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 cross-modal retrieval methods assume the multi-modal training data is complete and has a one-to-one correspondence. However, in the real world, multi-modal data generally suffers from missing modality information due to the uncertainty of data collection and storage processes, which limits the practical application of existing cross-modal retrieval methods. Although some solutions have been proposed to generate the missing modality data using a single pseudo sample, this may lead to incomplete semantic restoration and sub-optimal retrieval results due to the limited semantic information it provides. To address this challenge, this article proposes an Incomplete Cross-Modal Retrieval with Deep Correlation Transfer (ICMR-DCT) method that can robustly model incomplete multi-modal data and dynamically capture the adjacency semantic correlation for cross-modal retrieval. Specifically, we construct intra-modal graph attention-based auto-encoder to learn modality-invariant representations by performing semantic reconstruction through intra-modality adjacency correlation mining. Then, we design dual cross-modal alignment constraints to project multi-modal representations into a common semantic space, thus bridging the heterogeneous modality gap and enhancing the discriminability of the common representation. We further introduce semantic preservation to enhance adjacency semantic information and achieve cross-modal semantic correlation. Moreover, we propose a nearest-neighbor weighting integration strategy with cross-modal correlation transfer to generate the missing modality data according to inter-modality mapping relations and adjacency correlations between each sample and its neighbors, which improves the robustness of our method against incomplete multi-modal training data. Extensive experiments on three widely tested benchmark datasets demonstrate the superior performance of our method in cross-modal retrieval tasks under both complete and incomplete retrieval scenarios. Our used datasets and source codes are available at https://github.com/shidan0122/DCT.git .

Deep hashing reaps the benefits of deep learning and hashing technology, and has become the mainstream of large-scale image retrieval. It generally encodes image into hash code with feature similarity preserving, that is, geometric-structure preservation, and achieves promising retrieval results. In this article, we find that existing geometric-structure preservation manner inadequately ensures feature discrimination, while improving feature discrimination of hash code essentially determines hash learning retrieval performance. This fact principally spurs us to propose a discriminative geometric-structure-based deep hashing method (DGDH), which investigates three novel loss terms based on class centers to induce the so-called discriminative geometrical structure. In detail, the margin-aware center loss assembles samples in the same class to the corresponding class centers for intraclass compactness, then a linear classifier based on class center serves to boost interclass separability, and the radius loss further puts different class centers on a hypersphere to tentatively reduce quantization errors. An efficient alternate optimization algorithm with guaranteed desirable convergence is proposed to optimize DGDH. We theoretically analyze the robustness and generalization of the proposed method. The experiments on five popular benchmark datasets demonstrate superior image retrieval performance of the proposed DGDH over several state of the arts.

Sequence logos are used to visually display conservations and variations in short sequences. They can indicate the fixed patterns or conserved motifs in a batch of DNA or protein sequences. However, most of the popular sequence logo generators are based on the assumption that all the input sequences are from the same homologous group, which will lead to an overlook of the heterogeneity among the sequences during the sequence logo making process. Heterogeneous groups of sequences may represent clades of different evolutionary origins, or genes families with different functions. Therefore, it is essential to divide the sequences into different phylogenetic or functional groups to reveal their specific sequence motifs and conservation patterns. To solve these problems, we developed MetaLogo, which can automatically cluster the input sequences after multiple sequence alignment and phylogenetic tree construction, and then output sequence logos for multiple groups and aligned them in one figure. User-defined grouping is also supported by MetaLogo to allow users to investigate functional motifs in a more delicate and dynamic perspective. MetaLogo can highlight both the homologous and nonhomologous sites among sequences. MetaLogo can also be used to annotate the evolutionary positions and gene functions of unknown sequences, together with their local sequence characteristics. We provide users a public MetaLogo web server (http://metalogo.omicsnet.org), a standalone Python package (https://github.com/labomics/MetaLogo), and also a built-in web server available for local deployment. Using MetaLogo, users can draw informative, customized and publishable sequence logos without any programming experience to present and investigate new knowledge on specific sequence sets.

Deep supervised hashing has greatly improved retrieval performance with the powerful learning capability of deep neural network. In multi-label image retrieval, existing deep hashing simply indicates whether two images are similar by constructing a similarity matrix. However, it ignores the dependency among multiple labels that has been shown important in multi-label application. To fulfill this gap, this paper proposes Deep Co-Image-Label Hashing (DCILH) to discover label dependency. Specifically, DCILH regards image and label as two views, and maps the two views into a common deep Hamming space. DCILH proposes to learn prototype for each label, and preserve similarity among images, labels, and prototypes. To exploit label dependency, DCILH further employs the label-correlation aware loss on the predicted labels, such that predicted output on positive label is enforced to be larger than that on negative label. Extensive experiments on several multi-label benchmarks demonstrate the proposed DCILH outperforms state-of-the-art deep supervised hashing on large-scale multi-label image retrieval.

