Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

BackgroundSingle-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve.ResultsWe introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods.ConclusionsSlingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression

Large Scale Spectral Clustering Using Approximate Commute Time Embedding

Spectral clustering is a novel clustering method which can detect complex shapes of data clusters. However, it requires the eigen decomposition of the graph Laplacian matrix, which is proportion to $O(n^3)$ and thus is not suitable for large scale systems. Recently, many methods have been proposed to accelerate the computational time of spectral clustering. These approximate methods usually involve sampling techniques by which a lot information of the original data may be lost. In this work, we propose a fast and accurate spectral clustering approach using an approximate commute time embedding, which is similar to the spectral embedding. The method does not require using any sampling technique and computing any eigenvector at all. Instead it uses random projection and a linear time solver to find the approximate embedding. The experiments in several synthetic and real datasets show that the proposed approach has better clustering quality and is faster than the state-of-the-art approximate spectral clustering methods

Geometry-Aware Neighborhood Search for Learning Local Models for Image Reconstruction

Local learning of sparse image models has proven to be very effective to solve inverse problems in many computer vision applications. To learn such models, the data samples are often clustered using the K-means algorithm with the Euclidean distance as a dissimilarity metric. However, the Euclidean distance may not always be a good dissimilarity measure for comparing data samples lying on a manifold. In this paper, we propose two algorithms for determining a local subset of training samples from which a good local model can be computed for reconstructing a given input test sample, where we take into account the underlying geometry of the data. The first algorithm, called Adaptive Geometry-driven Nearest Neighbor search (AGNN), is an adaptive scheme which can be seen as an out-of-sample extension of the replicator graph clustering method for local model learning. The second method, called Geometry-driven Overlapping Clusters (GOC), is a less complex nonadaptive alternative for training subset selection. The proposed AGNN and GOC methods are evaluated in image super-resolution, deblurring and denoising applications and shown to outperform spectral clustering, soft clustering, and geodesic distance based subset selection in most settings.Comment: 15 pages, 10 figures and 5 table