Sérgio Matos

Orcid: 0000-0003-1941-3983

Affiliations:
  • University of Aveiro, Aveiro, Portugal


According to our database1, Sérgio Matos authored at least 92 papers between 2006 and 2024.

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Bibliography

2024
Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes.
Database J. Biol. Databases Curation, January, 2024

Towards discovery: an end-to-end system for uncovering novel biomedical relations.
Database J. Biol. Databases Curation, January, 2024

SPARe: Supercharged Lexical Retrievers on GPU with Sparse Kernels.
Proceedings of the Advances in Information Retrieval, 2024

Exploring efficient zero-shot synthetic dataset generation for Information Retrieval.
Proceedings of the Findings of the Association for Computational Linguistics: EACL 2024, 2024

Analyzing a Decade of Evolution: Trends in Natural Language Processing.
Proceedings of the Big Data Analytics and Knowledge Discovery, 2024

BIT.UA at MultiCardioNER: Adapting a Multi-head CRF for Cardiology.
Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2024), 2024

Towards a Hyperparameter-Free QUBO Formulation for Feature Selection in IR.
Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2024), 2024

BIT.UA at BioASQ 12: From Retrieval to Answer Generation.
Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2024), 2024

HealthDBFinder: a question-answering task for health database discovery.
Proceedings of the 37th IEEE International Symposium on Computer-Based Medical Systems, 2024

2023
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., July, 2023

DyPrune: Dynamic Pruning Rates for Neural Networks.
Proceedings of the Progress in Artificial Intelligence, 2023

Exploring Kolmogorov Complexity Approximations for Data Analysis: Insights and Applications.
Proceedings of the Technological Innovation for Connected Cyber Physical Spaces, 2023

BIT.UA at MedProcNer: Discovering Medical Procedures in Spanish Using Transformer Models with MCRF and Augmentation.
Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2023), 2023

BIT.UA at BioASQ 11B: Two-Stage IR with Synthetic Training and Zero-Shot Answer Generation.
Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2023), 2023

2022
Modelling patient trajectories using multimodal information.
J. Biomed. Informatics, 2022

Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics.
Database J. Biol. Databases Curation, 2022

The NAD Interactome, Identification of Putative New NAD-Binding Proteins.
Proceedings of the Practical Applications of Computational Biology and Bioinformatics, 2022

Feature-Based Classification of Archaeal Sequences Using Compression-Based Methods.
Proceedings of the Pattern Recognition and Image Analysis - 10th Iberian Conference, 2022

Deep Learning solutions based on fixed contextualized embeddings from PubMedBERT on BioASQ 10b and traditional IR in Synergy.
Proceedings of the Working Notes of CLEF 2022 - Conference and Labs of the Evaluation Forum, Bologna, Italy, September 5th - to, 2022

Portuguese Twitter Dataset on COVID-19.
Proceedings of the IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, 2022

2021
Automatic analysis of artistic paintings using information-based measures.
Pattern Recognit., 2021

A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases.
J. Biomed. Informatics, 2021

A Recommender System to Help Refining Clinical Research Studies.
Proceedings of the Public Health and Informatics, 2021

Benchmarking a transformer-FREE model for ad-hoc retrieval.
Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Main Volume, 2021

Universal Passage Weighting Mecanism (UPWM) in BioASQ 9b.
Proceedings of the Working Notes of CLEF 2021 - Conference and Labs of the Evaluation Forum, Bucharest, Romania, September 21st - to, 2021

BioASQ Synergy: A strong and simple baseline rooted in relevance feedback.
Proceedings of the Working Notes of CLEF 2021 - Conference and Labs of the Evaluation Forum, Bucharest, Romania, September 21st - to, 2021

Patient Trajectory Modelling in Longitudinal Data: A Review on Existing Solutions.
Proceedings of the 34th IEEE International Symposium on Computer-Based Medical Systems, 2021

