Francisco M. Couto

ORCID

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 70

Top Venues

Publications

Matilde Pato, Márcia Barros, Francisco M. Couto
Survey on Recommender Systems for Biomedical Items in Life and Health Sciences. ACM Comput. Surv. 56 (6) (2024)
Christopher Anaya, Maria Fernandes, Francisco M. Couto
LLM Fine-Tuning With Biomedical Open-Source Data. CLEF (Working Notes) (2024)
Pedro Ruas, Fernando Gallego, Francisco J. Veredas, Francisco M. Couto
Hybrid X-Linker: Automated Data Generation and Extreme Multi-label Ranking for Biomedical Entity Linking. CoRR (2024)
Muhammad Asif, Hugo F. M. C. Martiniano, Andre Lamurias, Samina Kausar, Francisco M. Couto
DGH-GO: dissecting the genetic heterogeneity of complex diseases using gene ontology. BMC Bioinform. 24 (1) (2023)
Sofia I R. Conceição, Diana F. Sousa, Pedro Silvestre, Francisco M. Couto
lasigeBioTM at SemEval-2023 Task 7: Improving Natural Language Inference Baseline Systems with Domain Ontologies. SemEval@ACL (2023)
Pedro Ruas, Diana F. Sousa, André Neves, Carlos Cruz, Francisco M. Couto
LASIGE and UNICAGE solution to the NASA LitCoin NLP Competition. CoRR (2023)
Diana F. Sousa, Francisco M. Couto
K-RET: knowledgeable biomedical relation extraction system. Bioinform. 39 (4) (2023)
Maria Fernandes, Jérémie Decouchant, Francisco M. Couto
Chapter Two - Security, privacy, and trust management in DNA computing. Adv. Comput. 129 (2023)
Pedro Ruas, Francisco M. Couto
NILINKER: Attention-based approach to NIL Entity Linking. J. Biomed. Informatics 132 (2022)
Diana Sousa, Francisco M. Couto
Biomedical Relation Extraction With Knowledge Graph-Based Recommendations. IEEE J. Biomed. Health Informatics 26 (8) (2022)
Margarida M. Campos, Francisco M. Couto
Post-processing BioBERT And Using Voting Methods for Biomedical Question Answering. CLEF (Working Notes) (2021)
Pedro Ruas, Vitor D. T. Andrade, Francisco M. Couto
Lasige-BioTM at ProfNER: BiLSTM-CRF and contextual Spanish embeddings for Named Entity Recognition and Tweet Binary Classification. SMM4H@NAACL-HLT (2021)
Márcia Barros, Francisco M. Couto, Matilde Pato, Pedro Ruas
Creating Recommender Systems Datasets in Scientific Fields. KDD (2021)
Pedro Ruas, Vitor D. T. Andrade, Francisco M. Couto
LASIGE-BioTM at MESINESP2: entity linking with semantic similarity and extreme multi-label classification on Spanish biomedical documents. CLEF (Working Notes) (2021)
Márcia Barros, André Moitinho, Francisco M. Couto
Hybrid semantic recommender system for chemical compounds in large-scale datasets. J. Cheminformatics 13 (1) (2021)
Daniel Faria, Beatriz Lima, Marta Contreiras Silva, Francisco M. Couto, Catia Pesquita
AML and AMLC results for OAEI 2021. OM@ISWC (2021)
Andre Lamurias, Sofia Jesus, Vanessa Neveu, Reza M. Salek, Francisco M. Couto
Information Retrieval Using Machine Learning for Biomarker Curation in the Exposome-Explorer. Frontiers Res. Metrics Anal. 6 (2021)
Pedro Ruas, André Lamúrias, Francisco M. Couto
Towards a Multilingual Corpus for Named Entity Linking Evaluation in the Clinical Domain. SIIRH@ECIR (2020)
Diana Sousa, Francisco M. Couto
BiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction. CoRR (2020)
Andre Lamurias, Diana Sousa, Francisco M. Couto
Generating Biomedical Question Answering Corpora From Q&A Forums. IEEE Access 8 (2020)
Fábio Colaço, Márcia Barros, Francisco M. Couto
