Elucidating genetic and molecular basis of altered higher-order brain structure-function coupling in major depressive disorder.

Previous studies have shown that major depressive disorder (MDD) patients exhibit structural and functional impairments, but few studies have investigated changes in higher-order coupling between structure and function. Here, we systematically investigated the effect of MDD on higher-order coupling between structural connectivity (SC) and functional connectivity (FC). Each brain region was mapped into embedding vector by the node2vec algorithm. We used support vector machine (SVM) with the brain region embedding vector to distinguish MDD patients from health controls (HCs) and identify the most discriminative brain regions. Our study revealed that MDD patients had decreased higher-order coupling in connections between the most discriminative brain regions and local connections in rich-club organization and increased higher-order coupling in connections between the ventral attentional network and limbic network compared with HCs. Interestingly, transcriptome-neuroimaging association analysis demonstrated the correlations between regional rSC-FC coupling variations between MDD patients and HCs and α/ß-hydrolase domain-containing 6 (ABHD6), ß 1,3-N-acetylglucosaminyltransferase-9(ß3GNT9), transmembrane protein 45B (TMEM45B), the correlation between regional dSC-FC coupling variations and retinoic acid early transcript 1E antisense RNA 1(RAET1E-AS1), and the correlations between regional iSC-FC coupling variations and ABHD6, ß3GNT9, katanin-like 2 protein (KATNAL2). In addition, correlation analysis with neurotransmitter receptor/transporter maps found that the rSC-FC and iSC-FC coupling variations were both correlated with neuroendocrine transporter (NET) expression, and the dSC-FC coupling variations were correlated with metabotropic glutamate receptor 5 (mGluR5). Further mediation analysis explored the relationship between genes, neurotransmitter receptor/transporter and MDD related higher-order coupling variations. These findings indicate that specific genetic and molecular factors underpin the observed disparities in higher-order SC-FC coupling between MDD patients and HCs. Our study confirmed that higher-order coupling between SC and FC plays an important role in diagnosing MDD. The identification of new biological evidence for MDD etiology holds promise for the development of innovative antidepressant therapies.

Advanced CKD detection through optimized metaheuristic modeling in healthcare informatics.

Data categorization is a top concern in medical data to predict and detect illnesses; thus, it is applied in modern healthcare informatics. In modern informatics, machine learning and deep learning models have enjoyed great attention for categorizing medical data and improving illness detection. However, the existing techniques, such as features with high dimensionality, computational complexity, and long-term execution duration, raise fundamental problems. This study presents a novel classification model employing metaheuristic methods to maximize efficient positives on Chronic Kidney Disease diagnosis. The medical data is initially massively pre-processed, where the data is purified with various mechanisms, including missing values resolution, data transformation, and the employment of normalization procedures. The focus of such processes is to leverage the handling of the missing values and prepare the data for deep analysis. We adopt the Binary Grey Wolf Optimization method, a reliable subset selection feature using metaheuristics. This operation is aimed at improving illness prediction accuracy. In the classification step, the model adopts the Extreme Learning Machine with hidden nodes through data optimization to predict the presence of CKD. The complete classifier evaluation employs established measures, including recall, specificity, kappa, F-score, and accuracy, in addition to the feature selection. Data related to the study show that the proposed approach records high levels of accuracy, which is better than the existing models.

Prediction of miRNAs and diseases association based on sparse autoencoder and MLP.

Introduction: MicroRNAs (miRNAs) are small and non-coding RNA molecules which have multiple important regulatory roles within cells. With the deepening research on miRNAs, more and more researches show that the abnormal expression of miRNAs is closely related to various diseases. The relationship between miRNAs and diseases is crucial for discovering the pathogenesis of diseases and exploring new treatment methods. Methods: Therefore, we propose a new sparse autoencoder and MLP method (SPALP) to predict the association between miRNAs and diseases. In this study, we adopt advanced deep learning technologies, including sparse autoencoder and multi-layer perceptron (MLP), to improve the accuracy of predicting miRNA-disease associations. Firstly, the SPALP model uses a sparse autoencoder to perform feature learning and extract the initial features of miRNAs and diseases separately, obtaining the latent features of miRNAs and diseases. Then, the latent features combine miRNAs functional similarity data with diseases semantic similarity data to construct comprehensive miRNAs-diseases datasets. Subsequently, the MLP model can predict the unknown association among miRNAs and diseases. Result: To verify the performance of our model, we set up several comparative experiments. The experimental results show that, compared with traditional methods and other deep learning prediction methods, our method has significantly improved the accuracy of predicting miRNAs-disease associations, with 94.61% accuracy and 0.9859 AUC value. Finally, we conducted case study of SPALP model. We predicted the top 30 miRNAs that might be related to Lupus Erythematosus, Ecute Myeloid Leukemia, Cardiovascular, Stroke, Diabetes Mellitus five elderly diseases and validated that 27, 29, 29, 30, and 30 of the top 30 are indeed associated. Discussion: The SPALP approach introduced in this study is adept at forecasting the links between miRNAs and diseases, addressing the complexities of analyzing extensive bioinformatics datasets and enriching the comprehension contribution to disease progression of miRNAs.

