Single-cell multi-omics sequencing represents an advanced technology capable of simultaneously measuring multiple omics data from the same cell. The joint clustering of single-cell multi-omics sequencing data enables a comprehensive depiction of cell states and uncovers intricate molecular mechanisms, holding immense significance in fields such as oncology, neurology, and developmental biology. However, the disparities in feature spaces across different omics layers and data noise present substantial challenges for achieving accurate clustering. To tackle these challenges, we introduce a novel clustering method for single-cell multi-omics data, termed scMSAC, which is grounded in a denoising subgraph attention autoencoder. The proposed method employs a weighted nearest neighbor graph strategy to ascertain the weights of multi-omics data, subsequently generating a similarity graph that holistically encapsulates intercellular connections through the weighted amalgamation of diverse omics perspectives. The scMSAC model captures the topological features of cells through the subgraph attention autoencoder, constructing relationships among cells. For the omics features extracted by the subgraph attention autoencoder, scMSAC incorporates an SCA (Spatial Channel Attention) mechanism for feature fusion to reduce the differences in feature spaces of different omics and achieve better clustering performance. Comparative experiments with various existing methods demonstrate that scMSAC has excellent clustering performance and performs well in detecting rare cell types and differential expression analysis.

Convolutional Neural Networks struggle with long-range dependencies modeling in medical image segmentation, and traditional Transformer models rely on Multi-Layer Perceptron (MLP) for channel information mixing, with performance issues as data dimensions increase. These issues prompt a reassessment of the model's design to enhance segmentation performance and effectively capture long-range dependencies. Consequently, this study presents the Kadformer, a novel network optimized for fine-grained multi-organ segmentation. The Kadformer model adopts an innovative U-shaped network architecture, which enhances the extraction of spatial and channel features in the encoder through the KAN-Enhanced Multi-Dimensional Attention (KMA) mechanism, effectively compensating for information loss during downsampling. We design a Dynamic Path Selection (DPS) strategy to mitigate the feature extraction discrepancies encountered by the linear attention mechanism when processing category-sparse and category-dense images while enhancing feature discrimination through long-range sequential modeling Mamba. Furthermore, we construct the Data Interaction (DAI) module to guide the dual-path encoder's channel and spatial information filtering and effectively integrate the semantically inconsistent features between the KMA and DPS modules. Our approach achieves more than 30% parameter reduction compared to state-of-the-art methods. In addition, the Kadformer network outperforms existing segmentation methods on six public datasets, demonstrating excellent performance. The code has been made available on GitHub: https://github.com/wxc9927/Kadformer.

Infectious diseases continue to pose a serious threat to public health, underscoring the urgent need for effective computational approaches to screen novel anti-infective agents. Oligopeptides have emerged as promising candidates in an-timicrobial research due to their structural simplicity, high bioavailability, and low susceptibility to resistance. Despite their potential, computational models specifically designed to predict associations between oligopeptides and infectious diseases remain scarce. We propose Prompt-Guided Graph Contrastive Learning for Oligopeptide-Disease Association Prediction (PGCLODA), a framework designed to predict potential associations between oligopeptides and infectious diseases. A tripartite graph is constructed to integrate oligopeptides, microbes, and diseases. To preserve informative structures, we introduce a prompt-based graph augmentation strategy. Our dual encoder, composed of a graph convolutional network and a Transformer, captures both local and global features. The fused representations are used for final classification. Experiments on a benchmark dataset show that our method consistently outperforms existing models and demonstrates strong generalization capability in discovering novel associations.

In multi-organ segmentation tasks, both local details and global contextual information are crucial. Existing main-stream methods based on CNN-Transformer hybrid architectures typically employ simple serial stacking, end-stage concatenation, or pointwise addition for feature fusion, which struggle to handle feature inconsistency and often lead to information conflict and loss. To address the aforementioned challenges, we innovatively propose TBHF-Unet. We design a three-branch hierarchical encoder that dynamically fuses multi-source features in parallel, achieving deep layer-wise integration of multi-source information. The hierarchical structure maintains the independence of each branch while avoiding feature degradation, enabling superior performance without the need for excessively deep networks. Additionally, we design a Local-Global Feature Fusion (LGFF) module to efficiently and accurately integrate local details with global semantics, effectively alleviating feature inconsistency and achieving more comprehensive feature representation. Experiments on five public datasets demonstrate that the proposed method outperforms existing segmentation techniques, showing higher segmentation accuracy and robustness.

