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Martin Krallinger
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2020 – today
- 2024
- [c43]Wen-wai Yim, Asma Ben Abacha, Yujuan Fu, Zhaoyi Sun, Fei Xia, Meliha Yetisgen, Martin Krallinger:
Overview of the MEDIQA-M3G 2024 Shared Task on Multilingual Multimodal Medical Answer Generation. ClinicalNLP@NAACL 2024: 581-589 - [c42]Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Martin Krallinger, Natalia V. Loukachevitch, Vera Davydova, Elena Tutubalina, Georgios Paliouras:
Overview of BioASQ 2024: The Twelfth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF (2) 2024: 3-27 - [c41]Salvador Lima-López, Eulàlia Farré-Maduell, Jan Rodríguez-Miret, Miguel Rodríguez-Ortega, Livia Lilli, Jacopo Lenkowicz, Giovanna Ceroni, Jonathan Kossof, Anoop Shah, Anastasios Nentidis, Anastasia Krithara, Georgios Katsimpras, Georgios Paliouras, Martin Krallinger:
Overview of MultiCardioNER task at BioASQ 2024 on Medical Specialty and Language Adaptation of Clinical NER Systems for Spanish, English and Italian. CLEF (Working Notes) 2024: 8-27 - [c40]Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras, Martin Krallinger, Luis Gascó Sánchez, Salvador Lima-López, Eulàlia Farré, Natalia V. Loukachevitch, Vera Davydova, Elena Tutubalina
:
BioASQ at CLEF2024: The Twelfth Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge. ECIR (5) 2024: 490-497 - [c39]Fernando Gallego Donoso
ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish. ICCS (5) 2024: 266-280 - [i7]Fernando Gallego Donoso, Guillermo López-García, Luis Gascó Sánchez, Martin Krallinger, Francisco J. Veredas:
ClinLinker: Medical Entity Linking of Clinical Concept Mentions in Spanish. CoRR abs/2404.06367 (2024) - 2023
- [j31]Antonio Miranda-Escalada
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations. Database J. Biol. Databases Curation 2023 (2023) - [j30]Salvador Lima-López, Eulàlia Farré-Maduell, Vicent Brivá-Iglesias, Luis Gascó Sánchez, Martin Krallinger:
MEDDOPLACE Shared Task overview: recognition, normalization and classification of locations and patient movement in clinical texts. Proces. del Leng. Natural 71: 301-311 (2023) - [c38]Salvador Lima-López, Eulàlia Farré-Maduell, Luis Gascó, Anastasios Nentidis, Anastasia Krithara, Georgios Katsimpras, Georgios Paliouras, Martin Krallinger:
Overview of MedProcNER Task on Medical Procedure Detection and Entity Linking at BioASQ 2023. CLEF (Working Notes) 2023: 1-18 - [c37]Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2023: The Eleventh BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF 2023: 227-250 - [c36]Anastasios Nentidis, Anastasia Krithara, Georgios Paliouras, Eulàlia Farré-Maduell
BioASQ at CLEF2023: The Eleventh Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge. ECIR (3) 2023: 577-584 - [i6]Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Salvador Lima-López, Eulàlia Farré-Maduell, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2023: The eleventh BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CoRR abs/2307.05131 (2023) - 2022
- [j29]Andrew Chatr-aryamontri, Lynette Hirschman
Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII. Database J. Biol. Databases Curation 2022(2022) (2022) - [j28]Graciela Gonzalez-Hernandez
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers. Database J. Biol. Databases Curation 2022(2022) (2022) - [j27]Antonio Miranda-Escalada, Eulàlia Farré-Maduell, Salvador Lima-López, Darryl Estrada, Luis Gascó, Martin Krallinger:
