Filters








408 Hits in 3.8 sec

BioNLP shared Task 2013 - An Overview of the Bacteria Biotope Task

Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Philippe Bessières, Claire Nédellec
2013 Workshop on Biomedical Natural Language Processing  
This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2013, which follows BioNLP-ST-11.  ...  The Bacteria Biotope task aims to extract the location of bacteria from scientific web pages and to characterize these locations with respect to the OntoBiotope ontology.  ...  Acknowledgments This work has been partially supported by the Quaero program, funded by OSEO, the French state agency for innovation and the INRA OntoBiotope Network.  ... 
dblp:conf/bionlp/BossyGRBN13 fatcat:xr76d7vwlvbidjzpvksfihmzzy

Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013

Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun'ichi Tsujii, Sophia Ananiadou
2015 BMC Bioinformatics  
In this paper, we present the Cancer Genetics (CG) and Pathway Curation (PC) tasks, two event extraction tasks introduced in the BioNLP Shared Task 2013.  ...  Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical  ...  Acknowledgements We wish to thank the BioNLP ST 2013 participants and supporting resource providers for their invaluable contributions to making these tasks a success.  ... 
doi:10.1186/1471-2105-16-s10-s2 pmid:26202570 pmcid:PMC4511510 fatcat:e7dhvpzwzbcmxm3hfilgrawj3i

TEES 2.1: Automated Annotation Scheme Learning in the BioNLP 2013 Shared Task

Jari Björne, Tapio Salakoski
2013 Workshop on Biomedical Natural Language Processing  
We participate in the BioNLP 2013 Shared Task with Turku Event Extraction System (TEES) version 2.1.  ...  TEES 2.1 is shown to have good generalizability and good performance across the BioNLP 2013 task corpora, achieving first place in four out of eight tasks.  ...  Acknowledgments We thank CSC -IT Center for Science Ltd, Espoo, Finland for providing computational resources.  ... 
dblp:conf/bionlp/BjorneS13 fatcat:xj5npgmo2renndkulaigwvjz2q

Overview of the Bacteria Biotope Task at BioNLP Shared Task 2016

Louise Delėger, Robert Bossy, Estelle Chaix, Mouhamadou Ba, Arnaud Ferrė, Philippe Bessières, Claire Nėdellec
2016 Proceedings of the 4th BioNLP Shared Task Workshop  
This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions.  ...  The task is motivated by the importance of the knowledge on bacteria habitats for fundamental research and applications in microbiology.  ...  The BB subtask was evaluated using the Slot Error Rate (SER), the same method as BioNLP-ST 2013 BB task 1 since the two tasks are the same.  ... 
doi:10.18653/v1/w16-3002 dblp:conf/bionlp/DelegerBCBFBN16 fatcat:azsnzy7ozngmjgkrwt6diswopi

VERSE: Event and Relation Extraction in the BioNLP 2016 Shared Task

Jake Lever, Steven JM Jones
2016 Proceedings of the 4th BioNLP Shared Task Workshop  
We present the Vancouver Event and Relation System for Extraction (VERSE) 1 as a competing system for three subtasks of the BioNLP Shared Task 2016.  ...  Acknowledgments This research was supported by a Vanier Canada Graduate Scholarship. The authors would like to thank ComputeCanada for computational resources used in this project.  ...  The pattern-based tool BioSem (Bui et al., 2013) in particular performed well in the Genia Event subtask of the BioNLP'13 Shared Task.  ... 
doi:10.18653/v1/w16-3005 dblp:conf/bionlp/LeverJ16 fatcat:z6vuka7t7fdcfgpfe24nubsxka

Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016

Farrokh Mehryary, Jari Björne, Sampo Pyysalo, Tapio Salakoski, Filip Ginter
2016 Proceedings of the 4th BioNLP Shared Task Workshop  
We present the TurkuNLP entry to the BioNLP Shared Task 2016 Bacteria Biotopes event extraction (BB3-event) subtask.  ...  Our method ranked second among the entries to the shared task, achieving an F-score of 52.1% with 62.3% precision and 44.8% recall.  ...  We would also like to thank the CSC IT Center for Science Ltd. for computational resources. This work has been supported in part by Medical Research Council grant MR/M013049/1.  ... 
doi:10.18653/v1/w16-3009 dblp:conf/bionlp/MehryaryBPSG16 fatcat:qerobb42mfgldjqddvpmmpffdq

Overview of the Regulatory Network of Plant Seed Development (SeeDev) Task at the BioNLP Shared Task 2016

Estelle Chaix, Bertrand Dubreucq, Abdelhak Fatihi, Dialekti Valsamou, Robert Bossy, Mouhamadou Ba, Louise Delėger, Pierre Zweigenbaum, Philippe Bessières, Loïc Lepiniec, Claire Nėdellec
2016 Proceedings of the 4th BioNLP Shared Task Workshop  
This paper presents the SeeDev Task of the BioNLP Shared Task 2016.  ...  The best F-score is 0.432, which is similar to the scores achieved in similar tasks on molecular biology.  ...  The IJPB benefits from the support of the Labex Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).  ... 
doi:10.18653/v1/w16-3001 dblp:conf/bionlp/ChaixDFVBBDZBLN16 fatcat:z5pm4gaakbca3j4l6eauu2k4jq

Overview of the gene regulation network and the bacteria biotope tasks in BioNLP'13 shared task

Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessières, Claire Nédellec
2015 BMC Bioinformatics  
We present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB).  ...  The 2013 tasks expand on the 2011 version by better addressing the biological knowledge modeling needs. New evaluation metrics were designed for the new goals.  ...  Acknowledgements This work has been partially supported by the Quaero program funded by OSEO, the French state agency for innovation, the Program Investing in the Future, Grant n°ANR-10-IDEX-0003-02» funded  ... 
doi:10.1186/1471-2105-16-s10-s1 pmid:26202448 pmcid:PMC4511173 fatcat:keakzqti2bftpdbtaoi6nhv2pu

