Enhancing Multivariate Data Classification Using Graph Convolutional Networks: A Comparative Evaluation with PCA and t-SNE

Sex classification is a major benchmark of previous work in learning on the structural connectome, a naturally occurring brain graph that has proven useful for studying cognitive function and impairment. While graph neural networks (GNNs), specifically graph convolutional networks (GCNs), have gained popularity lately for their effectiveness in learning on graph data, achieving strong performance in adult sex classification tasks, their application to pediatric populations remains unexplored. We seek to characterize the capacity for GNN models to learn connectomic patterns on pediatric data through an exploration of training techniques and architectural design choices. Two datasets comprising an adult BRIGHT dataset (N = 147 Hodgkin's lymphoma survivors and N = 162 age similar controls) and a pediatric Human Connectome Project in Development (HCP-D) dataset (N = 135 healthy subjects) were utilized. Two GNN models (GCN simple and GCN residual), a deep neural network (multi-layer perceptron), and two standard machine learning models (random forest and support vector machine) were trained. Architecture exploration experiments were conducted to evaluate the impact of network depth, pooling techniques, and skip connections on the ability of GNN models to capture connectomic patterns. Models were assessed across a range of metrics including accuracy, AUC score, and adversarial robustness. GNNs outperformed other models across both populations. Notably, adult GNN models achieved 85.1% accuracy in sex classification on unseen adult participants, consistent with prior studies. The extension of the adult models to the pediatric dataset and training on the smaller pediatric dataset were sub-optimal in their performance. Using adult data to augment pediatric models, the best GNN achieved comparable accuracy across unseen pediatric (83.0%) and adult (81.3%) participants. Adversarial sensitivity experiments showed that the simple GCN remained the most robust to perturbations, followed by the multi-layer perceptron and the residual GCN. These findings underscore the potential of GNNs in advancing our understanding of sex-specific neurological development and disorders and highlight the importance of data augmentation in overcoming challenges associated with small pediatric datasets. Further, they highlight relevant tradeoffs in the design landscape of connectomic GNNs. For example, while the simpler GNN model tested exhibits marginally worse accuracy and AUC scores in comparison to the more complex residual GNN, it demonstrates a higher degree of adversarial robustness.

LightGCAN: A lightweight graph convolutional attention network for user preference modeling and personalized recommendation

Automatic building extraction from optical imagery remains a challenge due to, for example, the complexity of building shapes. Semantic segmentation is an efficient approach for this task. The latest development in deep convolutional neural networks (DCNNs) has made accurate pixel-level classification tasks possible. Yet one central issue remains: the precise delineation of boundaries. Deep architectures generally fail to produce fine-grained segmentation with accurate boundaries due to their progressive down-sampling. Hence, we introduce a generic framework to overcome the issue, integrating the graph convolutional network (GCN) and deep structured feature embedding (DSFE) into an end-to-end workflow. Furthermore, instead of using a classic graph convolutional neural network, we propose a gated graph convolutional network, which enables the refinement of weak and coarse semantic predictions to generate sharp borders and fine-grained pixel-level classification. Taking the semantic segmentation of building footprints as a practical example, we compared different feature embedding architectures and graph neural networks. Our proposed framework with the new GCN architecture outperforms state-of-the-art approaches. Although our main task in this work is building footprint extraction, the proposed method can be generally applied to other binary or multi-label segmentation tasks.

