颜林林 (2022-09-19 22:00):
#paper doi:10.1038/s41598-022-17585-2 Scientific Reports, 2022, Recursive integration of synergised graph representations of multi‑omics data for cancer subtypes identification. 随着高通量测序技术在不同组学水平上的应用,肿瘤研究也早已进入多组学研究阶段。如何将多组学高维数据进行有效整合,一直是一项有挑战的工作。与此相关的方法学研发工作,大多聚焦于单组学数据的各类降维和特征提取。本文开发了一个名为RISynG(Recursive Integration of Synergised Graph-representations)的方法,通过从原始的组学数据中提取Gramian和Laplacian两个表征矩阵(representation matrices),使整合不同组学之间更加有效。相比过去大多数将多组学数据进行简单串联堆叠的方式,能够取得更好的分类效果,实现基于肿瘤多组学数据(如TCGA)进行肿瘤分型。
IF:3.800Q1 Scientific reports, 2022-09-17. DOI: 10.1038/s41598-022-17585-2 PMID: 36115864
Recursive integration of synergised graph representations of multi-omics data for cancer subtypes identification
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Abstract:
Cancer subtypes identification is one of the critical steps toward advancing personalized anti-cancerous therapies. Accumulation of a massive amount of multi-platform omics data measured across the same set of samples provides an opportunity to look into this deadly disease from several views simultaneously. Few integrative clustering approaches are developed to capture shared information from all the views to identify cancer subtypes. However, they have certain limitations. The challenge here is identifying the most relevant feature space from each omic view and systematically integrating them. Both the steps should lead toward a global clustering solution with biological significance. In this respect, a novel multi-omics clustering algorithm named RISynG (Recursive Integration of Synergised Graph-representations) is presented in this study. RISynG represents each omic view as two representation matrices that are Gramian and Laplacian. A parameterised combination function is defined to obtain a synergy matrix from these representation matrices. Then a recursive multi-kernel approach is applied to integrate the most relevant, shared, and complementary information captured via the respective synergy matrices. At last, clustering is applied to the integrated subspace. RISynG is benchmarked on five multi-omics cancer datasets taken from The Cancer Genome Atlas. The experimental results demonstrate RISynG's efficiency over the other approaches in this domain.
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