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An Interaction Pattern Kernel Approach for Protein-Protein Interaction Extraction from Biomedical Literature [chapter]

Yung-Chun Chang, Yu-Chen Su, Nai-Wen Chang, Wen-Lian Hsu
2014 Lecture Notes in Computer Science  
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

Huanhuan Yu, Longhua Qian, Guodong Zhou, Qiaoming Zhu
2009 2009 2nd International Conference on Biomedical Engineering and Informatics  
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

Timur Fayruzov, Martine De Cock, Chris Cornelis, Veronique Hoste
2009 BMC Bioinformatics  
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

Gurusamy Murugesan, Sabenabanu Abdulkadhar, Jeyakumar Natarajan, Bin Liu
2017 PLoS ONE  
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]

Peilei Liu, Ting Wang
2014 arXiv   pre-print
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

Timur Fayruzov, Martine De Cock, Chris Cornelis, Veronique Hoste
2008 Proceeding of the 2nd international workshop on Data and text mining in bioinformatics - DTMBIO '08  
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]

Timur Fayruzov, Martine De Cock, Chris Cornelis, Véronique Hoste
2008 Lecture Notes in Computer Science  
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

Peng Chen, Jianyi Guo, Zhengtao Yu, Sichao Wei, Feng Zhou, Xin Yan
2013 Journal of Computer and Communications  
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

Ying Li, Lizheng Wei, Cankun Wang, Jianing Zhao, Siyu Han, Yu Zhang, Wei Du
2022 BMC Bioinformatics  
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

Lishuang Li, Panpan Zhang, Tianfu Zheng, Hongying Zhang, Zhenchao Jiang, Degen Huang, Yu Xue
2014 PLoS ONE  
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]

Yung-Chun Chang, Chien Chin Chen, Wen-Lian Hsu
2013 Lecture Notes in Computer Science  
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]

Gerold Schneider, Kaarel Kaljurand, Fabio Rinaldi
2009 Lecture Notes in Computer Science  
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

Zhihao Yang, Hongfei Lin, Yanpeng Li
2010 Journal of Biomedical Informatics  
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

Yung-Chun Chang, Zhong-Yong Chen, Chien-Chin Chen, Wen-Lian Hsu
2015 International Journal of Languages, Literature and Linguistics  
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]

Elham Shahab
2017 arXiv   pre-print
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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