Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot. - Frédéric Ehrler; Antoine Geissbühler; Antonio Jimeno-Yepes; Patrick Ruch (BMC Bioinform., 2005)

Report on the TREC 2006 Experiment: Genomics Track. - Patrick Ruch; Frédéric Ehrler; Julien Gobeill; Imad Tbahriti; Antonio Jimeno-Yepes (TREC, 2006)

Information Retrieval and Information Extraction in TREC Genomics 2007. - Antonio Jimeno-Yepes; Piotr Pezik (TREC, 2007)

Use of Shared Lexical Resources for Efficient Ontological Engineering. - Antonio Jimeno-Yepes; Ernesto Jiménez-Ruiz; Rafael Berlanga Llavori; Dietrich Rebholz-Schuhmann (SWAT4LS, 2008)

Text processing through Web services: calling Whatizit. - Dietrich Rebholz-Schuhmann; Miguel Arregui; Sylvain Gaudan; Harald Kirsch; Antonio Jimeno-Yepes (Bioinform., 2008)

Assessment of disease named entity recognition on a corpus of annotated sentences. - Antonio Jimeno-Yepes; Ernesto Jiménez-Ruiz; Vivian Lee; Sylvain Gaudan; Rafael Berlanga Llavori; Dietrich Rebholz-Schuhmann (BMC Bioinform., 2008)

Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text. - Sylvain Gaudan; Antonio Jimeno-Yepes; Vivian Lee; Dietrich Rebholz-Schuhmann (EURASIP J. Bioinform. Syst. Biol., 2008)

Using Biomedical Terminological Resources for Information Retrieval. - Piotr Pezik; Antonio Jimeno-Yepes; Dietrich Rebholz-Schuhmann (Information Retrieval in Biomedicine, 2009)

Reuse of terminological resources for efficient ontological engineering in Life Sciences. - Antonio Jimeno-Yepes; Ernesto Jiménez-Ruiz; Rafael Berlanga Llavori; Dietrich Rebholz-Schuhmann (BMC Bioinform., 2009)

Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb. - Kevin Nagel; Antonio Jimeno-Yepes; Dietrich Rebholz-Schuhmann (BMC Bioinform., 2009)

Ontology refinement for improved information retrieval in the biomedical domain. - Antonio Jimeno-Yepes (2009)

Applications of Ontologies and Text Mining in the Biomedical Domain. - Antonio Jimeno-Yepes; Rafael Berlanga Llavori; Dietrich Rebholz-Schuhmann (Ontology Theory, Management and Design, 2010)

Query Expansion for UMLS Metathesaurus Disambiguation Based on Automatic Corpus Extraction. - Antonio Jimeno-Yepes; Alan R. Aronson (ICMLA, 2010)

The CALBC Silver Standard Corpus for Biomedical Named Entities - A Study in Harmonizing the Contributions from Four Independent Named Entity Taggers. - Dietrich Rebholz-Schuhmann; Antonio José Jimeno-Yepes; Erik M. van Mulligen; Ning Kang 002; Jan A. Kors; David Milward; Peter T. Corbett; Ekaterina Buyko; Katrin Tomanek; Elena Beisswanger; Udo Hahn (LREC, 2010)

Knowledge-based biomedical word sense disambiguation: comparison of approaches. - Antonio Jimeno-Yepes; Alan R. Aronson (BMC Bioinform., 2010)

Ontology refinement for improved information retrieval. - Antonio Jimeno-Yepes; Rafael Berlanga Llavori; Dietrich Rebholz-Schuhmann (Inf. Process. Manag., 2010)

Calbc Silver Standard Corpus. - Dietrich Rebholz-Schuhmann; Antonio Jimeno-Yepes; Erik M. van Mulligen; Ning Kang 002; Jan A. Kors; David Milward; Peter T. Corbett; Ekaterina Buyko; Elena Beisswanger; Udo Hahn (J. Bioinform. Comput. Biol., 2010)

Measuring prediction capacity of individual verbs for the identification of protein interactions. - Dietrich Rebholz-Schuhmann; Antonio Jimeno-Yepes; Miguel Arregui; Harald Kirsch (J. Biomed. Informatics, 2010)

