Amid recent advances for multivariate time series forecasting, self-supervised learning has emerged as a promising paradigm for deriving transferable knowledge from multi-domain data. Despite its effectiveness, existing approaches exhibit two critical limitations: (1) Underestimating the significance of multivariate dependencies in learning generalizable representations and (2) Failing to reconcile the complementary strengths of autoregressive and one-shot generative paradigms. In this work, we propose TimeCAP, a novel channel-aware pre-training framework that internalizes latent causal relationships among variables inherent in multi-domain data, and effectively transfers the acquired knowledge to downstream applications. Technically, we present a flexible channel-grouping learning approach, complemented by an adaptive meta-routing mechanism, enabling TimeCAP to parallel recognize intra-group local patterns while maintaining global coherence. Intra- and inter-group multivariate dependencies are captured through the self- and cross-attention with channel-aware mask, which strictly confine interactions among time-aligned, fine-grained multivariate tokens. To seamlessly unify two advanced generative paradigms, we propose a novel dynamic dual-head decoding and optimization strategy, empowering TimeCAP to leverage critical dependencies in the output series while avoiding cumulative errors over time. In the few-shot evaluation, TimeCAP achieves average MSE and MAE reductions of 11.8% and 6% over leading baselines, while also outperforming state-of-the-art models in full-shot and zero-shot settings by large margins.

Single-cell RNA sequencing technology holds significant importance in biomedical research, yet its inherent characteristics—including high dimensionality, technical noise, and sparsity—pose substantial challenges for cellular clustering analysis. To address these limitations, this paper introduces scDVCC, a novel deep clustering framework for scRNA-seq data based on dual-view contrastive learning. Our approach constructs dual views through K-nearest neighbor graphs and diffusion maps, employs graph neural networks integrated with zero-inflated negative binomial distribution for data modeling, and incorporates an dual-contrastive learning mechanism encompassing both instance-level and cluster-level discrimination enhancement. Experimental validation demonstrates that scDVCC significantly outperforms seven advanced methods across nine benchmark datasets. This advancement holds strong potential to facilitate applications of single-cell data analysis in deciphering cellular heterogeneity and elucidating disease mechanisms.

Graph neural networks (GNNs), as a rising star in machine learning, are widely used in relational data models and have achieved outstanding performance in graph tasks. GNN continuously takes inspiration from mature models in other domains such as computer vision and natural language processing to motivate the development of graph algorithms. However, due to the various data structures from different domains, the cross-domain migration of models has to go through a long period of disassembly and reconstruction, which may not yield the desired results. To preserve the excellent properties of convolution and optimize the migration process from convolutional neural networks (CNNs) to GNNs, we propose a convolution bridge. The convolution bridge realizes the data alignment from CNN to GNN, so that the CNN-based model can be efficiently migrated to the graph structure model. To demonstrate the effectiveness of our migration strategy, we migrated the inception module and U-Net architecture from CNNs to GNNs, named GraInc and GraU-Net, for the node-level task and the graph-level task, respectively. Experimental results show that GraInc and GraU-Net are highly competitive compared to the current state-of-the-art models, particularly on dense graph datasets.

Cluster assignment is crucial for analyzing single-cell RNA sequencing (scRNA-seq) data, essential for studying cell diversity and biological functions at the single-cell level. Deep learning-based clustering methods have been extensively applied in scRNA-seq data analysis. However, current deep models frequently overlook the deep exploration of potential gene correlation, resulting in networks lacking guidance from gene correlation information when learning hidden layer features. This paper proposes an adaptive feedback fuzzy clustering method based on deep gene correlation mining(scDCMAC). The deep gene correlation mining network employs contrast learning to compute the contrast loss on two cell similarity matrices, constructed from denoised autoencoder hidden layer features and original input features, to uncover potential gene correlation. The adaptive feedback clustering network further denoises the hidden layer features using a self-attention mechanism, computes the affiliation matrix, and supervises the denoising autoencoder’s dimensionality reduction using the affiliation matrix. Experiments on 13 real scRNA-seq datasets demonstrate that scDCMAC excels in clustering accuracy and stability, showing great potential in scRNA-seq sample analysis.

Single-cell sequencing technologies allow for a high-resolution examination of various biological activities, such as the genome, transcriptome, and epigenetic modifications, across thousands of cells. In contrast, single-omics approaches fall short in fully capturing the intricate molecular mechanisms. In this regrad, integrating multi-omics data can potentially provide a more comprehensive understanding of fundamental biological processes. Although sequencing technologies have emerged that can simultaneously obtain different omics from single cells, they are limited by throughput and the types of omics. A more common scenario is that data from different omics are measured independently, resulting in unpaired cell compositions. Therefore, efficient algorithms are needed to integrate and analyze unpaired multi-omics data.In this study, we propose a novel framework for integrating unpaired single-cell multi-omics data based on the Kolmogorov-Arnold deep embedding model (scKADE). This framework introduces Kolmogorov–Arnold Networks (KAN) to map different omics data to a unified common feature space for adversarial alignment. Furthermore, to assess the contribution of different cells in data integration, we employ an unsupervised weight estimation algorithm to enhance the alignment quality.