Improved Intrusion Detection Based on Hybrid Deep Learning Models and Federated Learning.

The security of the Industrial Internet of Things (IIoT) is of vital importance, and the Network Intrusion Detection System (NIDS) plays an indispensable role in this. Although there is an increasing number of studies on the use of deep learning technology to achieve network intrusion detection, the limited local data of the device may lead to poor model performance because deep learning requires large-scale datasets for training. Some solutions propose to centralize the local datasets of devices for deep learning training, but this may involve user privacy issues. To address these challenges, this study proposes a novel federated learning (FL)-based approach aimed at improving the accuracy of network intrusion detection while ensuring data privacy protection. This research combines convolutional neural networks with attention mechanisms to develop a new deep learning intrusion detection model specifically designed for the IIoT. Additionally, variational autoencoders are incorporated to enhance data privacy protection. Furthermore, an FL framework enables multiple IIoT clients to jointly train a shared intrusion detection model without sharing their raw data. This strategy significantly improves the model's detection capability while effectively addressing data privacy and security issues. To validate the effectiveness of the proposed method, a series of experiments were conducted on a real-world Internet of Things (IoT) network intrusion dataset. The experimental results demonstrate that our model and FL approach significantly improve key performance metrics such as detection accuracy, precision, and false-positive rate (FPR) compared to traditional local training methods and existing models.

Ethereum Phishing Scam Detection Based on Data Augmentation Method and Hybrid Graph Neural Network Model.

The rapid advancement of blockchain technology has fueled the prosperity of the cryptocurrency market. Unfortunately, it has also facilitated certain criminal activities, particularly the increasing issue of phishing scams on blockchain platforms such as Ethereum. Consequently, developing an efficient phishing detection system is critical for ensuring the security and reliability of cryptocurrency transactions. However, existing methods have shortcomings in dealing with sample imbalance and effective feature extraction. To address these issues, this study proposes an Ethereum phishing scam detection method based on DA-HGNN (Data Augmentation Method and Hybrid Graph Neural Network Model), validated by real Ethereum datasets to prove its effectiveness. Initially, basic node features consisting of 11 attributes were designed. This study applied a sliding window sampling method based on node transactions for data augmentation. Since phishing nodes often initiate numerous transactions, the augmented samples tended to balance. Subsequently, the Temporal Features Extraction Module employed Conv1D (One-Dimensional Convolutional neural network) and GRU-MHA (GRU-Multi-Head Attention) models to uncover intrinsic relationships between features from the time sequences and to mine adequate local features, culminating in the extraction of temporal features. The GAE (Graph Autoencoder) concept was then leveraged, with SAGEConv (Graph SAGE Convolution) as the encoder. In the SAGEConv reconstruction module, by reconstructing the relationships between transaction graph nodes, the structural features of the nodes were learned, obtaining reconstructed node embedding representations. Ultimately, phishing fraud nodes were further identified by integrating temporal features, basic features, and embedding representations. A real Ethereum dataset was collected for evaluation, and the DA-HGNN model achieved an AUC-ROC (Area Under the Receiver Operating Characteristic Curve) of 0.994, a Recall of 0.995, and an F1-score of 0.994, outperforming existing methods and baseline models.

iDNA-OpenPrompt: OpenPrompt learning model for identifying DNA methylation.

