Detection of cough signals in continuous audio recordings using hidden Markov models. - Sérgio Matos; Surinder S. Birring; Ian D. Pavord; David H. Evans 001 (IEEE Trans. Biomed. Eng., 2006)

An Automated System for 24-h Monitoring of Cough Frequency: The Leicester Cough Monitor. - Sérgio Matos; Surinder S. Birring; Ian D. Pavord; David H. Evans 001 (IEEE Trans. Biomed. Eng., 2007)

Syntactic Parsing for Bio-molecular Event Detection from Scientific Literature. - Sérgio Matos; Anabela Barreiro; José Luís Oliveira (EPIA, 2009)

Recognition of Gene/Protein Names using Conditional Random Fields. - David Campos 001; Sérgio Matos; José Luís Oliveira (KDIR, 2010)

Improving Cross Mapping in Biomedical Databases. - Joel Arrais; João E. Pereira; Pedro Lopes 002; Sérgio Matos; José Luís Oliveira (IWPACBB, 2010)

Expanding Gene-Based PubMed Queries. - Sérgio Matos; Joel Arrais; José Luís Oliveira (IWPACBB, 2010)

Concept-based query expansion for retrieving gene related publications from MEDLINE. - Sérgio Matos; Joel Arrais; João Maia-Rodrigues; José Luís Oliveira (BMC Bioinform., 2010)

Prioritizing Literature Search Results Using a Training Set of Classified Documents. - Sérgio Matos; José Luís Oliveira (PACBB, 2011)

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. - 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; et al. (BMC Bioinform., 2011)

The gene normalization task in BioCreative III. - 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; et al. (BMC Bioinform., 2011)

Classification methods for finding articles describing protein-protein interactions in PubMed. - Sérgio Matos; José Luís Oliveira (J. Integr. Bioinform., 2011)

Harmonization of gene/protein annotations: towards a gold standard MEDLINE. - David Campos 001; Sérgio Matos; Ian Lewin; José Luís Oliveira; Dietrich Rebholz-Schuhmann (Bioinform., 2012)

Structuring and Exploring the Biomedical Literature Using Latent Semantics. - Sérgio Matos; Hugo Araújo; José Luís Oliveira (DCAI, 2013)

Computational Approach to Predict Inter-Species Oral Protein-Protein Interactions. - Edgar D. Coelho; Joel Arrais; Sérgio Matos; Nuno Rosa; Maria José Correia; Marlene Barros; José Luís Oliveira (IWBBIO, 2013)

Predicting Flu Incidence from Portuguese Tweets. - José Carlos Santos; Sérgio Matos (IWBBIO, 2013)

Analysing Relevant Diseases from Iberian Tweets. - Víctor M. Prieto; Sérgio Matos; Manuel Álvarez; Fidel Cacheda; José Luís Oliveira (PACBB, 2013)

BeCAS: biomedical concept recognition services and visualization. - Tiago Nunes; David Campos 001; Sérgio Matos; José Luís Oliveira (Bioinform., 2013)

Gimli: open source and high-performance biomedical name recognition. - David Campos 001; Sérgio Matos; José Luís Oliveira (BMC Bioinform., 2013)

A modular framework for biomedical concept recognition. - David Campos 001; Sérgio Matos; José Luís Oliveira (BMC Bioinform., 2013)

Extracting Sentences Describing Biomolecular Events from the Biomedical Literature. - Tiago Nunes; Sérgio Matos; José Luís Oliveira (DCAI, 2014)

BioinformaticsUA: Concept Recognition in Clinical Narratives Using a Modular and Highly Efficient Text Processing Framework. - Sérgio Matos; Tiago Nunes; José Luís Oliveira (SemEval@COLING, 2014)

Egas: a collaborative and interactive document curation platform. - David Campos 001; Jóni Lourenço; Sérgio Matos; José Luís Oliveira (Database J. Biol. Databases Curation, 2014)

Computational prediction of the human-microbial oral interactome. - Edgar D. Coelho; Joel Arrais; Sérgio Matos; Carlos Pereira; Nuno Rosa; Maria José Correia; Marlene Barros; José Luís Oliveira (BMC Syst. Biol., 2014)

TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. - David Campos 001; Quoc-Chinh Bui; Sérgio Matos; José Luís Oliveira (Source Code Biol. Medicine, 2014)

Incremental Learning Versus Batch Learning for Classification of User's Behaviour in Medical Imaging. - Carlos Viana-Ferreira; Sérgio Matos; Carlos Costa 001 (HEALTHINF, 2015)