Single-cell RNA sequencing (scRNA-seq) provides transcriptome profiling of individual cells, allowing for in-depth studies of cell heterogeneity at cell resolution. While cell clustering lays the basic foundation of scRNA-seq data analysis, the high-dimensionality and frequent dropout events of the data raise great challenges. Although plenty of dedicated clustering methods have been proposed, they often fail to fully explore the underlying data structure. Here, we introduce scMCGF, a new multi-view clustering algorithm based on graph fusion. It utilizes multi-view data generated from transcriptomic data to learn the consistent and complementary information across different view, ultimately constructing a unified graph matrix for robust cell clustering. Specifically, scMCGF utilizes two-dimensional-reduction methods (principal component analysis and diffusion maps) to capture both linear and non-linear characteristics of the data. Additionally, it calculates a cell-pathway score matrix to incorporate pathway-level information. These three features, along with the pre-processed gene expression data, form the multi-view data. scMCGF iteratively refines the structure of similarity graphs of each view through adaptive learning and learns a unified graph matrix by weighting and fusing the individual similarity graph matrix. The final clustering results are obtained by applying the rank constraint on the Laplacian matrix of the unified graph matrix. Experiments results of 13 real data sets reveal that scMCGF outperforms eight state-of-the-art methods in clustering accuracy and robustness. Furthermore, biological analysis validates that the clustering results of scMCGF provide a reliable foundation for downstream investigations.

Intracranial aneurysm (IA) is a vascular disease of the brain arteries caused by pathological vascular dilation, which can result in subarachnoid hemorrhage if ruptured. Automatically classification and segmentation of intracranial aneurysms are essential for their diagnosis and treatment. However, the majority of current research is focused on two-dimensional images, ignoring the 3D spatial information that is also critical. In this work, we propose a novel dual-branch fusion network called the Point Cloud and Multi-View Medical Neural Network (PMMNet) for IA classification and segmentation. Specifically, one branch based on 3D point clouds serves the purpose of extracting spatial features, whereas the other branch based on multi-view images acquires 2D pixel features. Ultimately, the two types of features are fused for IA classification and segmentation. To extract both local and global features from 3D point clouds, Multilayer Perceptron (MLP) and the attention mechanism are used in parallel. In addition, a SPSA module is proposed for multi-view image feature learning, which extracts more exquisite channel and spatial multi-scale features from 2D images. Experiments conducted on the IntrA dataset outperform other state-of-the-art methods, demonstrating that the proposed PMMNet exhibits strong superiority on the medical 3D dataset. We also obtain competitive results on public datasets, including ModelNet40, ModelNet10, and ShapeNetPart, which further validate the robustness and generality of the PMMNet.

Segmentation of thoracic and abdominal organs is crucial for accurate disease diagnosis, surgical planning, and long-term health management of patients. Deep learning often depends on large quantities of high-quality training data to achieve superior results. However, the inherent complexity and sparsity of medical images require advanced models with greater learning capabilities. Additionally, significant morphological differences between organs often result in inaccurate and false-positive segmentation. To alleviate these issues, we propose a Dual Attention (DA) and Multi-Resolution Inputs (MI) based network (DAMNet) for the segmentation of thoracic and abdominal organs. Specially, DAMNet utilizes a single encoder and dual decoders. The encoder integrates MI with the Transformer to achieve multi-level feature fusion and capture global image relationships, improving the model’s capability to process intricate image data. In the decoders, Residual U-blocks (RSU) and the DA module consisting of Spatial Multi-Scale Cross-Axis Attention (SMCA) and Convolutional Self-Attention (CSA) are used as two decoder branches, respectively. The design of decoders allows the model to extract detailed information from different encoding layers from two perspectives, thereby reducing inaccuracies in segmentation. We perform thorough experiments and evaluations using three publicly available datasets: Synapse, SegTHOR, and THoracic. The experimental results indicate that our proposed DAMNet model demonstrates exceptional proficiency in segmenting thoracic and abdominal organs.

