Graph-linked unified embedding
WebGraph-linked unified embedding for single-cell multi-omics data integration For more details, please check out our publication. Directory structure WebMulti-omics single-cell data integration and regulatory inference with graph-linked embedding. ZJ Cao, G Gao. Nature Biotechnology 40 (10), 1458-1466, 2024. 54: ...
Graph-linked unified embedding
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WebRecently, Cao and Gao developed a computational method, named GLUE (graph-linked unified embedding), 8 to fill the gap through modelling regulatory interactions across … WebA consensus graph is adaptively learned and embedded via the reverse graph regularization to guarantee the common local structure of multiple views and in turn can further align the incomplete views and inferred views. Moreover, an adaptive weighting strategy is designed to capture the importance of different views.
WebMay 1, 2024 · A new study presents GLUE (graph-linked unified embedding), a generalizable computational framework for integrating unpaired single-cell multi-omics … WebFeb 3, 2024 · Graph embeddings are calculated using machine learning algorithms. Like other machine learning systems, the more training data we have, the better our embedding will embody the uniqueness of an item. The process of creating a new embedding vector is called “encoding” or “encoding a vertex”.
WebSep 6, 2024 · With the ever-increasing amount of single-cell multi-omics data accumulated during the past years, effective and efficient computational integration is becoming a … We assume that there are K different omics layers to be integrated, each with a distinct feature set \({{{\mathcal{V}}}}_k,k = 1,2, \ldots ,K\). For example, in scRNA-seq, \({\mathcal{V}}_k\) is the set of genes, while in scATAC-seq, \({{{\mathcal{V}}}}_k\) is the set of chromatin regions. The data … See more As shown in previous work31, canonical adversarial alignment amounts to minimizing a generalized form of Jensen–Shannon divergence among the cell embedding distributions of different omics layers: where … See more We applied linear dimensionality reduction using canonical methods such as PCA (for scRNA-seq) or LSI (latent semantic indexing, for scATAC … See more To handle batch effect within omics layers, we incorporate batch as a covariate of the data decoders. Assuming \(b \in \left\{ {1,2, \ldots ,B} \right\}\), is the batch index, where B is the total number of batches, the decoder … See more The integration consistency score is a measure of consistency between the integrated multi-omics data and the guidance graph. First, we jointly cluster cells from all omics layers in the aligned cell embedding … See more
WebHere, we propose a computational framework called GLUE (graph-linked unified embedding), which bridges the gap by modeling regulatory interactions across omics …
WebJul 10, 2024 · The core of our algorithm is the use of vertex embeddings created from our Knowledge Graph. Representing vertices with embeddings allows encoding in a low-dimensional space the complex topological relationships that … cities around kansas city moWebMay 19, 2024 · A new study presents GLUE (graph-linked unified embedding), a generalizable computational framework for integrating unpaired single-cell multi … diarium mood trackerWebHere, we propose a computational framework called GLUE (graph-linked unified embedding), which bridges the gap by modeling regulatory interactions across omics layers explicitly. Systematic... cities around houston tx mapWebMay 2, 2024 · Here, we propose a computational framework called GLUE (graph-linked unified embedding), which bridges the gap by modeling regulatory interactions across omics layers explicitly. Systematic benchmarking demonstrated that GLUE is more accurate, robust and scalable than state-of-the-art tools for heterogeneous single-cell multi-omics … cities around lancaster paWebJun 15, 2024 · Graph clustering is a fundamental task which discovers communities or groups in networks. Recent studies have mostly focused on developing deep learning … diarmaid flynnWeb(graph-linked unified embedding), which bridges the gap by modeling regulatory interactions across omics layers explicitly. Systematic benchmarking demonstrated that … cities around la crosse wiWebMar 24, 2024 · A graph embedding, sometimes also called a graph drawing, is a particular drawing of a graph. Graph embeddings are most commonly drawn in the plane, but may … cities around lima ohio