Introduction: DNA methylation is a critical epigenetic modification involving the addition of a methyl group to the DNA molecule, playing a key role in regulating gene expression without changing the DNA sequence. The main difficulty in identifying DNA methylation sites lies in the subtle and complex nature of methylation patterns, which may vary across different tissues, developmental stages, and environmental conditions. Traditional methods for methylation site identification, such as bisulfite sequencing, are typically labor-intensive, costly, and require large amounts of DNA, hindering high-throughput analysis. Moreover, these methods may not always provide the resolution needed to detect methylation at specific sites, especially in genomic regions that are rich in repetitive sequences or have low levels of methylation. Furthermore, current deep learning approaches generally lack sufficient accuracy. Methods: This study introduces the iDNA-OpenPrompt model, leveraging the novel OpenPrompt learning framework. The model combines a prompt template, prompt verbalizer, and Pre-trained Language Model (PLM) to construct the prompt-learning framework for DNA methylation sequences. Moreover, a DNA vocabulary library, BERT tokenizer, and specific label words are also introduced into the model to enable accurate identification of DNA methylation sites. Results and Discussion: An extensive analysis is conducted to evaluate the predictive, reliability, and consistency capabilities of the iDNA-OpenPrompt model. The experimental outcomes, covering 17 benchmark datasets that include various species and three DNA methylation modifications (4mC, 5hmC, 6mA), consistently indicate that our model surpasses outstanding performance and robustness approaches.

Breast cancer diagnosis using support vector machine optimized by improved quantum inspired grey wolf optimization.

A prompt diagnosis of breast cancer in its earliest phases is necessary for effective treatment. While Computer-Aided Diagnosis systems play a crucial role in automated mammography image processing, interpretation, grading, and early detection of breast cancer, existing approaches face limitations in achieving optimal accuracy. This study addresses these limitations by hybridizing the improved quantum-inspired binary Grey Wolf Optimizer with the Support Vector Machines Radial Basis Function Kernel. This hybrid approach aims to enhance the accuracy of breast cancer classification by determining the optimal Support Vector Machine parameters. The motivation for this hybridization lies in the need for improved classification performance compared to existing optimizers such as Particle Swarm Optimization and Genetic Algorithm. Evaluate the efficacy of the proposed IQI-BGWO-SVM approach on the MIAS dataset, considering various metric parameters, including accuracy, sensitivity, and specificity. Furthermore, the application of IQI-BGWO-SVM for feature selection will be explored, and the results will be compared. Experimental findings demonstrate that the suggested IQI-BGWO-SVM technique outperforms state-of-the-art classification methods on the MIAS dataset, with a resulting mean accuracy, sensitivity, and specificity of 99.25%, 98.96%, and 100%, respectively, using a tenfold cross-validation datasets partition.

BC-QNet: A quantum-infused ELM model for breast cancer diagnosis.

The timely and accurate diagnosis of breast cancer is pivotal for effective treatment, but current automated mammography classification methods have their constraints. In this study, we introduce an innovative hybrid model that marries the power of the Extreme Learning Machine (ELM) with FuNet transfer learning, harnessing the potential of the MIAS dataset. This novel approach leverages an Enhanced Quantum-Genetic Binary Grey Wolf Optimizer (Q-GBGWO) within the ELM framework, elevating its performance. Our contributions are twofold: firstly, we employ a feature fusion strategy to optimize feature extraction, significantly enhancing breast cancer classification accuracy. The proposed methodological motivation stems from optimizing feature extraction for improved breast cancer classification accuracy. The Q-GBGWO optimizes ELM parameters, demonstrating its efficacy within the ELM classifier. This innovation marks a considerable advancement beyond traditional methods. Through comparative evaluations against various optimization techniques, the exceptional performance of our Q-GBGWO-ELM model becomes evident. The classification accuracy of the model is exceptionally high, with rates of 96.54 % for Normal, 97.24 % for Benign, and 98.01 % for Malignant classes. Additionally, the model demonstrates a high sensitivity with rates of 96.02 % for Normal, 96.54 % for Benign, and 97.75 % for Malignant classes, and it exhibits impressive specificity with rates of 96.69 % for Normal, 97.38 % for Benign, and 98.16 % for Malignant classes. These metrics are reflected in its ability to classify three different types of breast cancer accurately. Our approach highlights the innovative integration of image data, deep feature extraction, and optimized ELM classification, marking a transformative step in advancing early breast cancer detection and enhancing patient outcomes.

NK cell transfer overcomes resistance to PD-(L)1 therapy in aged mice.

