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An Interaction Pattern Kernel Approach for Protein-Protein Interaction Extraction from Biomedical Literature
[chapter]
2014
Lecture Notes in Computer Science
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text features for PPI extraction. ...
. Among biomedical relation types, protein-protein interaction (PPI) extraction is becoming critical in the field of molecular biology due to demands for automatic discovery of molecular pathways and ...
Thanks for listening! ...
doi:10.1007/978-3-319-13987-6_4
fatcat:icvbitylmvfqbatlrmygm35lce
Extracting Protein-Protein Interaction from Biomedical Text Using Additional Shallow Parsing Information
2009
2009 2nd International Conference on Biomedical Engineering and Informatics
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This paper explores protein-protein interaction extraction from biomedical literature using Support Vector Machines (SVM). ...
Besides common lexical features, various overlap features and base phrase chunking information are used to improve the performance. ...
For future work, we will further investigate deep syntactic information from full parse trees and dependency trees for feature-based protein-protein interaction extraction. ...
doi:10.1109/bmei.2009.5302220
dblp:conf/bmei/YuQZZ09
fatcat:6kbvvffejzg3jhnhg6vk6kxt7u
Linguistic feature analysis for protein interaction extraction
2009
BMC Bioinformatics
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The rapid growth of the amount of publicly available reports on biomedical experimental results has recently caused a boost of text mining approaches for protein interaction extraction. ...
., lexical and syntactic, data extracted from text. However, only few attempts have been made to evaluate the contribution of the different feature types. ...
To the best of our knowledge, besides us, only [7] [8] [9] have looked into the impact of syntactic in addition to lexical features for the protein interaction extraction task (all in the context of ...
doi:10.1186/1471-2105-10-374
pmid:19909518
pmcid:PMC2781821
fatcat:pw2ro6fkmrcmvls2rz6kixrtra
Distributed smoothed tree kernel for protein-protein interaction extraction from the biomedical literature
2017
PLoS ONE
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Automatic extraction of protein-protein interaction (PPI) pairs from biomedical literature is a widely examined task in biological information extraction. ...
In this paper, we present a special type of tree kernel for PPI extraction which exploits both syntactic (structural) and semantic vectors information known as Distributed Smoothed Tree kernel (DSTK). ...
[18] examined the combination of lexical, syntactic and dependency information based features for PPI extraction. ...
doi:10.1371/journal.pone.0187379
pmid:29099838
pmcid:PMC5669485
fatcat:z3i4byob55hwlenus43pmdr6qu
Automatic Extraction of Protein Interaction in Literature
[article]
2014
arXiv
pre-print
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2014 pre-print arXiv:1406.1953v1 fatcat:dqgqtyrcazd57m4wfwt66vq6f4
The results show that dependency features are import for the protein-protein interaction extraction and features related to the interaction word are effective for the interaction direction judgment. ...
Protein-protein interaction extraction is the key precondition of the construction of protein knowledge network, and it is very important for the research in the biomedicine. ...
Then, this paper extracted some features related to the interaction word, and decided the interaction direction, which provided more effective information for the construction of protein knowledge network ...
arXiv:1406.1953v2
fatcat:uln33dq6sreynemnjpfyz5vcxu
The role of syntactic features in protein interaction extraction
2008
Proceeding of the 2nd international workshop on Data and text mining in bioinformatics - DTMBIO '08
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Most approaches for protein interaction mining from biomedical texts use both lexical and syntactic features. ...
To this end, we strip this approach down to an algorithm that uses only a subset of the initial syntactic features. ...
Acknowledgement Chris Cornelis would like to thank the Research Foundation-Flanders for funding his research. ...
doi:10.1145/1458449.1458463
dblp:conf/cikm/FayruzovCCH08
fatcat:zy3qbuv24bhytck4u2zzm62c6a
DEEPER: A Full Parsing Based Approach to Protein Relation Extraction
[chapter]
2008
Lecture Notes in Computer Science
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Evaluation on benchmark datasets shows that our method is competitive with existing state-of-the-art algorithms for the extraction of protein interactions. ...
machine learning algorithms in deciding whether a sentence describes a protein interaction or not. ...
Acknowledgement Chris Cornelis would like to thank the Research Foundation{Flanders for funding his research. ...
doi:10.1007/978-3-540-78757-0_4
fatcat:nvrmmvojzfh77n642465eozcsa
Protein-Protein Interaction Extraction Based on Convex Combination Kernel Function
2013
Journal of Computer and Communications
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Owing to the effect of classified models was different in Protein-Protein Interaction (PPI) extraction, which was made by different single kernel functions, and only using single kernel function hardly ...
