Unmanned aerial vehicle (UAV) swarms find extensive applications in diverse fields, including search and rescue, logistics delivery, and environmental surveillance, necessitating meticulous task and temporal scheduling to meet intricate spatiotemporal requirements. A market-based strategy emerges as a suitable option for self-organizing swarm coordination. However, the consensus mechanisms employed by most market-based algorithms necessitate synchronous communication, leading to waiting times. Researchers have turned to asynchronous approaches for enhanced efficiency, yet the communication burden of existing asynchronous methods escalates swiftly with the growth of the swarm size. Therefore, this paper proposes an Asynchronous Harmony-based Decentralized Auctions (AHDA) method for networked UAV swarm to reduce the communication load and scheduling time required by a market-based approach. First, proximity communication is proposed to reduce the broadcast range and content of UAVs. Second, new conflict resolution protocols are designed to eliminate task conflict between UAVs faster. Third, propagation rules are designed to limit the scope of task information diffusion. Ultimately, it brings a decrease in communication load and scheduling time because it is expected to achieve the minimum requirement of no task conflict between UAVs, rather than swarm scheduling consistency. Monte Carlo simulations spanning 32 to 128 UAVs demonstrate that compared with the Asynchronous Consensus-Based Bundle Algorithm (ACBBA), the proposed AHDA achieves reductions of up to 70.16% in transmitted messages, 75.78% in communication traffic, and 63.12% in scheduling time.

Distributed task allocation in the UAV swarm is sensitive to excessive communication overhead and frequent transmissions. Combining reinforcement learning and task allocation demonstrates great potential in enhancing algorithm performance and optimizing communication. However, existing studies rely on ideal communication assumptions and the nonphysical environment, making training and validation impractical in applying networked swarms. This paper proposes the Communication-Aware Task Allocation, which aims to train a gating mechanism policy to coordinate the transmission timing, improving robustness and timelessness of the task allocation. First, the policy learning problem is formalized as a POMDP, for which the channel access and other features are designed for observations, actions are inter-agent adaptive gating mechanisms, and the shared reward reflects global task conflicts. Second, to address the asynchronous learning under the CTDE, an asynchronous experience collection and splicing method is proposed to align trajectories. Then, the MOCPPO is proposed, which combines a primal-dual operator with proximal policy optimization, updating the optimal Lagrange multiplier and strategy parameters to simultaneously minimize task conflicts and communication overhead. Finally, sim-to-real experiments are conducted in the HIL environment, and results illustrate the best trade-off optimization of the proposed method over all state-of-the-art approaches.

The advent of single-cell RNA sequencing (scRNA-seq) has offering unprecedented insights at the single-cell level. This groundbreaking technology has opened new pathways for understanding cellular diversity and revealing novel insights into disease mechanisms. However, the analysis of scRNA-seq data is challenging, primarily due to dropout events caused by technical noise. Developing effective imputation methods is crucial for the reliable and informative analysis of scRNA-seq data. While deep learning-based approaches have been proposed for scRNA-seq data imputation, they often fall short of optimal performance, especially in identifying rare cell types. Here we propose a novel self-supervised deep learning model named scGANCL for scRNA-seq data imputation. scGANCL combines bidirectional generative adversarial network (BiGAN) with contrastive learning (CL) to enhance imputation performance. To fully exploit gene expression profiles, a contrastive learning module is introduced to enhance the representation learning of cells by minimizing the discrepancy between the distributions of real and generated data. Comprehensive experiments have been conducted on ten simulated and seven real datasets to validate scGANCL's effectiveness. The results demonstrated scGANCL consistently outperformed seven state-of-the-art methods across various downstream tasks. Ablation studies further validated the contribution of each component to the overall performance of the model.