Improving an automatically extracted corpus for UMLS Metathesaurus word sense disambiguation. - Antonio Jimeno-Yepes; Alan R. Aronson (Proces. del Leng. Natural, 2010)

Self-training and co-training in biomedical word sense disambiguation. - Antonio Jimeno-Yepes; Alan R. Aronson (BioNLP@ACL, 2011)

Preliminary Results for Biomedical Word Sense Disambiguation Based on Semantic Clustering. - Tamara Martín-Wanton; Rafael Berlanga Llavori; Antonio Jimeno-Yepes (DEXA Workshops, 2011)

A Knowledge-Based Approach to Medical Records Retrieval. - Dina Demner-Fushman; Swapna Abhyankar; Antonio Jimeno-Yepes; Russell F. Loane; Bastien Rance; François-Michel Lang; Nicholas C. Ide; Emilia Apostolova; Alan R. Aronson (TREC, 2011)

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. - Dietrich Rebholz-Schuhmann; Antonio Jimeno-Yepes; Chen Li 011; Senay Kafkas; Ian Lewin; Ning Kang 002; Peter T. Corbett; David Milward; Ekaterina Buyko; Elena Beisswanger; Kerstin Hornbostel; Alexandre Kouznetsov; et al. (J. Biomed. Semant., 2011)

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. - Antonio José Jimeno-Yepes; Bridget T. McInnes; Alan R. Aronson (BMC Bioinform., 2011)

Collocation analysis for UMLS knowledge-based word sense disambiguation. - Antonio Jimeno-Yepes; Bridget T. McInnes; Alan R. Aronson (BMC Bioinform., 2011)

Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts. - Laura Plaza; Antonio José Jimeno-Yepes; Alberto Díaz 001; Alan R. Aronson (BMC Bioinform., 2011)

Integration of UMLS and MEDLINE in Unsupervised Word Sense Disambiguation. - Antonio Jimeno-Yepes; Alan R. Aronson (AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text, 2012)

Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation. - Antonio Jimeno-Yepes; Alan R. Aronson (IHI, 2012)

MEDLINE MeSH indexing: lessons learned from machine learning and future directions. - Antonio Jimeno-Yepes; James G. Mork; Bartlomiej Wilkowski; Dina Demner-Fushman; Alan R. Aronson (IHI, 2012)

Disambiguating automatically-generated semantic annotations for Life Science open registries. - Antonio Jimeno-Yepes; Rafael Berlanga Llavori; María Pérez Catalán (E-LKR, 2012)

NLM at TREC 2012 Medical Records Track. - Dina Demner-Fushman; Swapna Abhyankar; Antonio Jimeno-Yepes; Russell F. Loane; François-Michel Lang; James G. Mork; Nicolas Ide; Alan R. Aronson (TREC, 2012)

A One-Size-Fits-All Indexing Method Does Not Exist: Automatic Selection Based on Meta-Learning. - Antonio Jimeno-Yepes; James G. Mork; Dina Demner-Fushman; Alan R. Aronson (J. Comput. Sci. Eng., 2012)

Impact of Corpus Diversity and Complexity on NER Performance. - Tatyana Shmanina; Ingrid Zukerman; Antonio Jimeno-Yepes; Lawrence Cavedon; Karin Verspoor (ALTA, 2013)

Comparison and combination of several MeSH indexing approaches. - Antonio Jimeno-Yepes; James G. Mork; Dina Demner-Fushman; Alan R. Aronson (AMIA, 2013)

Using the Argumentative Structure of Scientific Literature to Improve Information Access. - Antonio Jimeno-Yepes; James G. Mork; Alan R. Aronson (BioNLP@ACL, 2013)

Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data. - Andrew MacKinlay; David Martínez 001; Antonio Jimeno-Yepes; Haibin Liu; W. John Wilbur; Karin Verspoor (BioNLP@ACL (Shared Task), 2013)

Identifying Publication Types Using Machine Learning. - Antonio Jimeno-Yepes; James G. Mork; Alan R. Aronson (BioASQ@CLEF, 2013)

