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Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles
•A deep learning technique for identifying molecular functions of clathrin with high performance.•The proposed idea is to transform the position-specific scoring matrices to 2D images and feed into 2D convolutional neural networks.•Compared with the other state-of-the-art techniques, our method had...
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| Published in: | Computer methods and programs in biomedicine 2019-08, Vol.177, p.81-88 |
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| cites | cdi_FETCH-LOGICAL-c466t-7d8a286aded32eb541dd0c37ba29dcc0fc37cc855d4be137928ea2f2d5ead3693 |
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| container_title | Computer methods and programs in biomedicine |
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| creator | Le, Nguyen Quoc Khanh Huynh, Tuan-Tu Yapp, Edward Kien Yee Yeh, Hui-Yuan |
| description | •A deep learning technique for identifying molecular functions of clathrin with high performance.•The proposed idea is to transform the position-specific scoring matrices to 2D images and feed into 2D convolutional neural networks.•Compared with the other state-of-the-art techniques, our method had a significant improvement in all of the measurement metrics.•A powerful model to help biologists discover the new sequences that belong to clathrin.•A basis for further research that can improve the performance of protein function prediction using deep neural networks.
Clathrin is an adaptor protein that serves as the principal element of the vesicle-coating complex and is important for the membrane cleavage to dispense the invaginated vesicle from the plasma membrane. The functional loss of clathrins has been tied to a lot of human diseases, i.e., neurodegenerative disorders, cancer, Alzheimer's diseases, and so on. Therefore, creating a precise model to identify its functions is a crucial step towards understanding human diseases and designing drug targets.
We present a deep learning model using a two-dimensional convolutional neural network (CNN) and position-specific scoring matrix (PSSM) profiles to identify clathrin proteins from high throughput sequences. Traditionally, the 2D CNNs take images as an input so we treated the PSSM profile with a 20 × 20 matrix as an image of 20 × 20 pixels. The input PSSM profile was then connected to our 2D CNN in which we set a variety of parameters to improve the performance of the model. Based on the 10-fold cross-validation results, hyper-parameter optimization process was employed to find the best model for our dataset. Finally, an independent dataset was used to assess the predictive ability of the current model.
Our model could identify clathrin proteins with sensitivity of 92.2%, specificity of 91.2%, accuracy of 91.8%, and MCC of 0.83 in the independent dataset. Compared to state-of-the-art traditional neural networks, our method achieved a significant improvement in all typical measurement metrics.
Throughout the proposed study, we provide an effective tool for investigating clathrin proteins and our achievement could promote the use of deep learning in biomedical research. We also provide source codes and dataset freely at https://www.github.com/khanhlee/deep-clathrin/. |
| doi_str_mv | 10.1016/j.cmpb.2019.05.016 |
| format | article |
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Clathrin is an adaptor protein that serves as the principal element of the vesicle-coating complex and is important for the membrane cleavage to dispense the invaginated vesicle from the plasma membrane. The functional loss of clathrins has been tied to a lot of human diseases, i.e., neurodegenerative disorders, cancer, Alzheimer's diseases, and so on. Therefore, creating a precise model to identify its functions is a crucial step towards understanding human diseases and designing drug targets.
We present a deep learning model using a two-dimensional convolutional neural network (CNN) and position-specific scoring matrix (PSSM) profiles to identify clathrin proteins from high throughput sequences. Traditionally, the 2D CNNs take images as an input so we treated the PSSM profile with a 20 × 20 matrix as an image of 20 × 20 pixels. The input PSSM profile was then connected to our 2D CNN in which we set a variety of parameters to improve the performance of the model. Based on the 10-fold cross-validation results, hyper-parameter optimization process was employed to find the best model for our dataset. Finally, an independent dataset was used to assess the predictive ability of the current model.
Our model could identify clathrin proteins with sensitivity of 92.2%, specificity of 91.2%, accuracy of 91.8%, and MCC of 0.83 in the independent dataset. Compared to state-of-the-art traditional neural networks, our method achieved a significant improvement in all typical measurement metrics.