Bilingual Emotion Analysis on Social Media throughout the COVID19 Pandemic in Portugal.
Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies, 2021

2020
Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model.
Entropy, 2020

BIT.UA@TREC 2020 Precision Medicine Track.
Proceedings of the Twenty-Ninth Text REtrieval Conference, 2020

2020 Deep Learning Track.
Proceedings of the Twenty-Ninth Text REtrieval Conference, 2020

Evaluating semantic textual similarity in clinical sentences using deep learning and sentence embeddings.
Proceedings of the SAC '20: The 35th ACM/SIGAPP Symposium on Applied Computing, online event, [Brno, Czech Republic], March 30, 2020

Rule-based extraction of family history information from clinical notes.
Proceedings of the SAC '20: The 35th ACM/SIGAPP Symposium on Applied Computing, online event, [Brno, Czech Republic], March 30, 2020

Clinical Concept Normalization on Medical Records Using Word Embeddings and Heuristics.
Proceedings of the Digital Personalized Health and Medicine - Proceedings of MIE 2020, Medical Informatics Europe, Geneva, Switzerland, April 28, 2020

Frugal neural reranking: evaluation on the Covid-19 literature.
Proceedings of the 1st Workshop on NLP for COVID-19@ EMNLP 2020, Online, December 2020, 2020

Understanding Depression from Psycholinguistic Patterns in Social Media Texts.
Proceedings of the Advances in Information Retrieval, 2020

Calling Attention to Passages for Biomedical Question Answering.
Proceedings of the Advances in Information Retrieval, 2020

BIT.UA at BioASQ 8: Lightweight Neural Document Ranking with Zero-shot Snippet Retrieval.
Proceedings of the Working Notes of CLEF 2020, 2020

Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information.
Proceedings of the Biomedical Engineering Systems and Technologies, 2020

Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes.
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020), 2020

2019
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine.
Database J. Biol. Databases Curation, 2019

Extraction of chemical-protein interactions from the literature using neural networks and narrow instance representation.
Database J. Biol. Databases Curation, 2019

Rule-based and Machine Learning Hybrid System for Patient Cohort Selection.
Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019), 2019

2018
Configurable web-services for biomedical document annotation.
J. Cheminformatics, 2018

SCREEN-DR: Collaborative platform for diabetic retinopathy.
Int. J. Medical Informatics, 2018

SCREEN-DR - Software Architecture for the Diabetic Retinopathy Screening.
Proceedings of the Building Continents of Knowledge in Oceans of Data: The Future of Co-Created eHealth, 2018

Automated ICD-9-CM medical coding of diabetic patient's clinical reports.
Proceedings of the First International Conference on Data Science, 2018

Recognition of genetic mutations in text using deep learning.
Proceedings of the First International Conference on Data Science, 2018

Ejection Fraction Classification in Transthoracic Echocardiography Using a Deep Learning Approach.
Proceedings of the 31st IEEE International Symposium on Computer-Based Medical Systems, 2018

2017
An Intelligent Cloud Storage Gateway for Medical Imaging.
J. Medical Syst., 2017

Protein-Protein Interaction Article Classification Using a Convolutional Recurrent Neural Network with Pre-trained Word Embeddings.
J. Integr. Bioinform., 2017

Supervised Learning and Knowledge-Based Approaches Applied to Biomedical Word Sense Disambiguation.
J. Integr. Bioinform., 2017

Improving Document Prioritization for Protein-Protein Interaction Extraction Using Shallow Linguistics and Word Embeddings.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

Biomedical Word Sense Disambiguation with Word Embeddings.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

2016
Pattern recognition for cache management in distributed medical imaging environments.
Int. J. Comput. Assist. Radiol. Surg., 2016

Overview of the interactive task in BioCreative V.
Database J. Biol. Databases Curation, 2016

Mining clinical attributes of genomic variants through assisted literature curation in Egas.
Database J. Biol. Databases Curation, 2016

