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A set of domain rules and a deep network for protein coreference resolution

Chen Li, Zhiqiang Rao, Qinghua Zheng, Xiangrong Zhang
2018 Database: The Journal of Biological Databases and Curation  
A set of domain rules and a deep network for protein coreference resolution. Abstract Current research of bio-text mining mainly focuses on event extractions.  ...  The first is a rule-based method, which creates a set of syntactic rules or semantic constraints for CR.  ...  So we explore a deep learning method to solve the protein CR task without hand-craft rules and too many features.  ... 
doi:10.1093/database/bay065 pmid:30010737 pmcid:PMC6041745 fatcat:xpx2b4ojmngsbj2mmctnbg6rcm

Coreference Resolution for the Biomedical Domain: A Survey [article]

Pengcheng Lu, Massimo Poesio
2021 arXiv   pre-print
Thus, the biomedical genre has long been the second most researched genre for coreference resolution after the news domain, and the subject of a great deal of research for NLP in general.  ...  Issues with coreference resolution are one of the most frequently mentioned challenges for information extraction from the biomedical literature.  ...  Acknowledgements This research was supported in part by the China Scholarship Council, and the DALI project, ERC Grant 695662.  ... 
arXiv:2109.12424v1 fatcat:tsuinvv5snburjgkkqkzyxoeky

Distinguished representation of identical mentions in bio-entity coreference resolution

Yufei Li, Xiangyu Zhou, Jie Ma, Xiaoyong Ma, Pengzhen Cheng, Tieliang Gong, Chen Li
2022 BMC Medical Informatics and Decision Making  
Results The experimental results show that the proposed model brings significant improvements on most of the baseline for coreference resolution and mention detection on the BioNLP dataset and CRAFT-CR  ...  Background Bio-entity Coreference Resolution (CR) is a vital task in biomedical text mining.  ...  rules, (2) hybrid models [13, 14] , which combine rule-based and machine learningbased methods for biomedical coreference resolution, (3) neural network-based models [7] [8] [9] [10] , which use deep  ... 
doi:10.1186/s12911-022-01862-1 pmid:35501781 pmcid:PMC9063119 fatcat:6e7addl6jvaaxoazwwidbwngma

Anaphora and Coreference Resolution: A Review [article]

Rhea Sukthanker, Soujanya Poria, Erik Cambria, Ramkumar Thirunavukarasu
2018 arXiv   pre-print
The area of entity resolution in NLP has seen proliferation of research in two separate sub-areas namely: anaphora resolution and coreference resolution.  ...  Entity resolution aims at resolving repeated references to an entity in a document and forms a core component of natural language processing (NLP) research.  ...  The Protein Coreference resolution task was a part of BioNLP-2011 shared task (Kim et al, 2011) .  ... 
arXiv:1805.11824v1 fatcat:ighrkr6f2nexphrw3qfojatmde

Scalable Bio-Molecular Event Extraction System towards Knowledge Acquisition

Pattabhi Rk Rao, Sindhuja Gopalan, Sobha Lalitha Devi
2017 International Conference on Natural Language Processing  
The system includes a robust anaphora and coreference resolution module, developed as part of this work.  ...  This paper presents a robust system for the automatic extraction of bio-molecular events from scientific texts.  ...  We have developed a biomedical domain anaphora coreference resolution module for resolving the protein coreference relations.  ... 
dblp:conf/icon-nlp/RaoGD17 fatcat:skgoptqgyvgifhfxstu5r3wama

Neural Mention Detection [article]

Juntao Yu, Bernd Bohnet, Massimo Poesio
2020 arXiv   pre-print
The first approach is based on the mention detection part of a state of the art coreference resolution system; the second uses ELMO embeddings together with a bidirectional LSTM and a biaffine classifier  ...  We then evaluate our models for coreference resolution by using mentions predicted by our best model in start-of-the-art coreference systems.  ...  The CONLL data set is the standard reference corpora for coreference resolution. The English subset consists of 2802, 342, and 348 documents for the train, development and test sets respectively.  ... 
arXiv:1907.12524v2 fatcat:bzrrxtyw2jgh3ozj3eaoldfqky

Swanson linking revisited: Accelerating literature-based discovery across domains using a conceptual influence graph

Gus Hahn-Powell, Marco A. Valenzuela-Escárcega, Mihai Surdeanu
2017 Proceedings of ACL 2017, System Demonstrations  
We introduce a modular approach for literature-based discovery consisting of a machine reading and knowledge assembly component that together produce a graph of influence relations (e.g., "A promotes B  ...  We demonstrate that this deep reading and search system reduces the effort needed to uncover "undiscovered public knowledge", and that with the aid of this tool a domain expert was able to drastically  ...  This interest has been properly disclosed to the University of Arizona Institutional Review Committee and is managed in accordance with its conflict of interest policies.  ... 
doi:10.18653/v1/p17-4018 dblp:conf/acl/Hahn-PowellVS17 fatcat:zydizkienbcedpdyunh55mqpum

Natural Language Processing for Information Extraction [article]

