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The gene regulatory structure of cells involves not only the regulatory relationship between two genes, but also the cooperative associations of multiple genes. However, most gene regulatory network inference methods for single cell only focus on and infer the regulatory relationships of pairs of genes, ignoring the global regulatory structure which is crucial to identify the regulations in the complex biological systems. Here, we proposed a graph-based Deep learning model for Regulatory networks Inference among Genes (DeepRIG) from single-cell RNA-seq data. To learn the global regulatory structure, DeepRIG builds a prior regulatory graph by transforming the gene expression of data into the co-expression mode. Then it utilizes a graph autoencoder model to embed the global regulatory information contained in the graph into gene latent embeddings and to reconstruct the gene regulatory network. Extensive benchmarking results demonstrate that DeepRIG can accurately reconstruct the gene regulatory networks and outperform existing methods on multiple simulated networks and real-cell regulatory networks. Additionally, we applied DeepRIG to the samples of human peripheral blood mononuclear cells and triple-negative breast cancer, and presented that DeepRIG can provide accurate cell-type-specific gene regulatory networks inference and identify novel regulators of progression and inhibition. Author summary: Although many methods have been proposed to infer the gene regulatory network of a single cell, they only focus on the regulatory relationships of pairs of genes and ignore the global regulatory structure. Here, we present a deep learning-based model to learn the global regulatory structure and reconstruct the gene regulatory networks from single-cell RNA sequencing data with a graph view. We utilize the weighted gene co-expression analysis to build a prior regulatory graph of gene and a graph autoencoder to deconstruct the latent regulatory structure among genes. We performed extensive experiments on varieties of single-cell RNA sequencing datasets and compared our method with 9 stat-of-the-art gene regulatory network inference method. The results show that our method can significantly improve the accuracy of gene regulatory network inference and can be applied to identify key regulators in a wide range of scenarios. [ABSTRACT FROM AUTHOR]

Emerging evidence indicates that circular RNAs (circRNAs) can provide new insights and potential therapeutic targets for disease diagnosis and treatment. However, traditional biological experiments are expensive and time-consuming. Recently, deep learning with a more powerful ability for representation learning enables it to be a promising technology for predicting disease-associated circRNAs. In this review, we mainly introduce the most popular databases related to circRNA, and summarize three types of deep learning-based circRNA-disease associations prediction methods: feature-generation-based, type-discrimination and hybrid-based methods. We further evaluate seven representative models on benchmark with ground truth for both balance and imbalance classification tasks. In addition, we discuss the advantages and limitations of each type of method and highlight suggested applications for future research. [ABSTRACT FROM AUTHOR]

Modeling-based anti-cancer drug sensitivity prediction has been extensively studied in recent years. While most drug sensitivity prediction models only use gene expression data, the remarkable impacts of gene mutation, methylation, and copy number variation on drug sensitivity are neglected. Drug sensitivity prediction can both help protect patients from some adverse drug reactions and improve the efficacy of treatment. Genomics data are extremely useful for drug sensitivity prediction task. This article reviews the role of drug sensitivity prediction, describes a variety of methods for predicting drug sensitivity. Moreover, the research significance of drug sensitivity prediction, as well as existing problems are well discussed. [ABSTRACT FROM AUTHOR]