Graph clustering aims to divide the graph into different clusters. The recently emerging deep graph clustering approaches are largely built on graph neural networks (GNN). However, GNN is designed for general graph encoding and there is a common issue of representation collapse in existing GNN-based deep graph clustering algorithms. We attribute two main reasons for such issue: (i) the inductive bias of GNN models: GNNs tend to generate similar representations for proximal nodes. Since graphs often contain a non-negligible amount of inter-cluster links, the bias results in error message passing and leads to biased clustering; (ii) the clustering guided loss function: most traditional approaches strive to make all samples closer to pre-learned cluster centers, which cause a degenerate solution assigning all data points to a single label thus make all samples and less discriminative. To address these challenges, we investigate graph clustering from a graph cut perspective and propose an innovative and non-GNN-based Deep Cut-informed Graph embedding and Clustering framework, namely DCGC. This framework includes two modules: (i) cut-informed graph encoding; (ii) self-supervised graph clustering via optimal transport. For the encoding module, we derive a cut-informed graph embedding objective to fuse graph structure and attributes by minimizing their joint normalized cut. For the clustering module, we utilize the optimal transport theory to obtain the clustering assignments, which can balance the guidance of proximity to the pre-learned cluster center. With the above two tailored designs, DCGC is more suitable for the graph clustering task, which can effectively alleviate the problem of representation collapse and achieve better performance. We conduct extensive experiments to demonstrate that our method is simple but effective compared with benchmarks.

This paper develops a comprehensive framework to address three critical trustworthy challenges in federated learning (FL): robustness against Byzantine attacks, fairness, and privacy preservation. To improve the system's defense against Byzantine attacks that send malicious information to bias the system's performance, we develop a Two-sided Norm Based Screening (TNBS) mechanism, which allows the central server to crop the gradients that have the l lowest norms and h highest norms. TNBS functions as a screening tool to filter out potential malicious participants whose gradients are far from the honest ones. To promote egalitarian fairness, we adopt the q-fair federated learning (q-FFL). Furthermore, we adopt a differential privacy-based scheme to prevent raw data at local clients from being inferred by curious parties. Convergence guarantees are provided for the proposed framework under different scenarios. Experimental results on real datasets demonstrate that the proposed framework effectively improves robustness and fairness while managing the trade-off between privacy and accuracy. This work appears to be the first study that experimentally and theoretically addresses fairness, privacy, and robustness in trustworthy FL.

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

Single-cell RNA sequencing (scRNA-seq) is essential for unraveling cellular heterogeneity and diversity, offering invaluable insights for bioinformatics advancements. Despite its potential, traditional clustering methods in scRNA-seq data analysis often neglect the structural information embedded in gene expression profiles, crucial for understanding cellular correlations and dependencies. Existing strategies, including graph neural networks, face challenges in handling the inefficiency due to scRNA-seq data's intrinsic high-dimension and high-sparsity. Addressing these limitations, we introduce scCDCG (single-cell RNA-seq Clustering via Deep Cut-informed Graph), a novel framework designed for efficient and accurate clustering of scRNA-seq data that simultaneously utilizes intercellular high-order structural information. scCDCG comprises three main components: (i) A graph embedding module utilizing deep cut-informed techniques, which effectively captures intercellular high-order structural information, overcoming the over-smoothing and inefficiency issues prevalent in prior graph neural network methods. (ii) A self-supervised learning module guided by optimal transport, tailored to accommodate the unique complexities of scRNA-seq data, specifically its high-dimension and high-sparsity. (iii) An autoencoder-based feature learning module that simplifies model complexity through effective dimension reduction and feature extraction. Our extensive experiments on 6 datasets demonstrate scCDCG's superior performance and efficiency compared to 7 established models, underscoring scCDCG's potential as a transformative tool in scRNA-seq data analysis. Our code is available at: https://github.com/XPgogogo/scCDCG.

This paper proposes a class of distributed event-triggered algorithms that solve the average consensus problem in multi-agent systems. By designing events such that a specifically chosen Lyapunov function is monotonically decreasing, event-triggered algorithms succeed in reducing communications among agents while still ensuring that the entire system converges to the desired state. However, depending on the chosen Lyapunov function the transient behaviors can be very different. Moreover, performance requirements also vary from application to application. Consequently, we are instead interested in considering a class of Lyapunov functions such that each Lyapunov function produces a different event-triggered coordination algorithm to solve the multi-agent average consensus problem. The proposed class of algorithms all guarantee exponential convergence of the resulting system and exclusion of Zeno behaviors. This allows us to easily implement different algorithms that all guarantee correctness to meet varying performance needs. We show that our findings can be applied to the practical clock synchronization problem in wireless sensor networks (WSNs) and further corroborate their effectiveness with simulation results.