Graph convolutional network – Long short term memory neural network- multi layer perceptron- Gaussian progress regression model: A new deep learning model for predicting ozone concertation

The study of graph neural networks has revealed that they can unleash new applications in a variety of disciplines using such a basic process that we cannot imagine in the context of other deep learning designs. Many limitations limit their expressiveness, and researchers are working to overcome them to fully exploit the power of graph data. There are a number of publications that explore graph neural networks (GNNs) restrictions and bottlenecks, but the common thread that runs through them all is that they can all be traced back to message passing, which is the key technique we use to train our graph models. We outline the general GNN design pipeline in this study as well as discuss solutions to the over-smoothing problem, categorize the solutions, and identify open challenges for further research. Abbreviations: CGNN: Continuous Graph Neural Networks; CNN: Convolution NeuralNetwork; DeGNN: Decomposition Graph Neural Network; DGN: Directional GraphNetworks; DGN: Differentiable Group Normalization; DL: Deep Learning; EGAI:Enhancing GNNs by a High-quality Aggregation of Beneficial Information; GAT: GraphAttention Network; GCN: Graph Convolutional Network; GDC: Graph Drop Connect; GDR: Group Distance Ratio; GNN: Graph Neural Network; GRAND: GraphRandom Neural Networks; IIG: Instance Information Gain; MAD: Man AverageDistance; PDE-GCN: Partial Differential Equations-GCN; PTDNet: ParameterizedTopological Denoising network; TDGNN: Tree Decomposition Graph NeuralNetwork;

The generalization error of graph convolutional networks may enlarge with more layers

The n-octanol/buffer solution distribution coefficient at pH = 7.4 (log D7.4) is an indicator of lipophilicity, and it influences a wide variety of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties and druggability of compounds. In log D7.4 prediction, graph neural networks (GNNs) can uncover subtle structure-property relationships (SPRs) by automatically extracting features from molecular graphs that facilitate the learning of SPRs, but their performances are often limited by the small size of available datasets. Herein, we present a transfer learning strategy called pretraining on computational data and then fine-tuning on experimental data (PCFE) to fully exploit the predictive potential of GNNs. PCFE works by pretraining a GNN model on 1.71 million computational log D data (low-fidelity data) and then fine-tuning it on 19,155 experimental log D7.4 data (high-fidelity data). The experiments for three GNN architectures (graph convolutional network (GCN), graph attention network (GAT), and Attentive FP) demonstrated the effectiveness of PCFE in improving GNNs for log D7.4 predictions. Moreover, the optimal PCFE-trained GNN model (cx-Attentive FP, Rtest2 = 0.909) outperformed four excellent descriptor-based models (random forest (RF), gradient boosting (GB), support vector machine (SVM), and extreme gradient boosting (XGBoost)). The robustness of the cx-Attentive FP model was also confirmed by evaluating the models with different training data sizes and dataset splitting strategies. Therefore, we developed a webserver and defined the applicability domain for this model. The webserver (http://tools.scbdd.com/chemlogd/) provides free log D7.4 prediction services. In addition, the important descriptors for log D7.4 were detected by the Shapley additive explanations (SHAP) method, and the most relevant substructures of log D7.4 were identified by the attention mechanism. Finally, the matched molecular pair analysis (MMPA) was performed to summarize the contributions of common chemical substituents to log D7.4, including a variety of hydrocarbon groups, halogen groups, heteroatoms, and polar groups. In conclusion, we believe that the cx-Attentive FP model can serve as a reliable tool to predict log D7.4 and hope that pretraining on low-fidelity data can help GNNs make accurate predictions of other endpoints in drug discovery.

Traffic flow prediction plays an important role in intelligent transportation systems and is of great significance in the applications of traffic control and urban planning. Due to the complexity of road traffic flow data, traffic flow prediction has been one of the challenging tasks to fully exploit the spatiotemporal characteristics of roads to improve prediction accuracy. In this study, a combined flow direction level traffic flow prediction graph convolutional network (GCN) and long short-term memory (LSTM) model based on spatiotemporal characteristics is proposed. First, a GCN model is employed to capture the topological structure of the data graph and extract the spatial features of road networks. Additionally, due to the capability to handle long-term dependencies, the long-term memory is used to predict the time series of traffic flow and extract the time features. The proposed model is evaluated using real-world data, which are obtained from the intersection of Liuquan Road and Zhongrun Avenue in the Zibo High-Tech Zone of China. The results show that the developed combined GCN-LSTM flow direction level traffic flow prediction model can perform better than the single models of the LSTM model and GCN model, and the combined ARIMA-LSTM model in traffic flow has a strong spatiotemporal correlation.