DRecPy: A Python Framework for Developing Deep Learning-Based Recommenders. RecSys (2020)
Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Jingqi Wang, Yuankai Ren, Zhi Zhang, Yaoyun Zhang, Mai Hoang Dao, Pedro Ruas, Andre Lamurias, Francisco M. Couto, Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro, Daniel M. Lowe, John Mayfield, Abdullatif Köksal, Hilal Dönmez, Elif Özkirimli, Arzucan Özgür, Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes, C. S. Malarkodi, Pattabhi Rk Rao, Sobha Lalitha Devi, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. CLEF (Working Notes) (2020)
André Neves, André Lamúrias, Francisco M. Couto
Biomedical Question Answering using Extreme Multi-Label Classification and Ontologies in the Multilingual Panorama. SIIRH@ECIR (2020)
Andre Lamurias, Diana Sousa, Francisco M. Couto
Generating Scientific Question Answering Corpora from Q&A forums. CoRR (2020)
Francisco M. Couto, Martin Krallinger
Report of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages. SIIRH@ECIR (2020)
Diana Sousa, Francisco M. Couto
BiOnt: Deep Learning Using Multiple Biomedical Ontologies for Relation Extraction. ECIR (2) (2020)
Pedro Ruas, Andre Lamurias, Francisco M. Couto
Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature. J. Cheminformatics 12 (1) (2020)
Maria Fernandes, Jérémie Decouchant, Marcus Völp, Francisco M. Couto, Paulo Jorge Esteves Veríssimo
DNA-SeAl: Sensitivity Levels to Optimize the Performance of Privacy-Preserving DNA Alignment. IEEE J. Biomed. Health Informatics 24 (3) (2020)
Francisco M. Couto, Martin Krallinger
Proposal of the First International Workshop on Semantic Indexing and Information Retrieval for Health from Heterogeneous Content Types and Languages (SIIRH). ECIR (2) (2020)
Pedro Ruas, Andre Lamurias, Francisco M. Couto
LasigeBioTM Team at CLEF2020 ChEMU Evaluation Lab: Named Entity Recognition and Event extraction from chemical reactions described in patents using BioBERT NER and RE. CLEF (Working Notes) (2020)
Sérgio Nunes, Suzanne Little, Sumit Bhatia, Ludovico Boratto, Guillaume Cabanac, Ricardo Campos, Francisco M. Couto, Stefano Faralli, Ingo Frommholz, Adam Jatowt, Alípio Jorge, Mirko Marras, Philipp Mayr, Giovanni Stilo
ECIR 2020 Workshops: Assessing the Impact of Going Online. CoRR (2020)
Pedro Ruas, André Neves, Vitor D. T. Andrade, Francisco M. Couto, Mario Ezra Aragón
LasigeBioTM at CANTEMIST: Named Entity Recognition and Normalization of Tumour Morphology Entities and Clinical Coding of Spanish Health-related Documents. IberLEF@SEPLN (2020)
Márcia Barros, André Moitinho, Francisco M. Couto
Hybrid Semantic Recommender System for Chemical Compounds. CoRR (2020)
Diana Sousa, Andre Lamurias, Francisco M. Couto
A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing. Database J. Biol. Databases Curation 2020 (2020)
Márcia Barros, André Moitinho, Francisco M. Couto
Hybrid Semantic Recommender System for Chemical Compounds. ECIR (2) (2020)
Beatriz Lima, Daniel Faria, Francisco M. Couto, Isabel F. Cruz, Catia Pesquita
OAEI 2020 results for AML and AMLC. OM@ISWC (2020)
Márcia Barros, Andre Lamurias, Diana Sousa, Pedro Ruas, Francisco M. Couto
COVID-19: A Semantic-Based Pipeline for Recommending Biomedical Entities. NLP4COVID@EMNLP (2020)
Sérgio Nunes, Suzanne Little, Sumit Bhatia, Ludovico Boratto, Guillaume Cabanac, Ricardo Campos, Francisco M. Couto, Stefano Faralli, Ingo Frommholz, Adam Jatowt, Alípio Jorge, Mirko Marras, Philipp Mayr, Giovanni Stilo