Finally, extracting PPI using the classified model made by this kernel function. ...
The phrase syntactic features selected specifically: Syntactic tree feature 1: the common root class of two proteins Syntactic tree feature 2: the number of nodes forms the first protein to the root protein ...
doi:10.4236/jcc.2013.15002
fatcat:y3vghaqaybbhzc5bmdxwfoukn4
LPInsider: a webserver for lncRNA–protein interaction extraction from the literature
2022
BMC Bioinformatics
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Results LPInsider is developed as the first webserver for extracting LPIs from biomedical literature texts based on multiple text features (semantic word vectors, syntactic structure vectors, distance ...
Identifying LncRNA–protein interactions (LPIs) is essential to understand the molecular mechanism and infer the functions of lncRNAs. ...
Therefore, the logistic regression classifier trained by LPI Corpus is used for lncRNA-protein interaction extraction. ...
doi:10.1186/s12859-022-04665-3
pmid:35428172
pmcid:PMC9013167
fatcat:4b46ziz73zfqzavjsezfofgd7m
Integrating Semantic Information into Multiple Kernels for Protein-Protein Interaction Extraction from Biomedical Literatures
2014
PLoS ONE
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Protein-Protein Interaction (PPI) extraction is an important task in the biomedical information extraction. ...
Presently, many machine learning methods for PPI extraction have achieved promising results. However, the performance is still not satisfactory. ...
[4] investigated the combination of diverse lexical, syntactic and particularly dependency information for feature-based protein-protein interaction extraction using SVM, achieving a promising F-score ...
doi:10.1371/journal.pone.0091898
pmid:24622773
pmcid:PMC3951470
fatcat:due44tp6wzgzbn235fpm3lgkgq
A Composite Kernel Approach for Detecting Interactive Segments in Chinese Topic Documents
[chapter]
2013
Lecture Notes in Computer Science
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What is person interactions?? Such interactions exemplify types of human behavior that make people consider each other or influence each other. ...
Examples of person interactions include compliments, criticism, collaboration, and competition. ...
, N.: Combining lexical, syntactic, and semantic features with maximum entropy models for extracting relations. ...
doi:10.1007/978-3-642-45068-6_19
fatcat:qezqyqo75fc5xbmpr3tyoeaio4
Detecting Protein-Protein Interactions in Biomedical Texts Using a Parser and Linguistic Resources
[chapter]
2009
Lecture Notes in Computer Science
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After automatically parsing the GENIA corpus, which is manually annotated for proteins, all syntactic paths between proteins are extracted. ...
We use a syntactic parser, a corpus annotated for proteins, and manual decisions as training material. ...
To extract meaningful features for the model construction, dependency parsing is often used. [7] extract sentences in which two proteins and an interaction word co-occur. ...
doi:10.1007/978-3-642-00382-0_33
fatcat:fcuofyrgr5advkk267xqnx35ve
BioPPISVMExtractor: A protein–protein interaction extractor for biomedical literature using SVM and rich feature sets
2010
Journal of Biomedical Informatics
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This system uses rich feature sets including word features, keyword feature, protein names distance feature and Link path feature for SVM classification. ...
However, the amount of biomedical literature regarding protein interactions is increasing rapidly and it is difficult for interaction database curators to detect and curate protein interaction information ...
David Corney for sharing the evaluation datasets and results. ...
doi:10.1016/j.jbi.2009.08.013
pmid:19706337
fatcat:rwb6ukl535dozaxtp3asbfrjna
Constructing Topic Person Interaction Networks Using a Tree Kernel-Based Method
2015
International Journal of Languages, Literature and Linguistics
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We proposed a rich interactive tree structure to represent syntactic, content, and semantic information in the text for extracting person interactions. ...
for comparison. ...
ACKNOWLEDGMENT We are grateful to the anonymous reviewers for insightful comments. ...
doi:10.18178/ijlll.2015.1.4.46
fatcat:2ag5tbvxirfsffu4jzvxsxfh5a
A Short Survey of Biomedical Relation Extraction Techniques
[article]
2017
arXiv
pre-print
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In the current research, we focus on different aspects of relation extraction techniques in biomedical domain and briefly describe the state-of-the-art for relation extraction between a variety of biological ...
Biomedical information is growing rapidly in the recent years and retrieving useful data through information extraction system is getting more attention. ...
BioNoculars uses a graph-based method to construct extraction patterns for extracting protein-protein interactions. ...
arXiv:1707.05850v3
fatcat:snyvtomcxbbeplkspqaucmpely
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