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.

我们通过严格的数学论点建设性地展示了GNN在紧凑型$ d $维欧几里得网格上的近似频带限制功能中的架构优于NN的架构。我们表明，前者只需要$ \ MATHCAL {m} $采样函数值就可以实现$ o_ {d}的均匀近似错误（2^{ - \ \ m athcal {m} {m}^{1/d/d/d}}}}} $从某种意义上说，这个错误率是最佳的，NNS可能会取得更糟的情况。

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}}}。

由于缺乏深度信息，单眼3D对象检测在自主驾驶中非常具有挑战性。本文提出了一种基于多尺度深度分层的单眼单目眼3D对象检测算法，它使用锚定方法检测每像素预测中的3D对象。在所提出的MDS-Net中，开发了一种新的基于深度的分层结构，以通过在对象的深度和图像尺寸之间建立数学模型来改善网络的深度预测能力。然后开发出新的角度损耗功能，以进一步提高角度预测的精度并提高训练的收敛速度。最终在后处理阶段最终应用优化的软，以调整候选盒的置信度。基蒂基准测试的实验表明，MDS-Net在3D检测中优于现有的单目3D检测方法，并在满足实时要求时进行3D检测和BEV检测任务。

Driven by improved architectures and better representation learning frameworks, the field of visual recognition has enjoyed rapid modernization and performance boost in the early 2020s. For example, modern ConvNets, represented by ConvNeXt, have demonstrated strong performance in various scenarios. While these models were originally designed for supervised learning with ImageNet labels, they can also potentially benefit from self-supervised learning techniques such as masked autoencoders (MAE). However, we found that simply combining these two approaches leads to subpar performance. In this paper, we propose a fully convolutional masked autoencoder framework and a new Global Response Normalization (GRN) layer that can be added to the ConvNeXt architecture to enhance inter-channel feature competition. This co-design of self-supervised learning techniques and architectural improvement results in a new model family called ConvNeXt V2, which significantly improves the performance of pure ConvNets on various recognition benchmarks, including ImageNet classification, COCO detection, and ADE20K segmentation. We also provide pre-trained ConvNeXt V2 models of various sizes, ranging from an efficient 3.7M-parameter Atto model with 76.7% top-1 accuracy on ImageNet, to a 650M Huge model that achieves a state-of-the-art 88.9% accuracy using only public training data.

A step-search sequential quadratic programming method is proposed for solving nonlinear equality constrained stochastic optimization problems. It is assumed that constraint function values and derivatives are available, but only stochastic approximations of the objective function and its associated derivatives can be computed via inexact probabilistic zeroth- and first-order oracles. Under reasonable assumptions, a high-probability bound on the iteration complexity of the algorithm to approximate first-order stationarity is derived. Numerical results on standard nonlinear optimization test problems illustrate the advantages and limitations of our proposed method.

Masked image modeling (MIM) has shown great promise for self-supervised learning (SSL) yet been criticized for learning inefficiency. We believe the insufficient utilization of training signals should be responsible. To alleviate this issue, we introduce a conceptually simple yet learning-efficient MIM training scheme, termed Disjoint Masking with Joint Distillation (DMJD). For disjoint masking (DM), we sequentially sample multiple masked views per image in a mini-batch with the disjoint regulation to raise the usage of tokens for reconstruction in each image while keeping the masking rate of each view. For joint distillation (JD), we adopt a dual branch architecture to respectively predict invisible (masked) and visible (unmasked) tokens with superior learning targets. Rooting in orthogonal perspectives for training efficiency improvement, DM and JD cooperatively accelerate the training convergence yet not sacrificing the model generalization ability. Concretely, DM can train ViT with half of the effective training epochs (3.7 times less time-consuming) to report competitive performance. With JD, our DMJD clearly improves the linear probing classification accuracy over ConvMAE by 5.8%. On fine-grained downstream tasks like semantic segmentation, object detection, etc., our DMJD also presents superior generalization compared with state-of-the-art SSL methods. The code and model will be made public at https://github.com/mx-mark/DMJD.

Considering the computation complexity, we propose a Guided Hybrid Quantization with One-to-one Self-Teaching (GHOST}) framework. More concretely, we first design a structure called guided quantization self-distillation (GQSD), which is an innovative idea for realizing lightweight through the synergy of quantization and distillation. The training process of the quantization model is guided by its full-precision model, which is time-saving and cost-saving without preparing a huge pre-trained model in advance. Second, we put forward a hybrid quantization (HQ) module to obtain the optimal bit width automatically under a constrained condition where a threshold for distribution distance between the center and samples is applied in the weight value search space. Third, in order to improve information transformation, we propose a one-to-one self-teaching (OST) module to give the student network a ability of self-judgment. A switch control machine (SCM) builds a bridge between the student network and teacher network in the same location to help the teacher to reduce wrong guidance and impart vital knowledge to the student. This distillation method allows a model to learn from itself and gain substantial improvement without any additional supervision. Extensive experiments on a multimodal dataset (VEDAI) and single-modality datasets (DOTA, NWPU, and DIOR) show that object detection based on GHOST outperforms the existing detectors. The tiny parameters (<9.7 MB) and Bit-Operations (BOPs) (<2158 G) compared with any remote sensing-based, lightweight or distillation-based algorithms demonstrate the superiority in the lightweight design domain. Our code and model will be released at https://github.com/icey-zhang/GHOST.

Automatic font generation without human experts is a practical and significant problem, especially for some languages that consist of a large number of characters. Existing methods for font generation are often in supervised learning. They require a large number of paired data, which are labor-intensive and expensive to collect. In contrast, common unsupervised image-to-image translation methods are not applicable to font generation, as they often define style as the set of textures and colors. In this work, we propose a robust deformable generative network for unsupervised font generation (abbreviated as DGFont++). We introduce a feature deformation skip connection (FDSC) to learn local patterns and geometric transformations between fonts. The FDSC predicts pairs of displacement maps and employs the predicted maps to apply deformable convolution to the low-level content feature maps. The outputs of FDSC are fed into a mixer to generate final results. Moreover, we introduce contrastive self-supervised learning to learn a robust style representation for fonts by understanding the similarity and dissimilarities of fonts. To distinguish different styles, we train our model with a multi-task discriminator, which ensures that each style can be discriminated independently. In addition to adversarial loss, another two reconstruction losses are adopted to constrain the domain-invariant characteristics between generated images and content images. Taking advantage of FDSC and the adopted loss functions, our model is able to maintain spatial information and generates high-quality character images in an unsupervised manner. Experiments demonstrate that our model is able to generate character images of higher quality than state-of-the-art methods.

Gaze estimation is the fundamental basis for many visual tasks. Yet, the high cost of acquiring gaze datasets with 3D annotations hinders the optimization and application of gaze estimation models. In this work, we propose a novel Head-Eye redirection parametric model based on Neural Radiance Field, which allows dense gaze data generation with view consistency and accurate gaze direction. Moreover, our head-eye redirection parametric model can decouple the face and eyes for separate neural rendering, so it can achieve the purpose of separately controlling the attributes of the face, identity, illumination, and eye gaze direction. Thus diverse 3D-aware gaze datasets could be obtained by manipulating the latent code belonging to different face attributions in an unsupervised manner. Extensive experiments on several benchmarks demonstrate the effectiveness of our method in domain generalization and domain adaptation for gaze estimation tasks.