Ann2RDF: moving annotations to semantic web. - Pedro Sernadela; Sérgio Matos; José Luís Oliveira (iiWAS, 2015)

A Semantic Layer for Unifying and Exploring Biomedical Document Curation Results. - Pedro Sernadela; Pedro Lopes 002; David Campos 001; Sérgio Matos; José Luís Oliveira (IWBBIO (1), 2015)

Long-Term Prefetching for Cloud Medical Imaging Repositories. - Carlos Viana-Ferreira; Sérgio Matos; Carlos Costa 001 (MIE, 2015)

BioinformaticsUA: Machine Learning and Rule-Based Recognition of Disorders and Clinical Attributes from Patient Notes. - Sérgio Matos; José Sequeira; José Luís Oliveira (SemEval@NAACL-HLT, 2015)

An Overview of Biomolecular Event Extraction from Scientific Documents. - Jorge A. Vanegas; Sérgio Matos; Fabio A. González 001; José Luís Oliveira (Comput. Math. Methods Medicine, 2015)

A document processing pipeline for annotating chemical entities in scientific documents. - David Campos 001; Sérgio Matos; José Luís Oliveira (J. Cheminformatics, 2015)

The CHEMDNER corpus of chemicals and drugs and its annotation principles. - 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; et al. (J. Cheminformatics, 2015)

Semantic Knowledge Base Construction from Radiology Reports. - Eriksson J. Melicio Monteiro; Pedro Sernadela; Sérgio Matos; Carlos Costa 001; José Luís Oliveira (HEALTHINF, 2016)

A Curation Pipeline and Web-Services for PDF Documents. - André Santos; Sérgio Matos; David Campos 001; José Luís Oliveira (SMBM, 2016)

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. - 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 001; et al. (Database J. Biol. Databases Curation, 2016)

Mining clinical attributes of genomic variants through assisted literature curation in Egas. - Sérgio Matos; David Campos 001; Renato P. Pinho; Raquel M. Silva; Matthew E. Mort; David N. Cooper; José Luís Oliveira (Database J. Biol. Databases Curation, 2016)

Overview of the interactive task in BioCreative V. - Qinghua Wang 003; Shabbir Syed-Abdul; Lara Almeida; Sophia Ananiadou; Yalbi I. Balderas-Martínez; Riza Batista-Navarro; David Campos 001; Lucy Chilton; Hui-Jou Chou; Gabriela Contreras; Laurel Cooper; Hong-Jie Dai; et al. (Database J. Biol. Databases Curation, 2016)

Pattern recognition for cache management in distributed medical imaging environments. - Carlos Viana-Ferreira; Luís S. Ribeiro; Sérgio Matos; Carlos Costa 001 (Int. J. Comput. Assist. Radiol. Surg., 2016)

Biomedical Word Sense Disambiguation with Word Embeddings. - Rui Antunes 002; Sérgio Matos (PACBB, 2017)

Improving Document Prioritization for Protein-Protein Interaction Extraction Using Shallow Linguistics and Word Embeddings. - Sérgio Matos (PACBB, 2017)

Supervised Learning and Knowledge-Based Approaches Applied to Biomedical Word Sense Disambiguation. - Rui Antunes 002; Sérgio Matos (J. Integr. Bioinform., 2017)

Protein-Protein Interaction Article Classification Using a Convolutional Recurrent Neural Network with Pre-trained Word Embeddings. - Sérgio Matos; Rui Antunes 002 (J. Integr. Bioinform., 2017)

An Intelligent Cloud Storage Gateway for Medical Imaging. - Carlos Viana-Ferreira; António Guerra; João Figueira Silva; Sérgio Matos; Carlos Costa 001 (J. Medical Syst., 2017)

Ejection Fraction Classification in Transthoracic Echocardiography Using a Deep Learning Approach. - João Figueira Silva; Jorge Miguel Silva; António Guerra; Sérgio Matos; Carlos Costa 001 (CBMS, 2018)

Recognition of genetic mutations in text using deep learning. - Pedro Matos; Sérgio Matos (DATA, 2018)

Automated ICD-9-CM medical coding of diabetic patient's clinical reports. - Vitor Pereira; Sérgio Matos; José Luís Oliveira (DATA, 2018)

SCREEN-DR - Software Architecture for the Diabetic Retinopathy Screening. - Micael Pedrosa; Jorge Miguel Silva; Sérgio Matos; Carlos Costa 001 (MIE, 2018)