Cluster assignment is vital to analyzing single-cell RNA sequencing (scRNA-seq) data to understand high-level biological processes. Deep learning-based clustering methods have recently been widely used in scRNA-seq data analysis. However, existing deep models often overlook the interconnections and interactions among network layers, leading to the loss of structural information within the network layers. Herein, we develop a new self-supervised clustering method based on an adaptive multi-scale autoencoder, called scAMAC. The self-supervised clustering network utilizes the Multi-Scale Attention mechanism to fuse the feature information from the encoder, hidden and decoder layers of the multi-scale autoencoder, which enables the exploration of cellular correlations within the same scale and captures deep features across different scales. The self-supervised clustering network calculates the membership matrix using the fused latent features and optimizes the clustering network based on the membership matrix. scAMAC employs an adaptive feedback mechanism to supervise the parameter updates of the multi-scale autoencoder, obtaining a more effective representation of cell features. scAMAC not only enables cell clustering but also performs data reconstruction through the decoding layer. Through extensive experiments, we demonstrate that scAMAC is superior to several advanced clustering and imputation methods in both data clustering and reconstruction. In addition, scAMAC is beneficial for downstream analysis, such as cell trajectory inference. Our scAMAC model codes are freely available at https://github.com/yancy2024/scAMAC.

Object detection in aerial images based on deep learning requires a large amount of labeled data, whereas manual annotation of aerial images is time-consuming and laborious. As a branch of machine learning, active learning can help humans find the valuable samples by designing some corresponding query strategies, which effectively reduces the cost of manual labeling. However, objects in aerial images are usually small, dense, and accompanied by the interference from complex backgrounds. These brings considerable challenges for active learning in selecting high-value aerial image samples. Currently, there is a relatively lack of study on active learning for aerial images object detection. Therefore, this paper proposes an novel active learning method, using global-margin uncertainty (GMU) and collaborative sampling (CS) to find out the high valuable aerial image samples to reduce the annotation cost and improve the training efficiency of models. In GMU, the predicted scores of categories are applied to calculate the global uncertainty and margin uncertainty of unlabeled aerial images, then those aerial images with high uncertainty scores are selected as the candidate samples. In CS, we train a main model and an auxiliary model respectively to detect the candidate samples, where the samples with large differences in detection results of the two models are selected for manual annotation. The experiments conduct on VisDrone2019 and DOTA-v1.5 datasets, which showes that the proposed method has a better performance compared with several state-of-the-art active learning methods.

This study focuses on building an intelligent decision-making attention mechanism in which the channel relationship and conduct feature maps among specific deep Dense ConvNet blocks are connected to each other. Thus, develop a novel freezing network with a pyramid spatial channel attention mechanism (FPSC-Net) in deep modeling. This model studies how specific design choices in the large-scale data-driven optimization and creation process affect the balance between the accuracy and effectiveness of the designed deep intelligent model. To this end, this study presents a novel architecture unit, which is termed as the "Activate-and-Freeze" block on popular and highly competitive datasets. In order to extract informative features by fusing spatial and channel-wise information together within local receptive fields and boost the representation power, this study constructs a Dense-attention module (pyramid spatial channel (PSC) attention) to perform feature recalibration, and through the PSC attention to model the interdependence among convolution feature channels. We join the PSC attention module in the activating and back-freezing strategy to search for one of the most important parts of the network for extraction and optimization. Experiments on various large-scale datasets demonstrate that the proposed method can achieve substantially better performance for improving the ConvNets representation power than the other state-of-the-art deep models.

Meter pointers exhibit stable and anti-interference capabilities, rendering them extensively utilized in industrial environments. However, automated reading poses a significant challenge due to the fact that current segmentation methods struggle to isolate the fine-grained pointers and scales for accurate reading calculations. This challenge can be alleviated by enhancing the feature extraction capability of the segmentation network. As is well-known that Attention plays an essential role in human vision by selectively focusing on convex parts, and attention-based methods have been applied to various computer vision tasks. Therefore, we propose a new image segmentation network called multipath attention network (MPANet) for pointer meter recognition in the complex industrial environments. The designed network employs an attention gate mechanism to proficiently capture local features stemming from various pathways during skip-connection and upsample processes. In addition, our network incorporates deep supervision by merging the outputs of the final three layers to extract abundant low-dimensional information. To further improve the performance of encoders and decoders, a residual U-block is employed, thereby forming an enhanced U-shaped network structure. In the experiments, we employ HD95, Dice, and Recall as evaluation metrics. MPANet demonstrates superior performance compared to state-of-the-art networks on three our self-collected datasets, showing improvements of over 1% across all metrics. In addition, we validate the efficacy of MPA as a plug-and-play module and the benefits of applying deep supervision to multidecoder network.