Mention detection, normalization & classification of species, pathogens, humans and food in clinical documents: Overview of the LivingNER shared task and resources. Proces. del Leng. Natural 69: 241-253 (2022) - [c35]Antonio Miranda-Escalada, Luis Gascó, Salvador Lima-López, Eulàlia Farré-Maduell, Darryl Estrada, Anastasios Nentidis, Anastasia Krithara, Georgios Katsimpras, Georgios Paliouras, Martin Krallinger:
Overview of DisTEMIST at BioASQ: Automatic detection and normalization of diseases from clinical texts: results, methods, evaluation and multilingual resources. CLEF (Working Notes) 2022: 179-203 - [c34]Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara
Overview of BioASQ 2022: The Tenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF 2022: 337-361 - [c33]Luis Gascó Sánchez, Darryl Estrada-Zavala, Eulàlia Farré-Maduell, Salvador Lima-López, Antonio Miranda-Escalada, Martin Krallinger:
The SocialDisNER shared task on detection of disease mentions in health-relevant content from social media: methods, evaluation, guidelines and corpora. SMM4H@COLING 2022: 182-189 - [c32]Davy Weissenbacher, Juan M. Banda, Vera Davydova, Darryl Estrada-Zavala, Luis Gascó Sánchez, Yao Ge, Yuting Guo, Ari Z. Klein, Martin Krallinger, Mathias Leddin, Arjun Magge, Raul Rodriguez-Esteban
Overview of the Seventh Social Media Mining for Health Applications (#SMM4H) Shared Tasks at COLING 2022. SMM4H@COLING 2022: 221-241 - [c31]Anastasios Nentidis, Anastasia Krithara
BioASQ at CLEF2022: The Tenth Edition of the Large-scale Biomedical Semantic Indexing and Question Answering Challenge. ECIR (2) 2022: 429-435 - [c30]Mariana Neves, Antonio Jimeno-Yepes, Amy Siu, Roland Roller, Philippe Thomas, Maika Vicente Navarro, Lana Yeganova, Dina Wiemann, Giorgio Maria Di Nunzio, Federica Vezzani, Christel Gérardin, Rachel Bawden, Darryl Estrada, Salvador Lima-López, Eulàlia Farré-Maduell, Martin Krallinger, Cristian Grozea, Aurélie Névéol:
Findings of the WMT 2022 Biomedical Translation Shared Task: Monolingual Clinical Case Reports. WMT 2022: 694-723 - [i5]Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Antonio Miranda-Escalada, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2022: The tenth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CoRR abs/2210.06852 (2022) - 2021
- [j26]Elizabeth T. Hobbs, Stephen M. Goralski
ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts. Frontiers Res. Metrics Anal. 6: 674205 (2021) - [j25]Salvador Lima-López, Eulàlia Farré-Maduell, Antonio Miranda-Escalada, Vicent Brivá-Iglesias, Martin Krallinger:
NLP applied to occupational health: MEDDOPROF shared task at IberLEF 2021 on automatic recognition, classification and normalization of professions and occupations from medical texts. Proces. del Leng. Natural 67: 243-256 (2021) - [c29]Luis Gascó, Anastasios Nentidis, Anastasia Krithara, Darryl Estrada-Zavala, Renato Toshiyuki Murasaki, Elena Primo-Peña, Cristina Bojo-Canales, Georgios Paliouras, Martin Krallinger:
Overview of BioASQ 2021-MESINESP track. Evaluation of advance hierarchical classification techniques for scientific literature, patents and clinical trials. CLEF (Working Notes) 2021: 165-187 - [c28]Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara
Overview of BioASQ 2021: The Ninth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF 2021: 239-263 - [c27]Anastasia Krithara
BioASQ at CLEF2021: Large-Scale Biomedical Semantic Indexing and Question Answering. ECIR (2) 2021: 624-630 - [c26]Antonio Miranda-Escalada, Eulàlia Farré-Maduell
The ProfNER shared task on automatic recognition of occupation mentions in social media: systems, evaluation, guidelines, embeddings and corpora. SMM4H@NAACL-HLT 2021: 13-20 - [c25]Arjun Magge, Ari Z. Klein, Antonio Miranda-Escalada, Mohammed Ali Al-Garadi, Ilseyar Alimova, Zulfat Miftahutdinov, Eulàlia Farré, Salvador Lima-López, Ivan Flores, Karen O'Connor, Davy Weissenbacher, Elena Tutubalina, Abeed Sarker
