CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification.

Single cell sequencing technology has provided unprecedented opportunities for comprehensively deciphering cell heterogeneity. Nevertheless, the high dimensionality and intricate nature of cell heterogeneity have presented substantial challenges to computational methods. Numerous novel clustering methods have been proposed to address this issue. However, none of these methods achieve the consistently better performance under different biological scenarios. In this study, we developed CAKE, a novel and scalable self-supervised clustering method, which consists of a contrastive learning model with a mixture neighborhood augmentation for cell representation learning, and a self-Knowledge Distiller model for the refinement of clustering results. These designs provide more condensed and cluster-friendly cell representations and improve the clustering performance in term of accuracy and robustness. Furthermore, in addition to accurately identifying the major type cells, CAKE could also find more biologically meaningful cell subgroups and rare cell types. The comprehensive experiments on real single-cell RNA sequencing datasets demonstrated the superiority of CAKE in visualization and clustering over other comparison methods, and indicated its extensive application in the field of cell heterogeneity analysis. Contact: Ruiqing Zheng. (rqzheng@csu.edu.cn).

Deep learning enables stochastic optical reconstruction microscopy-like superresolution image reconstruction from conventional microscopy.

Despite its remarkable potential for transforming low-resolution images, deep learning faces significant challenges in achieving high-quality superresolution microscopy imaging from wide-field (conventional) microscopy. Here, we present X-Microscopy, a computational tool comprising two deep learning subnets, UR-Net-8 and X-Net, which enables STORM-like superresolution microscopy image reconstruction from wide-field images with input-size flexibility. X-Microscopy was trained using samples of various subcellular structures, including cytoskeletal filaments, dot-like, beehive-like, and nanocluster-like structures, to generate prediction models capable of producing images of comparable quality to STORM-like images. In addition to enabling multicolour superresolution image reconstructions, X-Microscopy also facilitates superresolution image reconstruction from different conventional microscopic systems. The capabilities of X-Microscopy offer promising prospects for making superresolution microscopy accessible to a broader range of users, going beyond the confines of well-equipped laboratories.

Contrastive Bayesian Analysis for Deep Metric Learning.

Recent methods for deep metric learning have been focusing on designing different contrastive loss functions between positive and negative pairs of samples so that the learned feature embedding is able to pull positive samples of the same class closer and push negative samples from different classes away from each other. In this work, we recognize that there is a significant semantic gap between features at the intermediate feature layer and class labels at the final output layer. To bridge this gap, we develop a contrastive Bayesian analysis to characterize and model the posterior probabilities of image labels conditioned by their features similarity in a contrastive learning setting. This contrastive Bayesian analysis leads to a new loss function for deep metric learning. To improve the generalization capability of the proposed method onto new classes, we further extend the contrastive Bayesian loss with a metric variance constraint. Our experimental results and ablation studies demonstrate that the proposed contrastive Bayesian metric learning method significantly improves the performance of deep metric learning in both supervised and pseudo-supervised scenarios, outperforming existing methods by a large margin.

Multi-Focus Image Fusion Based on Multi-Scale Generative Adversarial Network.

The methods based on the convolutional neural network have demonstrated its powerful information integration ability in image fusion. However, most of the existing methods based on neural networks are only applied to a part of the fusion process. In this paper, an end-to-end multi-focus image fusion method based on a multi-scale generative adversarial network (MsGAN) is proposed that makes full use of image features by a combination of multi-scale decomposition with a convolutional neural network. Extensive qualitative and quantitative experiments on the synthetic and Lytro datasets demonstrated the effectiveness and superiority of the proposed MsGAN compared to the state-of-the-art multi-focus image fusion methods.

Local Semantic Correlation Modeling Over Graph Neural Networks for Deep Feature Embedding and Image Retrieval.

Deep feature embedding aims to learn discriminative features or feature embeddings for image samples which can minimize their intra-class distance while maximizing their inter-class distance. Recent state-of-the-art methods have been focusing on learning deep neural networks with carefully designed loss functions. In this work, we propose to explore a new approach to deep feature embedding. We learn a graph neural network to characterize and predict the local correlation structure of images in the feature space. Based on this correlation structure, neighboring images collaborate with each other to generate and refine their embedded features based on local linear combination. Graph edges learn a correlation prediction network to predict the correlation scores between neighboring images. Graph nodes learn a feature embedding network to generate the embedded feature for a given image based on a weighted summation of neighboring image features with the correlation scores as weights. Our extensive experimental results under the image retrieval settings demonstrate that our proposed method outperforms the state-of-the-art methods by a large margin, especially for top-1 recalls.

Zero-Shot Learning to Index on Semantic Trees for Scalable Image Retrieval.

In this study, we develop a new approach, called zero-shot learning to index on semantic trees (LTI-ST), for efficient image indexing and scalable image retrieval. Our method learns to model the inherent correlation structure between visual representations using a binary semantic tree from training images which can be effectively transferred to new test images from unknown classes. Based on predicted correlation structure, we construct an efficient indexing scheme for the whole test image set. Unlike existing image index methods, our proposed LTI-ST method has the following two unique characteristics. First, it does not need to analyze the test images in the query database to construct the index structure. Instead, it is directly predicted by a network learnt from the training set. This zero-shot capability is critical for flexible, distributed, and scalable implementation and deployment of the image indexing and retrieval services at large scales. Second, unlike the existing distance-based index methods, our index structure is learnt using the LTI-ST deep neural network with binary encoding and decoding on a hierarchical semantic tree. Our extensive experimental results on benchmark datasets and ablation studies demonstrate that the proposed LTI-ST method outperforms existing index methods by a large margin while providing the above new capabilities which are highly desirable in practice.

Supervised Deep Feature Embedding With Handcrafted Feature.

Image representation methods based on deep convolutional neural networks (CNNs) have achieved the state-of-the-art performance in various computer vision tasks, such as image retrieval and person re-identification. We recognize that more discriminative feature embeddings can be learned with supervised deep metric learning and handcrafted features for image retrieval and similar applications. In this paper, we propose a new supervised deep feature embedding with a handcrafted feature model. To fuse handcrafted feature information into CNNs and realize feature embeddings, a general fusion unit is proposed (called Fusion-Net). We also define a network loss function with image label information to realize supervised deep metric learning. Our extensive experimental results on the Stanford online products' data set and the in-shop clothes retrieval data set demonstrate that our proposed methods outperform the existing state-of-the-art methods of image retrieval by a large margin. Moreover, we also explore the applications of the proposed methods in person re-identification and vehicle re-identification; the experimental results demonstrate both the effectiveness and efficiency of the proposed methods.