BACKGROUND: Cancer is the leading cause of death among older adults. Although the integration of immunotherapy has revolutionized the therapeutic landscape of cancer, the complex interactions between age and immunotherapy efficacy remain incompletely defined. Here, we aimed to elucidate the relationship between aging and immunotherapy resistance. METHODS: Flow cytometry was performed to evaluate the infiltration of immune cells in the tumor microenvironment (TME). In vivo T cell proliferation, cytotoxicity and migration assays were performed to evaluate the antitumor capacity of tumor antigen-specific CD8+ T cells in mice. Real-time quantitative PCR (qPCR) was used to investigate the expression of IFN-γ-associated gene and natural killer (NK)-associated chemokine. Adoptive NK cell transfer was adopted to evaluate the effects of NK cells from young mice in overcoming the immunotherapy resistance of aged mice. RESULTS: We found that elderly patients with advanced non-small cell lung cancer (aNSCLC) aged ≥ 75 years exhibited poorer progression-free survival (PFS), overall survival (OS) and a lower clinical response rate after immunotherapy. Mechanistically, we showed that the infiltration of NK cells was significantly reduced in aged mice compared to younger mice. Furthermore, the aged NK cells could also suppress the activation of tumor antigen-specific CD8+ T cells by inhibiting the recruitment and activation of CD103+ dendritic cells (DCs). Adoptive transfer of NK cells from young mice to aged mice promoted TME remodeling, and reversed immunotherapy resistance. CONCLUSION: Our findings revealed the decreased sensitivity of elderly patients to immunotherapy, as well as in aged mice. This may be attributed to the reduction of NK cells in aged mice, which inhibits CD103+ DCs recruitment and its CD86 expression and ultimately leads to immunotherapy resistance.

Residual graph transformer for autism spectrum disorder prediction.

Brain functional connectivity (FC) based on resting-state functional magnetic resonance imaging (rs-fMRI) has been in vogue to predict Autism Spectrum Disorder (ASD), which is a neuropsychiatric disease up the plight of locating latent biomarkers for clinical diagnosis. Albeit massive endeavors have been made, most studies are fed up with several chronic issues, such as the intractability of harnessing the interaction flourishing within brain regions, the astriction of representation due to vanishing gradient within deeper network architecture, and the poor interpretability leading to unpersuasive diagnosis. To ameliorate these issues, a FC-learned Residual Graph Transformer Network, namely RGTNet, is proposed. Specifically, we design a Graph Encoder to extract temporal-related features with long-range dependencies, from which interpretable FC matrices would be modeled. Besides, the residual trick is introduced to deepen the GCN architecture, thereby learning the higher-level information. Moreover, a novel Graph Sparse Fitting followed by weighted aggregation is proposed to ease dimensionality explosion. Empirically, the results on two types of ABIDE data sets demonstrate the meliority of RGTNet. Notably, the achieved ACC metric reaches 73.4%, overwhelming most competitors with merely 70.9% on the AAL atlas using a five-fold cross-validation policy. Moreover, the investigated biomarkers concord closely with the authoritative medical knowledge, paving a viable way for ASD-clinical diagnosis. Our code is available at https://github.com/CodeGoat24/RGTNet.

NIMEQ-SACNet: A novel self-attention precision medicine model for vision-threatening diabetic retinopathy using image data.

In the realm of precision medicine, the potential of deep learning is progressively harnessed to facilitate intricate clinical decision-making, especially when navigating multifaceted datasets encompassing Omics, Clinical, image, device, social, and environmental dimensions. This study accentuates the criticality of image data, given its instrumental role in detecting and classifying vision-threatening diabetic retinopathy (VTDR) - a predominant global contributor to vision impairment. The timely identification of VTDR is a linchpin for efficacious interventions and the mitigation of vision loss. Addressing this, This study introduces "NIMEQ-SACNet," a novel hybrid model by the prowess of the Enhanced Quantum-Inspired Binary Grey Wolf Optimizer (EQI-BGWO) with a self-attention capsule network. The proposed approach is characterized by two pivotal advancements: firstly, the augmentation of the Binary Grey Wolf Optimization through Quantum Computing methodologies, and secondly, the deployment of the enhanced EQI-BGWO to adeptly calibrate the SACNet's parameters, culminating in a notable uplift in VTDR classification accuracy. The proposed model's ability to handle binary, 5-stage, and 7-stage VTDR classifications adroitly is noteworthy. Rigorous assessments on the fundus image dataset, underscored by metrics such as Accuracy, Sensitivity, Specificity, Precision, F1-Score, and MCC, bear testament to NIMEQ-SACNet's pre-eminence over prevailing algorithms and classification frameworks.