Context-Dependent Semantic Annotation in Cross-Lingual Biomedical Resources. - Rafael Berlanga Llavori; Antonio Jimeno-Yepes; María Pérez Catalán; Dietrich Rebholz-Schuhmann (CLEF, 2013)

An Evaluation of the Concept Retrieval Annotation for Spanish-English CLEFER Parallel Corpora. - Rafael Berlanga Llavori; Antonio Jimeno-Yepes; María Pérez Catalán; Dietrich Rebholz-Schuhmann (CLEF (Working Notes), 2013)

The NLM Medical Text Indexer System for Indexing Biomedical Literature. - James G. Mork; Antonio Jimeno-Yepes; Alan R. Aronson (BioASQ@CLEF, 2013)

Entity Recognition in Parallel Multi-lingual Biomedical Corpora: The CLEF-ER Laboratory Overview. - Dietrich Rebholz-Schuhmann; Simon Clematide; Fabio Rinaldi 001; Senay Kafkas; Erik M. van Mulligen; Quoc-Chinh Bui; Johannes Hellrich; Ian Lewin; David Milward; Michael Poprat; Antonio Jimeno-Yepes; Udo Hahn; et al. (CLEF, 2013)

Multilingual Semantic Resources and Parallel Corpora in the Biomedical Domain: the CLEF-ER Challenge. - Dietrich Rebholz-Schuhmann; Simon Clematide; Fabio Rinaldi 001; Senay Kafkas; Erik M. van Mulligen; Quoc-Chinh Bui; Johannes Hellrich; Ian Lewin; David Milward; Michael Poprat; Antonio Jimeno-Yepes; Udo Hahn; et al. (CLEF (Working Notes), 2013)

PCorral - interactive mining of protein interactions from MEDLINE. - Chen Li 011; Antonio Jimeno-Yepes; Miguel Arregui; Harald Kirsch; Dietrich Rebholz-Schuhmann (Database J. Biol. Databases Curation, 2013)

Annotating the biomedical literature for the human variome. - Karin Verspoor; Antonio Jimeno-Yepes; Lawrence Cavedon; Tara McIntosh; Asha Herten-Crabb; Zoë Thomas; John-Paul Plazzer (Database J. Biol. Databases Curation, 2013)

Monitoring named entity recognition: the League Table. - Dietrich Rebholz-Schuhmann; Senay Kafkas; Jee-Hyub Kim; Antonio Jimeno-Yepes; Ian Lewin (J. Biomed. Semant., 2013)

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. - Dietrich Rebholz-Schuhmann; Senay Kafkas; Jee-Hyub Kim; Chen Li 011; Antonio Jimeno-Yepes; Robert Hoehndorf; Rolf Backofen; Ian Lewin (J. Biomed. Semant., 2013)

MeSH indexing based on automatically generated summaries. - Antonio José Jimeno-Yepes; Laura Plaza; James G. Mork; Alan R. Aronson; Alberto Díaz 001 (BMC Bioinform., 2013)

Combining MEDLINE and publisher data to create parallel corpora for the automatic translation of biomedical text. - Antonio Jimeno-Yepes; Élise Prieur-Gaston; Aurélie Névéol (BMC Bioinform., 2013)

GeneRIF indexing: sentence selection based on machine learning. - Antonio Jimeno-Yepes; J. Caitlin Sticco; James G. Mork; Alan R. Aronson (BMC Bioinform., 2013)

Identifying Twitter Location Mentions. - Bo Han 002; Antonio Jimeno-Yepes; Andrew MacKinlay; Qiang Chen (ALTA, 2014)

Deep Belief Networks and Biomedical Text Categorisation. - Antonio Jimeno-Yepes; Andrew MacKinlay; Justin Bedo; Rahil Garvani; Qiang Chen (ALTA, 2014)

BioC interoperability track overview. - Donald C. Comeau; Riza Theresa Batista-Navarro; Hong-Jie Dai; Rezarta Islamaj Dogan; Antonio Jimeno-Yepes; Ritu Khare; Zhiyong Lu; Hernani Marques; Carolyn J. Mattingly; Mariana L. Neves; Yifan Peng 002; Rafal Rak; et al. (Database J. Biol. Databases Curation, 2014)

