Open AccessProceedings Article
Overview of BioNLP Shared Task 2013
Claire Nédellec,Robert Bossy,Jin-Dong Kim,Jung-Jae Kim,Tomoko Ohta,Sampo Pyysalo,Pierre Zweigenbaum +6 more
- pp 1-7
TLDR
The BioNLP Shared Task 2013 shows advances in the state of the art and demonstrates that extraction methods can be successfully generalized in various aspects.Citations
More filters
Posted Content
NER-BERT: A Pre-trained Model for Low-Resource Entity Tagging.
TL;DR: Zhang et al. as mentioned in this paper constructed a massive NER corpus with a relatively high quality, and they pre-trained a NER-BERT model based on the created dataset.
Posted Content
In Layman's Terms: Semi-Open Relation Extraction from Scientific Texts
TL;DR: In this paper, the authors combine the output of both types of systems to achieve Semi-Open Relation Extraction, a new task that they explore in the Biology domain. But narrow IE systems extract only a fraction of the information captured, and Open IE systems do not perform well on the long and complex sentences encountered in scientific texts.
Posted Content
Extracting Biological Pathway Models From NLP Event Representations
TL;DR: This paper describes an an open-source software system for the automatic conversion of NLP event representations to system biology structured data interchange formats such as SBML and BioPAX.
Proceedings Article
Improving clinical document understanding on COVID-19 research with spark NLP
Veysel Kocaman,David Talby +1 more
TL;DR: In this paper, a clinical text mining system is presented, which can recognize over 100 different entity types including social determinants of health, anatomy, risk factors, and adverse events in addition to other commonly used clinical and biomedical entities.
Proceedings ArticleDOI
GADGET: Using Gated GRU for Biomedical Event Trigger Detection
TL;DR: This paper proposes a novel model based on gate mechanism, which identifies trigger and non-trigger words in the first stage, and introduces additional fusion layer in order to incorporate sentence level information for event trigger detection.
References
More filters
Proceedings ArticleDOI
Coarse-to-Fine n-Best Parsing and MaxEnt Discriminative Reranking
Eugene Charniak,Mark Johnson +1 more
TL;DR: This paper describes a simple yet novel method for constructing sets of 50- best parses based on a coarse-to-fine generative parser that generates 50-best lists that are of substantially higher quality than previously obtainable.
Proceedings ArticleDOI
Overview of BioNLP'09 Shared Task on Event Extraction
TL;DR: The design and implementation of the BioNLP'09 Shared Task is presented, indicating that state-of-the-art performance is approaching a practically applicable level and revealing some remaining challenges.
Performance measures for information extraction
TL;DR: An error measure is defined, the slot error rate, which combines the different types of error directly, without having to resort to precision and recall as preliminary measures.
Book ChapterDOI
PANTHER Pathway: An Ontology-Based Pathway Database Coupled with Data Analysis Tools
Huaiyu Mi,Paul Thomas +1 more
TL;DR: This chapter first discusses how biological knowledge is represented, particularly the importance of ontologies or standards in systems biology research, and uses PANTHER Pathway as an example to illustrate how ontologies and standards play a role in data modeling, data entry, and data display.
Journal ArticleDOI
Evaluating temporal relations in clinical text: 2012 i2b2 Challenge.
TL;DR: A corpus of discharge summaries annotated with temporal information was provided to be used for the development and evaluation of temporal reasoning systems, and the best systems overwhelmingly adopted a rule based approach for value normalization.