Brendan Sullivan, Patricia S Langan, Rick Archibald, Leighton Coates, Venu Gopal Vadavasi, Vickie Lynch
{"title":"Volumetric Segmentation <i>via</i> Neural Networks Improves Neutron Crystallography Data Analysis.","authors":"Brendan Sullivan, Patricia S Langan, Rick Archibald, Leighton Coates, Venu Gopal Vadavasi, Vickie Lynch","doi":"10.1109/CCGRID.2019.00070","DOIUrl":"10.1109/CCGRID.2019.00070","url":null,"abstract":"<p><p>Crystallography is the powerhouse technique for molecular structure determination, with applications in fields ranging from energy storage to drug design. Accurate structure determination, however, relies partly on determining the precise locations and integrated intensities of Bragg peaks in the resulting data. Here, we describe a method for Bragg peak integration that is accomplished using neural networks. The network is based on a U-Net and identifies peaks in three-dimensional reciprocal space through segmentation, allowing prediction of the full 3D peak shape from noisy data that is commonly difficult to process. The procedure for generating appropriate training sets is detailed. Trained networks achieve Dice coefficients of 0.82 and mean IoUs of 0.69. Carrying out integration over entire datasets, it is demonstrated that integrating neural network-predicted peaks results in improved intensity statistics. Furthermore, using a second dataset, the possibility of transfer learning between datasets is shown. Given the ubiquity and growing complexity of crystallography, we anticipate integration by machine learning to play an increasingly important role across the physical sciences. These early results demonstrate the applicability of deep learning techniques for integrating crystallography data and suggest a possible role in the next generation of crystallography experiments.</p>","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"2019 ","pages":"549-555"},"PeriodicalIF":0.0,"publicationDate":"2019-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/CCGRID.2019.00070","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37500058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Introduction: Business and Technological Drivers of Grid Computing","authors":"K. Stanoevska-Slabeva, T. Wozniak","doi":"10.1007/978-3-642-05193-7_1","DOIUrl":"https://doi.org/10.1007/978-3-642-05193-7_1","url":null,"abstract":"","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"23 1","pages":"3-11"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74460436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Grid Basics","authors":"K. Stanoevska-Slabeva, T. Wozniak","doi":"10.1007/978-3-642-05193-7_3","DOIUrl":"https://doi.org/10.1007/978-3-642-05193-7_3","url":null,"abstract":"","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"47 1","pages":"23-45"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77728695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Organizational and Governance Challenges for Grid Computing in Companies - Summary of Findings from Business Experiments","authors":"K. Stanoevska-Slabeva, T. Wozniak","doi":"10.1007/978-3-642-05193-7_13","DOIUrl":"https://doi.org/10.1007/978-3-642-05193-7_13","url":null,"abstract":"","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"27 1","pages":"213-222"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77181408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
U. Heindl, A. Jacob, Marcus Mueller, P. Rácz, B. Stiller, E. Volk, M. Waldburger
{"title":"AgroGrid - Grid Technologies in Agro Food Business","authors":"U. Heindl, A. Jacob, Marcus Mueller, P. Rácz, B. Stiller, E. Volk, M. Waldburger","doi":"10.1007/978-3-642-05193-7_11","DOIUrl":"https://doi.org/10.1007/978-3-642-05193-7_11","url":null,"abstract":"","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"268 1","pages":"173-190"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79832320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Practical Guidelines for Evolving IT Infrastructure towards Grids and Clouds","authors":"K. Stanoevska-Slabeva, T. Wozniak, V. Hoyer","doi":"10.1007/978-3-642-05193-7_14","DOIUrl":"https://doi.org/10.1007/978-3-642-05193-7_14","url":null,"abstract":"","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"21 1","pages":"225-243"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73400092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Juan-Carlos Cuesta, Karita Luokkanen-Rabetino, K. Stanoevska-Slabeva
{"title":"Grid Value Chains - What is a Grid Solution?","authors":"Juan-Carlos Cuesta, Karita Luokkanen-Rabetino, K. Stanoevska-Slabeva","doi":"10.1007/978-3-642-05193-7_6","DOIUrl":"https://doi.org/10.1007/978-3-642-05193-7_6","url":null,"abstract":"","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"27 1","pages":"83-96"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74403768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Common Capabilities for Service Oriented Infrastructures - Grid and Cloud Computing","authors":"T. Dimitrakos","doi":"10.1007/978-3-642-05193-7_8","DOIUrl":"https://doi.org/10.1007/978-3-642-05193-7_8","url":null,"abstract":"","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"9 1","pages":"123-145"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79356502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cloud Basics - An Introduction to Cloud Computing","authors":"K. Stanoevska-Slabeva, T. Wozniak","doi":"10.1007/978-3-642-05193-7_4","DOIUrl":"https://doi.org/10.1007/978-3-642-05193-7_4","url":null,"abstract":"","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"35 1","pages":"47-61"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89971644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The BEinGRID Project","authors":"T. Dimitrakos","doi":"10.1007/978-3-642-05193-7_2","DOIUrl":"https://doi.org/10.1007/978-3-642-05193-7_2","url":null,"abstract":"","PeriodicalId":92904,"journal":{"name":"IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing. IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing","volume":"9 1","pages":"13-17"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91103149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}