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Enhancing the Performance of Feature Selection using a Hybrid Genetic Algorithm

N. Vanjulavalli, A. Kovalan
2015 International Journal of Computer Applications  
Ontologies help to overcome the disambiguate nature of the natural language by the use of standard terms that relate to specific concepts.  ...  In natural language, many words are ambiguous giving different meanings based on the context and situation.  ...  Ontologies used for Query Expansion Query expansion is the method of supplementing the user's query with additional terms to improve results during retrieval.  ... 
doi:10.5120/ijca2015905700 fatcat:nuefibci65cnzoxlweiokimidi

Biomedical ontologies in action: role in knowledge management, data integration and decision support

O Bodenreider
2008 IMIA Yearbook of Medical Informatics  
While ontologies are used primarily as a source of vocabulary for standardization and integration purposes, many applications also use them as a source of computable knowledge.  ...  Barriers to the use of ontologies in biomedical applications are discussed.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
pmid:18660879 pmcid:PMC2592252 fatcat:axl74koixzbffmfi6m3txvlwqu

Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

O. Bodenreider
2008 IMIA Yearbook of Medical Informatics  
While ontologies are used primarily as a source of vocabulary for standardization and integration purposes, many applications also use them as a source of computable knowledge.  ...  ); data integration, exchange and semantic interoperability; and decision support and reasoning (data selection and aggregation, decision support, natural language processing applications, knowledge discovery  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
doi:10.1055/s-0038-1638585 fatcat:r7vz4bruq5fpxa5nhhgcxohd2e

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience

M. Krallinger, F. Leitner, M. Vazquez, D. Salgado, C. Marcelle, M. Tyers, A. Valencia, A. Chatr-aryamontri
2012 Database: The Journal of Biological Databases and Curation  
Two ontologies that have been successfully used for this purpose are the Gene Ontology (GO) for annotating aspects of gene products and the Molecular Interaction ontology (PSI-MI) used by databases that  ...  Here, we provide a general overview of current text-mining methods to automatically extract annotations of GO and PSI-MI ontology terms in the context of the BioCreative (Critical Assessment of Information  ...  to determine the functional similarity between genes annotated with those terms.  ... 
doi:10.1093/database/bas017 pmid:22438567 pmcid:PMC3309177 fatcat:3q2zwcobxfaebl4rw4hsnddid4

Semantic Search based on the Online Integration of NLP Techniques

Katsuya Masuda, Takuya Matsuzaki, Jun'ichi Tsujii
2011 Procedia - Social and Behavioral Sciences  
This paper introduces a framework for semantic information retrieval based on the integration of various natural language processing (NLP) techniques, each of which annotates a base text with di erent  ...  The query language is based on a variant of the region algebra, in which we can specify a substructure in the annotated text that may involve different kinds of annotations.  ...  We plan to improve scoring methods by using a probabilistic model and automatic query construction methods using annotated informations.  ... 
doi:10.1016/j.sbspro.2011.10.609 fatcat:tw2fk5kcjnbdnih7gwtyncabam

FlexNER: A Flexible LSTM-CNN Stack Framework for Named Entity Recognition [article]

Hongyin Zhu, Wenpeng Hu, Yi Zeng
2019 arXiv   pre-print
We conduct experiments on five languages, such as English, German, Spanish, Dutch and Chinese, and biomedical fields, such as identifying the chemicals and gene/protein terms from scientific works.  ...  Inspired by the idea of distant supervision (DS), this paper enhances the representation by increasing the entity-context diversity without relying on external resources.  ...  Acknowledgement This study is supported by the Strategic Priority Research Program of Chinese Academy of Sciences (Grant No.XDB32070100).  ... 
arXiv:1908.05009v1 fatcat:zgl5pf5pyvghxjyo3oru7pukgq

Learning for Biomedical Information Extraction: Methodological Review of Recent Advances [article]

Feifan Liu, Jinying Chen, Abhyuday Jagannatha, Hong Yu
2016 arXiv   pre-print
In addition, we dive into open information extraction and deep learning, two emerging and influential techniques and envision next generation of BioIE.  ...  Unlike existing reviews covering a holistic view on BioIE, this review focuses on mainly recent advances in learning based approaches, by systematically summarizing them into different aspects of methodological  ...  Experiments of using CrowdTruth on medical relation extraction task show that the crowd performs just as well as medical experts in terms of quality and efficacy of annotation, and also indicate that at  ... 
arXiv:1606.07993v1 fatcat:7d5om7zxxzhoviiriasrfwg3xi

