BackgroundVariations in DNA copy number have an important contribution to the development of several diseases, including autism, schizophrenia and cancer. Single-cell sequencing technology allows the dissection of genomic heterogeneity at the single-cell level, thereby providing important evolutionary information about cancer cells. In contrast to traditional bulk sequencing, single-cell sequencing requires the amplification of the whole genome of a single cell to accumulate enough samples for sequencing. However, the amplification process inevitably introduces amplification bias, resulting in an over-dispersing portion of the sequencing data. Recent study has manifested that the over-dispersed portion of the single-cell sequencing data could be well modelled by negative binomial distributions.ResultsWe developed a read-depth based method, nbCNV to detect the copy number variants (CNVs). The nbCNV method uses two constraints-sparsity and smoothness to fit the CNV patterns under the assumption that the read signals are negatively binomially distributed. The problem of CNV detection was formulated as a quadratic optimization problem, and was solved by an efficient numerical solution based on the classical alternating direction minimization method.ConclusionsExtensive experiments to compare nbCNV with existing benchmark models were conducted on both simulated data and empirical single-cell sequencing data. The results of those experiments demonstrate that nbCNV achieves superior performance and high robustness for the detection of CNVs in single-cell sequencing data.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1239-7) contains supplementary material, which is available to authorized users.

Both the shared and individual patterns can be uniquely characterized as well as effectively decomposed within the wavelet space.

In this paper, a plane spiral orbital angular momentum (PS-OAM) mode-groups (MGs) based multi-user multiple-input-multiple-output (MIMO) non-orthogonal multiple access (NOMA) system is studied, where a base station (BS) transmits date to multiple users by utilizing the generated PSOAM beams. For such scenario, the interference between users in different PSOAM-mode groups can be avoided, which leads to a significant performance enhancement. We aim to maximize the energy efficiency (EE) of the system subject to the total transmission power constraint and the minimum rate constraint. This design problem is non-convex by optimizing the power allocation, and thus is quite difficult to tackle directly. To solve this issue, we present a bisection-based power allocation algorithm where the bisection method is exploited in the outer layer to obtain the optimal EE and a power distributed iterative algorithm is exploited in the inner layer to optimize the transmit power. Simulation results validate the theoretical findings and demonstrate the proposed system can achieve better performance than the traditional multi-user MIMO system in terms of EE.

Revealing data with intrinsically diagonal block structures is particularly useful for analyzing groups of highly correlated variables. Earlier researches based on non-negative matrix factorization (NMF) have been shown to be effective in representing such data by decomposing the observed data into two factors, where one factor is considered to be the feature and the other the expansion loading from a linear algebra perspective. If the data are sampled from multiple independent subspaces, the loading factor would possess a diagonal structure under an ideal matrix decomposition. However, the standard NMF method and its variants have not been reported to exploit this type of data via direct estimation. To address this issue, a non-negative matrix factorization with multiple constraints model is proposed in this paper. The constraints include an sparsity norm on the feature matrix and a total variational norm on each column of the loading matrix. The proposed model is shown to be capable of efficiently recovering diagonal block structures hidden in observed samples. An efficient numerical algorithm using the alternating direction method of multipliers model is proposed for optimizing the new model. Compared with several benchmark models, the proposed method performs robustly and effectively for simulated and real biological data.

Plane spiral orbital angular momentum (PSOAM) mode-groups (MGs) and multiple-input multiple-output nonorthogonal multiple access (MIMO-NOMA) serve as two emerging techniques for achieving high spectral efficiency (SE) in the next-generation networks. In this paper, a PSOAM MGs based multi-user MIMO-NOMA system is studied, where the base station transmits data to users by utilizing the generated PSOAM beams. For such scenario, the interference between users in different PSOAM mode groups can be avoided, which leads to a significant performance enhancement. We aim to maximize the energy efficiency (EE) of the system subject to the constraints of the total transmission power and the minimum data rate. This designed optimization problem is non-convex owing to the interference among users, and hence is quite difficult to tackle directly. To solve this issue, we develop a dual layer resource allocation algorithm where the bisection method is exploited in the outer layer to obtain the optimal EE and a resource distributed iterative algorithm is exploited in the inner layer to optimize the transmit power. Besides, an alternative resource allocation algorithm with Deep Belief Networks (DBN) is proposed to cope with the requirement for low computational complexity. Simulation results verify the theoretical findings and demonstrate the proposed algorithms on the PSOAM MGs based MIMO-NOMA system can obtain a better performance comparing to the conventional MIMO-NOMA system in terms of EE.