A universal framework for single-cell multi-omics data integration with graph convolutional networks.

Single-cell omics data are growing at an unprecedented rate, whereas effective integration of them remains challenging due to different sequencing methods, quality, and expression pattern of each omics data. In this study, we propose a universal framework for the integration of single-cell multi-omics data based on graph convolutional network (GCN-SC). Among the multiple single-cell data, GCN-SC usually selects one data with the largest number of cells as the reference and the rest as the query dataset. It utilizes mutual nearest neighbor algorithm to identify cell-pairs, which provide connections between cells both within and across the reference and query datasets. A GCN algorithm further takes the mixed graph constructed from these cell-pairs to adjust count matrices from the query datasets. Finally, dimension reduction is performed by using non-negative matrix factorization before visualization. By applying GCN-SC on six datasets, we show that GCN-SC can effectively integrate sequencing data from multiple single-cell sequencing technologies, species or different omics, which outperforms the state-of-the-art methods, including Seurat, LIGER, GLUER and Pamona.

Predicting drug-protein interactions by preserving the graph information of multi source data.

Examining potential drug-target interactions (DTIs) is a pivotal component of drug discovery and repurposing. Recently, there has been a significant rise in the use of computational techniques to predict DTIs. Nevertheless, previous investigations have predominantly concentrated on assessing either the connections between nodes or the consistency of the network's topological structure in isolation. Such one-sided approaches could severely hinder the accuracy of DTI predictions. In this study, we propose a novel method called TTGCN, which combines heterogeneous graph convolutional neural networks (GCN) and graph attention networks (GAT) to address the task of DTI prediction. TTGCN employs a two-tiered feature learning strategy, utilizing GAT and residual GCN (R-GCN) to extract drug and target embeddings from the diverse network, respectively. These drug and target embeddings are then fused through a mean-pooling layer. Finally, we employ an inductive matrix completion technique to forecast DTIs while preserving the network's node connectivity and topological structure. Our approach demonstrates superior performance in terms of area under the curve and area under the precision-recall curve in experimental comparisons, highlighting its significant advantages in predicting DTIs. Furthermore, case studies provide additional evidence of its ability to identify potential DTIs.

Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks.

BACKGROUND: Cell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation atlas to TOO detection in low depth cfDNA samples. METHODS: We constructed a tumor-specific methylation atlas (TSMA) using whole-genome bisulfite sequencing (WGBS) data from five types of tumor tissues (breast, colorectal, gastric, liver and lung cancer) and paired white blood cells (WBC). TSMA was used with a non-negative least square matrix factorization (NNLS) deconvolution algorithm to identify the abundance of tumor tissue types in a WGBS sample. We showed that TSMA worked well with tumor tissue but struggled with cfDNA samples due to the overwhelming amount of WBC-derived DNA. To construct a model for TOO, we adopted the multi-modal strategy and used as inputs the combination of deconvolution scores from TSMA with other features of cfDNA. RESULTS: Our final model comprised of a graph convolutional neural network using deconvolution scores and genome-wide methylation density features, which achieved an accuracy of 69% in a held-out validation dataset of 239 low-depth cfDNA samples. CONCLUSIONS: In conclusion, we have demonstrated that our TSMA in combination with other cfDNA features can improve TOO detection in low-depth cfDNA samples.

Clinical research text summarization method based on fusion of domain knowledge.

OBJECTIVE: The objective of this study is to integrate PICO knowledge into the clinical research text summarization process, aiming to enhance the model's comprehension of biomedical texts while capturing crucial content from the perspective of summary readers, ultimately improving the quality of summaries. METHODS: We propose a clinical research text summarization method called DKGE-PEGASUS (Domain-Knowledge and Graph Convolutional Enhanced PEGASUS), which is based on integrating domain knowledge. The model mainly consists of three components: a PICO label prediction module, a text information re-mining unit based on Graph Convolutional Neural Networks (GCN), and a pre-trained summarization model. First, the PICO label prediction module is used to identify PICO elements in clinical research texts while obtaining word embeddings enriched with PICO knowledge. Then, we use GCN to reinforce the encoder of the pre-trained summarization model to achieve deeper text information mining while explicitly injecting PICO knowledge. Finally, the outputs of the PICO label prediction module, the GCN text information re-mining unit, and the encoder of the pre-trained model are fused to produce the final coding results, which are then decoded by the decoder to generate summaries. RESULTS: Experiments conducted on two datasets, PubMed and CDSR, demonstrated the effectiveness of our method. The Rouge-1 scores achieved were 42.64 and 38.57, respectively. Furthermore, the quality of our summarization results was found to significantly outperform the baseline model in comparisons of summarization results for a segment of biomedical text. CONCLUSION: The method proposed in this paper is better equipped to identify critical elements in clinical research texts and produce a higher-quality summary.