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
Database J. Biol. Databases Curation, 2016

A Curation Pipeline and Web-Services for PDF Documents.
Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, 2016

Semantic Knowledge Base Construction from Radiology Reports.
Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016), 2016

2015
The CHEMDNER corpus of chemicals and drugs and its annotation principles.
J. Cheminformatics, 2015

A document processing pipeline for annotating chemical entities in scientific documents.
J. Cheminformatics, 2015

An Overview of Biomolecular Event Extraction from Scientific Documents.
Comput. Math. Methods Medicine, 2015

BioinformaticsUA: Machine Learning and Rule-Based Recognition of Disorders and Clinical Attributes from Patient Notes.
Proceedings of the 9th International Workshop on Semantic Evaluation, 2015

Long-Term Prefetching for Cloud Medical Imaging Repositories.
Proceedings of the Digital Healthcare Empowering Europeans, 2015

A Semantic Layer for Unifying and Exploring Biomedical Document Curation Results.
Proceedings of the Bioinformatics and Biomedical Engineering, 2015

Ann2RDF: moving annotations to semantic web.
Proceedings of the 17th International Conference on Information Integration and Web-based Applications & Services, 2015

Incremental Learning Versus Batch Learning for Classification of User's Behaviour in Medical Imaging.
Proceedings of the HEALTHINF 2015, 2015

2014
TrigNER: automatically optimized biomedical event trigger recognition on scientific documents.
Source Code Biol. Medicine, 2014

Computational prediction of the human-microbial oral interactome.
BMC Syst. Biol., 2014

Egas: a collaborative and interactive document curation platform.
Database J. Biol. Databases Curation, 2014

BioinformaticsUA: Concept Recognition in Clinical Narratives Using a Modular and Highly Efficient Text Processing Framework.
Proceedings of the 8th International Workshop on Semantic Evaluation, 2014

Extracting Sentences Describing Biomolecular Events from the Biomedical Literature.
Proceedings of the Distributed Computing and Artificial Intelligence, 2014

2013
A modular framework for biomedical concept recognition.
BMC Bioinform., 2013

Gimli: open source and high-performance biomedical name recognition.
BMC Bioinform., 2013

BeCAS: biomedical concept recognition services and visualization.
Bioinform., 2013

Analysing Relevant Diseases from Iberian Tweets.
Proceedings of the 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2013

Predicting Flu Incidence from Portuguese Tweets.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

Computational Approach to Predict Inter-Species Oral Protein-Protein Interactions.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

Structuring and Exploring the Biomedical Literature Using Latent Semantics.
Proceedings of the Distributed Computing and Artificial Intelligence, 2013

2012
Harmonization of gene/protein annotations: towards a gold standard MEDLINE.
Bioinform., 2012

2011
Classification methods for finding articles describing protein-protein interactions in PubMed.
J. Integr. Bioinform., 2011

The gene normalization task in BioCreative III.
BMC Bioinform., 2011

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

Prioritizing Literature Search Results Using a Training Set of Classified Documents.
Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2011

2010
Concept-based query expansion for retrieving gene related publications from MEDLINE.
BMC Bioinform., 2010

Expanding Gene-Based PubMed Queries.
Proceedings of the Advances in Bioinformatics, 2010

Improving Cross Mapping in Biomedical Databases.
Proceedings of the Advances in Bioinformatics, 2010

Recognition of Gene/Protein Names using Conditional Random Fields.
Proceedings of the KDIR 2010, 2010

2009
Syntactic Parsing for Bio-molecular Event Detection from Scientific Literature.
Proceedings of the Progress in Artificial Intelligence, 2009

2007
An Automated System for 24-h Monitoring of Cough Frequency: The Leicester Cough Monitor.
IEEE Trans. Biomed. Eng., 2007

2006
Detection of cough signals in continuous audio recordings using hidden Markov models.
IEEE Trans. Biomed. Eng., 2006


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