Benchmarking algorithms for single-cell multi-omics prediction and integration.

The development of single-cell multi-omics technology has greatly enhanced our understanding of biology, and in parallel, numerous algorithms have been proposed to predict the protein abundance and/or chromatin accessibility of cells from single-cell transcriptomic information and to integrate various types of single-cell multi-omics data. However, few studies have systematically compared and evaluated the performance of these algorithms. Here, we present a benchmark study of 14 protein abundance/chromatin accessibility prediction algorithms and 18 single-cell multi-omics integration algorithms using 47 single-cell multi-omics datasets.

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution.

Spatial transcriptomics approaches have substantially advanced our capacity to detect the spatial distribution of RNA transcripts in tissues, yet it remains challenging to characterize whole-transcriptome-level data for single cells in space. Addressing this need, researchers have developed integration methods to combine spatial transcriptomic data with single-cell RNA-seq data to predict the spatial distribution of undetected transcripts and/or perform cell type deconvolution of spots in histological sections. However, to date, no independent studies have comparatively analyzed these integration methods to benchmark their performance.

WEDGE: imputation of gene expression values from single-cell RNA-seq datasets using biased matrix decomposition.

The low capture rate of expressed RNAs from single-cell sequencing technology is one of the major obstacles to downstream functional genomics analyses. Recently, a number of imputation methods have emerged for single-cell transcriptome data, however, recovering missing values in very sparse expression matrices remains a substantial challenge. Here, we propose a new algorithm, WEDGE (WEighted Decomposition of Gene Expression), to impute gene expression matrices by using a biased low-rank matrix decomposition method.

Spectral Mesh Segmentation via l Gradient Minimization.

Mesh segmentation is a process of partitioning a mesh model into meaningful parts - a fundamental problem in various disciplines. This paper introduces a novel mesh segmentation method inspired by sparsity pursuit. Based on the local geometric and topological information of a given mesh, we build a Laplacian matrix whose Fiedler vector is used to characterize the uniformity among elements of the same segment.

Diffusion equations over arbitrary triangulated surfaces for filtering and texture applications.

In computer graphics, triangular mesh representations of surfaces have become very popular. Compared with parametric and implicit forms of surfaces, triangular mesh surfaces have many advantages, such as easy to render, convenient to store and the ability to model geometric objects with arbitrary topology. In this paper, we are interested in data processing over triangular mesh surfaces through PDEs (partial differential equations).