Francisco M. Couto

According to our database1, Francisco M. Couto authored at least 121 papers between 2003 and 2021.

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Bibliography

2021
Using Neural Networks for Relation Extraction from Biomedical Literature.
Proceedings of the Artificial Neural Networks - Third Edition., 2021

2020
DNA-SeAl: Sensitivity Levels to Optimize the Performance of Privacy-Preserving DNA Alignment.
IEEE J. Biomed. Health Informatics, 2020

Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature.
J. Cheminformatics, 2020

ECIR 2020 Workshops: Assessing the Impact of Going Online.
CoRR, 2020

Generating Scientific Question Answering Corpora from Q&A forums.
CoRR, 2020

Generating Biomedical Question Answering Corpora From Q&A Forums.
IEEE Access, 2020

LasigeBioTM at CANTEMIST: Named Entity Recognition and Normalization of Tumour Morphology Entities and Clinical Coding of Spanish Health-related Documents.
Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020) co-located with 36th Conference of the Spanish Society for Natural Language Processing (SEPLN 2020), 2020

DRecPy: A Python Framework for Developing Deep Learning-Based Recommenders.
Proceedings of the RecSys 2020: Fourteenth ACM Conference on Recommender Systems, 2020

COVID-19: A Semantic-Based Pipeline for Recommending Biomedical Entities.
Proceedings of the 1st Workshop on NLP for COVID-19@ EMNLP 2020, Online, December 2020, 2020

BiOnt: Deep Learning Using Multiple Biomedical Ontologies for Relation Extraction.
Proceedings of the Advances in Information Retrieval, 2020

Towards a Multilingual Corpus for Named Entity Linking Evaluation in the Clinical Domain.
Proceedings of the Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages co-located with 42nd European Conference on Information Retrieval, 2020

Biomedical Question Answering using Extreme Multi-Label Classification and Ontologies in the Multilingual Panorama.
Proceedings of the Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages co-located with 42nd European Conference on Information Retrieval, 2020

Report of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages.
Proceedings of the Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages co-located with 42nd European Conference on Information Retrieval, 2020

Proposal of the First International Workshop on Semantic Indexing and Information Retrieval for Health from Heterogeneous Content Types and Languages (SIIRH).
Proceedings of the Advances in Information Retrieval, 2020

Hybrid Semantic Recommender System for Chemical Compounds.
Proceedings of the Advances in Information Retrieval, 2020

LasigeBioTM Team at CLEF2020 ChEMU Evaluation Lab: Named Entity Recognition and Event extraction from chemical reactions described in patents using BioBERT NER and RE.
Proceedings of the Working Notes of CLEF 2020, 2020

Extreme Multi-Label Classification applied to the Biomedical and Multilingual Panorama.
Proceedings of the Working Notes of CLEF 2020, 2020


2019
Text Mining for Bioinformatics Using Biomedical Literature.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 1, 2019

Semantic Similarity Definition.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 1, 2019

Using Neural Networks for Relation Extraction from Biomedical Literature.
CoRR, 2019

PPR-SSM: personalized PageRank and semantic similarity measures for entity linking.
BMC Bioinform., 2019

Multi-domain semantic similarity in biomedical research.
BMC Bioinform., 2019

Using Research Literature to Generate Datasets of Implicit Feedback for Recommending Scientific Items.
IEEE Access, 2019

AML and AMLC Results for OAEI 2019.
Proceedings of the 14th International Workshop on Ontology Matching co-located with the 18th International Semantic Web Conference (ISWC 2019), 2019

A Silver Standard Corpus of Human Phenotype-Gene Relations.
Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2019

LasigeBioTM at MEDIQA 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition.
Proceedings of the 18th BioNLP Workshop and Shared Task, 2019

2018
MER: a shell script and annotation server for minimal named entity recognition and linking.
J. Cheminformatics, 2018

Accurate filtering of privacy-sensitive information in raw genomic data.
J. Biomed. Informatics, 2018

Tackling the challenges of matching biomedical ontologies.
J. Biomed. Semant., 2018

Results of AML participation in OAEI 2018.
Proceedings of the 13th International Workshop on Ontology Matching co-located with the 17th International Semantic Web Conference, 2018

2017
Assessing Public Metabolomics Metadata, Towards Improving Quality.
J. Integr. Bioinform., 2017

MRA - Proof of Concept of a Multilingual Report Annotator Web Application.
CoRR, 2017

Impact of translation on named-entity recognition in radiology texts.
Database J. Biol. Databases Curation, 2017

Results of AML in OAEI 2017.
Proceedings of the 12th International Workshop on Ontology Matching co-located with the 16th International Semantic Web Conference (ISWC 2017), 2017

MoRS at SemEval-2017 Task 3: Easy to use SVM in Ranking Tasks.
Proceedings of the 11th International Workshop on Semantic Evaluation, 2017

ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events.
Proceedings of the 11th International Workshop on Semantic Evaluation, 2017

Metadata Analyser: Measuring Metadata Quality.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

Cloud-Assisted Read Alignment and Privacy.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

How Can Photo Sharing Inspire Sharing Genomes?
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

Anthropometric Data Analytics: A Portuguese Case Study.
Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

2016
WS4A: a Biomedical Question and Answering System based on public Web Services and Ontologies.
CoRR, 2016

Knowledge Ratings in MetaboLights.
CoRR, 2016

A Large-Scale Characterization of User Behaviour in Cable TV.
CoRR, 2016

A Flexible Recommendation System for Cable TV.
CoRR, 2016

Functional coherence metrics in protein families.
J. Biomed. Semant., 2016

OAEI 2016 results of AML.
Proceedings of the 11th International Workshop on Ontology Matching co-located with the 15th International Semantic Web Conference (ISWC 2016), 2016

ULISBOA at SemEval-2016 Task 12: Extraction of temporal expressions, clinical events and relations using IBEnt.
Proceedings of the 10th International Workshop on Semantic Evaluation, 2016

Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision.
Proceedings of the 4th BioNLP Shared Task Workshop, BioNLP 2016, 2016

2015
Improving chemical entity recognition through h-index based semantic similarity.
J. Cheminformatics, 2015

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

Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora.
Database J. Biol. Databases Curation, 2015

The semantic web in translational medicine: current applications and future directions.
Briefings Bioinform., 2015

A High-Throughput Method to Detect Privacy-Sensitive Human Genomic Data.
Proceedings of the 14th ACM Workshop on Privacy in the Electronic Society, 2015

AML results for OAEI 2015.
Proceedings of the 10th International Workshop on Ontology Matching collocated with the 14th International Semantic Web Conference (ISWC 2015), 2015

ULisboa: Recognition and Normalization of Medical Concepts.
Proceedings of the 9th International Workshop on Semantic Evaluation, 2015

IICE: Web Tool for Automatic Identification of Chemical Entities and Interactions.
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2015

Annotating biomedical ontology terms in electronic health records using crowd-sourcing.
Proceedings of the International Conference on Biomedical Ontology, 2015

Social Impact - Identifying Quotes of Literary Works in Social Networks.
Proceedings of the Progress in Artificial Intelligence, 2015

2014
Identifying interactions between chemical entities in biomedical text.
J. Integr. Bioinform., 2014

The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources.
J. Biomed. Semant., 2014

Friendsourcing the unmet needs of people with dementia.
Proceedings of the International Web for All Conference, 2014

Learning temporal-dependent ranking models.
Proceedings of the 37th International ACM SIGIR Conference on Research and Development in Information Retrieval, 2014

Building reference alignments for compound matching of multiple ontologies using OBO cross-products.
Proceedings of the 9th International Workshop on Ontology Matching collocated with the 13th International Semantic Web Conference (ISWC 2014), 2014

AgreementMakerLight 2.0: Towards Efficient Large-Scale Ontology Matching.
Proceedings of the ISWC 2014 Posters & Demonstrations Track a track within the 13th International Semantic Web Conference, 2014

AgreementMakerLight results for OAEI 2014.
Proceedings of the 9th International Workshop on Ontology Matching collocated with the 13th International Semantic Web Conference (ISWC 2014), 2014

Towards Annotating Potential Incoherences in BioPortal Mappings.
Proceedings of the Semantic Web - ISWC 2014, 2014

Rating, Recognizing and Rewarding Metadata Integration and Sharing on the Semantic Web.
Proceedings of the 10th International Workshop on Uncertainty Reasoning for the Semantic Web (URSW 2014) co-located with the 13th International Semantic Web Conference (ISWC 2014), 2014

ULisboa: Identification and Classification of Medical Concepts.
Proceedings of the 8th International Workshop on Semantic Evaluation, 2014

Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical Features.
Proceedings of the 8th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2014

Towards Visualizing the Alignment of Large Biomedical Ontologies.
Proceedings of the Data Integration in the Life Sciences - 10th International Conference, 2014

2013
Tracking politics with POWER.
Program, 2013

The Next Generation of Similarity Measures that Fully Explore the Semantics in Biomedical Ontologies.
J. Bioinform. Comput. Biol., 2013

Benchmarking some Portuguese S&T system research units
CoRR, 2013

Ontology alignment repair through modularization and confidence-based heuristics.
CoRR, 2013

CIDS country rankings: comparing documents and citations of USA, UK and China top researchers.
CoRR, 2013

Enrichment analysis applied to disease prognosis.
J. Biomed. Semant., 2013

Exploiting disjointness axioms to improve semantic similarity measures.
Bioinform., 2013

A survey of web archive search architectures.
Proceedings of the 22nd International World Wide Web Conference, 2013