Improving Graph Convolutional Network with Learnable Edge Weights and Edge-Node Co-Embedding for Graph Anomaly Detection.

The era of Industry 4.0 is gradually transforming our society into a data-driven one, which can help us uncover valuable information from accumulated data, thereby improving the level of social governance. The detection of anomalies, is crucial for maintaining societal trust and fairness, yet it poses significant challenges due to the ubiquity of anomalies and the difficulty in identifying them accurately. This paper aims to enhance the performance of the current Graph Convolutional Network (GCN)-based Graph Anomaly Detection (GAD) algorithm on datasets with extremely low proportions of anomalous labels. This goal is achieved through modifying the GCN network structure and conducting feature extraction, thus fully utilizing three types of information in the graph: node label information, node feature information, and edge information. Firstly, we theoretically demonstrate the relationship between label propagation and feature convolution, indicating that the Label Propagation Algorithm (LPA) can serve as a regularization penalty term for GCN, aiding in training and enabling learnable edge weights, providing a basis for incorporating node label information into GCN networks. Secondly, we introduce a method to aggregate node and edge features, thereby incorporating edge information into GCN networks. Finally, we design different GCN trainable weights for node features and co-embedding features. This design allows different features to be projected into different spaces, greatly enhancing model expressiveness. Experimental results on the DGraph dataset demonstrate superior AUC performance compared to baseline models, highlighting the feasibility and efficacy of the proposed approach in addressing GAD tasks in the scene with extremely low proportions of anomalous data.

Real-World Spatial Synchronization of Event-CMOS Cameras through Deep Learning: A Novel CNN-DGCNN Approach.

This paper presents a new deep-learning architecture designed to enhance the spatial synchronization between CMOS and event cameras by harnessing their complementary characteristics. While CMOS cameras produce high-quality imagery, they struggle in rapidly changing environments-a limitation that event cameras overcome due to their superior temporal resolution and motion clarity. However, effective integration of these two technologies relies on achieving precise spatial alignment, a challenge unaddressed by current algorithms. Our architecture leverages a dynamic graph convolutional neural network (DGCNN) to process event data directly, improving synchronization accuracy. We found that synchronization precision strongly correlates with the spatial concentration and density of events, with denser distributions yielding better alignment results. Our empirical results demonstrate that areas with denser event clusters enhance calibration accuracy, with calibration errors increasing in more uniformly distributed event scenarios. This research pioneers scene-based synchronization between CMOS and event cameras, paving the way for advancements in mixed-modality visual systems. The implications are significant for applications requiring detailed visual and temporal information, setting new directions for the future of visual perception technologies.

Identifying cancer driver genes based on multi-view heterogeneous graph convolutional network and self-attention mechanism.

BACKGROUND: Correctly identifying the driver genes that promote cell growth can significantly assist drug design, cancer diagnosis and treatment. The recent large-scale cancer genomics projects have revealed multi-omics data from thousands of cancer patients, which requires to design effective models to unlock the hidden knowledge within the valuable data and discover cancer drivers contributing to tumorigenesis. RESULTS: In this work, we propose a graph convolution network-based method called MRNGCN that integrates multiple gene relationship networks to identify cancer driver genes. First, we constructed three gene relationship networks, including the gene-gene, gene-outlying gene and gene-miRNA networks. Then, genes learnt feature presentations from the three networks through three sharing-parameter heterogeneous graph convolution network (HGCN) models with the self-attention mechanism. After that, these gene features pass a convolution layer to generate fused features. Finally, we utilized the fused features and the original feature to optimize the model by minimizing the node and link prediction losses. Meanwhile, we combined the fused features, the original features and the three features learned from every network through a logistic regression model to predict cancer driver genes. CONCLUSIONS: We applied the MRNGCN to predict pan-cancer and cancer type-specific driver genes. Experimental results show that our model performs well in terms of the area under the ROC curve (AUC) and the area under the precision-recall curve (AUPRC) compared to state-of-the-art methods. Ablation experimental results show that our model successfully improved the cancer driver identification by integrating multiple gene relationship networks.

