{"title":"Tuning hyperparameters of doublet-detection methods for single-cell RNA sequencing data","authors":"N. Xi, Angelos Vasilopoulos","doi":"10.15302/j-qb-022-0324","DOIUrl":"https://doi.org/10.15302/j-qb-022-0324","url":null,"abstract":"The existence of doublets in single-cell RNA sequencing (scRNA-seq) data poses a great challenge in downstream data analysis. Computational doublet-detection methods have been developed to remove doublets from scRNA-seq data. Yet, the default hyperparameter settings of those methods may not provide optimal performance. Here, we propose a strategy to tune hyperparameters for a cutting-edge doublet-detection method. We utilize a full factorial design to explore the relationship between hyperparameters and detection accuracy on 16 real scRNA-seq datasets. The optimal hyperparameters are obtained by a response surface model and convex optimization. We show that the optimal hyperparameters provide top performance across scRNA-seq datasets under various biological conditions. Our tuning strategy can be applied to other computational doublet-detection methods. It also offers insights into hyperparameter tuning for broader computational methods in scRNA-seq data analysis.","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46420397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Implementing Toy Models in Microsoft Excel","authors":"A. Kimura","doi":"10.1007/978-981-16-5018-5_4","DOIUrl":"https://doi.org/10.1007/978-981-16-5018-5_4","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51118971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Self-Organization of the Cell","authors":"A. Kimura","doi":"10.1007/978-981-16-5018-5_9","DOIUrl":"https://doi.org/10.1007/978-981-16-5018-5_9","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51119544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Implementing Toy Models in Python","authors":"A. Kimura","doi":"10.1007/978-981-16-5018-5_5","DOIUrl":"https://doi.org/10.1007/978-981-16-5018-5_5","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"67 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51119040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mechanics of the Cell","authors":"A. Kimura","doi":"10.1007/978-981-16-5018-5_3","DOIUrl":"https://doi.org/10.1007/978-981-16-5018-5_3","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51118936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Diversity of the Cell","authors":"A. Kimura","doi":"10.1007/978-981-16-5018-5_7","DOIUrl":"https://doi.org/10.1007/978-981-16-5018-5_7","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"49 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51119511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development of the Cell over Time (Perspectives)","authors":"A. Kimura","doi":"10.1007/978-981-16-5018-5_11","DOIUrl":"https://doi.org/10.1007/978-981-16-5018-5_11","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51118820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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