SCREEN-DR: Collaborative platform for diabetic retinopathy. - Micael Pedrosa; Jorge Miguel Silva; João Figueira Silva; Sérgio Matos; Carlos Costa 001 (Int. J. Medical Informatics, 2018)

Configurable web-services for biomedical document annotation. - Sérgio Matos (J. Cheminformatics, 2018)

Rule-based and Machine Learning Hybrid System for Patient Cohort Selection. - Rui Antunes 002; João Figueira Silva; Arnaldo Pereira; Sérgio Matos (HEALTHINF, 2019)

Extraction of chemical-protein interactions from the literature using neural networks and narrow instance representation. - Rui Antunes 002; Sérgio Matos (Database J. Biol. Databases Curation, 2019)

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. - Rezarta Islamaj Dogan; Sun Kim; Andrew Chatr-aryamontri; Chih-Hsuan Wei; Donald C. Comeau; Rui Antunes 002; Sérgio Matos; Qingyu Chen 001; Aparna Elangovan; Nagesh C. Panyam; Karin Verspoor; Hongfang Liu; et al. (Database J. Biol. Databases Curation, 2019)

Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes. - João Rafael Almeida; João Figueira Silva; Alejandro Pazos Sierra; Sérgio Matos; José Luís Oliveira (HEALTHINF, 2020)

Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information. - João Rafael Almeida; João Figueira Silva; Alejandro Pazos Sierra; Sérgio Matos; José Luís Oliveira (BIOSTEC (Selected Papers), 2020)

BIT.UA at BioASQ 8: Lightweight Neural Document Ranking with Zero-shot Snippet Retrieval. - Tiago Melo Almeida; Sérgio Matos (CLEF (Working Notes), 2020)

Calling Attention to Passages for Biomedical Question Answering. - Tiago Melo Almeida; Sérgio Matos (ECIR (2), 2020)

Understanding Depression from Psycholinguistic Patterns in Social Media Texts. - Alina Trifan; Rui Antunes 002; Sérgio Matos; José Luís Oliveira (ECIR (2), 2020)

Frugal neural reranking: evaluation on the Covid-19 literature. - Tiago Melo Almeida; Sérgio Matos (NLP4COVID@EMNLP, 2020)

Clinical Concept Normalization on Medical Records Using Word Embeddings and Heuristics. - João Figueira Silva; Rui Antunes 002; João Rafael Almeida; Sérgio Matos (MIE, 2020)

Rule-based extraction of family history information from clinical notes. - João Rafael Almeida; Sérgio Matos (SAC, 2020)

Evaluating semantic textual similarity in clinical sentences using deep learning and sentence embeddings. - Rui Antunes 002; João Figueira Silva; Sérgio Matos (SAC, 2020)

2020 Deep Learning Track. - Tiago Melo Almeida; Sérgio Matos (TREC, 2020)

BIT.UA@TREC 2020 Precision Medicine Track. - Tiago Melo Almeida; Sérgio Matos (TREC, 2020)

Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model. - Jorge Miguel Silva; Eduardo Pinho; Sérgio Matos; Diogo Pratas (Entropy, 2020)

Bilingual Emotion Analysis on Social Media throughout the COVID19 Pandemic in Portugal. - Alina Trifan; Sérgio Matos; Pedro Morgado 002; José Luís Oliveira (HEALTHINF, 2021)

Patient Trajectory Modelling in Longitudinal Data: A Review on Existing Solutions. - João Figueira Silva; Sérgio Matos (CBMS, 2021)

BioASQ Synergy: A strong and simple baseline rooted in relevance feedback. - Tiago Melo Almeida; Sérgio Matos (CLEF (Working Notes), 2021)

Universal Passage Weighting Mecanism (UPWM) in BioASQ 9b. - Tiago Melo Almeida; Sérgio Matos (CLEF (Working Notes), 2021)

Benchmarking a transformer-FREE model for ad-hoc retrieval. - Tiago Melo Almeida; Sérgio Matos (EACL, 2021)

A Recommender System to Help Refining Clinical Research Studies. - João Rafael Almeida; João Figueira Silva; Sérgio Matos; Alejandro Pazos; José Luís Oliveira (MIE, 2021)

A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases. - João Rafael Almeida; João Figueira Silva; Sérgio Matos; José Luís Oliveira (J. Biomed. Informatics, 2021)

Automatic analysis of artistic paintings using information-based measures. - Jorge Miguel Silva; Diogo Pratas; Rui Antunes 002; Sérgio Matos; Armando J. Pinho (Pattern Recognit., 2021)