ECIR 2020 workshops: assessing the impact of going online. SIGIR Forum 54 (1) (2020)
André Neves, André Lamúrias, Francisco M. Couto
Extreme Multi-Label Classification applied to the Biomedical and Multilingual Panorama. CLEF (Working Notes) (2020)
João D. Ferreira, Francisco M. Couto
Multi-domain semantic similarity in biomedical research. BMC Bioinform. (10) (2019)
Daniel Faria, Catia Pesquita, Teemu Tervo, Francisco M. Couto, Isabel F. Cruz
AML and AMLC Results for OAEI 2019. OM@ISWC (2019)
Diana Sousa, Andre Lamurias, Francisco M. Couto
A Silver Standard Corpus of Human Phenotype-Gene Relations. NAACL-HLT (1) (2019)
Andre Lamurias, Diana Sousa, Luka A. Clarke, Francisco M. Couto
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. BMC Bioinform. 20 (1) (2019)
Diana Sousa, Andre Lamurias, Francisco M. Couto
A Silver Standard Corpus of Human Phenotype-Gene Relations. CoRR (2019)
Márcia Barros, André Moitinho, Francisco M. Couto
Using Research Literature to Generate Datasets of Implicit Feedback for Recommending Scientific Items. IEEE Access 7 (2019)
Diana Sousa, Andre Lamurias, Francisco M. Couto
Using Neural Networks for Relation Extraction from Biomedical Literature. CoRR (2019)
Andre Lamurias, Francisco M. Couto
LasigeBioTM at MEDIQA 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition. BioNLP@ACL (2019)
Andre Lamurias, Pedro Ruas, Francisco M. Couto
PPR-SSM: personalized PageRank and semantic similarity measures for entity linking. BMC Bioinform. 20 (1) (2019)
Francisco M. Couto, Andre Lamurias
MER: a shell script and annotation server for minimal named entity recognition and linking. J. Cheminformatics 10 (1) (2018)
Daniel Faria, Catia Pesquita, Booma Sowkarthiga Balasubramani, Teemu Tervo, David Carriço, Rodrigo Garrilha, Francisco M. Couto, Isabel F. Cruz
Results of AML participation in OAEI 2018. OM@ISWC (2018)
Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M. Couto, Isabel F. Cruz
Tackling the challenges of matching biomedical ontologies. J. Biomed. Semant. 9 (1) (2018)
Jérémie Decouchant, Maria Fernandes, Marcus Völp, Francisco M. Couto, Paulo Jorge Esteves Veríssimo
Accurate filtering of privacy-sensitive information in raw genomic data. J. Biomed. Informatics 82 (2018)
Luís Campos, Vasco Pedro, Francisco M. Couto
Impact of translation on named-entity recognition in radiology texts. Database J. Biol. Databases Curation 2017 (2017)
Daniel Faria, Booma S. Balasubramani, Vivek R. Shivaprabhu, Isabela Mott, Catia Pesquita, Francisco M. Couto, Isabel F. Cruz
Results of AML in OAEI 2017. OM@ISWC (2017)
Vinicius Vielmo Cogo, Alysson Bessani, Francisco M. Couto, Margarida Gama-Carvalho, Maria Fernandes, Paulo Jorge Esteves Veríssimo
How Can Photo Sharing Inspire Sharing Genomes? PACBB (2017)
Luís Campos, Francisco M. Couto
MRA - Proof of Concept of a Multilingual Report Annotator Web Application. CoRR (2017)
João D. Ferreira, Bruno Inácio, Reza M. Salek, Francisco M. Couto
Assessing Public Metabolomics Metadata, Towards Improving Quality. J. Integr. Bioinform. 14 (4) (2017)
Maria Fernandes, Jérémie Decouchant, Francisco M. Couto, Paulo Jorge Esteves Veríssimo
Cloud-Assisted Read Alignment and Privacy. PACBB (2017)
Andre Lamurias, Diana Sousa, Sofia Pereira, Luka A. Clarke, Francisco M. Couto
ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events. SemEval@ACL (2017)
