Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.

知识图（kgs）由于能够存储适用于许多领域的关系知识的能力，因此有助于多种应用。尽管在创造和维护方面进行了巨大的努力，但即使是最大的公斤也远非完整。因此，KG完成（KGC）已成为KG研究最关键的任务之一。最近，该领域的大量文献围绕着使用图神经网络（GNN）学习强大的嵌入，从而利用KGS中的拓扑结构。具体而言，已经做出了专门的努力，以扩展GNN，通常是为简单的同质和单一相关图设计的，以通过设计更复杂的聚合方案而不是相邻节点（关键的节点）（通过设计更复杂的聚合方案）（为GNN绩效）适当利用多关系信息。这些方法的成功自然归因于GNN在简单的多层感知器（MLP）模型上使用，这是由于它们的附加聚合功能。在这项工作中，我们发现简单的MLP模型能够达到与GNN的可比性能，这表明聚集可能并不像以前那样重要。通过进一步的探索，我们显示出仔细的评分功能和损失功能设计对KGC模型性能的影响要大得多，并且实际上不需要聚集。这表明了评分功能设计，损失功能设计和先前工作中的聚集结合，并有很有希望的见解当今最先进的KGC方法的可伸缩性，以及对KGC任务更合适的聚合设计的仔细注意明天。该实现可在线获得：https：//github.com/juanhui28/are_mpnns_helpful。

多模式单细胞技术的最新进展已使从同一细胞中的多个OMICS数据同时采集，从而更深入地了解细胞状态和动力学。但是，从多模式数据，模拟模式之间的关系并更重要的是，将大量的单模式数据集纳入下游分析是一项挑战。为了应对这些挑战并相应地促进了多模式的单细胞数据分析，已经引入了三个关键任务：$ \ textit {模式预测} $，$ \ textit {modital {modital {modational conterative} $和$ \ textit {intimit {interion {intim interding} $。在这项工作中，我们提出了一个通用图形神经网络框架$ \ textit {scmognn} $来解决这三个任务，并表明$ \ textit {scmognn} $与最新的任务相比，在所有三个任务中都表现出了卓越的结果。艺术和传统方法。我们的方法是\ textit {模式预测}的整体排名的官方获奖者，来自神经2021竞赛\ footNote {\ url {https://openproblems.bio/neurips_2021/}}，我们的所有方法都已整合到我们的所有实现中舞蹈软件包\ footNote {\ url {https://github.com/omicsml/dance}}}。

Different people speak with diverse personalized speaking styles. Although existing one-shot talking head methods have made significant progress in lip sync, natural facial expressions, and stable head motions, they still cannot generate diverse speaking styles in the final talking head videos. To tackle this problem, we propose a one-shot style-controllable talking face generation framework. In a nutshell, we aim to attain a speaking style from an arbitrary reference speaking video and then drive the one-shot portrait to speak with the reference speaking style and another piece of audio. Specifically, we first develop a style encoder to extract dynamic facial motion patterns of a style reference video and then encode them into a style code. Afterward, we introduce a style-controllable decoder to synthesize stylized facial animations from the speech content and style code. In order to integrate the reference speaking style into generated videos, we design a style-aware adaptive transformer, which enables the encoded style code to adjust the weights of the feed-forward layers accordingly. Thanks to the style-aware adaptation mechanism, the reference speaking style can be better embedded into synthesized videos during decoding. Extensive experiments demonstrate that our method is capable of generating talking head videos with diverse speaking styles from only one portrait image and an audio clip while achieving authentic visual effects. Project Page: https://github.com/FuxiVirtualHuman/styletalk.

Unmanned aerial vehicle (UAV) swarms are considered as a promising technique for next-generation communication networks due to their flexibility, mobility, low cost, and the ability to collaboratively and autonomously provide services. Distributed learning (DL) enables UAV swarms to intelligently provide communication services, multi-directional remote surveillance, and target tracking. In this survey, we first introduce several popular DL algorithms such as federated learning (FL), multi-agent Reinforcement Learning (MARL), distributed inference, and split learning, and present a comprehensive overview of their applications for UAV swarms, such as trajectory design, power control, wireless resource allocation, user assignment, perception, and satellite communications. Then, we present several state-of-the-art applications of UAV swarms in wireless communication systems, such us reconfigurable intelligent surface (RIS), virtual reality (VR), semantic communications, and discuss the problems and challenges that DL-enabled UAV swarms can solve in these applications. Finally, we describe open problems of using DL in UAV swarms and future research directions of DL enabled UAV swarms. In summary, this survey provides a comprehensive survey of various DL applications for UAV swarms in extensive scenarios.