Portuguese Twitter Dataset on COVID-19. - Richard Adolph Aires Jonker; Roshan Poudel; Olga Fajarda; Sérgio Matos; José Luís Oliveira; Rui Pedro Lopes (ASONAM, 2022)

Deep Learning solutions based on fixed contextualized embeddings from PubMedBERT on BioASQ 10b and traditional IR in Synergy. - Tiago Melo Almeida; André Pinho; Rodrigo Pereira; Sérgio Matos (CLEF (Working Notes), 2022)

Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods. - Jorge Miguel Silva; Diogo Pratas; Tânia Caetano; Sérgio Matos (IbPRIA, 2022)

The NAD Interactome, Identification of Putative New NAD-Binding Proteins. - Sara Duarte-Pereira; Sérgio Matos; José Luís Oliveira; Raquel M. Silva (PACBB, 2022)

Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics. - Tiago Melo Almeida; Rui Antunes 002; João Figueira Silva; João Rafael Almeida; Sérgio Matos (Database J. Biol. Databases Curation, 2022)

Modelling patient trajectories using multimodal information. - João Figueira Silva; Sérgio Matos (J. Biomed. Informatics, 2022)

BIT.UA at BioASQ 11B: Two-Stage IR with Synthetic Training and Zero-Shot Answer Generation. - Tiago Melo Almeida; Richard Adolph Aires Jonker; Roshan Poudel; Jorge Miguel Silva; Sérgio Matos (CLEF (Working Notes), 2023)

BIT.UA at MedProcNer: Discovering Medical Procedures in Spanish Using Transformer Models with MCRF and Augmentation. - Tiago Melo Almeida; Richard Adolph Aires Jonker; Roshan Poudel; Jorge Miguel Silva; Sérgio Matos (CLEF (Working Notes), 2023)

Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications. - Jorge Miguel Silva; Diogo Pratas; Sérgio Matos (DoCEIS, 2023)

DyPrune: Dynamic Pruning Rates for Neural Networks. - Richard Adolph Aires Jonker; Roshan Poudel; Olga Fajarda; José Luís Oliveira; Rui Pedro Lopes; Sérgio Matos (EPIA (1), 2023)

Study of NAD-interacting proteins highlights the extent of NAD regulatory roles in the cell and its potential as a therapeutic target. - Sara Duarte-Pereira; Sérgio Matos; José Luís Oliveira; Raquel M. Silva (J. Integr. Bioinform., 2023)

HealthDBFinder: a question-answering task for health database discovery. - João Rafael Almeida; Jorge Miguel Silva; Luís Carlos Afonso; Tiago Melo Almeida; Rui Antunes 002; Richard A. A. Jonker; João António Reis; Dimitri Alexandre da Silva; Sérgio Matos; José Luís Oliveira (CBMS, 2024)

BIT.UA at BioASQ 12: From Retrieval to Answer Generation. - Tiago Melo Almeida; Richard A. A. Jonker; João António Reis; João Rafael Almeida; Sérgio Matos (CLEF (Working Notes), 2024)

Towards a Hyperparameter-Free QUBO Formulation for Feature Selection in IR. - Tiago Melo Almeida; Sérgio Matos (CLEF (Working Notes), 2024)

BIT.UA at MultiCardioNER: Adapting a Multi-head CRF for Cardiology. - Richard A. A. Jonker; Tiago Melo Almeida; Sérgio Matos (CLEF (Working Notes), 2024)

Analyzing a Decade of Evolution: Trends in Natural Language Processing. - Richard A. A. Jonker; Tiago Melo Almeida; Sérgio Matos (DaWaK, 2024)

Exploring efficient zero-shot synthetic dataset generation for Information Retrieval. - Tiago Melo Almeida; Sérgio Matos (EACL (Findings), 2024)

SPARe: Supercharged Lexical Retrievers on GPU with Sparse Kernels. - Tiago Melo Almeida; Sérgio Matos (ECIR (3), 2024)

Towards discovery: an end-to-end system for uncovering novel biomedical relations. - Tiago Melo Almeida; Richard Adolph Aires Jonker; Rui Antunes 002; João Rafael Almeida; Sérgio Matos (Database J. Biol. Databases Curation, 2024)

Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes. - Richard A. A. Jonker; Tiago Melo Almeida; Rui Antunes 002; João Rafael Almeida; Sérgio Matos (Database J. Biol. Databases Curation, 2024)

Value Creation for Healthcare Ecosystems through Artificial Intelligence Applied to Physician-to-Physician Communication: A Systematic Review. - Beny Rubinstein; Sérgio Matos (Neural Process. Lett., 2025)