Sérgio Matos

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 64

Top Topics

Word Sense Disambiguation

Kolmogorov Complexity

Protein Interaction

Top Venues

CLEF (Working Notes)

Database J. Biol. Databases Curation

Publications

Tiago Almeida, Sérgio Matos
Towards a Hyperparameter-Free QUBO Formulation for Feature Selection in IR. CLEF (Working Notes) (2024)
Tiago Almeida, Sérgio Matos
Exploring efficient zero-shot synthetic dataset generation for Information Retrieval. EACL (Findings) (2024)
Tiago Almeida, Sérgio Matos
SPARe: Supercharged Lexical Retrievers on GPU with Sparse Kernels. ECIR (3) (2024)
Richard A. A. Jonker, Tiago Almeida, Sérgio Matos
Analyzing a Decade of Evolution: Trends in Natural Language Processing. DaWaK (2024)
Tiago Almeida, Richard A. A. Jonker, João António Reis, João Rafael Almeida, Sérgio Matos
BIT.UA at BioASQ 12: From Retrieval to Answer Generation. CLEF (Working Notes) (2024)
João Rafael Almeida, Jorge Miguel Silva, Luís Carlos Afonso, Tiago Melo Almeida, Rui Antunes, Richard A. A. Jonker, João António Reis, Dimitri Silva, Sérgio Matos, José Luís Oliveira
HealthDBFinder: a question-answering task for health database discovery. CBMS (2024)
Tiago Almeida, Richard Adolph Aires Jonker, Rui Antunes, João Rafael Almeida, Sérgio Matos
Towards discovery: an end-to-end system for uncovering novel biomedical relations. Database J. Biol. Databases Curation 2024 (2024)
Richard A. A. Jonker, Tiago Almeida, Sérgio Matos
BIT.UA at MultiCardioNER: Adapting a Multi-head CRF for Cardiology. CLEF (Working Notes) (2024)
Richard A. A. Jonker, Tiago Almeida, Rui Antunes, João Rafael Almeida, Sérgio Matos
Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes. Database J. Biol. Databases Curation 2024 (2024)
Sara Duarte-Pereira, Sérgio Matos, José Luís Oliveira, Raquel M. Silva
Study of NAD-interacting proteins highlights the extent of NAD regulatory roles in the cell and its potential as a therapeutic target. J. Integr. Bioinform. 20 (2) (2023)
Tiago Almeida, Richard Adolph Aires Jonker, Roshan Poudel, Jorge M. Silva, Sérgio Matos
BIT.UA at BioASQ 11B: Two-Stage IR with Synthetic Training and Zero-Shot Answer Generation. CLEF (Working Notes) (2023)
Asal Kiazadeh, Jonas Deuermeier, Emanuel Carlos, Rodrigo Martins, Sérgio Matos, Fabio Martinho Cardoso, Luis Manuel Pessoa
Concept paper on novel radio frequency resistive switches. NANOARCH (2023)
Richard Adolph Aires Jonker, Roshan Poudel, Olga Fajarda, José Luís Oliveira, Rui Pedro Lopes, Sérgio Matos
DyPrune: Dynamic Pruning Rates for Neural Networks. EPIA (1) (2023)
Jorge Miguel Silva, Diogo Pratas, Sérgio Matos
Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications. DoCEIS (2023)
Tiago Almeida, Richard A. A. Jonker, Roshan Poudel, Jorge M. Silva, Sérgio Matos
BIT.UA at MedProcNer: Discovering Medical Procedures in Spanish Using Transformer Models with MCRF and Augmentation. CLEF (Working Notes) (2023)
Tiago Almeida, André Pinho, Rodrigo Pereira, Sérgio Matos
Deep Learning solutions based on fixed contextualized embeddings from PubMedBERT on BioASQ 10b and traditional IR in Synergy. CLEF (Working Notes) (2022)
Jorge Miguel Silva, Diogo Pratas, Tânia Caetano, Sérgio Matos
Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods. IbPRIA (2022)
Tiago Almeida, Rui Antunes, João Figueira Silva, João Rafael Almeida, Sérgio Matos
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics. Database J. Biol. Databases Curation 2022 (2022) (2022)
João Figueira Silva, Sérgio Matos
Modelling Patient Trajectories Using Multimodal Information. CoRR (2022)
João Figueira Silva, Sérgio Matos
Modelling patient trajectories using multimodal information. J. Biomed. Informatics 134 (2022)
Richard Adolph Aires Jonker, Roshan Poudel, Olga Fajarda, Sérgio Matos, José Luís Oliveira, Rui Pedro Lopes
Portuguese Twitter Dataset on COVID-19. ASONAM (2022)
Sara Duarte-Pereira, Sérgio Matos, José Luís Oliveira, Raquel M. Silva
