Single-cell consensus clustering (SC3) provides user-friendly, robust and accurate cell clustering as well as downstream analysis for single-cell RNA-seq data. Single-cell RNA-seq enables the quantitative characterization of cell types based on global transcriptome profiles. We present single-cell consensus clustering (SC3), a user-friendly tool for unsupervised clustering, which achieves high accuracy and robustness by combining multiple clustering solutions through a consensus approach ( http://bioconductor.org/packages/SC3 ). We demonstrate that SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.

We quantify the dynamical implications of the small-world phenomenon by considering the generic synchronization of oscillator networks of arbitrary topology. The linear stability of the synchronous state is linked to an algebraic condition of the Laplacian matrix of the network. Through numerics and analysis, we show how the addition of random shortcuts translates into improved network synchronizability. Applied to networks of low redundancy, the small-world route produces synchronizability more efficiently than standard deterministic graphs, purely random graphs, and ideal constructive schemes. However, the small-world property does not guarantee synchronizability: the synchronization threshold lies within the boundaries, but linked to the end of the small-world region.

The complexity of biological, social, and engineering networks makes it desirable to find natural partitions into clusters (or communities) that can provide insight into the structure of the overall system and even act as simplified functional descriptions. Although methods for community detection abound, there is a lack of consensus on how to quantify and rank the quality of partitions. We introduce here the stability of a partition, a measure of its quality as a community structure based on the clustered autocovariance of a dynamic Markov process taking place on the network. Because the stability has an intrinsic dependence on time scales of the graph, it allows us to compare and rank partitions at each time and also to establish the time spans over which partitions are optimal. Hence the Markov time acts effectively as an intrinsic resolution parameter that establishes a hierarchy of increasingly coarser communities. Our dynamical definition provides a unifying framework for several standard partitioning measures: modularity and normalized cut size can be interpreted as one-step time measures, whereas Fiedler’s spectral clustering emerges at long times. We apply our method to characterize the relevance of partitions over time for constructive and real networks, including hierarchical graphs and social networks, and use it to obtain reduced descriptions for atomic-level protein structures over different time scales.

Most methods proposed to uncover communities in complex networks rely on combinatorial graph properties. Usually an edge-counting quality function, such as modularity, is optimized over all partitions of the graph compared against a null random graph model. Here we introduce a systematic dynamical framework to design and analyze a wide variety of quality functions for community detection. The quality of a partition is measured by its Markov Stability, a time-parametrized function defined in terms of the statistical properties of a Markov process taking place on the graph. The Markov process provides a dynamical sweeping across all scales in the graph, and the time scale is an intrinsic parameter that uncovers communities at different resolutions. This dynamic-based community detection leads to a compound optimization, which favours communities of comparable centrality (as defined by the stationary distribution), and provides a unifying framework for spectral algorithms, as well as different heuristics for community detection, including versions of modularity and Potts model. Our dynamic framework creates a systematic link between different stochastic dynamics and their corresponding notions of optimal communities under distinct (node and edge) centralities. We show that the Markov Stability can be computed efficiently to find multi-scale community structure in large networks.

We introduce the concept of natural connectivity as a measure of structural robustness in complex networks. The natural connectivity characterizes the redundancy of alternative routes in a network by quantifying the weighted number of closed walks of all lengths. This definition leads to a simple mathematical formulation that links the natural connectivity to the spectrum of a network. The natural connectivity can be regarded as an average eigenvalue that changes strictly monotonically with the addition or deletion of edges. We calculate both analytically and numerically the natural connectivity of three typical networks: regular ring lattices, random graphs, and random scale-free networks. We also compare the proposed natural connectivity to other structural robustness measures within a scenario of edge elimination and demonstrate that the natural connectivity provides sensitive discrimination of structural robustness that agrees with our intuition.