Assessing Graph‐based Deep Learning Models for Predicting Flash Point
Flash points of organic molecules play an important role in preventing flammability hazards and large databases of measured values exist, although millions of compounds remain unmeasured. To rapidly extend existing data to new compounds many researchers have used quantitative structure‐property rela...
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Veröffentlicht in: | Molecular informatics 2020-06, Vol.39 (6), p.e1900101-n/a |
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creator | Sun, Xiaoyu Krakauer, Nathaniel J. Politowicz, Alexander Chen, Wei‐Ting Li, Qiying Li, Zuoyi Shao, Xianjia Sunaryo, Alfred Shen, Mingren Wang, James Morgan, Dane |
description | Flash points of organic molecules play an important role in preventing flammability hazards and large databases of measured values exist, although millions of compounds remain unmeasured. To rapidly extend existing data to new compounds many researchers have used quantitative structure‐property relationship (QSPR) analysis to effectively predict flash points. In recent years graph‐based deep learning (GBDL) has emerged as a powerful alternative method to traditional QSPR. In this paper, GBDL models were implemented in predicting flash point for the first time. We assessed the performance of two GBDL models, message‐passing neural network (MPNN) and graph convolutional neural network (GCNN), by comparing against 12 previous QSPR studies using more traditional methods. Our result shows that MPNN both outperforms GCNN and yields slightly worse but comparable performance with previous QSPR studies. The average R2
and Mean Absolute Error (MAE) scores of MPNN are, respectively, 2.3 % lower and 2.0 K higher than previous comparable studies. To further explore GBDL models, we collected the largest flash point dataset to date, which contains 10575 unique molecules. The optimized MPNN gives a test data R2
of 0.803 and MAE of 17.8 K on the complete dataset. We also extracted 5 datasets from our integrated dataset based on molecular types (acids, organometallics, organogermaniums, organosilicons, and organotins) and explore the quality of the model in these classes. |
doi_str_mv | 10.1002/minf.201900101 |
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and Mean Absolute Error (MAE) scores of MPNN are, respectively, 2.3 % lower and 2.0 K higher than previous comparable studies. To further explore GBDL models, we collected the largest flash point dataset to date, which contains 10575 unique molecules. The optimized MPNN gives a test data R2
of 0.803 and MAE of 17.8 K on the complete dataset. We also extracted 5 datasets from our integrated dataset based on molecular types (acids, organometallics, organogermaniums, organosilicons, and organotins) and explore the quality of the model in these classes.</description><identifier>ISSN: 1868-1743</identifier><identifier>EISSN: 1868-1751</identifier><identifier>DOI: 10.1002/minf.201900101</identifier><identifier>PMID: 32077235</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Artificial neural networks ; Datasets ; Deep learning ; Domain of applicability ; Flammability ; Flash point ; Machine learning ; Message passing ; Neural network ; Neural networks ; Organic chemistry ; Organometallic compounds ; Quantitative structure-property relationship ; Robust model prediction</subject><ispartof>Molecular informatics, 2020-06, Vol.39 (6), p.e1900101-n/a</ispartof><rights>2020 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim</rights><rights>2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4101-d31033d292145a520b9cdc8d3356b4a192e67df4a7cd0ab344cb3fc4465384db3</citedby><cites>FETCH-LOGICAL-c4101-d31033d292145a520b9cdc8d3356b4a192e67df4a7cd0ab344cb3fc4465384db3</cites><orcidid>0000-0002-4911-0046</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fminf.201900101$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fminf.201900101$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27922,27923,45572,45573</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32077235$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sun, Xiaoyu</creatorcontrib><creatorcontrib>Krakauer, Nathaniel J.