Joint Multidimensional Pattern for Spectrum Prediction Using GNN.

In general, judging the use/idle state of the wireless spectrum is the foundation for cognitive radio users (secondary users, SUs) to access limited spectrum resources efficiently. Rich information can be mined by the inherent correlation of electromagnetic spectrum data from SUs in time, frequency, space, and other dimensions. Therefore, how to efficiently use the spectrum status of each SU implementation of reception multidimensional combination forecasting is the core of this paper. In this paper, we propose a deep-learning hybrid model called TensorGCN-LSTM based on the tensor data structure. The model treats SUs deployed at different spatial locations under the same frequency, and the spectrum status of SUs themselves under different frequencies in the task area as nodes and constructs two types of graph structures. Graph convolutional operations are used to sequentially extract corresponding spatial-domain and frequency-domain features from the two types of graph structures. Then, the long short-term memory (LSTM) model is used to fuse the spatial, frequency, and temporal features of the cognitive radio environment data. Finally, the prediction task of the spectrum distribution situation is accomplished through fully connected layers. Specifically, the model constructs a tensor graph based on the spatial similarity of SUs' locations and the frequency correlation between different frequency signals received by SUs, which describes the electromagnetic wave's dependency relationship in spatial and frequency domains. LSTM is used to capture the electromagnetic wave's dependency relationship in the temporal domain. To evaluate the effectiveness of the model, we conducted ablation experiments on LSTM, GCN, GC-LSTM, and TensorGCN-LSTM models using simulated data. The experimental results showed that our model achieves better prediction performance in RMSE, and the correlation coefficient R2 of 0.8753 also confirms the feasibility of the model.

Application of Graph Convolutional Neural Networks Combined with Single-Model Decision-Making Fusion Neural Networks in Structural Damage Recognition.

In cases with a large number of sensors and complex spatial distribution, correctly learning the spatial characteristics of the sensors is vital for structural damage identification. Graph convolutional neural networks (GCNs), unlike other methods, have the ability to learn the spatial characteristics of the sensors, which is targeted at the above problems in structural damage identification. However, under the influence of environmental interference, sensor instability, and other factors, part of the vibration signal can easily change its fundamental characteristics, and there is a possibility of misjudging structural damage. Therefore, on the basis of building a high-performance graphical convolutional deep learning model, this paper considers the integration of data fusion technology in the model decision-making layer and proposes a single-model decision-making fusion neural network (S_DFNN) model. Through experiments involving the frame model and the self-designed cable-stayed bridge model, it is concluded that this method has a better performance of damage recognition for different structures, and the accuracy is improved based on a single model and has good damage recognition performance. The method has better damage identification performance in different structures, and the accuracy rate is improved based on the single model, which has a very good damage identification effect. It proves that the structural damage diagnosis method proposed in this paper with data fusion technology combined with deep learning has a strong generalization ability and has great potential in structural damage diagnosis.

HGT: A Hierarchical GCN-Based Transformer for Multimodal Periprosthetic Joint Infection Diagnosis Using Computed Tomography Images and Text.

Prosthetic joint infection (PJI) is a prevalent and severe complication characterized by high diagnostic challenges. Currently, a unified diagnostic standard incorporating both computed tomography (CT) images and numerical text data for PJI remains unestablished, owing to the substantial noise in CT images and the disparity in data volume between CT images and text data. This study introduces a diagnostic method, HGT, based on deep learning and multimodal techniques. It effectively merges features from CT scan images and patients' numerical text data via a Unidirectional Selective Attention (USA) mechanism and a graph convolutional network (GCN)-based Feature Fusion network. We evaluated the proposed method on a custom-built multimodal PJI dataset, assessing its performance through ablation experiments and interpretability evaluations. Our method achieved an accuracy (ACC) of 91.4% and an area under the curve (AUC) of 95.9%, outperforming recent multimodal approaches by 2.9% in ACC and 2.2% in AUC, with a parameter count of only 68 M. Notably, the interpretability results highlighted our model's strong focus and localization capabilities at lesion sites. This proposed method could provide clinicians with additional diagnostic tools to enhance accuracy and efficiency in clinical practice.

Automated freezing of gait assessment with marker-based motion capture and multi-stage spatial-temporal graph convolutional neural networks.

