Heterogeneous graph convolutional neural network for protein-ligand scoring

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

Heterogeneous graphs are an essential structure that models real-world data through different types of nodes and relationships between them, including multimodality, which comprises different types of data such as text, image, and audio. Graph Neural Networks (GNNs) are a prominent graph representation learning method that takes advantage of the graph structure and its attributes that, when applied to the multimodal heterogeneous graph, learn a unique semantic space for the different modalities. Consequently, it allows multimodal fusion through simple operators such as sum, average, or multiplication, generating unified representations considering the supplementary and complementarity relationships between the modalities. In multimodal heterogeneous graphs, the labeling process tends to be even more costly due to the multiple modalities analyzed, in addition to the imbalance of classes inherent to some applications. In order to overcome these problems in applications that comprise a class of interest, One-Class Learning (OCL) is used. Given the lack of studies on multimodal early fusion in heterogeneous graphs for OCL tasks, we proposed a method based on unsupervised GNN for heterogeneous graphs and evaluated different early fusion operators. In this paper, we extend another work by evaluating the behavior of the main GNN convolutions in the method. We highlight that using operators such as average, addition, and subtraction were the best early fusion operators. In addition, GNN layers that do not use an attention mechanism performed better. In this way, we argue for heterogeneous graph neural networks in multimodal using early fusion simple operators instead of well-often-used concatenation and less complex convolutions.

A multi-agent artificial intelligence (AI) model is developed to automate the discovery of new metallic alloys, integrating multimodal data and external knowledge, including insights from physics via atomistic simulations. The system consists of (a) large language models (LLMs) for tasks such as reasoning and planning, (b) AI agents with distinct roles collaborating dynamically, and (c) a newly developed graph neural network (GNN) model for rapid retrieval of physical properties. We chose the ternary NbMoTa body-centered-cubic alloy as our model system and developed the GNN to predict two fundamental materials properties: the Peierls barrier and the solute/screw dislocation interaction energy. Our GNN model efficiently predicts these properties, reducing reliance on costly brute-force calculations and alleviating the computational demands on the multi-agent system. By combining the predictive capabilities of GNNs with the collaborative intelligence of LLM-driven reasoning agents, the system autonomously explores vast alloy design spaces, identifies trends in atomic-scale properties, and predicts macroscale mechanical strength, as demonstrated by several computational experiments. This synergistic approach accelerates the discovery of advanced alloys and holds promise for broader applications in other complex systems, marking a step forward in automated materials discovery and design. Impact statement Traditional deep learning models, such as graph neural networks and convolutional neural networks, operate within the confines of their training data sets, making single-step inferences for regression or classification. Our work introduces a multi-agent strategy that transcends these limitations by integrating deep learning with reasoning and decision-making capabilities. This intelligent system actively interprets results, determines subsequent actions, and iteratively refines predictions, accelerating the materials design process. We demonstrate its effectiveness in exploring the vast compositional space of a ternary alloy, where the model dynamically solicits data, analyzes trends, generates visualizations, and derives insights into materials behavior. By enabling accurate predictions of key alloy characteristics, our approach advances the discovery of novel metallic systems and underscores the critical role of solid-solution alloying. More broadly, it represents a major step toward integrating artificial intelligence with scientific reasoning, moving closer to artificial general intelligence in engineering. This paradigm shift has profound implications for materials science, enabling more efficient, autonomous, and intelligent exploration of complex materials spaces. Graphical Abstract

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 (GCN) based approaches have achieved significant progress for solving complex, graph-structured problems. GCNs incorporate the graph structure information and the node (or edge) features through message passing and computes ‘deep’ node representations. Despite significant progress in the field, designing GCN architectures for heterogeneous graphs still remains an open challenge. Due to the schema of a heterogeneous graph, useful information may reside multiple hops away. A key question is how to perform message passing to incorporate information of neighbors multiple hops away while avoiding the well-known over-smoothing problem in GCNs. To address this question, we propose our GCN framework Deep Heterogeneous Graph Convolutional Network (DHGCN), which takes advantage of the schema of a heterogeneous graph and uses a hierarchical approach to effectively utilize information many hops away. It first computes representations of the target nodes based on their schema-derived ego-network (SEN). It then links the nodes of the same type with various pre-defined metapaths and performs message passing along these links to compute final node representations. Our design choices naturally capture the way a heterogeneous graph is generated from the schema. The experimental results on real and synthetic datasets corroborate the design choice and illustrate the performance gains relative to competing alternatives.