Summary Monitoring carbon dioxide (CO2) saturation plume movement and pressure buildup is critical for ensuring the environmental safety of geological carbon storage (GCS) projects. High-fidelity numerical simulations provide accurate modeling of CO2 plume dynamics, but they are often computationally intensive. Recent advancements in data-driven models have enabled the rapid prediction of CO2 plume movement. By leveraging available simulation data sets, these models offer a more efficient alternative without compromising accuracy. In this study, we adopt the U-Net enhanced graph convolutional neural network (UGCN) to predict the spatial and temporal evolution of CO2 plume saturation and pressure buildup in saline aquifers. Utilizing the U-Net architecture, which incorporates skip connections, enables UGCN to capture high-level features and fine-grained details concurrently. We have created physics-based numerical simulation models that account for both CO2 injection and post-injection periods. By employing the Latin-hypercube sampling method, we generated a diverse range of reservoir and decision parameters, resulting in a comprehensive simulation database. We trained and tested the UGCN model on two different data sets, including a 2D radial reservoir model (Scenario 1) and a realistic Society of Petroleum Engineers Comparative Solution Project b (SPE 11b, Scenario 2) model to train and validate the UGCN model. The performance of the UGCN model was compared with other standard graph neural networks (GNNs), such as graph convolution network (GCN) and graph attention network (GAT). Notably, the UGCN model demonstrated robust performances on the blind testing dataset, achieving an R2 score of 0.993 and 0.989 for saturation predictions in Scenarios 1 and 2, respectively. Similarly, for pressure buildup the new model achieved an R2 of 0.989 and 0.999 for Scenarios 1 and 2, respectively. These prediction results indicate the effectiveness of the trained models in predicting the temporal and spatial evolution of CO2 saturation and pressure buildup predictions. Moreover, the prediction central processing unit (CPU) time for the deep learning (DL) models is significantly lower (0.02 seconds per case) than the physics-based reservoir simulator (on average, 10–15 minutes per case). This underscores the capability of the proposed method to provide predictions as accurate as physics-based simulations while reducing substantial computational costs.

AI-Driven molecule generation and bioactivity prediction: A multi-model approach combining VAE, graph and language-based neural networks.

Graph neural networks (GNNs) is an information - processing system that uses message passing among graph nodes. In recent years, GNN variants including graph attention network (GAT), graph convolutional network (GCN), and graph recurrent network (GRN) have shown revolutionary performance in computer vision applications using deep learning and artificial intelligence. These neural network model extensions, collect information in the form of graphs. GNN may be divided into three groups based on the challenges it solves: link prediction, node classification, graph classification. Machines can differentiate and recognise objects in image and video using standard CNNs. Extensive amount of research work needs to be done before robots can have same visual intuition as humans. GNN architectures, on the other hand, may be used to solve various image categorization and video challenges. The number of GNN applications in computer vision not limited, continues to expand. Human-object interaction, actin understanding, image categorization from a few shots and many more. In this paper use of GNN in image and video understanding, design aspects, architecture, applications and implementation challenges towards computer vision is described. GNN is a strong tool for analysing graph data and is still a relatively active area that needs further researches attention to solve many computer vision applications.