The NAD Interactome, Identification of Putative New NAD-Binding Proteins. PACBB (2022)
Alina Trifan, Sérgio Matos, Pedro Morgado, José Luís Oliveira
Bilingual Emotion Analysis on Social Media throughout the COVID19 Pandemic in Portugal. HEALTHINF (2021)
João Rafael Almeida, João Figueira Silva, Sérgio Matos, Alejandro Pazos, José Luís Oliveira
A Recommender System to Help Refining Clinical Research Studies. MIE (2021)
Jorge Miguel Silva, Diogo Pratas, Rui Antunes, Sérgio Matos, Armando J. Pinho
Automatic analysis of artistic paintings using information-based measures. CoRR (2021)
Tiago Almeida, Sérgio Matos
Benchmarking a transformer-FREE model for ad-hoc retrieval. EACL (2021)
Tiago Almeida, Sérgio Matos
BioASQ Synergy: A strong and simple baseline rooted in relevance feedback. CLEF (Working Notes) (2021)
Tiago Almeida, Sérgio Matos
Universal Passage Weighting Mecanism (UPWM) in BioASQ 9b. CLEF (Working Notes) (2021)
João Figueira Silva, Sérgio Matos
Patient Trajectory Modelling in Longitudinal Data: A Review on Existing Solutions. CBMS (2021)
Jorge Miguel Silva, Diogo Pratas, Rui Antunes, Sérgio Matos, Armando J. Pinho
Automatic analysis of artistic paintings using information-based measures. Pattern Recognit. 114 (2021)
João Rafael Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira
A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases. J. Biomed. Informatics 120 (2021)
Tiago Almeida, Sérgio Matos
Calling Attention to Passages for Biomedical Question Answering. ECIR (2) (2020)
Alina Trifan, Rui Antunes, Sérgio Matos, José Luís Oliveira
Understanding Depression from Psycholinguistic Patterns in Social Media Texts. ECIR (2) (2020)
Tiago Almeida, Sérgio Matos
BIT.UA at BioASQ 8: Lightweight Neural Document Ranking with Zero-shot Snippet Retrieval. CLEF (Working Notes) (2020)
Tiago Almeida, Sérgio Matos
Frugal neural reranking: evaluation on the Covid-19 literature. NLP4COVID@EMNLP (2020)
João Rafael Almeida, João Figueira Silva, Alejandro Pazos Sierra, Sérgio Matos, José Luís Oliveira
Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes. HEALTHINF (2020)
João Rafael Almeida, Sérgio Matos
Rule-based extraction of family history information from clinical notes. SAC (2020)
Tiago Almeida, Sérgio Matos
2020 Deep Learning Track. TREC (2020)
João Rafael Almeida, João Figueira Silva, Alejandro Pazos Sierra, Sérgio Matos, José Luís Oliveira
Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information. BIOSTEC (Selected Papers) (2020)
Jorge Miguel Silva, Eduardo Pinho, Sérgio Matos, Diogo Pratas
Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model. Entropy 22 (1) (2020)
Tiago Almeida, Sérgio Matos
BIT.UA@TREC 2020 Precision Medicine Track. TREC (2020)
Rui Antunes, João Figueira Silva, Sérgio Matos
Evaluating semantic textual similarity in clinical sentences using deep learning and sentence embeddings. SAC (2020)
João Figueira Silva, Rui Antunes, João Rafael Almeida, Sérgio Matos
Clinical Concept Normalization on Medical Records Using Word Embeddings and Heuristics. MIE (2020)
Rui Antunes, Sérgio Matos
Extraction of chemical-protein interactions from the literature using neural networks and narrow instance representation. Database J. Biol. Databases Curation 2019 (2019)
Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019 (2019)
Rui Antunes, João Figueira Silva, Arnaldo Pereira, Sérgio Matos
Rule-based and Machine Learning Hybrid System for Patient Cohort Selection. HEALTHINF (2019)
Sérgio Matos
Configurable web-services for biomedical document annotation. J. Cheminformatics 10 (1) (2018)
Micael Pedrosa, Jorge Miguel Silva, Sérgio Matos, Carlos Costa
SCREEN-DR - Software Architecture for the Diabetic Retinopathy Screening. MIE (2018)
Micael Pedrosa, Jorge Miguel Silva, João Figueira Silva, Sérgio Matos, Carlos Costa
SCREEN-DR: Collaborative platform for diabetic retinopathy. Int. J. Medical Informatics 120 (2018)
Vitor Pereira, Sérgio Matos, José Luís Oliveira