Miguel J. Rodrigues, Francisco M. Couto
MoRS at SemEval-2017 Task 3: Easy to use SVM in Ranking Tasks. SemEval@ACL (2017)
António Barata, Lucília Carvalho, Francisco M. Couto
Anthropometric Data Analytics: A Portuguese Case Study. PACBB (2017)
Bruno Inácio, João D. Ferreira, Francisco M. Couto
Metadata Analyser: Measuring Metadata Quality. PACBB (2017)
Diogo Gonçalves, Miguel Costa, Francisco M. Couto
A Flexible Recommendation System for Cable TV. CoRR (2016)
Camila Ramos, Marco Louro, Miguel Santos, Francisco M. Couto
Knowledge Ratings in MetaboLights. CoRR (2016)
Daniel Faria, Catia Pesquita, Booma S. Balasubramani, Catarina Martins, João Cardoso, Hugo Curado, Francisco M. Couto, Isabel F. Cruz
OAEI 2016 results of AML. OM@ISWC (2016)
Andre Lamurias, Miguel J. Rodrigues, Luka A. Clarke, Francisco M. Couto
Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision. BioNLP (Shared Task) (2016)
Hugo P. Bastos, Lisete Sousa, Luka A. Clarke, Francisco M. Couto
Functional coherence metrics in protein families. J. Biomed. Semant. 7 (2016)
Miguel J. Rodrigues, Miguel Falé, Andre Lamurias, Francisco M. Couto
WS4A: a Biomedical Question and Answering System based on public Web Services and Ontologies. CoRR (2016)
Márcia Barros, Andre Lamurias, Gonçalo Figueiró, Marta Antunes, Joana Teixeira, Alexandre Pinheiro, Francisco M. Couto
ULISBOA at SemEval-2016 Task 12: Extraction of temporal expressions, clinical events and relations using IBEnt. SemEval@NAACL-HLT (2016)
Diogo Gonçalves, Miguel Costa, Francisco M. Couto
A Large-Scale Characterization of User Behaviour in Cable TV. CoRR (2016)
Andre Lamurias, Luka A. Clarke, Francisco M. Couto
IICE: Web Tool for Automatic Identification of Chemical Entities and Interactions. ECML/PKDD (3) (2015)
Andre Lamurias, João D. Ferreira, Francisco M. Couto
Improving chemical entity recognition through h-index based semantic similarity. J. Cheminformatics 7 (S-1) (2015)
Tudor Groza, Sebastian Köhler, Sandra C. Doelken, Nigel Collier, Anika Oellrich, Damian Smedley, Francisco M. Couto, Gareth Baynam, Andreas Zankl, Peter N. Robinson
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora. Database J. Biol. Databases Curation 2015 (2015)
Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V. Ramanan, P. Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Ravikumar Komandur Elayavilli, Andre Lamurias, Francisco M. Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J. Cheminformatics 7 (S-1) (2015)
André Leal, Bruno Martins, Francisco M. Couto
ULisboa: Recognition and Normalization of Medical Concepts. SemEval@NAACL-HLT (2015)
Catia M. Machado, Dietrich Rebholz-Schuhmann, Ana T. Freitas, Francisco M. Couto
The semantic web in translational medicine: current applications and future directions. Briefings Bioinform. 16 (1) (2015)
Andre Lamurias, Vasco Pedro, Luka A. Clarke, Francisco M. Couto
Annotating biomedical ontology terms in electronic health records using crowd-sourcing. ICBO (2015)
Daniel Faria, Catarina Martins, Amruta Nanavaty, Daniela Oliveira, Booma Sowkarthiga, Aynaz Taheri, Catia Pesquita, Francisco M. Couto, Isabel F. Cruz
AML results for OAEI 2015. OM (2015)
Vinicius Vielmo Cogo, Alysson Bessani, Francisco M. Couto, Paulo Veríssimo
A High-Throughput Method to Detect Privacy-Sensitive Human Genomic Data. WPES@CCS (2015)
Carlos Barata, Mónica Abreu, Pedro Torres, Jorge Teixeira, Tiago João Guerreiro, Francisco M. Couto
