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A Unified Framework of Medical Information Annotation and Extraction for Chinese Clinical Text
[article]
2022
arXiv
pre-print
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Specifically, the annotation scheme is comprehensive, and compatible between tasks, especially for the medical relations. ...
This study presents an engineering framework of medical entity recognition, relation extraction and attribute extraction, which are unified in annotation, modeling and evaluation. ...
We highly appreciate the constructive comments on the annotation scheme by Xiaofen Zhao. We sincerely thank Xin Wei for his efforts in EMR data cleaning and parsing. ...
arXiv:2203.03823v1
fatcat:gwc3634ahbev7be76azgc5vbna
tieval: An Evaluation Framework for Temporal Information Extraction Systems
2023
Proceedings of the 46th International ACM SIGIR Conference on Research and Development in Information Retrieval
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On the one hand, different datasets have different annotation schemes, which hinders the comparison between competitors across different corpora. ...
While most research works adopt traditional metrics such as precision, recall, and 𝐹 1 , a few others prefer temporal awareness -a metric tailored to be more comprehensive on the evaluation of temporal ...
ACKNOWLEDGMENTS We would like to acknowledge the financial support received during the development of this project. ...
doi:10.1145/3539618.3591892
fatcat:5heg6iemsvadhomu6nm3pmxwbe
tieval: An Evaluation Framework for Temporal Information Extraction Systems
[article]
2023
arXiv
pre-print
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On the one hand, different datasets have different annotation schemes, thus hindering the comparison between competitors across different corpora. ...
While most research works adopt traditional metrics such as precision, recall, and F_1, a few others prefer temporal awareness – a metric tailored to be more comprehensive on the evaluation of temporal ...
Some used the TimeML annotation scheme to create new corpora, such as AQUAINT Graff [2002] and the Platinum corpus UzZaman et al. ...
arXiv:2301.04643v1
fatcat:5s47vuzxifapzb2ptmss5etl5u
Annotated Corpora and Annotation Tools
[chapter]
2016
Anaphora Resolution
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In this Chapter we review the currently available corpora to study anaphoric interpretation, and the tools that can be used to create new ones. ...
Acknowledgements This work was supported in part by a PhD studentship offered by Cogito / Expert Systems (Kepa Rodriguez), in part by the LIVEMEMORIES project (Poesio), and in part by the SENSEI project ...
In some of these schemes (including ACE, GNOME, and ARRAU), special attributes are used to mark the semantic function of the markable. ...
doi:10.1007/978-3-662-47909-4_4
dblp:series/tanlp/PoesioPRRV16
fatcat:4dnly5kz6zar7bfboduulhu66a
Coreference Annotation in the Russian Clinical Pear Stories Corpus: Annotation Features and Preliminary Results
2016
Social Science Research Network
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of an entity, and the inclusion of epistemic markers into NPs. ...
The study summarizes the comprehensive annotation schema developed for this task and the preliminary research of the referential choice features based on the corpus. ...
We took the ready-made scheme used for corpora annotation in NLP tasks. ...
doi:10.2139/ssrn.2885814
fatcat:g3mfagwcnzfp5hrxhciacg7fai
A French clinical corpus with comprehensive semantic annotations: development of the Medical Entity and Relation LIMSI annOtated Text corpus (MERLOT)
2017
Language Resources and Evaluation
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Six annotators contributed to the corpus annotation, using a comprehensive annotation scheme covering 21 entities, 11 attributes and 37 relations. ...
All annotators trained on a small, common portion of the corpus before proceeding independently. An automatic tool was used to produce entity and attribute pre-annotations. ...
The authors specially wish to acknowledge Dr. Griffon for his critical appraisal of the annotation scheme and its application to the corpus. ...
doi:10.1007/s10579-017-9382-y
fatcat:gujff6rkqveklm3snqigp55364
Corpora for computational linguistics Corpora for computational linguistics
2008
Ilha do Desterro
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This paper offers a survey of how they are currently used in different fields of the discipline, with particular emphasis on anaphora and coreference resolution, automatic summarisation and term extraction ...
This paper offers a survey of how they are currently used in different fields of the discipline, with particular emphasis on anaphora and coreference resolution, automatic summarisation and term extraction ...
The annotation process requires the markup in text of items that have a special meaning for some purpose, using an annotation scheme. ...
doaj:13213d8008b948a5959e49ccf3d045f8
fatcat:iyq6iauxevf4bpx3lalo575f3q
hPP Corpus: A Tagged Biomedical Corpus for Automatic Extraction of Human Protein Phosphorylation for Understanding Cellular Functions
2020
Journal of Embryology & Stem Cell Research
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The corpus is annotated with named entities, event relationship and syntactic dependencies, and freely available at http:// www.biominingbu.org/hPPcorpus/hPP_corpus.xml. ...