Edge features contain important information about graphs. However, current state-of-the-art neural network models designed for graph learning, e.g. graph convolutional networks (GCN) and graph attention networks (GAT), adequately utilize edge features, especially multi-dimensional edge features. In this paper, we build a new framework for a family of new graph neural network models that can more sufficiently exploit edge features, including those of undirected or multi-dimensional edges. The proposed framework can consolidate current graph neural network models; e.g. graph convolutional networks (GCN) and graph attention networks (GAT). The proposed framework and new models have the following novelties: First, we propose to use doubly stochastic normalization of graph edge features instead of the commonly used row or symmetric normalization approches used in current graph neural networks. Second, we construct new formulas for the operations in each individual layer so that they can handle multi-dimensional edge features. Third, for the proposed new framework, edge features are adaptive across network layers. As a result, our proposed new framework and new models can exploit a rich source of graph information. We apply our new models to graph node classification on several citation networks, whole graph classification, and regression on several molecular datasets. Compared with the current state-of-the-art methods, i.e. GCNs and GAT, our models obtain better performance, which testify to the importance of exploiting edge features in graph neural networks.

Skeleton-based action recognition aims to project skeleton sequences to action categories, where skeleton sequences are derived from multiple forms of pre-detected points. Compared with earlier methods that focus on exploring single-form skeletons via Graph Convolutional Networks (GCNs), existing methods tend to improve GCNs by leveraging multi-form skeletons due to their complementary cues. However, these methods (either adapting structure of GCNs or model ensemble) require the co-existence of all forms of skeletons during both training and inference stages, while a typical situation in real life is the existence of only partial forms for inference. To tackle this issue, we present Adaptive Cross-Form Learning (ACFL), which empowers well-designed GCNs to generate complementary representation from single-form skeletons without changing model capacity. Specifically, each GCN model in ACFL not only learns action representation from the single-form skeletons, but also adaptively mimics useful representations derived from other forms of skeletons. In this way, each GCN can learn how to strengthen what has been learned, thus exploiting model potential and facilitating action recognition as well. Extensive experiments conducted on three challenging benchmarks, i.e., NTU-RGB+D 120, NTU-RGB+D 60 and UAV-Human, demonstrate the effectiveness and generalizability of the proposed method. Specifically, the ACFL significantly improves various GCN models (i.e., CTR-GCN, MS-G3D, and Shift-GCN), achieving a new record for skeleton-based action recognition.

Chronic obstructive pulmonary disease (COPD) is a common disease with high morbidity and mortality, where early detection benefits the population. However, the early diagnosis rate of COPD is low due to the absence or slight early symptoms. In this paper, a novel method based on graph convolution network (GCN) for early detection of COPD is proposed, which uses small and weakly labeled chest computed tomography image data from the publicly available Danish Lung Cancer Screening Trial database. The key idea is to construct a graph using regions of interest randomly selected from the segmented lung parenchyma and then input it into the GCN model for COPD detection. In this way, the model can not only extract the feature information of each region of interest but also the topological structure information between regions of interest, that is, graph structure information. The proposed GCN model achieves an acceptable performance with an accuracy of 0.77 and an area under a curve of 0.81, which is higher than the previous studies on the same dataset. GCN model also outperforms several state-of-the-art methods trained at the same time. As far as we know, it is also the first time using the GCN model on this dataset for COPD detection.Graphical abstract

In recent years, tremendous efforts have been made to explore features contained in user-item graphs for recommendation based on Graph Neural Networks (GNN). However, most existing recommendation methods based on GNN use weighted sum of directly-linked node’s features only, assuming that neighboring nodes are independent individuals, neglecting possible correlations between neighboring nodes, which may result in failure of capturing co-occurrence signals. Therefore, in this paper, we propose a novel Graph Convolutional Network with Neighbor complex Interactions for Recommendation (GCNNIRec) focused upon capturing possible co-occurrence signals between node neighbors. Specifically, two types of modules, the Linear-Aggregator module and the Interaction-Aggregator module are both inside GCNNIRec. The former module linearly aggregates the features of neighboring nodes to obtain the representation of target node. The latter utilizes the interactions between neighbors to aggregate the co-occurrence features of nodes to capture co-occurrence features. Furthermore, empirical results on three real datasets confirm not only the state-of-the-art performance of GCNNIRec but also the performance gains achieved by introducing Interaction-Aggregator module into GNN.