Automated ICD-9-CM medical coding of diabetic patient's clinical reports. DATA (2018)
Pedro Matos, Sérgio Matos
Recognition of genetic mutations in text using deep learning. DATA (2018)
João Figueira Silva, Jorge Miguel Silva, António Guerra, Sérgio Matos, Carlos Costa
Ejection Fraction Classification in Transthoracic Echocardiography Using a Deep Learning Approach. CBMS (2018)
Sérgio Matos
Improving Document Prioritization for Protein-Protein Interaction Extraction Using Shallow Linguistics and Word Embeddings. PACBB (2017)
Carlos Viana-Ferreira, António Guerra, João Figueira Silva, Sérgio Matos, Carlos Costa
An Intelligent Cloud Storage Gateway for Medical Imaging. CoRR (2017)
Sérgio Matos, Rui Antunes
Protein-Protein Interaction Article Classification Using a Convolutional Recurrent Neural Network with Pre-trained Word Embeddings. J. Integr. Bioinform. 14 (4) (2017)
Carlos Viana-Ferreira, António Guerra, João Figueira Silva, Sérgio Matos, Carlos Costa
An Intelligent Cloud Storage Gateway for Medical Imaging. J. Medical Syst. 41 (9) (2017)
Rui Antunes, Sérgio Matos
Biomedical Word Sense Disambiguation with Word Embeddings. PACBB (2017)
Rui Antunes, Sérgio Matos
Supervised Learning and Knowledge-Based Approaches Applied to Biomedical Word Sense Disambiguation. J. Integr. Bioinform. 14 (4) (2017)
Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios V. Gkoutos, Afroza Khanam Irin, Lars Juhl Jensen, Silvia Jimenez, Toni Rose Jue, Ingrid M. Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew E. Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel M. Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole A. Vasilevsky, Xiaodong Wang, Andrew Chatr-aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna R. McEntyre, Sandra E. Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary L. Schaeffer, Cathy H. Wu, Lynette Hirschman, Cecilia N. Arighi
Overview of the interactive task in BioCreative V. Database J. Biol. Databases Curation 2016 (2016)
Carlos Viana-Ferreira, Luís S. Ribeiro, Sérgio Matos, Carlos Costa
Pattern recognition for cache management in distributed medical imaging environments. Int. J. Comput. Assist. Radiol. Surg. 11 (2) (2016)
Sérgio Matos, David Campos, Renato P. Pinho, Raquel M. Silva, Matthew E. Mort, David N. Cooper, José Luís Oliveira
Mining clinical attributes of genomic variants through assisted literature curation in Egas. Database J. Biol. Databases Curation 2016 (2016)
Eriksson J. Melicio Monteiro, Pedro Sernadela, Sérgio Matos, Carlos Costa, José Luís Oliveira
Semantic Knowledge Base Construction from Radiology Reports. HEALTHINF (2016)
André Santos, Sérgio Matos, David Campos, José Luís Oliveira
A Curation Pipeline and Web-Services for PDF Documents. SMBM (2016)
Sun Kim, Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, Donald C. Comeau
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation 2016 (2016)
Carlos Viana-Ferreira, Sérgio Matos, Carlos Costa
Long-Term Prefetching for Cloud Medical Imaging Repositories. MIE (2015)
Sérgio Matos, José Sequeira, José Luís Oliveira
BioinformaticsUA: Machine Learning and Rule-Based Recognition of Disorders and Clinical Attributes from Patient Notes. SemEval@NAACL-HLT (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)
Pedro Sernadela, Sérgio Matos, José Luís Oliveira
Ann2RDF: moving annotations to semantic web. iiWAS (2015)
Jorge A. Vanegas, Sérgio Matos, Fabio A. González, José Luís Oliveira
An Overview of Biomolecular Event Extraction from Scientific Documents. Comput. Math. Methods Medicine 2015 (2015)
David Campos, Sérgio Matos, José Luís Oliveira
A document processing pipeline for annotating chemical entities in scientific documents. J. Cheminformatics 7 (S-1) (2015)
Pedro Sernadela, Pedro Lopes, David Campos, Sérgio Matos, José Luís Oliveira
A Semantic Layer for Unifying and Exploring Biomedical Document Curation Results. IWBBIO (1) (2015)
Carlos Viana-Ferreira, Sérgio Matos, Carlos Costa