Social Impact - Identifying Quotes of Literary Works in Social Networks. EPIA (2015)
Catia Pesquita, João D. Ferreira, Francisco M. Couto, Mário J. Silva
The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. J. Biomed. Semant. 5 (2014)
Andre Lamurias, João D. Ferreira, Francisco M. Couto
Identifying interactions between chemical entities in biomedical text. J. Integr. Bioinform. 11 (3) (2014)
Daniel Faria, Catia Pesquita, Emanuel Santos, Isabel F. Cruz, Francisco M. Couto
AgreementMakerLight 2.0: Towards Efficient Large-Scale Ontology Matching. ISWC (Posters & Demos) (2014)
Catia Pesquita, Daniel Faria, Emanuel Santos, Jean-Marc Neefs, Francisco M. Couto
Towards Visualizing the Alignment of Large Biomedical Ontologies. DILS (2014)
Andre Lamurias, João D. Ferreira, Francisco M. Couto
Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical Features. PACBB (2014)
Daniel Faria, Catarina Martins, Amruta Nanavaty, Aynaz Taheri, Catia Pesquita, Emanuel Santos, Isabel F. Cruz, Francisco M. Couto
AgreementMakerLight results for OAEI 2014. OM (2014)
Daniel Faria, Ernesto Jiménez-Ruiz, Catia Pesquita, Emanuel Santos, Francisco M. Couto
Towards Annotating Potential Incoherences in BioPortal Mappings. ISWC (2) (2014)
Catia Pesquita, Michelle Cheatham, Daniel Faria, Joana Barros, Emanuel Santos, Francisco M. Couto
Building reference alignments for compound matching of multiple ontologies using OBO cross-products. OM (2014)
João Martins, José Carilho, Oliver Schnell, Carlos Duarte, Francisco M. Couto, Luís Carriço, Tiago João Guerreiro
Friendsourcing the unmet needs of people with dementia. W4A (2014)
André Leal, Diogo Gonçalves, Bruno Martins, Francisco M. Couto
ULisboa: Identification and Classification of Medical Concepts. SemEval@COLING (2014)
Francisco M. Couto
Rating, Recognizing and Rewarding Metadata Integration and Sharing on the Semantic Web. URSW (2014)
Miguel Costa, Francisco M. Couto, Mário J. Silva
Learning temporal-dependent ranking models. SIGIR (2014)
Catia Pesquita, Daniel Faria, Emanuel Santos, Francisco M. Couto
To repair or not to repair: reconciling correctness and coherence in ontology reference alignments. OM (2013)
Francisco M. Couto
CIDS country rankings: comparing documents and citations of USA, UK and China top researchers. CoRR (2013)
João D. Ferreira, Janna Hastings, Francisco M. Couto
Exploiting disjointness axioms to improve semantic similarity measures. Bioinform. 29 (21) (2013)
João D. Ferreira, Catia Pesquita, Francisco M. Couto, Mário J. Silva
Digital preservation of epidemic resources: coupling metadata and ontologies. iPRES (2013)
Catia Pesquita, Daniel Faria, Cosmin Stroe, Emanuel Santos, Isabel F. Cruz, Francisco M. Couto
What's in a 'nym'? Synonyms in Biomedical Ontology Matching. ISWC (1) (2013)
Miguel Costa, Daniel Gomes, Francisco M. Couto, Mário J. Silva
A survey of web archive search architectures. WWW (Companion Volume) (2013)
Silvio Moreira, João Filgueiras, Bruno Martins, Francisco M. Couto, Mário J. Silva
REACTION: A naive machine learning approach for sentiment classification. SemEval@NAACL-HLT (2013)
Emanuel Santos, Daniel Faria, Catia Pesquita, Francisco M. Couto
Ontology alignment repair through modularization and confidence-based heuristics. CoRR (2013)

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Publication Activity (10 Years)

Top Topics

Top Venues

Francisco M. Couto