Improved Support Vector Machine based on CNN-SVD for vision-threatening diabetic retinopathy detection and classification.

The integration of artificial intelligence (AI) in diagnosing diabetic retinopathy, a major contributor to global vision impairment, is becoming increasingly pronounced. Notably, the detection of vision-threatening diabetic retinopathy (VTDR) has been significantly fortified through automated techniques. Traditionally, the reliance on manual analysis of retinal images, albeit slow and error-prone, constituted the conventional approach. Addressing this, our study introduces a novel methodology that amplifies the robustness and precision of the detection process. This is complemented by the groundbreaking Hierarchical Block Attention (HBA) and HBA-U-Net architecture, which notably propel attention mechanisms in image segmentation. This innovative model refines image processing without imposing excessive computational demands by honing in on individual pixel intricacies, spatial relationships, and channel-specific attention. Building upon this innovation, our proposed method employs a multi-stage strategy encompassing data pre-processing, feature extraction via a hybrid CNN-SVD model, and classification employing an amalgamation of Improved Support Vector Machine-Radial Basis Function (ISVM-RBF), DT, and KNN techniques. Rigorously tested on the IDRiD dataset classified into five severity tiers, the hybrid model yields remarkable performance, achieving a 99.18% accuracy, 98.15% sensitivity, and 100% specificity in VTDR detection, thus surpassing existing methods. These results underscore a more potent avenue for diagnosing and addressing this crucial ocular condition while underscoring AI's transformative potential in medical care, particularly in ophthalmology.

Tumor-associated myeloid cells in cancer immunotherapy.

Tumor-associated myeloid cells (TAMCs) are among the most important immune cell populations in the tumor microenvironment, and play a significant role on the efficacy of immune checkpoint blockade. Understanding the origin of TAMCs was found to be the essential to determining their functional heterogeneity and, developing cancer immunotherapy strategies. While myeloid-biased differentiation in the bone marrow has been traditionally considered as the primary source of TAMCs, the abnormal differentiation of splenic hematopoietic stem and progenitor cells, erythroid progenitor cells, and B precursor cells in the spleen, as well as embryo-derived TAMCs, have been depicted as important origins of TAMCs. This review article provides an overview of the literature with a focus on the recent research progress evaluating the heterogeneity of TAMCs origins. Moreover, this review summarizes the major therapeutic strategies targeting TAMCs with heterogeneous sources, shedding light on their implications for cancer antitumor immunotherapies.

PLSNet: Position-aware GCN-based autism spectrum disorder diagnosis via FC learning and ROIs sifting.

Brain function connectivity, derived from functional magnetic resonance imaging (fMRI), has enjoyed high popularity in the studies of Autism Spectrum Disorder (ASD) diagnosis. Albeit rapid progress has been made, most studies still suffer from several knotty issues: (1) the hardship of modeling the sophisticated brain neuronal connectivity; (2) the mismatch of identically graph node setup to the variations of different brain regions; (3) the dimensionality explosion resulted from excessive voxels in each fMRI sample; (4) the poor interpretability giving rise to unpersuasive diagnosis. To ameliorate these issues, we propose a position-aware graph-convolution-network-based model, namely PLSNet, with superior accuracy and compelling built-in interpretability for ASD diagnosis. Specifically, a time-series encoder is designed for context-rich feature extraction, followed by a function connectivity generator to model the correlation with long range dependencies. In addition, to discriminate the brain nodes with different locations, the position embedding technique is adopted, giving a unique identity to each graph region. We then embed a rarefying method to sift the salient nodes during message diffusion, which would also benefit the reduction of the dimensionality complexity. Extensive experiments conducted on Autism Brain Imaging Data Exchange demonstrate that our PLSNet achieves state-of-the-art performance. Notably, on CC200 atlas, PLSNet reaches an accuracy of 76.4% and a specificity of 78.6%, overwhelming the previous state-of-the-art with 2.5% and 6.5% under five-fold cross-validation policy. Moreover, the most salient brain regions predicted by PLSNet are closely consistent with the theoretical knowledge in the medical domain, providing potential biomarkers for ASD clinical diagnosis. Our code is available at https://github.com/CodeGoat24/PLSNet.

DRSN4mCPred: accurately predicting sites of DNA N4-methylcytosine using deep residual shrinkage network for diagnosis and treatment of gastrointestinal cancer in the precision medicine era.

