Single-cell multimodal data can simultaneously provide cellular features at different levels, such as gene expression, chromatin accessibility, and spatial location. The integration of multimodal data can efficiently utilize the information from various views, thereby enhancing the reliability and accuracy of cellular research. The current integration methods mainly focus on obtaining the representation of cells but neglect the representation of genes, not beneficial to cell type-specific gene module analyses. Besides, some integration algorithms only can integrate multi-omics data and cannot be applied to spatial transcriptome data for integrating transcriptomic data and spatial location. To this end, we propose MISF, a Multimodal data Integration algorithm based on adaptive Similarity network learning and matrix Factorization. MISF integrates multimodal data and learns the lower-dimensional representations of cells and genes. We validate the feasibility of MISF on multiple single-cell multi-omics data and spatial transcriptome data and compare it with the existing multi-omics data integration methods as well as spatial transcriptome data analysis algorithms. The results demonstrate that MISF can effectively integrate multimodal data, localize different types of cell clusters, and outline cellular spatial distribution pattern. Furthermore, MISF facilitates cell clustering and cell type-specific gene module analyses, providing new insights for the study of cellular heterogeneity.

Face Recognition (FR) models are vulnerable to adversarial examples that subtly manipulate benign face images, underscoring the urgent need to improve the transferability of adversarial attacks in order to expose the blind spots of these systems. Existing adversarial attack methods often overlook the potential benefits of augmenting the surrogate model with diverse initializations, which limits the transferability of the generated adversarial examples. To address this gap, we propose a novel method called Diverse Parameters Augmentation (DPA) attack method, which enhances surrogate models by incorporating diverse parameter initializations, resulting in a broader and more diverse set of surrogate models. Specifically, DPA consists of two key stages: Diverse Parameters Optimization (DPO) and Hard Model Aggregation (HMA). In the DPO stage, we initialize the parameters of the surrogate model using both pre-trained and random parameters. Subsequently, we save the models in the intermediate training process to obtain a diverse set of surrogate models. During the HMA stage, we enhance the feature maps of the diversified surrogate models by incorporating beneficial perturbations, thereby further improving the transferability. Experimental results demonstrate that our proposed attack method can effectively enhance the transferability of the crafted adversarial face examples.

Adversarial attacks on Face Recognition (FR) systems have demonstrated significant effectiveness against standalone FR models. However, their practicality diminishes in complete FR systems that incorporate Face Anti-Spoofing (FAS) models, as these models can detect and mitigate a substantial number of adversarial examples. To address this critical yet under-explored challenge, we introduce a novel attack setting that targets both FR and FAS models simultaneously, thereby enhancing the practicability of adversarial attacks on integrated FR systems. Specifically, we propose a new attack method, termed Reference-free Multi-level Alignment (RMA), designed to improve the capacity of black-box attacks on both FR and FAS models. The RMA framework is built upon three key components. Firstly, we propose an Adaptive Gradient Maintenance module to address the imbalances in gradient contributions between FR and FAS models. Secondly, we develop a Reference-free Intermediate Biasing module to improve the transferability of adversarial examples against FAS models. In addition, we introduce a Multi-level Feature Alignment module to reduce feature discrepancies at various levels of representation. Extensive experiments showcase the superiority of our proposed attack method to state-of-the-art adversarial attacks.

Adversarial face examples possess two critical properties: Visual Quality and Transferability. However, existing approaches rarely address these properties simultaneously, leading to subpar results. To address this issue, we propose a novel adversarial attack technique known as Adversarial Restoration (AdvRestore), which enhances both visual quality and transferability of adversarial face examples by leveraging a face restoration prior. In our approach, we initially train a Restoration Latent Diffusion Model (RLDM) designed for face restoration. Subsequently, we employ the inference process of RLDM to generate adversarial face examples. The adversarial perturbations are applied to the intermediate features of RLDM. Additionally, by treating RLDM face restoration as a sibling task, the transferability of the generated adversarial face examples is further improved. Our experimental results validate the effectiveness of the proposed attack method.