BACKGROUND: Freezing of gait (FOG) is a common and debilitating gait impairment in Parkinson's disease. Further insight into this phenomenon is hampered by the difficulty to objectively assess FOG. To meet this clinical need, this paper proposes an automated motion-capture-based FOG assessment method driven by a novel deep neural network. METHODS: Automated FOG assessment can be formulated as an action segmentation problem, where temporal models are tasked to recognize and temporally localize the FOG segments in untrimmed motion capture trials. This paper takes a closer look at the performance of state-of-the-art action segmentation models when tasked to automatically assess FOG. Furthermore, a novel deep neural network architecture is proposed that aims to better capture the spatial and temporal dependencies than the state-of-the-art baselines. The proposed network, termed multi-stage spatial-temporal graph convolutional network (MS-GCN), combines the spatial-temporal graph convolutional network (ST-GCN) and the multi-stage temporal convolutional network (MS-TCN). The ST-GCN captures the hierarchical spatial-temporal motion among the joints inherent to motion capture, while the multi-stage component reduces over-segmentation errors by refining the predictions over multiple stages. The proposed model was validated on a dataset of fourteen freezers, fourteen non-freezers, and fourteen healthy control subjects. RESULTS: The experiments indicate that the proposed model outperforms four state-of-the-art baselines. Moreover, FOG outcomes derived from MS-GCN predictions had an excellent (r = 0.93 [0.87, 0.97]) and moderately strong (r = 0.75 [0.55, 0.87]) linear relationship with FOG outcomes derived from manual annotations. CONCLUSIONS: The proposed MS-GCN may provide an automated and objective alternative to labor-intensive clinician-based FOG assessment. Future work is now possible that aims to assess the generalization of MS-GCN to a larger and more varied verification cohort.

Deep Neural Network for 3D Shape Classification Based on Mesh Feature.

Virtual reality, driverless cars, and robotics all make extensive use of 3D shape classification. One of the most popular ways to represent 3D data is with polygonal meshes. In particular, triangular mesh is frequently employed. A triangular mesh has more features than 3D data formats such as voxels, multi-views, and point clouds. The current challenge is to fully utilize and extract useful information from mesh data. In this paper, a 3D shape classification network based on triangular mesh and graph convolutional neural networks was suggested. The triangular face of this model was viewed as a unit. By obtaining an adjacency matrix from mesh data, graph convolutional neural networks can be utilized to process mesh data. The studies were performed on the ModelNet40 dataset with an accuracy of 91.0%, demonstrating that the classification network in this research may produce effective results.

Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition.

In the last decade, machine learning and artificial intelligence applications have received a significant boost in performance and attention in both academic research and industry. The success behind most of the recent state-of-the-art methods can be attributed to the latest developments in deep learning. When applied to various scientific domains that are concerned with the processing of non-tabular data, for example, image or text, deep learning has been shown to outperform not only conventional machine learning but also highly specialized tools developed by domain experts. This review aims to summarize AI-based research for GPCR bioactive ligand discovery with a particular focus on the most recent achievements and research trends. To make this article accessible to a broad audience of computational scientists, we provide instructive explanations of the underlying methodology, including overviews of the most commonly used deep learning architectures and feature representations of molecular data. We highlight the latest AI-based research that has led to the successful discovery of GPCR bioactive ligands. However, an equal focus of this review is on the discussion of machine learning-based technology that has been applied to ligand discovery in general and has the potential to pave the way for successful GPCR bioactive ligand discovery in the future. This review concludes with a brief outlook highlighting the recent research trends in deep learning, such as active learning and semi-supervised learning, which have great potential for advancing bioactive ligand discovery.

Classification of alkaloids according to the starting substances of their biosynthetic pathways using graph convolutional neural networks.