Incremental Learning Versus Batch Learning for Classification of User's Behaviour in Medical Imaging. HEALTHINF (2015)
Sérgio Matos, Tiago Nunes, José Luís Oliveira
BioinformaticsUA: Concept Recognition in Clinical Narratives Using a Modular and Highly Efficient Text Processing Framework. SemEval@COLING (2014)
Edgar D. Coelho, Joel Arrais, Sérgio Matos, Carlos Pereira, Nuno Rosa, Maria José Correia, Marlene Barros, José Luís Oliveira
Computational prediction of the human-microbial oral interactome. BMC Syst. Biol. 8 (2014)
David Campos, Jóni Lourenço, Sérgio Matos, José Luís Oliveira
Egas: a collaborative and interactive document curation platform. Database J. Biol. Databases Curation 2014 (2014)
Tiago Nunes, Sérgio Matos, José Luís Oliveira
Extracting Sentences Describing Biomolecular Events from the Biomedical Literature. DCAI (2014)
David Campos, Quoc-Chinh Bui, Sérgio Matos, José Luís Oliveira
TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. Source Code Biol. Medicine 9 (2014)
Víctor M. Prieto, Sérgio Matos, Manuel Álvarez, Fidel Cacheda, José Luís Oliveira
Analysing Relevant Diseases from Iberian Tweets. PACBB (2013)
José Carlos Santos, Sérgio Matos
Predicting Flu Incidence from Portuguese Tweets. IWBBIO (2013)
David Campos, Sérgio Matos, José Luís Oliveira
A modular framework for biomedical concept recognition. BMC Bioinform. 14 (2013)
David Campos, Sérgio Matos, José Luís Oliveira
Gimli: open source and high-performance biomedical name recognition. BMC Bioinform. 14 (2013)
Tiago Nunes, David Campos, Sérgio Matos, José Luís Oliveira
BeCAS: biomedical concept recognition services and visualization. Bioinform. 29 (15) (2013)
Sérgio Matos, Hugo Araújo, José Luís Oliveira
Structuring and Exploring the Biomedical Literature Using Latent Semantics. DCAI (2013)
Edgar D. Coelho, Joel Arrais, Sérgio Matos, Nuno Rosa, Maria José Correia, Marlene Barros, José Luís Oliveira
Computational Approach to Predict Inter-Species Oral Protein-Protein Interactions. IWBBIO (2013)
David Campos, Sérgio Matos, Ian Lewin, José Luís Oliveira, Dietrich Rebholz-Schuhmann
Harmonization of gene/protein annotations: towards a gold standard MEDLINE. Bioinform. 28 (9) (2012)
Sérgio Matos, José Luís Oliveira
Prioritizing Literature Search Results Using a Training Set of Classified Documents. PACBB (2011)
Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sérgio Matos, Sun Kim, W. John Wilbur, Luis Mateus Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinform. 12 (S-8) (2011)
Sérgio Matos, José Luís Oliveira
Classification methods for finding articles describing protein-protein interactions in PubMed. J. Integr. Bioinform. 8 (3) (2011)
Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sérgio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, W. John Wilbur
The gene normalization task in BioCreative III. BMC Bioinform. 12 (S-8) (2011)
David Campos, Sérgio Matos, José Luís Oliveira
Recognition of Gene/Protein Names using Conditional Random Fields. KDIR (2010)
Sérgio Matos, Joel Arrais, João Maia-Rodrigues, José Luís Oliveira
Concept-based query expansion for retrieving gene related publications from MEDLINE. BMC Bioinform. 11 (2010)
Joel Arrais, João E. Pereira, Pedro Lopes, Sérgio Matos, José Luís Oliveira
Improving Cross Mapping in Biomedical Databases. IWPACBB (2010)
Sérgio Matos, Joel Arrais, José Luís Oliveira
Expanding Gene-Based PubMed Queries. IWPACBB (2010)
Sérgio Matos, Anabela Barreiro, José Luís Oliveira
Syntactic Parsing for Bio-molecular Event Detection from Scientific Literature. EPIA (2009)
Sérgio Matos, Surinder S. Birring, Ian D. Pavord, David H. Evans
An Automated System for 24-h Monitoring of Cough Frequency: The Leicester Cough Monitor. IEEE Trans. Biomed. Eng. 54 (8) (2007)
Sérgio Matos, Surinder S. Birring, Ian D. Pavord, David H. Evans
Detection of cough signals in continuous audio recordings using hidden Markov models. IEEE Trans. Biomed. Eng. 53 (6) (2006)