Literature mining of genetic variants for curation: quantifying the importance of supplementary material. - Antonio Jimeno-Yepes; Karin Verspoor (Database J. Biol. Databases Curation, 2014)

Mutation extraction tools can be combined for robust recognition of genetic variants in the literature. - Antonio Jimeno-Yepes; Karin Verspoor (F1000Research, 2014)

Investigating Public Health Surveillance using Twitter. - Antonio Jimeno-Yepes; Andrew MacKinlay; Bo Han 002 (BioNLP@IJCNLP, 2015)

Identification and Analysis of Medical Entity Co-occurrences in Twitter. - Andrew MacKinlay; Antonio Jimeno-Yepes; Bo Han 002 (DTMBIO@CIKM, 2015)

Identifying Diseases, Drugs, and Symptoms in Twitter. - Antonio Jimeno-Yepes; Andrew MacKinlay; Bo Han 002; Qiang Chen (MedInfo, 2015)

Feature engineering for MEDLINE citation categorization with MeSH. - Antonio Jimeno-Yepes; Laura Plaza; Jorge Carrillo de Albornoz; James G. Mork; Alan R. Aronson (BMC Bioinform., 2015)

Knowledge based word-concept model estimation and refinement for biomedical text mining. - Antonio Jimeno-Yepes; Rafael Berlanga Llavori (J. Biomed. Informatics, 2015)

Temporal Modelling of Geospatial Words in Twitter. - Bo Han 002; Antonio Jimeno-Yepes; Andrew MacKinlay; Lianhua Chi (ALTA, 2016)

Syndromic Surveillance using Generic Medical Entities on Twitter. - Pin Huang; Andrew MacKinlay; Antonio Jimeno-Yepes (ALTA, 2016)

NER for Medical Entities in Twitter using Sequence to Sequence Neural Networks. - Antonio Jimeno-Yepes; Andrew MacKinlay (ALTA, 2016)

Decoding EEG and LFP signals using deep learning: heading TrueNorth. - Ewan Nurse; Benjamin S. Mashford; Antonio Jimeno-Yepes; Isabell Kiral-Kornek; Stefan Harrer; Dean R. Freestone (Conf. Computing Frontiers, 2016)

Weighted Population Code for low power neuromorphic image classification. - Antonio Jimeno-Yepes; Jianbin Tang; Shreya Saxena; Tobias Brosch; Arnon Amir (IJCNN, 2016)

The Scielo Corpus: a Parallel Corpus of Scientific Publications for Biomedicine. - Mariana L. Neves; Antonio Jimeno-Yepes; Aurélie Névéol (LREC, 2016)

Findings of the 2016 Conference on Machine Translation. - Ondrej Bojar; Rajen Chatterjee; Christian Federmann; Yvette Graham; Barry Haddow; Matthias Huck; Antonio Jimeno-Yepes; Philipp Koehn; Varvara Logacheva; Christof Monz; Matteo Negri; Aurélie Névéol; et al. (WMT, 2016)

Higher order features and recurrent neural networks based on Long-Short Term Memory nodes in supervised biomedical word sense disambiguation. - Antonio Jimeno-Yepes (CoRR, 2016)

Improving energy efficiency and classification accuracy of neuromorphic chips by learning binary synaptic crossbars. - Antonio Jimeno-Yepes; Jianbin Tang (CoRR, 2016)

Knowledge-Based Biomedical Word Sense Disambiguation with Neural Concept Embeddings and Distant Supervision. - A. K. M. Sabbir; Antonio Jimeno-Yepes; Ramakanth Kavuluru (CoRR, 2016)

Detection of adverse drug reactions using medical named entities on Twitter. - Andrew MacKinlay; Hafsah Aamer; Antonio Jimeno-Yepes (AMIA, 2017)

Knowledge-Based Biomedical Word Sense Disambiguation with Neural Concept Embeddings. - Akm Sabbir; Antonio Jimeno-Yepes; Ramakanth Kavuluru (BIBE, 2017)

