With the rapid advance of spatial multi-omics technologies, it has become possible to simultaneously profile transcripts, proteins and chromatin states at their native spatial coordinates, thereby uncovering molecular architecture that transcends any single-omics perspective. However, the resulting data matrices are often highly sparse and suffer from unstable dimensionality. Graph-based neural methods capture only local neighborhood information, whereas conventional Transformers, although capable of modelling long-range dependencies, incur prohibitive computational costs on such data. To overcome these limitations, we propose TLAGC—a Taylor-Linear-Attention-Guided Graph Convolutional framework that couples a Taylor-expanded linear attention (TLA) mechanism with graph convolutional networks. By eliminating the soft-max operation and linking the LocalGCN via residual connections, TLA preserves local structural information while enabling the integration of global and local contexts, thereby alleviating ineffective information propagation between spatially distant yet transcriptionally similar regions. Theoretical analysis confirms that TLA indeed reduces computational complexity, and extensive experiments on multiple spatial multi-omics benchmarks demonstrate that TLAGC consistently outperforms state-of-the-art baselines in delineating spatial domains.

Lysine crotonylation (Kcr) is an important protein modification occurring after translation in biology, serving an essential function in a range of biological processes in both plants and animals, including the regulation of gene expression, the maintenance of cellular metabolic balance, and the enhancement of photosynthesis. Exploring the detection of Kcr sites is essential for uncovering their biological functions. Nonetheless, conventional experimental approaches for detection are often time-consuming, expensive, and hindered by various technical constraints, making the precise identification of Kcr sites a significant challenge. This study seeks to develop a computational approach for the rapid and accurate prediction of Kcr sites in plant non-histone proteins. We introduce a novel deep learning framework named DeepNhKcr, which integrates the protein language model (ESM2) with a bidirectional long short-term memory (BiLSTM) network. To address the challenge of data imbalance, the model replaces the conventional cross-entropy loss with the focal loss function. In addition, DeepNhKcr combines advanced deep learning approaches with traditional protein encoding strategies to enable effective feature extraction and integration. This method not only significantly boosts the accuracy of predicting Kcr sites in non-histone proteins of plants. but also provides interpretability, shedding light on the potential links between key sequence characteristics and their biological roles. DeepNhKcr delivers outstanding results, surpassing existing machine learning and deep learning models, and demonstrating excellent performance in both five-fold cross-validation and independent test experiments. Moreover, the model integrates interpretability analysis techniques to investigate the connections between important sequence features and their biological roles. DeepNhKcr acts as a powerful method for detecting Kcr sites in plant non-histone proteins and is anticipated to greatly advance future studies in plant Kcr site prediction.

Spatial transcriptomics analysis methods offer an opportunity to investigate highly diverse biological tissues. Cell-cell communication is fundamental for maintaining physiological homeostasis in organisms and coordinating complex biological processes. Identifying cell-cell interactions is critical for understanding cellular activities. The interaction of a cell with other cells depends on several factors, and most of the existing methods that consider only gene expression information of neighbouring cells and spatial location information are somewhat limited. In this paper, we propose a network architecture based on graph convolution network and long short-term memory attention module-GCNLA, which contains graph convolution layer, long short-term memory network, attention module, and residual connections. GCNLA not only learns the spatial structure of cells but also captures interaction information between distal cells, the attention module further extracting and enhancing features related to cell-cell interactions. Finally, the inner product decoding calculates the cosine similarity, which is used to infer cell-cell interactions. In addition, GCNLA is capable of reconstructing the complete cell-cell interaction network. The experimental results on seqFISH and MERFISH demonstrate that the GCNLA network structure has better robustness and noise immunity. The potential features learned by GCNLA enable other downstream analyses, including single-cell resolution cell clustering based on spatial information resolving cell heterogeneity.

Engine data management is of great significance for ensuring data security and sharing, as well as facilitating multi-party collaborative learning. Traditional data management approaches often involve decentralized data storage that is vulnerable to tampering, making it challenging to conduct multi-party collaborative learning under privacy protection conditions and fully leverage the value of data. Moreover, data with compromised integrity can lead to incorrect results if used for model training. Therefore, this paper aims to break down data sharing barriers and fully utilize decentralized data for multi-party collaborative learning under privacy protection conditions. We propose a trustworthy engine data management method based on blockchain technology to ensure data immutability and non-repudiation. To address the issue of limited data samples for some users resulting in poor model performance, we introduce swarm learning techniques based on centralized machine learning and design a trustworthy data management method for swarm learning, achieving trustworthy regulation of the entire process. We conduct research on engine models under swarm learning based on the NASA open dataset, effectively organizing decentralized data samples for collaborative training while ensuring data privacy and fully leveraging the value of data.