</creatorcontrib><creatorcontrib>Politowicz, Alexander</creatorcontrib><creatorcontrib>Chen, Wei‐Ting</creatorcontrib><creatorcontrib>Li, Qiying</creatorcontrib><creatorcontrib>Li, Zuoyi</creatorcontrib><creatorcontrib>Shao, Xianjia</creatorcontrib><creatorcontrib>Sunaryo, Alfred</creatorcontrib><creatorcontrib>Shen, Mingren</creatorcontrib><creatorcontrib>Wang, James</creatorcontrib><creatorcontrib>Morgan, Dane</creatorcontrib><title>Assessing Graph‐based Deep Learning Models for Predicting Flash Point</title><title>Molecular informatics</title><addtitle>Mol Inform</addtitle><description>Flash points of organic molecules play an important role in preventing flammability hazards and large databases of measured values exist, although millions of compounds remain unmeasured. To rapidly extend existing data to new compounds many researchers have used quantitative structure‐property relationship (QSPR) analysis to effectively predict flash points. In recent years graph‐based deep learning (GBDL) has emerged as a powerful alternative method to traditional QSPR. In this paper, GBDL models were implemented in predicting flash point for the first time. We assessed the performance of two GBDL models, message‐passing neural network (MPNN) and graph convolutional neural network (GCNN), by comparing against 12 previous QSPR studies using more traditional methods. Our result shows that MPNN both outperforms GCNN and yields slightly worse but comparable performance with previous QSPR studies. The average R2
and Mean Absolute Error (MAE) scores of MPNN are, respectively, 2.3 % lower and 2.0 K higher than previous comparable studies. To further explore GBDL models, we collected the largest flash point dataset to date, which contains 10575 unique molecules. The optimized MPNN gives a test data R2
of 0.803 and MAE of 17.8 K on the complete dataset. We also extracted 5 datasets from our integrated dataset based on molecular types (acids, organometallics, organogermaniums, organosilicons, and organotins) and explore the quality of the model in these classes.</description><subject>Artificial neural networks</subject><subject>Datasets</subject><subject>Deep learning</subject><subject>Domain of applicability</subject><subject>Flammability</subject><subject>Flash point</subject><subject>Machine learning</subject><subject>Message passing</subject><subject>Neural network</subject><subject>Neural networks</subject><subject>Organic chemistry</subject><subject>Organometallic compounds</subject><subject>Quantitative structure-property relationship</subject><subject>Robust model prediction</subject><issn>1868-1743</issn><issn>1868-1751</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNqFkD1PwzAQhi0EolXpyogisbCk-CtxPFaFlkotdIDZcmyHpsoXdiPUjZ_Ab-SX4KilSCzccqe7517dvQBcIjhCEOLbMq-yEYaIQ4ggOgF9lMRJiFiETo81JT0wdG4DfRAcs4Sfgx7BkDFMoj6YjZ0zzuXVazCzsll_fXym0hkd3BnTBAsjbdXNlrU2hQuy2gYra3Sutl13Wki3DlZ1Xm0vwFkmC2eGhzwAL9P758lDuHiazSfjRaioPzHUBEFCNOYY0UhGGKZcaZVoQqI4pRJxbGKmMyqZ0lCmhFKVkkxRGkckoTolA3Cz121s_dYatxVl7pQpClmZunXCP8UJJ4Qhj17_QTd1ayt_ncAUJozHMceeGu0pZWvnrMlEY_NS2p1AUHQui85lcXTZL1wdZNu0NPqI_3jqAb4H3vPC7P6RE8v54_RX_BtCB4eS</recordid><startdate>202006</startdate><enddate>202006</enddate><creator>Sun, Xiaoyu</creator><creator>Krakauer, Nathaniel J.</creator><creator>Politowicz, Alexander</creator><creator>Chen, Wei‐Ting</creator><creator>Li, Qiying</creator><creator>Li, Zuoyi</creator><creator>Shao, Xianjia</creator><creator>Sunaryo, Alfred</creator><creator>Shen, Mingren</creator><creator>Wang, James</creator><creator>Morgan, Dane</creator><general>Wiley Subscription Services, Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7TM</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>JQ2</scope><scope>K9.