In this work, we focus on instance-level open vocabulary segmentation, intending to expand a segmenter for instance-wise novel categories without mask annotations. We investigate a simple yet effective framework with the help of image captions, focusing on exploiting thousands of object nouns in captions to discover instances of novel classes. Rather than adopting pretrained caption models or using massive caption datasets with complex pipelines, we propose an end-to-end solution from two aspects: caption grounding and caption generation. In particular, we devise a joint Caption Grounding and Generation (CGG) framework based on a Mask Transformer baseline. The framework has a novel grounding loss that performs explicit and implicit multi-modal feature alignments. We further design a lightweight caption generation head to allow for additional caption supervision. We find that grounding and generation complement each other, significantly enhancing the segmentation performance for novel categories. We conduct extensive experiments on the COCO dataset with two settings: Open Vocabulary Instance Segmentation (OVIS) and Open Set Panoptic Segmentation (OSPS). The results demonstrate the superiority of our CGG framework over previous OVIS methods, achieving a large improvement of 6.8% mAP on novel classes without extra caption data. Our method also achieves over 15% PQ improvements for novel classes on the OSPS benchmark under various settings.

Non-line-of-sight (NLOS) imaging aims to reconstruct the three-dimensional hidden scenes from the data measured in the line-of-sight, which uses photon time-of-flight information encoded in light after multiple diffuse reflections. The under-sampled scanning data can facilitate fast imaging. However, the resulting reconstruction problem becomes a serious ill-posed inverse problem, the solution of which is of high possibility to be degraded due to noises and distortions. In this paper, we propose two novel NLOS reconstruction models based on curvature regularization, i.e., the object-domain curvature regularization model and the dual (i.e., signal and object)-domain curvature regularization model. Fast numerical optimization algorithms are developed relying on the alternating direction method of multipliers (ADMM) with the backtracking stepsize rule, which are further accelerated by GPU implementation. We evaluate the proposed algorithms on both synthetic and real datasets, which achieve state-of-the-art performance, especially in the compressed sensing setting. All our codes and data are available at https://github.com/Duanlab123/CurvNLOS.

Stance detection refers to the task of extracting the standpoint (Favor, Against or Neither) towards a target in given texts. Such research gains increasing attention with the proliferation of social media contents. The conventional framework of handling stance detection is converting it into text classification tasks. Deep learning models have already replaced rule-based models and traditional machine learning models in solving such problems. Current deep neural networks are facing two main challenges which are insufficient labeled data and information in social media posts and the unexplainable nature of deep learning models. A new pre-trained language model chatGPT was launched on Nov 30, 2022. For the stance detection tasks, our experiments show that ChatGPT can achieve SOTA or similar performance for commonly used datasets including SemEval-2016 and P-Stance. At the same time, ChatGPT can provide explanation for its own prediction, which is beyond the capability of any existing model. The explanations for the cases it cannot provide classification results are especially useful. ChatGPT has the potential to be the best AI model for stance detection tasks in NLP, or at least change the research paradigm of this field. ChatGPT also opens up the possibility of building explanatory AI for stance detection.

Motivated by the problem of matching vertices in two correlated Erd\H{o}s-R\'enyi graphs, we study the problem of matching two correlated Gaussian Wigner matrices. We propose an iterative matching algorithm, which succeeds in polynomial time as long as the correlation between the two Gaussian matrices does not vanish. Our result is the first polynomial time algorithm that solves a graph matching type of problem when the correlation is an arbitrarily small constant.

Existing solutions to network scheduling typically assume that the instantaneous link rates are completely known before a scheduling decision is made or consider a bandit setting where the accurate link quality is discovered only after it has been used for data transmission. In practice, the decision maker can obtain (relatively accurate) channel information, e.g., through beamforming in mmWave networks, right before data transmission. However, frequent beamforming incurs a formidable overhead in densely deployed mmWave WLANs. In this paper, we consider the important problem of throughput optimization with joint link probing and scheduling. The problem is challenging even when the link rate distributions are pre-known (the offline setting) due to the necessity of balancing the information gains from probing and the cost of reducing the data transmission opportunity. We develop an approximation algorithm with guaranteed performance when the probing decision is non-adaptive, and a dynamic programming based solution for the more challenging adaptive setting. We further extend our solutions to the online setting with unknown link rate distributions and develop a contextual-bandit based algorithm and derive its regret bound. Numerical results using data traces collected from real-world mmWave deployments demonstrate the efficiency of our solutions.