Unsupervised hashing without supervision easily deteriorates in the case of grossly corrupted data. Motivated by robust optimization, this paper proposes a dual-graph regularized robust hashing (DGRH) based on both manifold smoothness and robust estimators in a more intuitive manner. Orthogonal to existing robust hashing methods, DGRH directly removes the outliers of datasets with M-estimator to exert robustness. In specific, it intends to recover low-rank representation from corrupted data via l1loss while preserving neighborhood relationships among samples with dual-graph regularization. Although DGRH seems a simple extension of robust PCA on graphs with hashing trick, it is easy to implement yet effective. Theory analysis is provided to support our claim. Experiments of image retrieval on three popular benchmark datasets show the efficacy of DGRH as compared to several well-behaved representative counterparts.

In unsupervised graph-based hashing for large-scale image retrieval, many efforts have been made to bridge the gap between the learned graph embedding and the corresponding binary codes. Relatively, few studies focus on the issue of the discrimination of graph embedding. In this paper, we firstly devise a discrete graph hashing model (DGH) that smooths graph embedding and simultaneously solving binary codes under the balanced discrete constraint, which equals a novel method of jointly learning graph embedding and spectral rotation, theoretically. To further induce discriminant graph embedding, we substitute affine transformation for spectral rotation in our DGH (abbreviated as ADGH). This is because affine transformation can accommodate both rotational angle and distance of graph embedding, while respecting the neighborhood structure among most samples. Besides, each subproblem of ADGH can yield the closed-form solution. Experiments of image retrieval on three benchmark datasets show that ADGH outperforms the representative hashing methods in quantity.

Current hashing methods for cross-modal retrieval generally attempt to learn the separate modality-specific transformation matrices to embed multi-modality data into a latent common subspace, and usually ignore the fact that respecting the diversity of multi-modality features in the latent subspace could be beneficial for retrieval improvements. To this, we propose a collaborative subspace graph hashing method (CSGH) to perform a two-stage collaborative learning framework for cross-modal retrieval. Particularly, CSGH first embeds multi-modality data into separate latent subspaces through individual modality-specific transformation matrices, and then connects these latent subspaces to a common Hamming space through a shared transformation matrix. In this framework, CSGH considers the modality-specific neighborhood structure and the cross-modal correlation within multi-modality data through the Laplacian regularization and the graph based correlation constraint, respectively. To solve CSGH, we develop an alternative procedure to optimize it, and fortunately, each sub-problem of CSGH has the elegant analytical solution. Experiments of cross-modal retrieval on Wiki, NUS-WIDE, Flickr25K and Flickr1M datasets show the effectiveness of CSGH compared with the state-of-the-art cross-modal hashing methods.

Road networks have significant impact on mobility and network characteristics of wireless ad hoc networks. Discovering their characteristics and effects on mobility and network performance in urban environments is a fundamental research task. In this paper, we firstly study the graph attributes of road networks by sampling real road networks in main cities of Europe and USA. We propose a new graph metric, called characteristic central length, in order to estimate the average shortest-path length of a large-scale spatial network. We find that real road networks from Europe and USA have different patterns with regard to some graph attributes and a simple grid model is inadequate to describe them. Considering the diverse patterns of urban road networks caused by obstacles and shortcuts, we propose a random road network model, called the GRE model. The model is validated through fitting it to real road network samples using a genetic algorithm and simulation of delay-tolerant networks. The simulation results have shown that by extending the grid model with new probabilistic parameters, the GRE model has better capability on approximating real road networks. The simulation results have also shown that delay-tolerant networks operating on road networks may have better performance than scenarios without road networks.

Mobility is an important issue in the research of mobile delay-tolerant networks (DTNs). A simple grid model has been frequently used to simulate urban road networks in geographical restricted mobility models. However, by analyzing graph attributes of some urban road networks in main cities of Europe and USA, we discovered the discrepancy between real road network samples and the grid model. Based on the finding, we proposed a random graph-based road network model, called the Grid Model with Random Edges (GRE). The GRE model extends the basic grid model with new probabilistic parameters and thus has better capabilities to approximate real-world road networks. The model was validated through optimizing model parameter values using a genetic algorithm and comparing graph attributes of road networks generated by the model. It was demonstrated that the GRE model has better capability on approximating real road networks than the grid model, thus providing a better foundation for mobility modeling in mobile DTNs.