</scope><scope>P64</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4911-0046</orcidid></search><sort><creationdate>202006</creationdate><title>Assessing Graph‐based Deep Learning Models for Predicting Flash Point</title><author>Sun, Xiaoyu ; Krakauer, Nathaniel J. ; Politowicz, Alexander ; Chen, Wei‐Ting ; Li, Qiying ; Li, Zuoyi ; Shao, Xianjia ; Sunaryo, Alfred ; Shen, Mingren ; Wang, James ; Morgan, Dane</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4101-d31033d292145a520b9cdc8d3356b4a192e67df4a7cd0ab344cb3fc4465384db3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Artificial neural networks</topic><topic>Datasets</topic><topic>Deep learning</topic><topic>Domain of applicability</topic><topic>Flammability</topic><topic>Flash point</topic><topic>Machine learning</topic><topic>Message passing</topic><topic>Neural network</topic><topic>Neural networks</topic><topic>Organic chemistry</topic><topic>Organometallic compounds</topic><topic>Quantitative structure-property relationship</topic><topic>Robust model prediction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sun, Xiaoyu</creatorcontrib><creatorcontrib>Krakauer, Nathaniel J.</creatorcontrib><creatorcontrib>Politowicz, Alexander</creatorcontrib><creatorcontrib>Chen, Wei‐Ting</creatorcontrib><creatorcontrib>Li, Qiying</creatorcontrib><creatorcontrib>Li, Zuoyi</creatorcontrib><creatorcontrib>Shao, Xianjia</creatorcontrib><creatorcontrib>Sunaryo, Alfred</creatorcontrib><creatorcontrib>Shen, Mingren</creatorcontrib><creatorcontrib>Wang, James</creatorcontrib><creatorcontrib>Morgan, Dane</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular informatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sun, Xiaoyu</au><au>Krakauer, Nathaniel J.</au><au>Politowicz, Alexander</au><au>Chen, Wei‐Ting</au><au>Li, Qiying</au><au>Li, Zuoyi</au><au>Shao, Xianjia</au><au>Sunaryo, Alfred</au><au>Shen, Mingren</au><au>Wang, James</au><au>Morgan, Dane</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Assessing Graph‐based Deep Learning Models for Predicting Flash Point</atitle><jtitle>Molecular informatics</jtitle><addtitle>Mol Inform</addtitle><date>2020-06</date><risdate>2020</risdate><volume>39</volume><issue>6</issue><spage>e1900101</spage><epage>n/a</epage><pages>e1900101-n/a</pages><issn>1868-1743</issn><eissn>1868-1751</eissn><abstract>Flash points of organic molecules play an important role in preventing flammability hazards and large databases of measured values exist, although millions of compounds remain unmeasured. To rapidly extend existing data to new compounds many researchers have used quantitative structure‐property relationship (QSPR) analysis to effectively predict flash points. In recent years graph‐based deep learning (GBDL) has emerged as a powerful alternative method to traditional QSPR. In this paper, GBDL models were implemented in predicting flash point for the first time. We assessed the performance of two GBDL models, message‐passing neural network (MPNN) and graph convolutional neural network (GCNN), by comparing against 12 previous QSPR studies using more traditional methods. Our result shows that MPNN both outperforms GCNN and yields slightly worse but comparable performance with previous QSPR studies. The average R2
and Mean Absolute Error (MAE) scores of MPNN are, respectively, 2.3 % lower and 2.0 K higher than previous comparable studies. To further explore GBDL models, we collected the largest flash point dataset to date, which contains 10575 unique molecules. The optimized MPNN gives a test data R2
of 0.803 and MAE of 17.8 K on the complete dataset. We also extracted 5 datasets from our integrated dataset based on molecular types (acids, organometallics, organogermaniums, organosilicons, and organotins) and explore the quality of the model in these classes.</abstract><cop>Germany</cop><pub>Wiley Subscription Services, Inc</pub><pmid>32077235</pmid><doi>10.1002/minf.201900101</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-4911-0046</orcidid></addata></record> |
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subjects | Artificial neural networks Datasets Deep learning Domain of applicability Flammability Flash point Machine learning Message passing Neural network Neural networks Organic chemistry Organometallic compounds Quantitative structure-property relationship Robust model prediction |
title | Assessing Graph‐based Deep Learning Models for Predicting Flash Point |
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