Face Recognition (FR) systems can be easily deceived by adversarial examples that manipulate benign face images through imperceptible perturbations. Adversarial attacks on FR encompass two types: impersonation (targeted) attacks and dodging (untargeted) attacks. Previous methods often achieve a successful impersonation attack on FR, however, it does not necessarily guarantee a successful dodging attack on FR in the black-box setting. In this paper, our key insight is that the generation of adversarial examples should perform both impersonation and dodging attacks simultaneously. To this end, we propose a novel attack method termed as Adversarial Pruning (Adv-Pruning), to fine-tune existing adversarial examples to enhance their dodging capabilities while preserving their impersonation capabilities. Adv-Pruning consists of Priming, Pruning, and Restoration stages. Concretely, we propose Adversarial Priority Quantification to measure the region-wise priority of original adversarial perturbations, identifying and releasing those with minimal impact on absolute model output variances. Then, Biased Gradient Adaptation is presented to adapt the adversarial examples to traverse the decision boundaries of both the attacker and victim by adding perturbations favoring dodging attacks on the vacated regions, preserving the prioritized features of the original perturbations while boosting dodging performance. As a result, we can maintain the impersonation capabilities of original adversarial examples while effectively enhancing dodging capabilities. Comprehensive experiments demonstrate the superiority of our method compared with state-of-the-art adversarial attack methods.

MOTIVATION: The rise of single-cell RNA sequencing (scRNA-seq) technology presents new opportunities for constructing detailed cell type-specific gene regulatory networks (GRNs) to study cell heterogeneity. However, challenges caused by noises, technical errors, and dropout phenomena in scRNA-seq data pose significant obstacles to GRN inference, making the design of accurate GRN inference algorithms still essential. The recent growth of both single-cell and spatial transcriptomic sequencing data enables the development of supervised deep learning methods to infer GRNs on these diverse single-cell datasets. RESULTS: In this study, we introduce a novel deep learning framework based on shared factor neighborhood and integrated neural network (SFINN) for inferring potential interactions and causalities between transcription factors and target genes from single-cell and spatial transcriptomic data. SFINN utilizes shared factor neighborhood to construct cellular neighborhood network based on gene expression data and additionally integrates cellular network generated from spatial location information. Subsequently, the cell adjacency matrix and gene pair expression are fed into an integrated neural network framework consisting of a graph convolutional neural network and a fully-connected neural network to determine whether the genes interact. Performance evaluation in the tasks of gene interaction and causality prediction against the existing GRN reconstruction algorithms demonstrates the usability and competitiveness of SFINN across different kinds of data. SFINN can be applied to infer GRNs from conventional single-cell sequencing data and spatial transcriptomic data. AVAILABILITY AND IMPLEMENTATION: SFINN can be accessed at GitHub: https://github.com/JGuan-lab/SFINN.

Face recognition (FR) models can be easily fooled by adversarial examples, which are crafted by adding imperceptible perturbations on benign face images. The existence of adversarial face examples poses a great threat to the security of society. To build a more sustainable digital nation, in this article, we improve the transferability of adversarial face examples to expose more blind spots of the existing FR models. Though generating hard samples has shown its effectiveness in improving the generalization of models in training tasks, the effectiveness of using this idea to improve the transferability of adversarial face examples remains unexplored. To this end, based on the property of hard samples and the symmetry between training tasks and adversarial attack tasks, we propose the concept of hard models, which have similar effects as hard samples for adversarial attack tasks. Using the concept of hard models, we propose a novel attack method called beneficial perturbation feature augmentation attack (BPFA), which reduces the overfitting of adversarial examples to surrogate FR models by constantly generating new hard models to craft the adversarial examples. Specifically, in the backpropagation, BPFA records the gradients on preselected feature maps and uses the gradient on the input image to craft the adversarial example. In the next forward propagation, BPFA leverages the recorded gradients to add beneficial perturbations on their corresponding feature maps to increase the loss. Extensive experiments demonstrate that BPFA can significantly boost the transferability of adversarial attacks on FR.

Person re-identifcation (Re-ID) based on unsupervised domain adaptation (UDA) aims to transfer the pre-trained model from one labeled source domain to an unlabeled target domain. Existing methods tackle this problem by using clustering methods to generate pseudo labels. However, pseudo labels produced by these techniques may be unstable and noisy, substantially deteriorating models’ performance. In this paper, we propose a Reliability Exploration with Self-ensemble Learning (RESL) framework for domain adaptive person ReID. First, to increase the feature diversity, multiple branches are presented to extract features from different data augmentations. Taking the temporally average model as a mean teacher model, online label refning is conducted by using its dynamic ensemble predictions from different branches as soft labels. Second, to combat the adverse effects of unreliable samples in clusters, sample reliability is estimated by evaluating the consistency of different clusters’ results, followed by selecting reliable instances for training and re-weighting sample contribution within Re-ID losses. A contrastive loss is also utilized with cluster-level memory features which are updated by the mean feature. The experiments demonstrate that our method can signifcantly surpass the state-of-the-art performance on the unsupervised domain adaptive person ReID.