Gene ontology annotation as text categorization: An empirical study

Kazuhiro Seki, Javed Mostafa
2008 Information Processing & Management  
Our experiments reveal that round-robin feature space allocation with eliminating negative terms substantially improves performance as GO terms become specific.  ...  We extract the words around the spotted gene occurrences and used them to represent the gene for GO domain code annotation.  ...  Also, we are grateful to the anonymous reviewers for their insightful feedback, which significantly improved the manuscript.  ... 
doi:10.1016/j.ipm.2008.05.003 fatcat:qef2huauxvcujl3crtqqcplmqy

A robust data-driven approach for gene ontology annotation

Y. Li, H. Yu
2014 Database: The Journal of Biological Databases and Curation  
BioCreative IV GO annotation task aims to evaluate the performance of system that automatically assigns GO terms to genes based on the narrative sentences in biomedical literature.  ...  Gene ontology (GO) and GO annotation are important resources for biological information management and knowledge discovery, but the speed of manual annotation became a major bottleneck of database curation  ...  Conflict of interest. None declared.  ... 
doi:10.1093/database/bau113 pmid:25425037 pmcid:PMC4243380 fatcat:7cfhl42k25cvrl7ia32fpojkee

Elsevier's approach to the bioCADDIE 2016 Dataset Retrieval Challenge

Antony Scerri, John Kuriakose, Amit Ajit Deshmane, Mark Stanger, Peter Cotroneo, Rebekah Moore, Raj Naik, Anita de Waard
2017 Database: The Journal of Biological Databases and Curation  
One stream was based on the principle of word embeddings, the other was rooted in ontology based indexing.  ...  Despite encountering several issues in the data, the evaluation procedure and the technologies used, the system performed quite well.  ...  Using full queries as provided with the natural language query processor followed by unigram query construction against an un-stemmed/lemmatized index, using the single aggregated text field (automatic  ... 
doi:10.1093/database/bax056 pmid:29220454 pmcid:PMC5737073 fatcat:lc5p2glorrc53jmj2djtfank6u

Biomedical Concept Recognition Using Deep Neural Sequence Models [article]

Negacy D. Hailu, Michael Bada, Asmelash Teka Hadgu, Lawrence E. Hunter
2019 bioRxiv   pre-print
Results: recently, applications of deep learning in natural language processing have demonstrated striking improvements over previously state-of-the-art performance in many related natural language processing  ...  For example, our best performing system improves the performance of the previous state-of-the-art in recognizing terms in the Gene Ontology Biological Process hierarchy, from a previous best F1 score of  ...  Gene Ontology Molecular Function (GO_MF): molecular functionalities possessed by genes or gene products, as well as the molecular bearers of these functionalities 6.  ... 
doi:10.1101/530337 fatcat:gnoomzairjc7rpv6lrkh64js4a

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B. Kell, Sampo Pyysalo, Sophia Ananiadou
2013 Bioinformatics  
Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature.  ...  We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches  ...  ACKNOWLEDGEMENTS The authors thank Yonghwa Jo and Hyeyeon Choi for their contributions to the development of the relevance judgment annotation criteria.  ... 
doi:10.1093/bioinformatics/btt227 pmid:23813008 pmcid:PMC3694679 fatcat:uisraousjjdv5a7c4fmh3odjhq

What makes a gene name? Named entity recognition in the biomedical literature

U. Leser, J. Hakenberg
2005 Briefings in Bioinformatics  
The recognition of biomedical concepts in natural text (named entity recognition, NER) is a key technology for automatic or semi-automatic analysis of textual resources.  ...  Acknowledgments This work is supported by the German Federal Ministry of Education and Research (BMBF) under grant contract 0312705B.  ...  of machine learning and of natural language processing.  ... 
doi:10.1093/bib/6.4.357 pmid:16420734 fatcat:fflhkkovwnetnccqd2zfgvlo64

The semantic web: year one

J. Euzenat, A. Napoli
2003 IEEE Intelligent Systems  
These approaches have been debated representations to that of genes, gene classes, directly and the relevant features are class- for years and are still discussed to determine and gene interactions  ...  the expression erates a function from the former to the of pair-rule and homeotic genes.  ... 
doi:10.1109/mis.2003.1249173 fatcat:wdozz4alo5hhbhzedkmc4qyufq

Frontiers of biomedical text mining: current progress

P. Zweigenbaum, D. Demner-Fushman, H. Yu, K. B. Cohen
2007 Briefings in Bioinformatics  
However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research.  ...  Some problems, such as abbreviationhandling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon.  ...  We wish to thank the journal's anonymous reviewers, whose insightful comments helped significantly improve this article.  ... 
doi:10.1093/bib/bbm045 pmid:17977867 pmcid:PMC2516302 fatcat:4nfbokb7lfdjbnkijw2v6754qy
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