Overview of the Sixth Social Media Mining for Health Applications (#SMM4H) Shared Tasks at NAACL 2021. SMM4H@NAACL-HLT 2021: 21-32 - [e3]Arjun Magge, Ari Z. Klein, Antonio Miranda-Escalada, Mohammed Ali Al-garadi, Ilseyar Alimova, Zulfat Miftahutdinov, Eulàlia Farré-Maduell, Salvador Lima-López, Ivan Flores, Karen O'Connor, Davy Weissenbacher, Elena Tutubalina, Abeed Sarker, Juan M. Banda, Martin Krallinger, Graciela Gonzalez-Hernandez:
Proceedings of the Sixth Social Media Mining for Health Workshop and Shared Task, SMM4H@NAACL-HLT 2021, Mexico City, Mexico, June 10, 2021. Association for Computational Linguistics 2021, ISBN 978-1-954085-31-2 [contents] - [i4]Anastasios Nentidis, Anastasia Krithara, Konstantinos Bougiatiotis, Martin Krallinger, Carlos Rodríguez Penagos, Marta Villegas, Georgios Paliouras:
Overview of BioASQ 2020: The eighth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CoRR abs/2106.14618 (2021) - [i3]Anastasios Nentidis, Georgios Katsimpras, Eirini Vandorou, Anastasia Krithara, Luis Gascó, Martin Krallinger, Georgios Paliouras:
Overview of BioASQ 2021: The ninth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CoRR abs/2106.14885 (2021) - [i2]Casimiro Pio Carrino, Jordi Armengol-Estapé, Ona De Gibert Bonet, Asier Gutiérrez-Fandiño
Spanish Biomedical Crawled Corpus: A Large, Diverse Dataset for Spanish Biomedical Language Models. CoRR abs/2109.07765 (2021) - 2020
- [c24]Antonio Miranda-Escalada, Aitor Gonzalez-Agirre, Jordi Armengol-Estapé, Martin Krallinger:
Overview of Automatic Clinical Coding: Annotations, Guidelines, and Solutions for non-English Clinical Cases at CodiEsp Track of CLEF eHealth 2020. CLEF (Working Notes) 2020 - [c23]Anastasios Nentidis, Anastasia Krithara
Overview of BioASQ 2020: The Eighth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. CLEF 2020: 194-214 - [c22]Lorraine Goeuriot
Overview of the CLEF eHealth Evaluation Lab 2020. CLEF 2020: 255-271 - [c21]Carlos Rodríguez Penagos, Anastasios Nentidis, Aitor Gonzalez-Agirre, Alejandro Asensio, Jordi Armengol-Estapé, Anastasia Krithara, Marta Villegas, Georgios Paliouras, Martin Krallinger:
Overview of MESINESP, a Spanish Medical Semantic Indexing Task within BioASQ 2020. CLEF (Working Notes) 2020 - [c20]Francisco M. Couto
Report of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages. SIIRH@ECIR 2020 - [c19]Martin Krallinger
BioASQ at CLEF2020: Large-Scale Biomedical Semantic Indexing and Question Answering. ECIR (2) 2020: 550-556 - [c18]Hanna Suominen
CLEF eHealth Evaluation Lab 2020. ECIR (2) 2020: 587-594 - [c17]Francisco M. Couto
Proposal of the First International Workshop on Semantic Indexing and Information Retrieval for Health from Heterogeneous Content Types and Languages (SIIRH). ECIR (2) 2020: 654-659 - [c16]Elizabeth T. Hobbs, Stephen M. Goralski, Ashley Mitchell, Andrew Simpson, Dorjan Leka, Emmanuel Kotey, Matt Sekira, James B. Munro, Suvarna Nadendla, Rebecca Jackson, Aitor Gonzalez-Agirre, Martin Krallinger, Michelle G. Giglio, Ivan Erill:
Corpora as Evolving Entities: Embedding Corpora in Biomedical Ontologies. ICBO/ODLS 2020: 1-11 - [c15]Antonio Miranda-Escalada, Eulàlia Farré, Martin Krallinger:
Named Entity Recognition, Concept Normalization and Clinical Coding: Overview of the Cantemist Track for Cancer Text Mining in Spanish, Corpus, Guidelines, Methods and Results. IberLEF@SEPLN 2020: 303-323 - [e2]Francisco M. Couto, Martin Krallinger:
