Multimodal omics provide deeper insight into the biological processes and cellular functions, especially transcriptomics and proteomics. Computational methods have been proposed for the integration of single-cell multimodal omics of transcriptomics and proteomics. However, existing methods primarily concentrate on the alignment of different omics, overlooking the unique information inherent in each omics type. Moreover, as the majority of single-cell cohorts only encompass one omics, it becomes critical to transfer the knowledge learnt from multimodal omics to enhance unimodal omics analysis. Therefore, we proposed a novel framework that leverages masked autoencoder with cross-attention mechanism, called scMMAE (single-cell multimodal masked autoencoder), to fuse multimodal omics and enhance unimodal omics analysis. scMMAE simultaneously captures both the shared features and the distinctive information of two single-cell omics modalities and transfers the knowledge to enhance single-cell transcriptome data. Comparative evaluations against benchmarking methods across various cohorts revealed a notable improvement, with an increase of up to 21% in the adjusted Rand index and up to 12% in normalized mutual information in the context of multimodal fusion. In the realm of unimodal omics, scMMAE demonstrated an overall enhancement of approximately 20% in the adjusted Rand index and nearly 10% in normalized mutual information. Other nine metrics, including the Fowlkes-Mallows index and silhouette coefficient, further underscored the high performance of scMMAE. Significantly, scMMAE exhibits an elevated level of proficiency in distinguishing between different cell types, particularly on CD4 and CD8 T cells. Availability and implementation: scMMAE source code at https://github.com/DM0815/scMMAE/.

Distributed machine learning (DML) enables model training on a large corpus of decentralized data from users and only collects local models or gradients for global synchronization on the cloud. Recent studies show that a third party can recover the training data in the DML system through publicly shared gradients. Our investigation has revealed that existing techniques (e.g., DLG) can only recover the training data on uniform weight distribution and fail to recover the training data on other weights initialization (e.g., normal distribution) or during the training stage. In this work, we provide an analysis of how weight distribution can affect the training data recovery from gradients. Based on this analysis, we propose a self-adaptive privacy attack from gradients, SAPAG—a general gradient attack algorithm that can recover the training data in DML with any weight initialization and in any training phase. Our algorithm exploits not only the gradients but also the variance of gradients. Specifically, we exploit the variance of gradients distribution and the Deep Neural Network (DNN) architecture and design an adaptive Gaussian kernel of gradient difference as a distance measure. Our experimental results on various benchmark datasets and tasks demonstrate the generalizability of SAPAG. SAPAG outperforms the state-of-the-art algorithms in terms of both the data recovery performance and the recovery speed.

Neural Ordinary Differential Equation (Neural ODE) has been proposed as a continuous approximation to the ResNet architecture. Some commonly used regularization mechanisms in discrete neural networks (e.g., dropout, Gaussian noise) are missing in current Neural ODE networks. In this paper, we propose a new continuous neural network framework called Neural Stochastic Differential Equation (Neural SDE), which naturally incorporates various commonly used regularization mechanisms based on random noise injection. For regularization purposes, our framework includes multiple types of noise patterns, such as dropout, additive, and multiplicative noise, which are common in plain neural networks. We provide some theoretical analyses explaining the improved robustness of our models against input perturbations. Furthermore, we demonstrate that the Neural SDE network can achieve better generalization than the Neural ODE and is more resistant to adversarial and non-adversarial input perturbations.

Data deduplication as an important middleware plays an essential role in current backup systems due to the high space efficiency, which however suffers from low restore performance, since the chunks are heavily fragmented. Existing systems leverage caching and rewriting schemes to reduce the number of container reads to restore the original data. However, when storing a large number of versions, the caching schemes become inefficient since each cached container consists of a few required chunks due to the exacerbated fragmentation, while the rewriting schemes consume more space to store the duplicate chunks.

Since the 1st discovery of transcriptional enhancers in 1981, their textbook definition has remained largely unchanged in the past 37 years. With the emergence of high-throughput assays and genome editing, which are switching the paradigm from bottom-up discovery and testing of individual enhancers to top-down profiling of enhancer activities genome-wide, it has become increasingly evidenced that this classical definition has left substantial gray areas in different aspects. Here we survey a representative set of recent research articles and report the definitions of enhancers they have adopted. The results reveal that a wide spectrum of definitions is used usually without the definition stated explicitly, which could lead to difficulties in data interpretation and downstream analyses. Based on these findings, we discuss the practical implications and suggestions for future studies.