Sonit Singh
2018 arXiv   pre-print
Various sub-tasks of IE such as Named Entity Recognition, Coreference Resolution, Named Entity Linking, Relation Extraction, Knowledge Base reasoning forms the building blocks of various high end Natural  ...  This explosion of information and need for more sophisticated and efficient information handling tools gives rise to Information Extraction(IE) and Information Retrieval(IR) technology.  ...  State-of-the-art in Coreference Resolution (CR) Coreference Resolution (CR) is the process of linking together multiple expressions of a given entity.  ... 
arXiv:1807.02383v1 fatcat:3bdyidbjp5hn7c2w4iqve4ajvi

Bridging Chasms In Hindustani Music Retrieval

Joe Cheri Ross, Preeti Rao, Pushpak Bhattacharyya
2018 Zenodo  
This research is motivated by the importance of a music recommendation system for Hindustani music.  ...  Our investigation on extracting meta-information from natural language text focuses on coreference resolution, with the aim of improving relation extraction from textual content.  ...  Recently, there were a few studies on applying deep learning for coreference resolution.  ... 
doi:10.5281/zenodo.1237568 fatcat:mrshrvhbcbb2lf4n7gys6e6plq

Bridging Chasms In Hindustani Music Retrieval

Joe Cheri Ross, Preeti Rao, Pushpak Bhattacharyya
2018 Zenodo  
This research is motivated by the importance of a music recommendation system for Hindustani music.  ...  Our investigation on extracting meta-information from natural language text focuses on coreference resolution, with the aim of improving relation extraction from textual content.  ...  Recently, there were a few studies on applying deep learning for coreference resolution.  ... 
doi:10.5281/zenodo.1239418 fatcat:uix3v2agqrajtcdrn5wm74tnq4

OUP accepted manuscript

2018 Database: The Journal of Biological Databases and Curation  
PubMed, a repository and search engine for biomedical literature, now indexes more than 1 million articles each year.  ...  We present Reach, a system for automated, large-scale machine reading of biomedical papers that can extract mechanistic descriptions of biological processes with relatively high precision at high throughput  ...  We are especially grateful to Tonia Korves and Lynette Hirschman for making these results available before their publication, and for the many clarification discussions.  ... 
doi:10.1093/database/bay098 fatcat:xpnrphqq6jgsbeuafu5pogr2uq

Coreference resolution: A review of general methodologies and applications in the clinical domain

Jiaping Zheng, Wendy W. Chapman, Rebecca S. Crowley, Guergana K. Savova
2011 Journal of Biomedical Informatics  
Our goal was to review recent advances in general purpose coreference resolution to lay the foundation for methodologies in the clinical domain, facilitated by the availability of a shared lexical resource  ...  Research on coreference resolution in the general English domain dates back to 1960s and 1970s. However, research on coreference resolution in the clinical free text has not seen major development.  ...  Acknowledgment The work was funded by Grant R01 CA127979 (The ODIE toolkit-software for Ontology Development and Information Extraction).  ... 
doi:10.1016/j.jbi.2011.08.006 pmid:21856441 pmcid:PMC3226856 fatcat:3t4j5t4fvvbrjlezjlirx3gz6e

Wide-coverage relation extraction from MEDLINE using deep syntax

Nhung TH Nguyen, Makoto Miwa, Yoshimasa Tsuruoka, Takashi Chikayama, Satoshi Tojo
2015 BMC Bioinformatics  
The entire collection of the relations extracted from MEDLINE is publicly available in machine-readable form, so that it can serve as a potential knowledge base for high-level text-mining applications.  ...  The extracted relations provide a quantitative understanding of what kinds of semantic relations are actually described in MEDLINE and can be ultimately extracted by (possibly type-specific) relation extraction  ...  Nguyen and Hoang Q. Vu for their careful work and fruitful feedback.  ... 
doi:10.1186/s12859-015-0538-8 pmid:25887686 pmcid:PMC4396593 fatcat:duue2xsssvblnghcoyqaxjym54

Bridging semantics and syntax with graph algorithms—state-of-the-art of extracting biomedical relations

Yuan Luo, Özlem Uzuner, Peter Szolovits
2017 Briefings in Bioinformatics  
In particular, they developed a rule-based coreference resolution system that consists of detecting rules for mention, antecedent and coreferential link.  ...  However, many of the reviewed approaches for relation and event extraction did not have a built-in coreference resolution component. Miwa et al.  ...  [118] No Association distance between pair of entities in a semantic network. No Chem2Bio2RDF [119] No Bui et al.  ... 
doi:10.1093/bib/bbx048 pmid:28472242 pmcid:PMC6080366 fatcat:3pu74myraffsnjttvnlgoy6kqq

Bridging semantics and syntax with graph algorithms—state-of-the-art of extracting biomedical relations

Yuan Luo, Özlem Uzuner, Peter Szolovits
2016 Briefings in Bioinformatics  
However, a number of problems at the frontiers of biomedical relation extraction continue to pose interesting challenges and present opportunities for great improvement and fruitful research.  ...  The ability to accurately capture both semantic and syntactic structures in text expressing these relations becomes increasingly critical to enable deep understanding of scientific papers and clinical  ...  for Cancer Data Analysis.  ... 
doi:10.1093/bib/bbw001 pmid:26851224 pmcid:PMC5221425 fatcat:z6sptxngubempdx6kthsyab7be
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