Throughout the proposed study, we provide an effective tool for investigating clathrin proteins and our achievement could promote the use of deep learning in biomedical research. We also provide source codes and dataset freely at https://www.github.com/khanhlee/deep-clathrin/.</description><identifier>ISSN: 0169-2607</identifier><identifier>EISSN: 1872-7565</identifier><identifier>DOI: 10.1016/j.cmpb.2019.05.016</identifier><identifier>PMID: 31319963</identifier><language>eng</language><publisher>Ireland: Elsevier B.V</publisher><subject>Adaptor protein complex ; Algorithms ; Cell Membrane - chemistry ; Clathrin - chemistry ; Clathrin coated pits ; Convolutional neural network ; Deep Learning ; Humans ; Molecular function ; Neural Networks, Computer ; Position specific scoring matrix ; Position-Specific Scoring Matrices ; Reproducibility of Results ; Sensitivity and Specificity ; Software ; Vesicular transport</subject><ispartof>Computer methods and programs in biomedicine, 2019-08, Vol.177, p.81-88</ispartof><rights>2019 Elsevier B.V.</rights><rights>Copyright © 2019 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c466t-7d8a286aded32eb541dd0c37ba29dcc0fc37cc855d4be137928ea2f2d5ead3693</citedby><cites>FETCH-LOGICAL-c466t-7d8a286aded32eb541dd0c37ba29dcc0fc37cc855d4be137928ea2f2d5ead3693</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31319963$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Le, Nguyen Quoc Khanh</creatorcontrib><creatorcontrib>Huynh, Tuan-Tu</creatorcontrib><creatorcontrib>Yapp, Edward Kien Yee</creatorcontrib><creatorcontrib>Yeh, Hui-Yuan</creatorcontrib><title>Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles</title><title>Computer methods and programs in biomedicine</title><addtitle>Comput Methods Programs Biomed</addtitle><description>•A deep learning technique for identifying molecular functions of clathrin with high performance.•The proposed idea is to transform the position-specific scoring matrices to 2D images and feed into 2D convolutional neural networks.•Compared with the other state-of-the-art techniques, our method had a significant improvement in all of the measurement metrics.•A powerful model to help biologists discover the new sequences that belong to clathrin.•A basis for further research that can improve the performance of protein function prediction using deep neural networks.
Clathrin is an adaptor protein that serves as the principal element of the vesicle-coating complex and is important for the membrane cleavage to dispense the invaginated vesicle from the plasma membrane. The functional loss of clathrins has been tied to a lot of human diseases, i.e., neurodegenerative disorders, cancer, Alzheimer's diseases, and so on. Therefore, creating a precise model to identify its functions is a crucial step towards understanding human diseases and designing drug targets.
We present a deep learning model using a two-dimensional convolutional neural network (CNN) and position-specific scoring matrix (PSSM) profiles to identify clathrin proteins from high throughput sequences. Traditionally, the 2D CNNs take images as an input so we treated the PSSM profile with a 20 × 20 matrix as an image of 20 × 20 pixels. The input PSSM profile was then connected to our 2D CNN in which we set a variety of parameters to improve the performance of the model. Based on the 10-fold cross-validation results, hyper-parameter optimization process was employed to find the best model for our dataset. Finally, an independent dataset was used to assess the predictive ability of the current model.
Our model could identify clathrin proteins with sensitivity of 92.2%, specificity of 91.2%, accuracy of 91.8%, and MCC of 0.83 in the independent dataset. Compared to state-of-the-art traditional neural networks, our method achieved a significant improvement in all typical measurement metrics.
Throughout the proposed study, we provide an effective tool for investigating clathrin proteins and our achievement could promote the use of deep learning in biomedical research. We also provide source codes and dataset freely at https://www.github.com/khanhlee/deep-clathrin/.</description><subject>Adaptor protein complex</subject><subject>Algorithms</subject><subject>Cell Membrane - chemistry</subject><subject>Clathrin - chemistry</subject><subject>Clathrin coated pits</subject><subject>Convolutional neural network</subject><subject>Deep Learning</subject><subject>Humans</subject><subject>Molecular function</subject><subject>Neural Networks, Computer</subject><subject>Position specific scoring matrix</subject><subject>Position-Specific Scoring Matrices</subject><subject>Reproducibility of Results</subject><subject>Sensitivity and Specificity</subject><subject>Software</subject><subject>Vesicular transport</subject><issn>0169-2607</issn><issn>1872-7565</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><recordid>eNp9kM1q3DAYRUVJaKZpX6CLomU2dvUzkm3oJoQmHUhIIOlayNLnjgZbciVNYfr0kZkky6wkLuceoYvQV0pqSqj8vqvNNPc1I7SriahL9AGtaNuwqhFSnKBVSbqKSdKcoU8p7QghTAj5EZ1xymnXSb5CaWPBZzc4o7MLHocBm1HnbXQezzFkcD7h_oCdNyHOIRbK_8Hbwwxx1lFPkCHiMGc3uf9HQylagBmPoKNfYO0tfnh8vFt8gxshfUangx4TfHk5z9Hv659PV7-q2_ubzdXlbWXWUuaqsa1mrdQWLGfQizW1lhje9Jp11hgylLsxrRB23QPlTcda0GxgVoC2XHb8HF0cveXhv3tIWU0uGRhH7SHsk2JMUramhPGCsiNqYkgpwqDm6CYdD4oStYytdmoZWy1jKyJUiUrp24t_309g3yqv6xbgxxGA8st_DqJKxoE3YF0Ek5UN7j3_Mz7Ck9U</recordid><startdate>201908</startdate><enddate>201908</enddate><creator>Le, Nguyen