BACKGROUND: Alkaloids, a class of organic compounds that contain nitrogen bases, are mainly synthesized as secondary metabolites in plants and fungi, and they have a wide range of bioactivities. Although there are thousands of compounds in this class, few of their biosynthesis pathways are fully identified. In this study, we constructed a model to predict their precursors based on a novel kind of neural network called the molecular graph convolutional neural network. Molecular similarity is a crucial metric in the analysis of qualitative structure-activity relationships. However, it is sometimes difficult for current fingerprint representations to emphasize specific features for the target problems efficiently. It is advantageous to allow the model to select the appropriate features according to data-driven decisions for extracting more useful information, which influences a classification or regression problem substantially. RESULTS: In this study, we applied a neural network architecture for undirected graph representation of molecules. By encoding a molecule as an abstract graph and applying "convolution" on the graph and training the weight of the neural network framework, the neural network can optimize feature selection for the training problem. By incorporating the effects from adjacent atoms recursively, graph convolutional neural networks can extract the features of latent atoms that represent chemical features of a molecule efficiently. In order to investigate alkaloid biosynthesis, we trained the network to distinguish the precursors of 566 alkaloids, which are almost all of the alkaloids whose biosynthesis pathways are known, and showed that the model could predict starting substances with an averaged accuracy of 97.5%. CONCLUSION: We have showed that our model can predict more accurately compared to the random forest and general neural network when the variables and fingerprints are not selected, while the performance is comparable when we carefully select 507 variables from 18000 dimensions of descriptors. The prediction of pathways contributes to understanding of alkaloid synthesis mechanisms and the application of graph based neural network models to similar problems in bioinformatics would therefore be beneficial. We applied our model to evaluate the precursors of biosynthesis of 12000 alkaloids found in various organisms and found power-low-like distribution.

A Spatial Adaptive Algorithm Framework for Building Pattern Recognition Using Graph Convolutional Networks.

Graph learning methods, especially graph convolutional networks, have been investigated for their potential applicability in many fields of study based on topological data. Their topological data processing capabilities have proven to be powerful. However, the relationships among separate entities include not only topological adjacency, but also correlation in vision, for example, the spatial vector data of buildings. In this study, we propose a spatial adaptive algorithm framework with a data-driven design to accomplish building group division and building group pattern recognition tasks, which is not sensitive to the difference in the spatial distribution of the buildings in various geographical regions. In addition, the algorithm framework has a multi-stage design, and processes the building group data from whole to parts, since the objective is closely related to multi-object detection on topological data. By using the graph convolution method and a deep neural network (DNN), the multitask model in this study can learn human thoughts through supervised training, and the whole process only depends upon the descriptive vector data of buildings without any ancillary data for building group partition. Experiments confirmed that the method for expressing buildings and the effect of the algorithm framework proposed are satisfactory. In summary, using deep learning methods to complete the tasks of building group division and building group pattern recognition is potentially effective, and the algorithm framework is worth further research.

Dual-channel deep graph convolutional neural networks.

The dual-channel graph convolutional neural networks based on hybrid features jointly model the different features of networks, so that the features can learn each other and improve the performance of various subsequent machine learning tasks. However, current dual-channel graph convolutional neural networks are limited by the number of convolution layers, which hinders the performance improvement of the models. Graph convolutional neural networks superimpose multi-layer graph convolution operations, which would occur in smoothing phenomena, resulting in performance decreasing as the increasing number of graph convolutional layers. Inspired by the success of residual connections on convolutional neural networks, this paper applies residual connections to dual-channel graph convolutional neural networks, and increases the depth of dual-channel graph convolutional neural networks. Thus, a dual-channel deep graph convolutional neural network (D2GCN) is proposed, which can effectively avoid over-smoothing and improve model performance. D2GCN is verified on CiteSeer, DBLP, and SDBLP datasets, the results show that D2GCN performs better than the comparison algorithms used in node classification tasks.

Exploiting the Role of Features for Antigens-Antibodies Interaction Site Prediction.

Antibodies are a class of proteins that recognize and neutralize pathogens by binding to their antigens. They are the most significant category of biopharmaceuticals for both diagnostic and therapeutic applications. Understanding how antibodies interact with their antigens plays a fundamental role in drug and vaccine design and helps to comprise the complex antigen binding mechanisms. Computational methods for predicting interaction sites of antibody-antigen are of great value due to the overall cost of experimental methods. Machine learning methods and deep learning techniques obtained promising results.In this work, we predict antibody interaction interface sites by applying HSS-PPI, a hybrid method defined to predict the interface sites of general proteins. The approach abstracts the proteins in terms of hierarchical representation and uses a graph convolutional network to classify the amino acids between interface and non-interface. Moreover, we also equipped the amino acids with different sets of physicochemical features together with structural ones to describe the residues. Analyzing the results, we observe that the structural features play a fundamental role in the amino acid descriptions. We compare the obtained performances, evaluated using standard metrics, with the ones obtained with SVM with 3D Zernike descriptors, Parapred, Paratome, and Antibody i-Patch.