What's in a 'nym'? Synonyms in Biomedical Ontology Matching.
Proceedings of the Semantic Web - ISWC 2013, 2013

To repair or not to repair: reconciling correctness and coherence in ontology reference alignments.
Proceedings of the 8th International Workshop on Ontology Matching co-located with the 12th International Semantic Web Conference (ISWC 2013), 2013

AgreementMakerLight results for OAEI 2013.
Proceedings of the 8th International Workshop on Ontology Matching co-located with the 12th International Semantic Web Conference (ISWC 2013), 2013

REACTION: A naive machine learning approach for sentiment classification.
Proceedings of the 7th International Workshop on Semantic Evaluation, 2013

LASIGE: using Conditional Random Fields and ChEBI ontology.
Proceedings of the 7th International Workshop on Semantic Evaluation, 2013

The AgreementMakerLight Ontology Matching System.
Proceedings of the On the Move to Meaningful Internet Systems: OTM 2013 Conferences, 2013

Digital preservation of epidemic resources: coupling metadata and ontologies.
Proceedings of the 10th International Conference on Digital Preservation, 2013

2012
Predicting the Extension of Biomedical Ontologies.
PLoS Comput. Biol., 2012

Testing the AgreementMaker System in the Anatomy Task of OAEI 2012
CoRR, 2012

Toponym Disambiguation Using Ontology-Based Semantic Similarity.
Proceedings of the Computational Processing of the Portuguese Language, 2012

Toward a Translational Medicine Approach for Hypertrophic Cardiomyopathy.
Proceedings of the Information Technology in Bio- and Medical Informatics, 2012

Identifying Chemical Entities based on ChEBI.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

Bringing epidemiology into the Semantic Web.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

2011
MEDCollector: Multisource Epidemic Data Collector.
Trans. Large Scale Data Knowl. Centered Syst., 2011

Disjunctive shared information between ontology concepts: application to Gene Ontology.
J. Biomed. Semant., 2011

REACTION at the Entity Linking task in KBP 2011.
Proceedings of the Fourth Text Analysis Conference, 2011

Using AgreementMaker to align ontologies for OAEI 2011.
Proceedings of the 6th International Workshop on Ontology Matching, 2011

The Biomedical Ontology Applications (BOA) Framework.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Where GO is Going and What it Means for Ontology Extension.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Generic Semantic Relatedness Measure for Biomedical Ontologies.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Biomedical Ontology Matching Using the AgreementMaker System.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2010
Semantic Similarity for Automatic Classification of Chemical Compounds.
PLoS Comput. Biol., 2010

Epidemic Marketplace: An e-Science Platform for Epidemic Modelling and Analysis.
ERCIM News, 2010

Unraveling Hypertrophic Cardiomyopathy Variability.
ERCIM News, 2010

BLOOMS on AgreementMaker: results for OAEI 2010.
Proceedings of the 5th International Workshop on Ontology Matching (OM-2010), 2010

Epidemic Marketplace: An Information Management System for Epidemiological Data.
Proceedings of the Information Technology in Bio- and Medical Informatics, 2010

Geographic signatures for semantic retrieval.
Proceedings of the 6th Workshop on Geographic Information Retrieval, 2010

2009
Semantic Similarity in Biomedical Ontologies.
PLoS Comput. Biol., 2009

Measuring coherence between electronic and manual annotations in biological databases.
Proceedings of the 2009 ACM Symposium on Applied Computing (SAC), 2009

Identifying Gene Ontology Areas for Automated Enrichment.
Proceedings of the Distributed Computing, 2009

GREAT: Gene Regulation EvAluation Tool.
Proceedings of the Distributed Computing, 2009

Identification of Chemical Entities in Patent Documents.
Proceedings of the Distributed Computing, 2009

Verification of Uncurated Protein Annotations.
Proceedings of the Information Retrieval in Biomedicine, 2009

2008
Metrics for GO based protein semantic similarity: a systematic evaluation.
BMC Bioinform., 2008

Identifying bioentity recognition errors of rule-based text-mining systems.
Proceedings of the Third IEEE International Conference on Digital Information Management (ICDIM), 2008

2007
Measuring semantic similarity between Gene Ontology terms.
Data Knowl. Eng., 2007

2006
Validating associations in biological databases.
Proceedings of the 2006 ACM CIKM International Conference on Information and Knowledge Management, 2006

2005
Finding genomic ontology terms in text using evidence content.
BMC Bioinform., 2005

Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors.
Proceedings of the 2005 ACM CIKM International Conference on Information and Knowledge Management, Bremen, Germany, October 31, 2005

2004
Classifying biological articles using web resources.
Proceedings of the 2004 ACM Symposium on Applied Computing (SAC), 2004

2003
ProFAL: PROtein Functional Annotation through Literature.
Proceedings of the VIII Jornadas Ingeniería del Software y Bases de Datos (JISBD 2003), 2003


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