Text mining researchers apply a variety of algorithms to extract such information. A standard annotated corpus is necessary to evaluate the performance of the text mining algorithms. ...
(iv) to confirm the event relationship between the related entities using a set of annotation rules. ...
doi:10.23880/jes-16000140
fatcat:nkz7treybnaqpmkgfqn2666nqi
BioInfer: a corpus for information extraction in the biomedical domain
2007
BMC Bioinformatics
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We describe an annotation scheme capturing named entities and their relationships along with a dependency analysis of sentence syntax. ...
The development and evaluation of such methods requires annotated domain corpora. ...
We are also grateful to Meelis Kolmer and Mauno Vihinen for consultation in creating the bioentity and relationship annotation schemes. ...
doi:10.1186/1471-2105-8-50
pmid:17291334
pmcid:PMC1808065
fatcat:hbjyjjsu4zhu7j67jn2l3obhya
KLUE: Korean Language Understanding Evaluation
[article]
2021
arXiv
pre-print
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KLUE is a collection of 8 Korean natural language understanding (NLU) tasks, including Topic Classification, SemanticTextual Similarity, Natural Language Inference, Named Entity Recognition, Relation Extraction ...
We make a few interesting observations from the preliminary experiments using the proposed KLUE benchmark suite, already demonstrating the usefulness of this new benchmark suite. ...
annotators in MRC dataset, and Sangah Park for careful consideration of data construction in DP, NER, and RE. ...
arXiv:2105.09680v4
fatcat:ejkvhzfldzhcbkhw4eakm7s634
PKDE4J: Entity and relation extraction for public knowledge discovery
2015
Journal of Biomedical Informatics
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In this paper, we present PKDE4J, a comprehensive text-mining system that integrates dictionary-based entity extraction and rule-based relation extraction in a highly flexible and extensible framework. ...
We demonstrate its competitive performance by evaluating it on many corpora and found that it surpasses existing systems with average F-measures of 85% for entity extraction and 81% for relation extraction ...
Acknowledgments This work was supported by the Bio-Synergy Research Project (NRF-2013M3A9C4078138) of the Ministry of Science, ICT, and Future Planning through the National Research Foundation. ...
doi:10.1016/j.jbi.2015.08.008
pmid:26277115
fatcat:sfgmji7zu5efbbo6xyarry7h4e
NEREL-BIO: A Dataset of Biomedical Abstracts Annotated with Nested Named Entities
[article]
2022
arXiv
pre-print
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Thus, NEREL-BIO comprises the following specific features: annotation of nested named entities, it can be used as a benchmark for cross-domain (NEREL -> NEREL-BIO) and cross-language (English -> Russian ...
This paper describes NEREL-BIO -- an annotation scheme and corpus of PubMed abstracts in Russian and smaller number of abstracts in English. ...
The authors thank all annotators for their contribution and Zulfat Miftahutdinov for his work on models trained on the MedMentions corpus. ...
arXiv:2210.11913v1
fatcat:n5qlhr5cknfu7gqkln54lso6ju
Constructing fine-grained entity recognition corpora based on clinical records of traditional Chinese medicine
2020
BMC Medical Informatics and Decision Making
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The final fine-grained annotated entity corpus consists of 1104 entities and 67,799 tokens. ...
We iteratively updated the guidelines until the inter-annotator agreement (IAA) exceeded a Cohen's kappa value of 0.9. Comprehensive annotations were performed while keeping the IAA value above 0.9. ...
The authors are grateful to the editor's and the reviewers' comments that help us to improve the quality and merit of this paper. ...
doi:10.1186/s12911-020-1079-2
pmid:32252745
fatcat:dcktu2lgejcjnliwrivzxlpgd4
An In-Depth Evaluation of Federated Learning on Biomedical Natural Language Processing
[article]
2023
arXiv
pre-print
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2023 pre-print arXiv:2307.11254v1 fatcat:j3s4yszjtnhilop3g5ti5wlzce
In this study, we evaluated FL on 2 biomedical NLP tasks encompassing 8 corpora using 6 LMs. ...
models using zero-/one-shot learning and offered lightning inference speed. ...
Three experts were used to annotate a set of 100 abstracts for each of the drug-disorder, drugtarget, and target-disorder relations. ...
arXiv:2307.11254v2
fatcat:nm6ljllrcjhszn4dyxx5jsfrri
JCBIE: a joint continual learning neural network for biomedical information extraction
2022
BMC Bioinformatics
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Previous biomedical knowledge extraction methods simply considered limited entity types and relations by using a task-specific training set, which is insufficient for large-scale BKGs development and downstream ...
Specifically, it allows us to adopt entity augmented inputs to establish the interaction between named entity recognition and relation extraction. ...
All auhtors read and approved the final manuscript. ...
doi:10.1186/s12859-022-05096-w
pmid:36536280
pmcid:PMC9761970
fatcat:jakzw44pujgx7himt5zmyeqlui
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