Recent methods often introduce attention mechanisms into the skip connections of U-shaped networks to capture features. However, these methods usually overlook spatial information extraction in skip connections and exhibit inefficiency in capturing spatial and channel information. This issue prompts us to reevaluate the design of the skip-connection mechanism and propose a new deep-learning network called the Fusing Spatial and Channel Attention Network, abbreviated as FSCA-Net. FSCA-Net is a novel U-shaped network architecture that utilizes the Parallel Attention Transformer (PAT) to enhance the extraction of spatial and channel features in the skip-connection mechanism, further compensating for downsampling losses. We design the Cross-Attention Bridge Layer (CAB) to mitigate excessive feature and resolution loss when downsampling to the lowest level, ensuring meaningful information fusion during upsampling at the lowest level. Finally, we construct the Dual-Path Channel Attention (DPCA) module to guide channel and spatial information filtering for Transformer features, eliminating ambiguities with decoder features and better concatenating features with semantic inconsistencies between the Transformer and the U-Net decoder. FSCA-Net is designed explicitly for fine-grained segmentation tasks of multiple organs and regions. Our approach achieves over 48% reduction in FLOPs and over 32% reduction in parameters compared to the state-of-the-art method. Moreover, FSCA-Net outperforms existing segmentation methods on seven public datasets, demonstrating exceptional performance.

Cluster assignment of large and complex datasets is a crucial but challenging task in pattern recognition and computer vision. In this study, we explore the possibility of employing fuzzy clustering in a deep neural network framework. Thus, we present a novel evolutionary unsupervised learning representation model with iterative optimization. It implements the deep adaptive fuzzy clustering (DAFC) strategy that learns a convolutional neural network classifier from given only unlabeled data samples. DAFC consists of a deep feature quality-verifying model and a fuzzy clustering model, where deep feature representation learning loss function and embedded fuzzy clustering with the weighted adaptive entropy is implemented. We joint fuzzy clustering to the deep reconstruction model, in which fuzzy membership is utilized to represent a clear structure of deep cluster assignments and jointly optimize for the deep representation learning and clustering. Also, the joint model evaluates current clustering performance by inspecting whether the resampled data from estimated bottleneck space have consistent clustering properties to improve the deep clustering model progressively. Experiments on various datasets show that the proposed method obtains a substantially better performance for both reconstruction and clustering quality compared to the other state-of-the-art deep clustering methods, as demonstrated with the in-depth analysis in the extensive experiments.

A large number of works have presented the single-cell RNA sequencing (scRNA-seq) to study the diversity and biological functions of cells at the single-cell level. Clustering identifies unknown cell types, which is essential for downstream analysis of scRNA-seq samples. However, the high dimensionality, high noise and pervasive dropout rate of scRNA-seq samples have a significant challenge to the cluster analysis of scRNA-seq samples. Herein, we propose a new adaptive fuzzy clustering model based on the denoising autoencoder and self-attention mechanism called the scDASFK. It implements the comparative learning to integrate cell similar information into the clustering method and uses a deep denoising network module to denoise the data. scDASFK consists of a self-attention mechanism for further denoising where an adaptive clustering optimization function for iterative clustering is implemented. In order to make the denoised latent features better reflect the cell structure, we introduce a new adaptive feedback mechanism to supervise the denoising process through the clustering results. Experiments on 16 real scRNA-seq datasets show that scDASFK performs well in terms of clustering accuracy, scalability and stability. Overall, scDASFK is an effective clustering model with great potential for scRNA-seq samples analysis. Our scDASFK model codes are freely available at https://github.com/LRX2022/scDASFK.

Inferential modeling has been of significance for modern manufacturing in estimating the quality-related process variables. As an effective inferential model, probabilistic slow feature analysis (PSFA) has gained attention in regression tasks to interpret dynamic properties with a slowness preference. However, PSFA is often challenged by the nonlinear sequential data due to its linear state-space structure. In this article, a new nonlinear extension of PSFA is proposed under the deep learning framework to enhance the dynamic feature extraction with limited labels, incorporating variational inference and Monte Carlo inference to derive the objective function. The proposed model considers the relevance of inputs with outputs as the input weights to upgrade prediction performance. The proposed model is verified through an industrial hydrocracking process to predict diesel yield with missing labels ranged from 0% to 50%, and the root mean squared error is reduced by at least 8.78% compared to PSFA.