DUTIR in BioNLP-ST 2016: Utilizing Convolutional Network and Distributed Representation to Extract Complicate Relations

Honglei Li, Jianhai Zhang, Jian Wang, Hongfei Lin, Zhihao Yang
2016 Proceedings of the 4th BioNLP Shared Task Workshop  
We participate in the two event extraction tasks of BioNLP 2016 Shared Task: binary relation extraction of SeeDev task and localization relations extraction of Bacteria Biotope task.  ...  The results with F-score of 0.370 and 0.478 in our participant tasks, which were evaluated on the test data set, show that our proposed method contributes to binary relation extraction effectively and  ...  Acknowledge This work is supported by the grants from the National Natural Science Foundation of China  ... 
doi:10.18653/v1/w16-3012 dblp:conf/bionlp/LiZWLY16 fatcat:spw3h7rquraxhb77qkgye46234

Deep Contextualized Biomedical Abbreviation Expansion

Qiao Jin, Jinling Liu, Xinghua Lu
2019 Proceedings of the 18th BioNLP Workshop and Shared Task  
It also surpasses human performance for expanding a sample abbreviation, and remains robust in imbalanced, low-resources and clinical settings.  ...  Acknowledgement We are grateful for the annonymous reviewers of BioNLP 2019 who gave us very insightful comments and suggestions. J.L. is supported by NLM training grant 5T15LM007059-32.  ...  Low-resources samples: We define abbreviations that have less than 1k training instances as low-resources samples.  ... 
doi:10.18653/v1/w19-5010 dblp:conf/bionlp/JinLL19 fatcat:sqprjlh33jfnzftgnnzvyx7opq

Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the CRAFT Structural Annotation Task

Thang Minh Ngo, Jenna Kanerva, Filip Ginter, Sampo Pyysalo
2019 Proceedings of The 5th Workshop on BioNLP Open Shared Tasks  
We present the approach taken by the TurkuNLP group in the CRAFT Structural Annotation task, a shared task on dependency parsing.  ...  To adapt the parser to the biomedical domain, we considered and evaluated a number of approaches, including the generation of custom word embeddings, combination with other in-domain resources, and the  ...  We are grateful to CSC -IT Center for Science for computational resources used to train our models.  ... 
doi:10.18653/v1/d19-5728 dblp:conf/bionlp/NgoKGP19 fatcat:45toz73fqnawtjqom6pq75m6jy

LitWay, Discriminative Extraction for Different Bio-Events

Chen Li, Zhiqiang Rao, Xiangrong Zhang
2016 Proceedings of the 4th BioNLP Shared Task Workshop  
It is tested on the SeeDev task of BioNLP-ST 2016, achieves the state-of-the-art performance with the F-score of 43.2%, ranking first of all participating teams.  ...  Scientific literature is one of the trustful resources delivering knowledge of these networks. We propose LitWay, a system for extracting semantic relations from texts.  ...  TEES (Björne and Salakoski, 2013 ) is a SVM based text mining system for the extraction of events and relations from natural language texts, it obtains good performance on a few tasks in BioNLP-ST 2013  ... 
doi:10.18653/v1/w16-3004 dblp:conf/bionlp/LiRZ16 fatcat:jqaqtfh4hjdz3ogowbzjpqi4ve

A Paraphrase Generation System for EHR Question Answering

Sarvesh Soni, Kirk Roberts
2019 Proceedings of the 18th BioNLP Workshop and Shared Task  
Acknowledgments This work was supported by the U.S.  ...  While this approach is capable of generating more variations of a given sentence, it is still a simplification task and hence not suitable to be incorporated in a QA system (Bhagat and Hovy, 2013) .  ...  Paraphrasing for Question Answering There are several question paraphrasing corpora available for the general domain such as WikiAnswers (Fader et al., 2013) , PPDB (Ganitkevitch et al., 2013) , PPDB  ... 
doi:10.18653/v1/w19-5003 dblp:conf/bionlp/SoniR19 fatcat:ve3jgrld7zbadjujonardalz4i

Extraction of Lactation Frames from Drug Labels and LactMed

Heath Goodrum, Meghana Gudala, Ankita Misra, Kirk Roberts
2019 Proceedings of the 18th BioNLP Workshop and Shared Task  
The ultimate goal of the project is to use such a system to identify discrepancies in lactation-related drug information between these resources.  ...  Acknowledgements This work was supported in part by the U.S. National Library of Medicine under award R00LM012104.  ...  Most notably, frame semantics have been operationalized in the large-scale resource FrameNet (Baker et al., 1998 (Baker et al., , 2003 , though this resource is not specific to biomedicine.  ... 
doi:10.18653/v1/w19-5020 dblp:conf/bionlp/GoodrumGMR19 fatcat:pobu2mjonva77byusm77zvsfly

Leveraging Sublanguage Features for the Semantic Categorization of Clinical Terms

Leonie Grön, Ann Bertels, Kris Heylen
2019 Proceedings of the 18th BioNLP Workshop and Shared Task  
Acknowledgements This work was supported by Internal Funds KU Leuven.  ...  Related research Especially in emerging domains and under-resourced languages, domain corpora are a valuable resource for terminology development.  ...  In a real-life scenario, it is unlikely that resources would be available for the manual coding of term features.  ... 
doi:10.18653/v1/w19-5022 dblp:conf/bionlp/GronBH19 fatcat:ayb343fofngojdf7bzfmivn62u
« Previous Showing results 1 — 15 out of 408 results