Introduction: The DNA N4-methylcytosine (4mC) site levels of those suffering from digestive system cancers were higher, and the pathogenesis of digestive system cancers may also be related to the changes in DNA 4mC levels. Identifying DNA 4mC sites is a very important step in studying the analysis of biological function and cancer prediction. Extracting accurate features from DNA sequences is the key to establishing a prediction model of effective DNA 4mC sites. This study sought to develop a new predictive model, DRSN4mCPred, which aimed to improve the performance of the predicting DNA 4mC sites. Methods: The model adopted multi-scale channel attention to extract features and used attention feature fusion (AFF) to fuse features. In order to capture features information more accurately and effectively, this model utilized Deep Residual Shrinkage Network with Channel-Wise thresholds (DRSN-CW) to eliminate noise-related features and achieve a more precise feature representation, thereby, distinguishing the sites in DNA with 4mC and non-4mC. Additionally, the predictive model incorporated an inverted residual block, a Multi-scale Channel Attention Module (MS-CAM), a Bi-directional Long Short Term Memory Network (Bi-LSTM), AFF, and DRSN-CW. Results and Discussion: The results indicated the predictive model DRSN4mCPred had extremely good performance in predicting the DNA 4mC sites across different species. This paper will potentially provide support for the diagnosis and treatment of gastrointestinal cancer based on artificial intelligence in the precise medical era.

A dichotomy color quantization algorithm for the HSI color space.

Color quantization is used to obtain an image with the same number of pixels as the original but represented using fewer colors. Most existing color quantization algorithms are based on the Red Green Blue (RGB) color space, and there are few color quantization algorithms for the Hue Saturation Intensity (HSI) color space with a simple uniform quantization algorithm. In this paper, we propose a dichotomy color quantization algorithm for the HSI color space. The proposed color quantization algorithm can display images with a smaller number of colors than other quantization methods of RGB color space. The proposed algorithm has three main steps as follows: first, a single-valued monotonic function of the Hue (H) component in the from RGB color space to HSI color space (RGB-HSI) color space conversion is constructed, which can avoid the partition calculation of the H component in the RGB-HSI color space; second, an iterative quantization algorithm based on the single-valued monotonic function is proposed; and third, a dichotomy quantization algorithm is proposed to improve the iterative quantization algorithm. Both visual and numerical evaluations reveal that the proposed method presents promising quantization results.

Synergistic immunotherapy targeting cancer-associated anemia: prospects of a combination strategy.

Cancer-associated anemia promotes tumor progression, leads to poor quality of life in patients with cancer, and even obstructs the efficacy of immune checkpoint inhibitors therapy. However, the precise mechanism for cancer-associated anemia remains unknown and the feasible strategy to target cancer-associated anemia synergizing immunotherapy needs to be clarified. Here, we review the possible mechanisms of cancer-induced anemia regarding decreased erythropoiesis and increased erythrocyte destruction, and cancer treatment-induced anemia. Moreover, we summarize the current paradigm for cancer-associated anemia treatment. Finally, we propose some prospective paradigms to slow down cancer-associated anemia and synergistic the efficacy of immunotherapy. Video Abstract.

Single-cell RNA-seq data analysis based on directed graph neural network.

Single-cell RNA sequencing (scRNA-seq) data scale surges with high-throughput sequencing technology development. However, although single-cell data analysis is a powerful tool, various issues have been reported, such as sequencing sparsity and complex differential patterns in gene expression. Statistical or traditional machine learning methods are inefficient, and the accuracy needs to be improved. The methods based on deep learning can not directly process non-Euclidean spatial data, such as cell diagrams. In this study, we have developed graph autoencoders and graph attention network for scRNA-seq analysis based on a directed graph neural network named scDGAE. Directed graph neural networks cannot only retain the connection properties of the directed graph but also expand the receptive field of the convolution operation. Cosine similarity, median L1 distance, and root-mean-squared error are used to measure the gene imputation performance of different methods with scDGAE. Furthermore, adjusted mutual information, normalized mutual information, completeness score, and Silhouette coefficient score are used to measure the cell clustering performance of different methods with scDGAE. Experiment results show that the scDGAE model achieves promising performance in gene imputation and cell clustering prediction on four scRNA-seq data sets with gold-standard cell labels. Furthermore, it is a robust framework that can be applied to general scRNA-Seq analyses.