Improving Classification Accuracy of Feedforward Neural Networks for Spiking Neuromorphic Chips. - Antonio Jimeno-Yepes; Jianbin Tang; Benjamin Scott Mashford (IJCAI, 2017)

Named Entity Recognition with Stack Residual LSTM and Trainable Bias Decoding. - Quan Tran; Andrew MacKinlay; Antonio Jimeno-Yepes (IJCNLP(1), 2017)

Findings of the WMT 2017 Biomedical Translation Shared Task. - Antonio Jimeno-Yepes; Aurélie Névéol; Mariana L. Neves; Karin Verspoor; Ondrej Bojar; Arthur Boyer; Cristian Grozea; Barry Haddow; Madeleine Kittner; Yvonne Lichtblau; Pavel Pecina; Roland Roller; et al. (WMT, 2017)

Neural-network-based analysis of EEG data using the neuromorphic TrueNorth chip for brain-machine interfaces. - Benjamin S. Mashford; Antonio Jimeno-Yepes; Isabell Kiral-Kornek; Jianbin Tang; Stefan Harrer (IBM J. Res. Dev., 2017)

Word embeddings and recurrent neural networks based on Long-Short Term Memory nodes in supervised biomedical word sense disambiguation. - Antonio Jimeno-Yepes (J. Biomed. Informatics, 2017)

A hybrid approach for automated mutation annotation of the extended human mutation landscape in scientific literature. - Antonio Jimeno-Yepes; Andrew D. MacKinlay; Natalie Gunn; Christine Schieber; Noel Faux; Matthew Downton; Benjamin Goudey; Richard L. Martin (AMIA, 2018)

Coarse-grained Semantic Characterization of Large Knowledge Resources. - Rafael Berlanga Llavori; Antonio Jimeno-Yepes; María Pérez; Indira Lanza-Cruz (CERI, 2018)

Parallel Corpora for the Biomedical Domain. - Aurélie Névéol; Antonio Jimeno-Yepes; Mariana L. Neves; Karin Verspoor (LREC, 2018)

Findings of the WMT 2018 Biomedical Translation Shared Task: Evaluation on Medline test sets. - Mariana L. Neves; Antonio Jimeno-Yepes; Aurélie Névéol; Cristian Grozea; Amy Siu; Madeleine Kittner; Karin Verspoor (WMT (shared task), 2018)

Confidence penalty, annealing Gaussian noise and zoneout for biLSTM-CRF networks for named entity recognition. - Antonio Jimeno-Yepes (CoRR, 2018)

Semantic Labeling Using a Low-Power Neuromorphic Platform. - Jianbin Tang; Benjamin Scott Mashford; Antonio Jimeno-Yepes (IEEE Geosci. Remote. Sens. Lett., 2018)

Neural Relation Extraction from Biomedical Literature. - Elaheh ShafieiBavani; Antonio Jimeno-Yepes (AMIA, 2019)

PubLayNet: Largest Dataset Ever for Document Layout Analysis. - Xu Zhong; Jianbin Tang; Antonio Jimeno-Yepes (ICDAR, 2019)

Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies. - Rachel Bawden; Kevin Bretonnel Cohen; Cristian Grozea; Antonio Jimeno-Yepes; Madeleine Kittner; Martin Krallinger; Nancy Mah; Aurélie Névéol; Mariana L. Neves; Felipe Soares; Amy Siu; Karin Verspoor; et al. (WMT (3), 2019)

Global Locality in Event Extraction. - Elaheh ShafieiBavani; Antonio Jimeno-Yepes; Xu Zhong (CoRR, 2019)

Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning. - Ying Xu; André Leier; Tatiana T. Marquez-Lago; Jue Xie; Antonio Jimeno-Yepes; James C. Whisstock; Campbell Wilson; Jiangning Song (AMIA, 2020)

Global Locality in Biomedical Relation and Event Extraction. - Elaheh ShafieiBavani; Antonio Jimeno-Yepes; Xu Zhong; David Martínez 001 (BioNLP, 2020)