Artificial Intelligence and High-Throughput Computational Workflows Empowering the Fast Screening of Metal-Organic Frameworks for Hydrogen Storage.

Metal-organic frameworks (MOFs) are one of the most promising hydrogen-storing materials due to their rich specific surface area, adjustable topological and pore structures, and modified functional groups. In this work, we developed automatically parallel computational workflows for high-throughput screening of ∼11,600 MOFs from the CoRE database and discovered 69 top-performing MOF candidates with work capacity greater than 1.00 wt % at 298.5 K and a pressure swing between 100 and 0.1 bar, which is at least twice that of MOF-5. In particular, ZITRUP, OQFAJ01, WANHOL, and VATYIZ showed excellent hydrogen storage performance of 4.48, 3.16, 2.19, and 2.16 wt %. We specifically analyzed the relationship between pore-limiting diameter, largest cavity diameter, void fraction, open metal sites, metal elements or nonmetallic atomic elements, and deliverable capacity and found that not only geometrical and physical features of crystalline but also chemical properties of adsorbate sites determined the H2 storage capacity of MOFs at room temperature. It is highlighted that we first proposed the modified crystal graph convolutional neural networks by incorporating the obtained geometrical and physical features into the convolutional high-dimensional feature vectors of period crystal structures for predicting H2 storage performance, which can improve the prediction accuracy of the neural network from the former mean absolute error (MAE) of 0.064 wt % to the current MAE of 0.047 wt % and shorten the consuming time to about 10-4 times of high-throughput computational screening. This work opens a new avenue toward high-throughput screening of MOFs for H2 adsorption capacity, which can be extended for the screening and discovery of other functional materials.

Graph neural networks for automatic extraction and labeling of the coronary artery tree in CT angiography.

Purpose: Automatic comprehensive reporting of coronary artery disease (CAD) requires anatomical localization of the coronary artery pathologies. To address this, we propose a fully automatic method for extraction and anatomical labeling of the coronary artery tree using deep learning. Approach: We include coronary CT angiography (CCTA) scans of 104 patients from two hospitals. Reference annotations of coronary artery tree centerlines and labels of coronary artery segments were assigned to 10 segment classes following the American Heart Association guidelines. Our automatic method first extracts the coronary artery tree from CCTA, automatically placing a large number of seed points and simultaneous tracking of vessel-like structures from these points. Thereafter, the extracted tree is refined to retain coronary arteries only, which are subsequently labeled with a multi-resolution ensemble of graph convolutional neural networks that combine geometrical and image intensity information from adjacent segments. Results: The method is evaluated on its ability to extract the coronary tree and to label its segments, by comparing the automatically derived and the reference labels. A separate assessment of tree extraction yielded an F1 score of 0.85. Evaluation of our combined method leads to an average F1 score of 0.74. Conclusions: The results demonstrate that our method enables fully automatic extraction and anatomical labeling of coronary artery trees from CCTA scans. Therefore, it has the potential to facilitate detailed automatic reporting of CAD.

Application of graph frequency attention convolutional neural networks in depression treatment response.

Depression, a prevalent global mental health disorder, necessitates precise treatment response prediction for the improvement of personalized care and patient prognosis. The Graph Convolutional Neural Networks (GCNs) have emerged as a promising technique for handling intricate signals and classification tasks owing to their end-to-end neural architecture and nonlinear processing capabilities. In this context, this article proposes a model named the Graph Frequency Attention Convolutional Neural Network (GFACNN). Primarily, the model transforms the EEG signals into graphs to depict the connections between electrodes and brain regions, while integrating a frequency attention module to accentuate brain rhythm information. The proposed approach delves into the application of graph neural networks in the classification of EEG data, aiming to evaluate the response to antidepressant treatment and discern between treatment-resistant and treatment-responsive cases. Experimental results obtained from an EEG dataset at Peking University People's Hospital demonstrate the notable performance of GFACNN in distinguishing treatment responses among depression patients, surpassing deep learning methodologies including CapsuleNet and GoogLeNet. This highlights the efficacy of graph neural networks in leveraging the connections within EEG signal data. Overall, GFACNN exhibits potential for the classification of depression EEG signals, thereby potentially aiding clinical diagnosis and treatment.