MOTIVATION: Recent advances in spatial transcriptomics technologies have enabled gene expression profiles while preserving spatial context. Accurately identifying spatial domains is crucial for downstream analysis and it requires the effective integration of gene expression profiles and spatial information. While increasingly computational methods have been developed for spatial domain detection, most of them cannot adaptively learn the complex relationship between gene expression and spatial information, leading to sub-optimal performance. RESULTS: To overcome these challenges, we propose a novel deep learning method named Spatial-MGCN for identifying spatial domains, which is a Multi-view Graph Convolutional Network (GCN) with attention mechanism. We first construct two neighbor graphs using gene expression profiles and spatial information, respectively. Then, a multi-view GCN encoder is designed to extract unique embeddings from both the feature and spatial graphs, as well as their shared embeddings by combining both graphs. Finally, a zero-inflated negative binomial decoder is used to reconstruct the original expression matrix by capturing the global probability distribution of gene expression profiles. Moreover, Spatial-MGCN incorporates a spatial regularization constraint into the features learning to preserve spatial neighbor information in an end-to-end manner. The experimental results show that Spatial-MGCN outperforms state-of-the-art methods consistently in several tasks, including spatial clustering and trajectory inference.

MOTIVATION: Single-cell RNA-sequencing (scRNA-seq) is widely used to reveal cellular heterogeneity, complex disease mechanisms and cell differentiation processes. Due to high sparsity and complex gene expression patterns, scRNA-seq data present a large number of dropout events, affecting downstream tasks such as cell clustering and pseudo-time analysis. Restoring the expression levels of genes is essential for reducing technical noise and facilitating downstream analysis. However, existing scRNA-seq data imputation methods ignore the topological structure information of scRNA-seq data and cannot comprehensively utilize the relationships between cells. RESULTS: Here, we propose a single-cell Graph Contrastive Learning method for scRNA-seq data imputation, named scGCL, which integrates graph contrastive learning and Zero-inflated Negative Binomial (ZINB) distribution to estimate dropout values. scGCL summarizes global and local semantic information through contrastive learning and selects positive samples to enhance the representation of target nodes. To capture the global probability distribution, scGCL introduces an autoencoder based on the ZINB distribution, which reconstructs the scRNA-seq data based on the prior distribution. Through extensive experiments, we verify that scGCL outperforms existing state-of-the-art imputation methods in clustering performance and gene imputation on 14 scRNA-seq datasets. Further, we find that scGCL can enhance the expression patterns of specific genes in Alzheimer's disease datasets. AVAILABILITY AND IMPLEMENTATION: The code and data of scGCL are available on Github: https://github.com/zehaoxiong123/scGCL. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

single-cell RNA-sequencing (scRNA-seq) technology can reveal cellular heterogeneity with high throughput and resolution, facilitating the profiling of single-cell transcriptomes. However, due to some experimental factors, a large number of missing values are generated in scRNA-seq data, which are called dropout events, and this phenomenon affects the downstream analysis. Imputation is an effective denoising method, but existing imputation methods still face a huge challenge: lack of interpretability. In this study, we propose single-cell Self-Attention Generative Adversarial Networks(scSAGAN), a semi-supervised imputation method for scRNA-seq data. scSAGAN mainly uses Semi-Supervised Learning (SSL) and Probabilistic Latent Semantic Analysis (PLSA), which can not only learn the potential characteristics of different types of cells but explain their imputation behavior. In clustering experiments, scSAGAN exhibits better clustering performance than all baselines on 7 datasets. Next, we interpret the imputation behavior of scSAGAN on datasets such as Alzheimer’s disease and find causative genes associated with the corresponding datasets. scSAGAN is currently an open-source method, available at https://github.com/zehaoxiongl23/scSAGAN.

MOTIVATION: Cell-type annotation plays a crucial role in single-cell RNA-seq (scRNA-seq) data analysis. As more and more well-annotated scRNA-seq reference data are publicly available, automatical label transference algorithms are gaining popularity over manual marker gene-based annotation methods. However, most existing methods fail to unify cell-type annotation with dimensionality reduction and are unable to generate deep latent representation from the perspective of data generation. RESULTS: In this article, we propose scSemiGAN, a single-cell semi-supervised cell-type annotation and dimensionality reduction framework based on a generative adversarial network, to overcome these challenges, modeling scRNA-seq data from the aspect of data generation. Our proposed scSemiGAN is capable of performing deep latent representation learning and cell-type label prediction simultaneously. Through extensive comparison with four state-of-the-art annotation methods on diverse simulated and real scRNA-seq datasets, scSemiGAN achieves competitive or superior performance in multiple downstream tasks including cell-type annotation, latent representation visualization, confounding factor removal and enrichment analysis. AVAILABILITY AND IMPLEMENTATION: The code and data of scSemiGAN are available on GitHub: https://github.com/rafa-nadal/scSemiGAN. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.