scholarly journals Coner: A Collaborative Approach for Long-Tail Named Entity Recognition in Scientific Publications

2019 ◽  
pp. 3-17
Author(s):  
Daniel Vliegenthart ◽  
Sepideh Mesbah ◽  
Christoph Lofi ◽  
Akiko Aizawa ◽  
Alessandro Bozzon
Keyword(s):  
Named Entity Recognition ◽  
Entity Recognition ◽  
Collaborative Approach ◽  
Scientific Publications ◽  
Long Tail ◽  
Named Entity

scholarly journals Unsupervised Technique for Automatically Extracting Components of References

2020 ◽  
Vol 9 (1) ◽  
pp. 1000-1004
Keyword(s):  
Machine Learning ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Supervised Machine Learning ◽  
Machine Learning Techniques ◽  
Scientific Publications ◽  
Standard Format ◽  
Named Entity ◽  
Learning Techniques ◽  
The Individual

The automatic extraction of bibliographic data remains a difficult task to the present day, when it's realized that the scientific publications are not in a standard format and every publications has its own template. There are many “regular expression” techniques and “supervised machine learning” techniques for extracting the entire details of the references mentioned within the bibliographic section. But there's no much difference within the percentage of their success. Our idea is to seek out whether unsupervised machine learning techniques can help us in increasing the share of success. This paper presents a technique for segregating and automatically extracting the individual components of references like Authors, Title of the references, publications details, etc., using “Unsupervised technique”, “Named-Entity recognition”(NER) technique and link these references to their corresponding full text article with the assistance of google

scholarly journals FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining

2017 ◽  
Author(s):  
John A Bachman ◽  
Benjamin M Gyori ◽  
Peter K Sorger
Keyword(s):  
Molecular Mechanisms ◽  
Named Entity Recognition ◽  
Biomedical Literature ◽  
Hierarchical Organization ◽  
Event Extraction ◽  
Entity Recognition ◽  
Biomedical Text ◽  
Protein Families ◽  
Scientific Publications ◽  
Named Entity

AbstractBackgroundFor automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers, a process known as named entity linking or “grounding.” Correct grounding is essential for resolving relationships among mined information, curated interaction databases, and biological datasets. The accuracy of this process is largely dependent on the availability of machine-readable resources associating synonyms and abbreviations commonly found in biomedical literature with uniform identifiers.ResultsIn a task involving automated reading of ∼215,000 articles using the REACH event extraction software we found that grounding was disproportionately inaccurate for multi-protein families (e.g., “AKT”) and complexes with multiple subunits (e.g.”NF-κB”). To address this problem we constructed FamPlex, a manually curated resource defining protein families and complexes as they are commonly encountered in biomedical text. In FamPlex the gene-level constituents of families and complexes are defined in a flexible format allowing for multi-level, hierarchical membership. To create FamPlex, text strings corresponding to entities were identified empirically from literature and linked manually to uniform identifiers; these identifiers were also mapped to equivalent entries in multiple related databases. FamPlex also includes curated prefix and suffix patterns that improve named entity recognition and event extraction. Evaluation of REACH extractions on a test corpus of ∼54,000 articles showed that FamPlex significantly increased grounding accuracy for families and complexes (from 15% to 71%). The hierarchical organization of entities in FamPlex also made it possible to integrate otherwise unconnected mechanistic information across families, subfamilies, and individual proteins. Applications of FamPlex to the TRIPS/DRUM reading system and the Biocreative VI Bioentity Normalization Task dataset demonstrated the utility of FamPlex in other settings.ConclusionFamPlex is an effective resource for improving named entity recognition, grounding, and relationship resolution in automated reading of biomedical text. The content in FamPlex is available in both tabular and Open Biomedical Ontology formats at https://github.com/sorgerlab/famplex under the Creative Commons CC0 license and has been integrated into the TRIPS/DRUM and REACH reading systems.

Arabic named entity recognition using optimized feature sets

2008 ◽  
Author(s):  
Yassine Benajiba ◽  
Mona Diab ◽  
Paolo Rosso
Keyword(s):  
Named Entity Recognition ◽  
Entity Recognition ◽  
Feature Sets ◽  
Named Entity

Developing a RadLex-based Named Entity Recognition Tool for Mining Textual Radiology Reports (Preprint)

2020 ◽  
Author(s):  
Shintaro Tsuji ◽  
Andrew Wen ◽  
Naoki Takahashi ◽  
Hongjian Zhang ◽  
Katsuhiko Ogasawara ◽  
...  
Keyword(s):  
Named Entity Recognition ◽  
Noun Phrases ◽  
General Purpose ◽  
Entity Recognition ◽  
Free Text ◽  
Clinical Text ◽  
Named Entity ◽  
Radiology Reports ◽  
Two Measures ◽  
F Measure

BACKGROUND Named entity recognition (NER) plays an important role in extracting the features of descriptions for mining free-text radiology reports. However, the performance of existing NER tools is limited because the number of entities depends on its dictionary lookup. Especially, the recognition of compound terms is very complicated because there are a variety of patterns. OBJECTIVE The objective of the study is to develop and evaluate a NER tool concerned with compound terms using the RadLex for mining free-text radiology reports. METHODS We leveraged the clinical Text Analysis and Knowledge Extraction System (cTAKES) to develop customized pipelines using both RadLex and SentiWordNet (a general-purpose dictionary, GPD). We manually annotated 400 of radiology reports for compound terms (Cts) in noun phrases and used them as the gold standard for the performance evaluation (precision, recall, and F-measure). Additionally, we also created a compound-term-enhanced dictionary (CtED) by analyzing false negatives (FNs) and false positives (FPs), and applied it for another 100 radiology reports for validation. We also evaluated the stem terms of compound terms, through defining two measures: an occurrence ratio (OR) and a matching ratio (MR). RESULTS The F-measure of the cTAKES+RadLex+GPD was 32.2% (Precision 92.1%, Recall 19.6%) and that of combined the CtED was 67.1% (Precision 98.1%, Recall 51.0%). The OR indicated that stem terms of “effusion”, "node", "tube", and "disease" were used frequently, but it still lacks capturing Cts. The MR showed that 71.9% of stem terms matched with that of ontologies and RadLex improved about 22% of the MR from the cTAKES default dictionary. The OR and MR revealed that the characteristics of stem terms would have the potential to help generate synonymous phrases using ontologies. CONCLUSIONS We developed a RadLex-based customized pipeline for parsing radiology reports and demonstrated that CtED and stem term analysis has the potential to improve dictionary-based NER performance toward expanding vocabularies.

Identification of Food Quality Descriptors in Customer Chat Conversations using Named Entity Recognition

2020 ◽  
Author(s):  
Aditya Kiran Brahma ◽  
Prathyush Potluri ◽  
Meghana Kanapaneni ◽  
Sumanth Prabhu ◽  
Sundeep Teki
Keyword(s):  
Food Quality ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Named Entity
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