This paper aims to study the deep clustering problem with heterogeneous features and unknown cluster number.To address this issue,a novel deep Bayesian clustering framework is proposed.In particular,a heterogeneous fe...This paper aims to study the deep clustering problem with heterogeneous features and unknown cluster number.To address this issue,a novel deep Bayesian clustering framework is proposed.In particular,a heterogeneous feature metric is first constructed to measure the similarity between different types of features.Then,a feature metric-restricted hierarchical sample generation process is established,in which sample with heterogeneous features is clustered by generating it from a similarity constraint hidden space.When estimating the model parameters and posterior probability,the corresponding variational inference algorithm is derived and implemented.To verify our model capability,we demonstrate our model on the synthetic dataset and show the superiority of the proposed method on some real datasets.Our source code is released on the website:Github.com/yexlwh/Heterogeneousclustering.展开更多
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of...RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes(e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.展开更多
基金This work was supported by the National Natural Science Foundation of China(Grant Nos.62006131,62071260)the National Natural Science Foundation of Zhejiang Province(LQ21F020009,LQ18F020001).
文摘This paper aims to study the deep clustering problem with heterogeneous features and unknown cluster number.To address this issue,a novel deep Bayesian clustering framework is proposed.In particular,a heterogeneous feature metric is first constructed to measure the similarity between different types of features.Then,a feature metric-restricted hierarchical sample generation process is established,in which sample with heterogeneous features is clustered by generating it from a similarity constraint hidden space.When estimating the model parameters and posterior probability,the corresponding variational inference algorithm is derived and implemented.To verify our model capability,we demonstrate our model on the synthetic dataset and show the superiority of the proposed method on some real datasets.Our source code is released on the website:Github.com/yexlwh/Heterogeneousclustering.
基金supported by the National Key Research and Development Program of China(2021YFE0114900)the National Natural Science Foundation of China(91940303,91940306,32025008,32170262,31922039,U1832215,32170229)+6 种基金the Natural Science Foundation of Zhejiang Province(LD21C050002)the Starry Night Science Fund at Shanghai Institute for Advanced Study of Zhejiang University(SN-ZJU-SIAS-009)the Beijing Advanced Innovation Center for Structural Biology,Shenzhen Basic Research Project(JCYJ20180507181642811)Research Grants Council of the Hong Kong SAR,China Projects(City U 11100421,City U 11101519,City U 11100218,N_City U110/17)Croucher Foundation Project(9509003)State Key Laboratory of Marine Pollution Director Discretionary Fund,City University of Hong Kong Projects(7005503,9667222,9680261)the United Kingdom Biotechnology and Biological Sciences Research Council(BBSRC:BBS/E/J/000PR9788)。
文摘RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes(e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
