MOTIVATION: Clustering analysis for single-cell RNA sequencing (scRNA-seq) data is an important step in revealing cellular heterogeneity. Many clustering methods have been proposed to discover heterogenous cell types from scRNA-seq data. However, adaptive clustering with accurate cluster number reflecting intrinsic biology nature from large-scale scRNA-seq data remains quite challenging. RESULTS: Here, we propose a single-cell Deep Adaptive Clustering (scDAC) model by coupling the Autoencoder (AE) and the Dirichlet Process Mixture Model (DPMM). By jointly optimizing the model parameters of AE and DPMM, scDAC achieves adaptive clustering with accurate cluster numbers on scRNA-seq data. We verify the performance of scDAC on five subsampled datasets with different numbers of cell types and compare it with 15 widely used clustering methods across nine scRNA-seq datasets. Our results demonstrate that scDAC can adaptively find accurate numbers of cell types or subtypes and outperforms other methods. Moreover, the performance of scDAC is robust to hyperparameter changes. AVAILABILITY AND IMPLEMENTATION: The scDAC is implemented in Python. The source code is available at https://github.com/labomics/scDAC.

Most existing multiview clustering methods require that graph matrices in different views are computed beforehand and that each graph is obtained independently. However, this requirement ignores the correlation between multiple views. In this letter, we tackle the problem of multiview clustering by jointly optimizing the graph matrix to make full use of the data correlation between views. With the interview correlation, a concept factorization-based multiview clustering method is developed for data integration, and the adaptive method correlates the affinity weights of all views. This method differs from nonnegative matrix factorization-based clustering methods in that it can be applicable to data sets containing negative values. Experiments are conducted to demonstrate the effectiveness of the proposed method in comparison with state-of-the-art approaches in terms of accuracy, normalized mutual information, and purity.

We propose a novel multi-view document clustering method with the graph-regularized concept factorization (MVCF). MVCF makes full use of multi-view features for more comprehensive understanding of the data and learns weights for each view adaptively. It also preserves the local geometrical structure of the manifolds for multi-view clustering. We have derived an efficient optimization algorithm to solve the objective function of MVCF and proven its convergence by utilizing the auxiliary function method. Experiments carried out on three benchmark datasets have demonstrated the effectiveness of MVCF in comparison to several state-of-the-art approaches in terms of accuracy, normalized mutual information and purity.

Inspired by gamma-band oscillations and other neurobiological discoveries, neural networks research shifts the emphasis toward temporal coding, which uses explicit times at which spikes occur as an essential dimension in neural representations. We present a feature-linking model (FLM) that uses the timing of spikes to encode information. The first spiking time of FLM is applied to image enhancement, and the processing mechanisms are consistent with the human visual system. The enhancement algorithm achieves boosting the details while preserving the information of the input image. Experiments are conducted to demonstrate the effectiveness of the proposed method. Results show that the proposed method is effective.

Spiking cortical model (SCM) is applied to image segmentation. A natural image is processed to produce a series of spike images by SCM, and the segmented result is obtained by the integration of the series of spike images. An appropriate maximum iterative times is selected to achieve an optimal threshold of SCM. In each iteration, neurons that produced spikes correspond to pixels with an intensity of the input natural image approximately. SCM synchronizes the output spikes via the fast linking synaptic modulation, which makes objects in the image as homogeneous as possible. Experimental results show that the output image not only separates objects and background well, but also pixels in each object are homogeneous. The proposed method performs well over other methods and the quantitative metrics are consistent with the visual performance.