Immunotherapy is an excellent treatment option for many solid tumors, and the therapeutic effect has been proved in clinical. Microsatellite instability (MSI) has been an important predictive marker for response to immune checkpoint inhibitors for Colorectal cancer (CRC). CRC patients with high-level MSI can be provided immunotherapy and benefit from it. Some studies have attempted to predict MSI using pathological images based on deep learning, but the accuracy of the prediction model needs to be improved. In this study, considering that different scales of pathological images contain various levels of information, we propose a novel method, named MSIUMP, to predict microsatellite instability using multi-scale pathological images. We first predict the MSI of a patient based on deep learning model using different scale pathological images, and then integrate the results by ensemble learning to improve the generalization and robustness. In addition, a convolutional neural network model modified on the basis of EfficientNet is used to extract the information of patches from pathological images at different scales. Our method achieved the areas under the receiver operating characteristic curves (AUC) of 0.9096 in the internal test dataset TCGA-CRC and the AUC of 0.9619 in the external independent validation dataset PAIP2020. These results demonstrate the potential of our method as a prediction tool for microsatellite instability in colorectal cancer.

Rapid development of single-cell RNA sequencing (scRNA-seq) technology has allowed researchers to explore biological phenomena at the cellular scale. Clustering is a crucial and helpful step for researchers to study the heterogeneity of cell. Although many clustering methods have been proposed, massive dropout events and the curse of dimensionality in scRNA-seq data make it still difficult to analysis because they reduce the accuracy of clustering methods, leading to misidentification of cell types. In this work, we propose the scHFC, which is a hybrid fuzzy clustering method optimized by natural computation based on Fuzzy C Mean (FCM) and Gath-Geva (GG) algorithms. Specifically, principal component analysis algorithm is utilized to reduce the dimensions of scRNA-seq data after it is preprocessed. Then, FCM algorithm optimized by simulated annealing algorithm and genetic algorithm is applied to cluster the data to output a membership matrix, which represents the initial clustering result and is taken as the input for GG algorithm to get the final clustering results. We also develop a cluster number estimation method called multi-index comprehensive estimation, which can estimate the cluster numbers well by combining four clustering effectiveness indexes. The performance of the scHFC method is evaluated on 17 scRNA-seq datasets, and compared with six state-of-the-art methods. Experimental results validate the better performance of our scHFC method in terms of clustering accuracy and stability of algorithm. In short, scHFC is an effective method to cluster cells for scRNA-seq data, and it presents great potential for downstream analysis of scRNA-seq data. The source code is available at https://github.com/WJ319/scHFC.

In this article, a source–grid–load-collabora tion-based control framework is proposed to improve the power quality of active distribution networks (ADNs) with high penetration of low-carbon energy. First, hybrid dynamics of ADNs are characterized by addressing the voltage regulation and operation economics in each operation mode, and the mode switching control is designed in line with the operation principle of the on-load tap changer, where voltage security events are used to build the event-triggered functions. Second, multiobjective optimization is formulated with consideration of the system-wide operation cost and distribution circuit loss of the ADN in a relatively slow time scale, while in the fast time scale, all the inverter-based distributed generators, energy storages, and static var compensator devices are coordinated at the source–load side, through which multiple voltage issues, including voltage profile issue and voltage increment issue, can be addressed in a fully distributed manner. Finally, simulation results validate the effectiveness and robustness of the proposed method based on the modified IEEE 33-bus system.

This paper investigates the event-triggered bipartite consensus for linear multi-gent systems (MASs) subject to quantized communication on the basis of a connected structurally balanced signed graph. Firstly, one proposes a control strategy combined of logarithmic quantizer and a dynamic event-triggered strategy. Then, based on Lyapunov function approach, sufficient conditions for the bounded bipartite consensus of MASs with event-trigger and relative quantized state measurements are derived. Furthermore, the Zeno behavior is excluded for the triggering time sequences. Finally, simulation study is given to verify the effectiveness of the proposed dynamic event-triggered control strategy with quantized relative state measurements.

This article presents a novel target detection method, which is named as circular target feature detection framework based on a deep convolutional neural network (DCNN). The central proposition of this method uses the optimized DCNN architecture to detect the target and locate the position of the circle accurately in the image field of view. In this article, a Hough transform based on threshold processing (HTP) is embedded into the optimized DCNN architecture, which calculates the center positions and radius of all circles by training the circular samples for each detected rectangular frame. It can efficiently identify small circular target materials in the industry and screen out unqualified particles. The experimental results show that the boundary information of the circles is obtained clearly from the complex noise background images, thereby accurately determining the location of the circle. It has some advantages over only using a specific circular recognition algorithm. We proposed the new study on HTP-DCNN, which has extremely high accuracy in the field of machine vision positioning with circles for industrial applications.