Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)最新文献

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Entropy vs. Content ( I ) 熵与内容(1)
{"title":"Entropy vs. Content (\u0000 I\u0000 )","authors":"","doi":"10.1002/9781119698005.ch16","DOIUrl":"https://doi.org/10.1002/9781119698005.ch16","url":null,"abstract":"","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82008765","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}
引用次数: 0
Index 指数
{"title":"Index","authors":"","doi":"10.1002/9781119698005.index","DOIUrl":"https://doi.org/10.1002/9781119698005.index","url":null,"abstract":"","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86399260","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}
引用次数: 0
Self‐Sequence Alignment ( I ) 自序列比对(1)
{"title":"Self‐Sequence Alignment (\u0000 I\u0000 )","authors":"","doi":"10.1002/9781119698005.ch5","DOIUrl":"https://doi.org/10.1002/9781119698005.ch5","url":null,"abstract":"","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"50 2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83674911","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}
引用次数: 0
Tree of Life: Genomes ( II ) 生命之树:基因组(II)
{"title":"Tree of Life: Genomes (\u0000 \u0000 II\u0000 \u0000 )","authors":"","doi":"10.1002/9781119698005.ch2","DOIUrl":"https://doi.org/10.1002/9781119698005.ch2","url":null,"abstract":"","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76576647","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}
引用次数: 0
Spectral Forecast ( I ) 频谱预测(I)
{"title":"Spectral Forecast (\u0000 I\u0000 )","authors":"","doi":"10.1002/9781119698005.ch15","DOIUrl":"https://doi.org/10.1002/9781119698005.ch15","url":null,"abstract":"","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90642919","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}
引用次数: 0
F orced Alignment ( II ) 强制对中(II)
{"title":"F\u0000 orced Alignment\u0000 (\u0000 II\u0000 )","authors":"","doi":"10.1002/9781119698005.ch4","DOIUrl":"https://doi.org/10.1002/9781119698005.ch4","url":null,"abstract":"","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"99 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83606585","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}
引用次数: 0
Jointly Embedding Multiple Single-Cell Omics Measurements. 联合嵌入多个单细胞组学测量。
Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble
{"title":"Jointly Embedding Multiple Single-Cell Omics Measurements.","authors":"Jie Liu,&nbsp;Yuanhao Huang,&nbsp;Ritambhara Singh,&nbsp;Jean-Philippe Vert,&nbsp;William Stafford Noble","doi":"10.4230/LIPIcs.WABI.2019.10","DOIUrl":"https://doi.org/10.4230/LIPIcs.WABI.2019.10","url":null,"abstract":"<p><p>Many single-cell sequencing technologies are now available, but it is still difficult to apply multiple sequencing technologies to the same single cell. In this paper, we propose an unsupervised manifold alignment algorithm, MMD-MA, for integrating multiple measurements carried out on disjoint aliquots of a given population of cells. Effectively, MMD-MA performs an <i>in silico</i> co-assay by embedding cells measured in different ways into a learned latent space. In the MMD-MA algorithm, single-cell data points from multiple domains are aligned by optimizing an objective function with three components: (1) a maximum mean discrepancy (MMD) term to encourage the differently measured points to have similar distributions in the latent space, (2) a distortion term to preserve the structure of the data between the input space and the latent space, and (3) a penalty term to avoid collapse to a trivial solution. Notably, MMD-MA does not require any correspondence information across data modalities, either between the cells or between the features. Furthermore, MMD-MA's weak distributional requirements for the domains to be aligned allow the algorithm to integrate heterogeneous types of single cell measures, such as gene expression, DNA accessibility, chromatin organization, methylation, and imaging data. We demonstrate the utility of MMD-MA in simulation experiments and using a real data set involving single-cell gene expression and methylation data.</p>","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"143 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8496402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39506853","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}
引用次数: 0
Jointly Embedding Multiple Single-Cell Omics Measurements 联合嵌入多个单细胞组学测量
Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble
{"title":"Jointly Embedding Multiple Single-Cell Omics Measurements","authors":"Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William Stafford Noble","doi":"10.1101/644310","DOIUrl":"https://doi.org/10.1101/644310","url":null,"abstract":"Many single-cell sequencing technologies are now available, but it is still difficult to apply multiple sequencing technologies to the same single cell. In this paper, we propose an unsupervised manifold alignment algorithm, MMD-MA, for integrating multiple measurements carried out on disjoint aliquots of a given population of cells. Effectively, MMD-MA performs an in silico co-assay by embedding cells measured in different ways into a learned latent space. In the MMD-MA algorithm, single-cell data points from multiple domains are aligned by optimizing an objective function with three components: (1) a maximum mean discrepancy (MMD) term to encourage the differently measured points to have similar distributions in the latent space, (2) a distortion term to preserve the structure of the data between the input space and the latent space, and (3) a penalty term to avoid collapse to a trivial solution. Notably, MMD-MA does not require any correspondence information across data modalities, either between the cells or between the features. Furthermore, MMD-MA’s weak distributional requirements for the domains to be aligned allow the algorithm to integrate heterogeneous types of single cell measures, such as gene expression, DNA accessibility, chromatin organization, methylation, and imaging data. We demonstrate the utility of MMD-MA in simulation experiments and using a real data set involving single-cell gene expression and methylation data.","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90396880","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}
引用次数: 73
Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures RNA二级结构玻尔兹曼系综中图距离的分布
R. Backofen, Markus Fricke, M. Marz, Jing Qin, P. Stadler
{"title":"Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures","authors":"R. Backofen, Markus Fricke, M. Marz, Jing Qin, P. Stadler","doi":"10.1007/978-3-642-40453-5_10","DOIUrl":"https://doi.org/10.1007/978-3-642-40453-5_10","url":null,"abstract":"","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"45 1","pages":"112 - 125"},"PeriodicalIF":0.0,"publicationDate":"2013-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91527492","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}
引用次数: 4
Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs 包括亲吻发夹基序的RNA二级结构预测
C. Theis, Stefan Janssen, R. Giegerich
{"title":"Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs","authors":"C. Theis, Stefan Janssen, R. Giegerich","doi":"10.1007/978-3-642-15294-8_5","DOIUrl":"https://doi.org/10.1007/978-3-642-15294-8_5","url":null,"abstract":"","PeriodicalId":93254,"journal":{"name":"Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)","volume":"23 1","pages":"52 - 64"},"PeriodicalIF":0.0,"publicationDate":"2010-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79809890","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}
引用次数: 26
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