Image-Based Table Recognition: Data, Model, and Evaluation. - Xu Zhong; Elaheh ShafieiBavani; Antonio Jimeno-Yepes (ECCV (21), 2020)

Forget Me Not: Reducing Catastrophic Forgetting for Domain Adaptation in Reading Comprehension. - Ying Xu; Xu Zhong; Antonio José Jimeno-Yepes; Jey Han Lau (IJCNN, 2020)

MEDLINE as a Parallel Corpus: a Survey to Gain Insight on French-, Spanish- and Portuguese-speaking Authors' Abstract Writing Practice. - Aurélie Névéol; Antonio Jimeno-Yepes; Mariana L. Neves (LREC, 2020)

Findings of the WMT 2020 Biomedical Translation Shared Task: Basque, Italian and Russian as New Additional Languages. - Rachel Bawden; Giorgio Maria Di Nunzio; Cristian Grozea; Inigo Jauregi Unanue; Antonio Jimeno-Yepes; Nancy Mah; David Martínez 001; Aurélie Névéol; Mariana L. Neves; Maite Oronoz; Olatz Perez-de-Viñaspre; Massimo Piccardi; et al. (WMT@EMNLP, 2020)

BioNorm: deep learning-based event normalization for the curation of reaction databases. - Peiliang Lou; Antonio Jimeno-Yepes; Zai Zhang 002; Qinghua Zheng; Xiangrong Zhang; Chen Li 011 (Bioinform., 2020)

Elephant in the Room: An Evaluation Framework for Assessing Adversarial Examples in NLP. - Ying Xu; Xu Zhong; Antonio José Jimeno-Yepes; Jey Han Lau (CoRR, 2020)

COVID-SEE: Scientific Evidence Explorer for COVID-19 Related Research. - Karin Verspoor; Simon Suster; Yulia Otmakhova 001; Shevon Mendis; Zenan Zhai; Biaoyan Fang; Jey Han Lau; Timothy Baldwin; Antonio Jimeno-Yepes; David Martínez 001 (CoRR, 2020)

Adverse drug event detection using reason assignments in FDA drug labels. - Corey Sutphin; Kahyun Lee; Antonio Jimeno-Yepes; Özlem Uzuner; Bridget T. McInnes (J. Biomed. Informatics, 2020)

Using Discourse Structure to Differentiate Focus Entities from Background Entities in Scientific Literature. - Antonio Jimeno-Yepes; Ameer Albahem; Karin Verspoor (ALTA, 2021)

Brief Description of COVID-SEE: The Scientific Evidence Explorer for COVID-19 Related Research. - Karin Verspoor; Simon Suster; Yulia Otmakhova 001; Shevon Mendis; Zenan Zhai; Biaoyan Fang; Jey Han Lau; Timothy Baldwin; Antonio Jimeno-Yepes; David Martínez 001 (ECIR (2), 2021)

ICDAR 2021 Competition on Scientific Literature Parsing. - Antonio Jimeno-Yepes; Peter Zhong; Douglas Burdick (ICDAR (4), 2021)

Impact of detecting clinical trial elements in exploration of COVID-19 literature. - Simon Suster; Karin Verspoor; Timothy Baldwin; Jey Han Lau; Antonio Jimeno-Yepes; David Martinez Iraola; Yulia Otmakhova 001 (ICHI, 2021)

Grey-box Adversarial Attack And Defence For Sentiment Classification. - Ying Xu; Xu Zhong; Antonio Jimeno-Yepes; Jey Han Lau (NAACL-HLT, 2021)

Findings of the WMT 2021 Biomedical Translation Shared Task: Summaries of Animal Experiments as New Test Set. - Lana Yeganova; Dina Wiemann; Mariana L. Neves; Federica Vezzani; Amy Siu; Inigo Jauregi Unanue; Maite Oronoz; Nancy Mah; Aurélie Névéol; David Martínez 001; Rachel Bawden; Giorgio Maria Di Nunzio; et al. (WMT@EMNLP, 2021)

A representation model for biological entities by fusing structured axioms with unstructured texts. - Peiliang Lou; Yuxin Dong; Antonio Jimeno-Yepes; Chen Li 011 (Bioinform., 2021)