Quoc Khanh</creator><creator>Huynh, Tuan-Tu</creator><creator>Yapp, Edward Kien Yee</creator><creator>Yeh, Hui-Yuan</creator><general>Elsevier B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>201908</creationdate><title>Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles</title><author>Le, Nguyen Quoc Khanh ; Huynh, Tuan-Tu ; Yapp, Edward Kien Yee ; Yeh, Hui-Yuan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c466t-7d8a286aded32eb541dd0c37ba29dcc0fc37cc855d4be137928ea2f2d5ead3693</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Adaptor protein complex</topic><topic>Algorithms</topic><topic>Cell Membrane - chemistry</topic><topic>Clathrin - chemistry</topic><topic>Clathrin coated pits</topic><topic>Convolutional neural network</topic><topic>Deep Learning</topic><topic>Humans</topic><topic>Molecular function</topic><topic>Neural Networks, Computer</topic><topic>Position specific scoring matrix</topic><topic>Position-Specific Scoring Matrices</topic><topic>Reproducibility of Results</topic><topic>Sensitivity and Specificity</topic><topic>Software</topic><topic>Vesicular transport</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Le, Nguyen Quoc Khanh</creatorcontrib><creatorcontrib>Huynh, Tuan-Tu</creatorcontrib><creatorcontrib>Yapp, Edward Kien Yee</creatorcontrib><creatorcontrib>Yeh, Hui-Yuan</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Computer methods and programs in biomedicine</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Le, Nguyen Quoc Khanh</au><au>Huynh, Tuan-Tu</au><au>Yapp, Edward Kien Yee</au><au>Yeh, Hui-Yuan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles</atitle><jtitle>Computer methods and programs in biomedicine</jtitle><addtitle>Comput Methods Programs Biomed</addtitle><date>2019-08</date><risdate>2019</risdate><volume>177</volume><spage>81</spage><epage>88</epage><pages>81-88</pages><issn>0169-2607</issn><eissn>1872-7565</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>•A deep learning technique for identifying molecular functions of clathrin with high performance.•The proposed idea is to transform the position-specific scoring matrices to 2D images and feed into 2D convolutional neural networks.•Compared with the other state-of-the-art techniques, our method had a significant improvement in all of the measurement metrics.•A powerful model to help biologists discover the new sequences that belong to clathrin.•A basis for further research that can improve the performance of protein function prediction using deep neural networks.
Clathrin is an adaptor protein that serves as the principal element of the vesicle-coating complex and is important for the membrane cleavage to dispense the invaginated vesicle from the plasma membrane. The functional loss of clathrins has been tied to a lot of human diseases, i.e., neurodegenerative disorders, cancer, Alzheimer's diseases, and so on. Therefore, creating a precise model to identify its functions is a crucial step towards understanding human diseases and designing drug targets.
We present a deep learning model using a two-dimensional convolutional neural network (CNN) and position-specific scoring matrix (PSSM) profiles to identify clathrin proteins from high throughput sequences. Traditionally, the 2D CNNs take images as an input so we treated the PSSM profile with a 20 × 20 matrix as an image of 20 × 20 pixels. The input PSSM profile was then connected to our 2D CNN in which we set a variety of parameters to improve the performance of the model. Based on the 10-fold cross-validation results, hyper-parameter optimization process was employed to find the best model for our dataset. Finally, an independent dataset was used to assess the predictive ability of the current model.
Our model could identify clathrin proteins with sensitivity of 92.2%, specificity of 91.2%, accuracy of 91.8%, and MCC of 0.83 in the independent dataset. Compared to state-of-the-art traditional neural networks, our method achieved a significant improvement in all typical measurement metrics.
Throughout the proposed study, we provide an effective tool for investigating clathrin proteins and our achievement could promote the use of deep learning in biomedical research. We also provide source codes and dataset freely at https://www.github.com/khanhlee/deep-clathrin/.</abstract><cop>Ireland</cop><pub>Elsevier B.V</pub><pmid>31319963</pmid><doi>10.1016/j.cmpb.2019.05.016</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| source | ScienceDirect Freedom Collection |
| subjects | Adaptor protein complex Algorithms Cell Membrane - chemistry Clathrin - chemistry Clathrin coated pits Convolutional neural network Deep Learning Humans Molecular function Neural Networks, Computer Position specific scoring matrix Position-Specific Scoring Matrices Reproducibility of Results Sensitivity and Specificity Software Vesicular transport |
| title | Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles |
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