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UZH in BioNLP 2013

Gerold Schneider, Simon Clematide, Tilia Ellendorff, Don Tuggener, Fabio Rinaldi, Gintare Grigonyte
2013
We describe a biological event detection method implemented for the Genia Event Extraction task of BioNLP 2013.  ...  Our participation in the Genia Event Extraction task of BioNLP 2013 (Kim et al., 2013) was motivated by the desire of testing our technologies on a more linguistically motivated task.  ...  Conclusions and Future work Our participation in the 2013 BioNLP shared task was a useful opportunity to revise components of the OntoGene pipeline and begin the implementation of a novel event generator  ... 
doi:10.5167/uzh-91884 fatcat:idyyvqaumza2fg2ezlzzonzcnm

Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task

Jin-Dong Kim, Jung-jae Kim, Xu Han, Dietrich Rebholz-Schuhmann
2015 BMC Bioinformatics  
The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme.  ...  Also, the Gene Regulation Ontology (GRO) task was newly introduced in the third edition. The final evaluation of the participating systems resulted in relatively low performance.  ...  2013.  ... 
doi:10.1186/1471-2105-16-s10-s3 pmid:26202680 pmcid:PMC4511578 fatcat:arzo5htwnrdihm72uhtfjchilu

COMETA: A Corpus for Medical Entity Linking in the Social Media [article]

Marco Basaldella, Fangyu Liu, Ehsan Shareghi, Nigel Collier
2020 arXiv   pre-print
Whilst there has been growing progress in Entity Linking (EL) for general language, existing datasets fail to address the complex nature of health terminology in layman's language.  ...  Meanwhile, there is a growing need for applications that can understand the public's voice in the health domain.  ...  UZH@CRAFT-ST: a sequence-labeling approach to concept recognition. In Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, pages 185-195, Hong Kong, China.  ... 
arXiv:2010.03295v2 fatcat:7zuoouy2erf3xaxjqx5aheiqsy

UZH@CRAFT-ST: a Sequence-labeling Approach to Concept Recognition

Lenz Furrer, Joseph Cornelius, Fabio Rinaldi
2019
In the cross-system comparison, BioBERT proves to be a strong basis for creating a concept-recognition system, although some entity types are predicted more accurately by the BiLSTM-based system.  ...  In the cross-system comparison, BioBERT proves to be a strong basis for creating a concept-recognition system, although some entity types are predicted more accurately by the BiLSTM-based system.  ...  Postprocessing Since our systems produce predictions in a CoNLL-like format, an additional conversion step was necessary to meet the requirements of the evaluation suite (BioNLP format).  ... 
doi:10.5167/uzh-176855 fatcat:dmnn3gc24ne7rfnvyejv5wcimq

Overview of the Fourth Social Media Mining for Health (SMM4H) Shared Tasks at ACL 2019

Davy Weissenbacher, Abeed Sarker, Arjun Magge, Ashlynn Daughton, Karen O'Connor, Michael J. Paul, Graciela Gonzalez-Hernandez
2019 Proceedings of the Fourth Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task   unpublished
(Lamb et al., 2013).  ...  (Lamb et al., 2013) Alex Lamb, Michael J. Paul, and Mark Dredze. 2013. Separating fact from fear: Tracking flu infections on twitter.  ... 
doi:10.18653/v1/w19-3203 fatcat:gmsnh7qrzbdmdmy7xheb5sfbaa

Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014)

S.N.
2014
and EFPIA companies' in kind contribution.  ...  IMI-JU under grants agreements n°115002 (eTOX) and nº115191 (Open PHACTS)], resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007(FP7/ -2013  ...  In the PC model chemi-4 http://2013.bionlp-st.org/ cal entities are required additionally.  ... 
doi:10.5167/uzh-98982 fatcat:avtlvr27hrdyfjfto47x2lfulu

COMETA: A Corpus for Medical Entity Linking in the Social Media

Marco Basaldella, Fangyu Liu, Ehsan Shareghi, Nigel Collier
2020 Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP)   unpublished
Whilst there has been growing progress in Entity Linking (EL) for general language, existing datasets fail to address the complex nature of health terminology in layman's language.  ...  Meanwhile, there is a growing need for applications that can understand the public's voice in the health domain.  ...  UZH@CRAFT-ST: a sequence-labeling approach to concept recognition. In Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, pages 185-195, Hong Kong, China.  ... 
doi:10.18653/v1/2020.emnlp-main.253 fatcat:2lmjco52xzae7fwnij2abcazjm