Understanding in Artificial Intelligence. - Stefan Maetschke; David Martinez Iraola; Pieter Barnard; Elaheh ShafieiBavani; Peter Zhong; Ying Xu; Antonio Jimeno-Yepes (CoRR, 2021)

Single versus Multiple Annotation for Named Entity Recognition of Mutations. - David Martinez Iraola; Antonio Jimeno-Yepes (CoRR, 2021)

Impact of detecting clinical trial elements in exploration of COVID-19 literature. - Simon Suster; Karin Verspoor; Timothy Baldwin; Jey Han Lau; Antonio Jimeno-Yepes; David Martínez 001; Yulia Otmakhova 001 (CoRR, 2021)

ICDAR 2021 Competition on Scientific Literature Parsing. - Antonio Jimeno-Yepes; Xu Zhong; Douglas Burdick (CoRR, 2021)

Distinguishing between focus and background entities in biomedical corpora using discourse structure and transformers. - Antonio Jimeno-Yepes; Karin Verspoor (LOUHI@EMNLP, 2022)

Modeling long-term dependencies and short-term correlations in patient journey data with temporal attention networks for health prediction. - Yuxi Liu; Zhenhao Zhang; Antonio Jimeno-Yepes; Flora D. Salim (BCB, 2022)

Integrated Convolutional and Recurrent Neural Networks for Health Risk Prediction using Patient Journey Data with Many Missing Values. - Yuxi Liu; Shaowen Qin; Antonio Jimeno-Yepes; Wei Shao 006; Zhenhao Zhang; Flora D. Salim (BIBM, 2022)

READ-BioMed@SocialDisNER: Adaptation of an Annotation System to Spanish Tweets. - Antonio Jimeno-Yepes; Karin Verspoor (SMM4H@COLING, 2022)

M3: Multi-level dataset for Multi-document summarisation of Medical studies. - Yulia Otmakhova 001; Karin Verspoor; Timothy Baldwin; Antonio Jimeno-Yepes; Jey Han Lau (EMNLP (Findings), 2022)

The READ-BioMed Team in LivingNER Task 1 (2022): Adaptation of an English Annotation System to Spanish. - Antonio Jimeno-Yepes; Karin Verspoor (IberLEF@SEPLN, 2022)

Findings of the WMT 2022 Biomedical Translation Shared Task: Monolingual Clinical Case Reports. - Mariana Neves 002; Antonio Jimeno-Yepes; Amy Siu; Roland Roller; Philippe Thomas 002; Maika Vicente Navarro; Lana Yeganova; Dina Wiemann; Giorgio Maria Di Nunzio; Federica Vezzani; Christel Gérardin; Rachel Bawden; et al. (WMT, 2022)

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Rezarta Islamaj; Jingcheng Du; Li Fang; Wang Kai; Shuo Xu 001; Yuefu Zhang; Parsa Bagherzadeh; Sabine Bergler; Aakash Bhatnagar; et al. (Database J. Biol. Databases Curation, 2022)

Hyperplane bounds for neural feature mappings. - Antonio Jimeno-Yepes (CoRR, 2022)

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. - Qingyu Chen 001; Alexis Allot; Robert Leaman; Rezarta Islamaj Dogan; Jingcheng Du; Li Fang; Wang Kai; Shuo Xu 001; Yuefu Zhang; Parsa Bagherzadeh; Sabine Bergler; Aakash Bhatnagar; et al. (CoRR, 2022)

Identification of focus versus background entities in scientific literature. - Antonio Jimeno-Yepes; Karin Verspoor (Zenodo, 2022)

Stacked Attention-based Networks for Accurate and Interpretable Health Risk Prediction. - Yuxi Liu; Zhenhao Zhang; Campbell Thompson; Richard Leibbrandt; Shaowen Qin; Antonio Jimeno-Yepes (IJCNN, 2023)