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, SIIRH@ECIR 2020, Lisbon, Portugal, April 14, 2020. CEUR Workshop Proceedings 2619, CEUR-WS.org 2020 [contents]
2010 – 2019
- 2019
- [j24]Martín Pérez-Pérez
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. J. Cheminformatics 11(1): 42:1-42:16 (2019) - [c14]Aitor Gonzalez-Agirre, Montserrat Marimon, Ander Intxaurrondo, Obdulia Rabal, Marta Villegas, Martin Krallinger:
PharmaCoNER: Pharmacological Substances, Compounds and proteins Named Entity Recognition track. BioNLP-OST@EMNLP-IJNCLP 2019: 1-10 - [c13]Montserrat Marimon, Aitor Gonzalez-Agirre, Ander Intxaurrondo, Heidy Rodriguez, Jose Lopez Martin, Marta Villegas, Martin Krallinger:
Automatic De-identification of Medical Texts in Spanish: the MEDDOCAN Track, Corpus, Guidelines, Methods and Evaluation of Results. IberLEF@SEPLN 2019: 618-638 - [c12]Rachel Bawden, Kevin Bretonnel Cohen, Cristian Grozea, Antonio Jimeno-Yepes, Madeleine Kittner, Martin Krallinger, Nancy Mah
Findings of the WMT 2019 Biomedical Translation Shared Task: Evaluation for MEDLINE Abstracts and Biomedical Terminologies. WMT (3) 2019: 29-53 - [c11]Felipe Soares, Martin Krallinger:
BSC Participation in the WMT Translation of Biomedical Abstracts. WMT (3) 2019: 175-178 - [e1]Miguel Ángel García Cumbreras, Julio Gonzalo, Eugenio Martínez Cámara, Raquel Martínez-Unanue, Paolo Rosso, Jorge Carrillo-de-Albornoz, Soto Montalvo, Luis Chiruzzo, Sandra Collovini, Yoan Gutiérrez, Salud M. Jiménez-Zafra, Martin Krallinger, Manuel Montes-y-Gómez, Reynier Ortega-Bueno, Aiala Rosá:
Proceedings of the Iberian Languages Evaluation Forum co-located with 35th Conference of the Spanish Society for Natural Language Processing, IberLEF@SEPLN 2019, Bilbao, Spain, September 24th, 2019. CEUR Workshop Proceedings 2421, CEUR-WS.org 2019 [contents] - [i1]Felipe Soares, Martin Krallinger:
BVS Corpus: A Multilingual Parallel Corpus of Biomedical Scientific Texts. CoRR abs/1905.01712 (2019) - 2018
- [j23]Jesus Santamaría, Martin Krallinger:
Construcción de recursos terminológicos médicos para el espa˜nol: el sistema de extracción de términos CUTEXT y los repositorios de términos biomédicos. Proces. del Leng. Natural 61: 49-56 (2018) - [c10]Ander Intxaurrondo, Montserrat Marimon, Aitor Gonzalez-Agirre, Jose Antonio López-Martín, Heidy Rodriguez, Jesus Santamaría, Marta Villegas, Martin Krallinger:
Finding Mentions of Abbreviations and Their Definitions in Spanish Clinical Cases: The BARR2 Shared Task Evaluation Results. IberEval@SEPLN 2018: 280-289 - 2017
- [j22]Andrés Cañada, Salvador Capella-Gutiérrez
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. Nucleic Acids Res. 45(Webserver-Issue): W484-W489 (2017) - [j21]Marta Villegas, Santiago de la Peña, Ander Intxaurrondo, Jesus Santamaría, Martin Krallinger:
Esfuerzos para fomentar la minería de textos en biomedicina más allá del inglés: el plan estratégico nacional español para las tecnologías del lenguaje. Proces. del Leng. Natural 59: 141-144 (2017) - [c9]Ander Intxaurrondo, Martín Pérez-Pérez, Gael Pérez Rodríguez, Jose Antonio López-Martín, Jesus Santamaría, Santiago de la Peña, Marta Villegas, Saber Ahmad Akhondi, Alfonso Valencia, Anália Lourenço, Martin Krallinger:
The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts. IberEval@SEPLN 2017: 230-246 - [c8]Ander Intxaurrondo, Martin Krallinger:
CNIO at BARR IberEval 2017: Exploring Three Biomedical Abbreviation Identifiers for Spanish Biomedical Publications. IberEval@SEPLN 2017: 278-285 - 2016
- [j20]Martín Pérez-Pérez
The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge. Database J. Biol. Databases Curation 2016 (2016) - [c7]Jose Camilla Sammartino, Martin Krallinger, Alfonso Valencia:
Annotation Process, Guidelines and Text Corpus of Small Non-Coding RNA Molecules: the MiNCor for MicroRNA Annotations. SMBM 2016: 56-63 - 2015
- [j19]Jonathan G. Lees, Jean-Karim Hériché
FUN-L: gene prioritization for RNAi screens. Bioinform. 31(12): 2052-2053 (2015) - [j18]Martin Krallinger
CHEMDNER: The drugs and chemical names extraction challenge. J. Cheminformatics 7(S-1): S1 (2015) - [j17]Martin Krallinger
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J. Cheminformatics 7(S-1): S2 (2015) - 2014
- [j16]Cecilia N. Arighi
BioCreative-IV virtual issue. Database J. Biol. Databases Curation 2014 (2014) - [c6]Martin Krallinger
Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis. PACBB 2014: 285-292 - 2013
- [j15]Cecilia N. Arighi
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013) - [j14]Donald C. Comeau, Rezarta Islamaj Dogan
BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 2013 (2013) - [c5]Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans:
Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Working Notes) 2013 - 2012
- [j13]Lynette Hirschman, Gully A. P. C. Burns
Text mining for the biocuration workflow. Database J. Biol. Databases Curation 2012 (2012) - [j12]Martin Krallinger
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. Database J. Biol. Databases Curation 2012 (2012) - [j11]Cathy H. Wu
BioCreative-2012 Virtual Issue. Database J. Biol. Databases Curation 2012 (2012) - [j10]David Salgado
MyMiner: a web application for computer-assisted biocuration and text annotation. Bioinform. 28(17): 2285-2287 (2012) - [c4]Roser Morante, Martin Krallinger, Alfonso Valencia, Walter Daelemans:
Machine Reading of Biomedical Texts about Alzheimer's Disease. CLEF (Online Working Notes/Labs/Workshop) 2012 - 2011
- [j9]Cecilia N. Arighi
Overview of the BioCreative III Workshop. BMC Bioinform. 12(S-8): S1 (2011) - [j8]Martin Krallinger
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): S3 (2011) - [j7]Cecilia N. Arighi
BioCreative III interactive task: an overview. BMC Bioinform. 12(S-8): S4 (2011) - 2010
- [j6]Martin Krallinger, Ashish V. Tendulkar, Florian Leitner, Andrew Chatr-aryamontri, Alfonso Valencia:
The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions. BMC Bioinform. 11(S-5): O1 (2010) - [j5]Florian Leitner
An Overview of BioCreative II.5. IEEE ACM Trans. Comput. Biol. Bioinform. 7(3): 385-399 (2010) - [c3]Martin Krallinger:
Importance of negations and experimental qualifiers in biomedical literature. NeSp-NLP@ACL 2010: 46-49
2000 – 2009
- 2009
- [j4]Martin Krallinger
Extraction of human kinase mutations from literature, databases and genotyping studies. BMC Bioinform. 10(S-8): 1 (2009) - [j3]Martin Krallinger
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. Nucleic Acids Res. 37(Web-Server-Issue): 160-165 (2009) - 2006
- [c2]Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter:
Refactoring Corpora. BioNLP@NAACL-HLT 2006: 116-117 - 2005
- [j2]Christian Blaschke, Eduardo Andrés León
Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinform. 6(S-1) (2005) - [j1]Martin Krallinger
A sentence sliding window approach to extract protein annotations from biomedical articles. BMC Bioinform. 6(S-1) (2005) - [p1]Martin Krallinger, Alfonso Valencia:
Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps. Data Analysis and Visualization in Genomics and Proteomics 2005: 41-59 - 2004
- [c1]Martin Krallinger, Maria Padron, Christian Blaschke, Alfonso Valencia:
Assessing the Correlation between Contextual Patterns and Biological Entity Tagging. NLPBA/BioNLP 2004
Coauthor Index
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