11/26 - Current Researcher (Research) Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
Universidade de Lisboa Faculdade de Ciências, Portugal
2019/07/27 - 2019/11/25 Research Trainee (Research) Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
Projects

Contract

Designation Funders
2019/11/26 - Current Dest: Deep Semantic Tagger
PTDC/CCI-BIO/28685/2017
Research Fellow
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
 Associação para a Inovação e Desenvolvimento da FCT
Ongoing
Outputs

Publications

Book chapter
  1. Pedro Ruas. "Deep Semantic Entity Linking". 2021.
    10.1007/978-3-030-72240-1_81
Conference paper
  1. Ruas, P.; Andrade, V.D.T.; Couto, F.M.. "LASIGE-BioTM at MESINESP2: Entity linking with semantic similarity and extreme multi-label classification on Spanish biomedical documents". 2021.
  2. Ruas, P.; Neves, A.; Andrade, V.D.T.; Couto, F.M.. "Lasigebiotm at cantemist: Named entity recognition and normalization of tumour morphology entities and clinical coding of Spanish health-related documents". 2020.
  3. Ruas, P.; Lamúrias, A.; Couto, F.M.. "Towards a multilingual corpus for named entity linking evaluation in the clinical domain". 2020.
  4. He, J.; Nguyen, D.Q.; Akhondi, S.A.; Druckenbrodt, C.; Thorne, C.; Hoessel, R.; Afzal, Z.; et al. "An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents". 2020.
  5. Ruas, P.; Lamurias, A.; Couto, F.M.. "LasigeBioTM team at CLEF2020 ChEMU evaluation lab: Named Entity Recognition and Event extraction from chemical reactions described in patents using BioBERT NER and RE". 2020.
Journal article
  1. Márcia Barros; Pedro Ruas; Diana Sousa; Ali Haider Bangash; Francisco M. Couto. "COVID-19 recommender system based on an annotated multilingual corpus". Genomics & Informatics (2021): https://doi.org/10.5808/gi.21008.
    10.5808/gi.21008
  2. "Creating Recommender Systems Datasets in Scientific Fields". Proceedings of the 27th ACM SIGKDD Conference on Knowledge Discovery & Data Mining (2021): http://dx.doi.org/10.1145/3447548.3470805.
    10.1145/3447548.3470805
  3. "Lasige-BioTM at ProfNER: BiLSTM-CRF and contextual Spanish embeddings for Named Entity Recognition and Tweet Binary Classification". Proceedings of the Sixth Social Media Mining for Health (#SMM4H) Workshop and Shared Task (2021): http://dx.doi.org/10.18653/v1/2021.smm4h-1.21.
    10.18653/v1/2021.smm4h-1.21
  4. Pedro Ruas; Andre Lamurias; Francisco M. Couto. "Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature". Journal of Cheminformatics (2020): https://doi.org/10.1186/s13321-020-00461-4.
    10.1186/s13321-020-00461-4
  5. Áurea Gabriel; Ana Valério-Bolas; Joana Palma-Marques; Patrícia Mourata-Gonçalves; Pedro Ruas; Tatiana Dias-Guerreiro; Gabriela Santos-Gomes. "Cutaneous Leishmaniasis: The Complexity of Host’s Effective Immune Response against a Polymorphic Parasitic Disease". Journal of Immunology Research 2019 (2019): 1-16. https://doi.org/10.1155/2019/2603730.
    10.1155/2019/2603730
  6. Andre Lamurias; Pedro Ruas; Francisco M. Couto. "PPR-SSM: personalized PageRank and semantic similarity measures for entity linking". BMC Bioinformatics 20 1 (2019): https://doi.org/10.1186%2Fs12859-019-3157-y.
    10.1186/s12859-019-3157-y
Thesis / Dissertation
  1. RUAS, PEDRO. "Exploring biomedical ontologies, personalized pagerank and semantic similarity in the entity linking task". Master, Universidade de Lisboa Faculdade de Ciências, 2019. https://repositorio.ul.pt/handle/10451/39624.
  2. RUAS, PEDRO. "Association of efflux pump inihibitors with antileishmanial drugs as an alternative treatment for leishmaniasis". Master, Universidade Nova de Lisboa Instituto de Higiene e Medicina Tropical, 2017. https://run.unl.pt/handle/10362/20657.

Other

Other output
  1. Towards a multilingual corpus for Named Entity Linking evaluation in the clinical domain (video). A Youtube video with the presentation of the short paper "Towards a multilingual corpus for Named Entity Linking evaluation in the clinical domain" in the context of the Semantic Indexing and Information Retrieval for Health 2020 workshop held in conjunction with the 42nd European Conference on Information Retrieval (ECIR2020). 2020. RUAS, PEDRO. https://www.youtube.com/watch?v=1SE7PY3sFtA.
  2. COVID-19: A Semantic-Based Pipeline for Recommending Biomedical Entities. 2020. Marcia Afonso Barros; Andre Lamurias; Diana Sousa; Pedro Ruas; Francisco M. Couto. https://doi.org/10.18653%2Fv1%2F2020.nlpcovid19-2.20.
    10.18653/v1/2020.nlpcovid19-2.20
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2020/04/14 Towards a multilingual corpus for Named Entity Linking evaluation in the clinical domain Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH) 2020 - Workshop held in conjunction with the 42nd European Conference on Information Retrieval (ECIR2020)
(Online due to Covid-19)

Committee member

Activity description
Role 		Institution / Organization
2020/04 - 2020/04 Review of submitted papers to the Workshop 'Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages 2020'
Member
Distinctions

Award

2011 Prémio de mérito do Ministério da Educação e Ciência