Class Specific Feature Disentanglement and Text Embeddings for Multi-label Generalized Zero Shot CXR Classification. - Dwarikanath Mahapatra; Antonio José Jimeno-Yepes; Shiba Kuanar; Sudipta Roy 002; Behzad Bozorgtabar; Mauricio Reyes 001; Zongyuan Ge (MICCAI (2), 2023)

Contrastive Learning-Based Imputation-Prediction Networks for In-hospital Mortality Risk Modeling Using EHRs. - Yuxi Liu; Zhenhao Zhang; Shaowen Qin; Flora D. Salim; Antonio Jimeno-Yepes (ECML/PKDD (6), 2023)

Findings of the WMT 2023 Biomedical Translation Shared Task: Evaluation of ChatGPT 3.5 as a Comparison System. - Mariana L. Neves; Antonio Jimeno-Yepes; Aurélie Névéol; Rachel Bawden; Giorgio Maria Di Nunzio; Roland Roller; Philippe Thomas 002; Federica Vezzani; Maika Vicente Navarro; Lana Yeganova; Dina Wiemann; Cristian Grozea (WMT, 2023)

Hypergraph Convolutional Networks for Fine-grained ICU Patient Similarity Analysis and Risk Prediction. - Yuxi Liu; Zhenhao Zhang; Shaowen Qin; Flora D. Salim; Antonio Jimeno-Yepes; Jun Shen 001 (CoRR, 2023)

Classifying literature mentions of biological pathogens as experimentally studied using natural language processing. - Antonio José Jimeno-Yepes; Karin Verspoor (J. Biomed. Semant., 2023)

Fine-grained Patient Similarity Measuring using Contrastive Graph Similarity Networks. - Yuxi Liu; Zhenhao Zhang; Shaowen Qin; Flora D. Salim; Jiang Bian; Antonio Jimeno-Yepes (ICHI, 2024)

Hypergraph Convolutional Networks for Fine-Grained lCU Patient Similarity Analysis and Risk Prediction. - Yuxi Liu; Zhenhao Zhang; Shaowen Qin; Flora D. Salim; Antonio Jimeno-Yepes; Jun Shen 001; Jiang Bian (ICHI, 2024)

Boosting Patient Representation Learning via Graph Contrastive Learning. - Zhenhao Zhang; Yuxi Liu; Jiang Bian; Antonio Jimeno-Yepes; Jun Shen 001; Fuyi Li; Guodong Long; Flora D. Salim (ECML/PKDD (9), 2024)

Findings of the WMT 2024 Biomedical Translation Shared Task: Test Sets on Abstract Level. - Mariana L. Neves; Cristian Grozea; Philippe Thomas 002; Roland Roller; Rachel Bawden; Aurélie Névéol; Steffen Castle; Vanessa Bonato; Giorgio Maria Di Nunzio; Federica Vezzani; Maika Vicente Navarro; Lana Yeganova; et al. (WMT, 2024)

Financial Report Chunking for Effective Retrieval Augmented Generation. - Antonio Jimeno-Yepes; Yao You; Jan Milczek; Sebastian Laverde; Renyu Li (CoRR, 2024)

Multi-Label Generalized Zero Shot Chest X-Ray Classification by Combining Image-Text Information With Feature Disentanglement. - Dwarikanath Mahapatra; Antonio Jimeno-Yepes; Behzad Bozorgtabar; Sudipta Roy 002; Zongyuan Ge; Mauricio Reyes 001 (IEEE Trans. Medical Imaging, 2025)

Assessing the Impact of the Quality of Textual Data on Feature Representation and Machine Learning Models. - Tabinda Sarwar; Antonio José Jimeno-Yepes; Lawrence Cavedon (CoRR, 2025)

Corrections to "Multi-Label Generalized Zero Shot Chest X-Ray Classification By Combining Image-Text Information With Feature Disentanglement". - Dwarikanath Mahapatra; Antonio Jimeno-Yepes; Behzad Bozorgtabar; Sudipta Roy 002; Zongyuan Ge; Mauricio Reyes 001 (IEEE Trans. Medical Imaging, 2025)

Evolutionary thoughts: integration of large language models and evolutionary algorithms. - Antonio Jimeno-Yepes; Pieter Barnard (CoRR, 2025)