Graph convolutional networks (GCN), aiming to learn meaningful representations for graph data, has been popularly used in recommender systems since user-item interactions can be represented by a bipartite graph. However, GCN often suffers from the over-smoothing issue when it goes deeper, which implies that long paths between users and items are not very useful to embedding learning in recommender systems. To deal with long paths, introducing user and item links is a promising way to shorten the average path between users and items. However, due to introducing the user and item linkages, the bipartite graph becomes a heterogeneous graph. To this end, we propose a multi-aspect heterogeneous GCN model, which is to power GCN towards recommendation tasks by introducing user-user and item-item links to build the heterogeneous user- item graph. Then, we decompose it into three subgraphs and keep the global heterogeneous graph to preserve the original structure information. Specifically, we apply GCN to learn user and item representations from both the subgraphs and the global graph. After that, we have multi-aspect attention to integrate the representations from GCN to obtain the final user and item representation. Extensive experiments on three real-world datasets show that the proposed approaches achieve significant improvements over state-of-the-art methods.

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.

Aspect-based sentiment analysis aims to predict sentiment polarities of given aspects in text. Most current approaches employ attention-based neural methods to capture semantic relationships between aspects and words in one sentence. However, these methods ignore the fact that sentences with the same aspect and sentiment polarity often share the structure and semantic information in a domain, which leads to lower model performance. To mitigate this problem, we propose a heterogeneous aspect graph neural network (HAGNN) to learn the structure and semantic knowledge from intersentence relationships. Our model is a heterogeneous graph neural network since it contains three different kinds of nodes: word nodes, aspect nodes, and sentence nodes. These nodes can pass structure and semantic information between each other and update their embeddings to improve the performance of our model. To the best of our knowledge, we are the first to use a heterogeneous graph to capture relationships between sentences and aspects. The experimental results on five public datasets show the effectiveness of our model outperforming some state-of-the-art models.

In recent years, heterogeneous network/graph representation learning/embedding (HNE) has drawn tremendous attentions from research communities in multiple disciplines. HNE has shown its outstanding performances in various networked data analysis and mining tasks. In fact, most of real-world information networks in multiple fields can be modelled as the heterogeneous information networks (HIN). Thus, the HNE-based techniques can sufficiently capture rich-structured and semantic latent features from the given information network in order to facilitate for different task-driven learning tasks. This is considered as fundamental success of HNE-based approach in comparing with previous traditional homogeneous network/graph based embedding techniques. However, there are recent studies have also demonstrated that the heterogeneous network/graph modelling and embedding through graph neural network (GNN) is not usually reliable. This challenge is original come from the fact that most of real-world heterogeneous networks are considered as incomplete and normally contain a large number of feature noises. Therefore, multiple attempts have proposed recently to overcome this limitation. Within this approach, the meta-path-based heterogeneous graph-structured latent features and GNN-based parameters are jointly learnt and optimized during the embedding process. However, this integrated GNN and heterogeneous graph structure (HGS) learning approach still suffered a challenge of effectively parameterizing and fusing different graph-structured latent features from both GNN- and HGS-based sides into better task-driven friendly and noise-reduced embedding spaces. Therefore, in this paper we proposed a novel attention-supplemented heterogeneous graph structure embedding approach, called as: AGSE. Our proposed AGSE model supports to not only achieve the combined rich heterogeneous structural and GNN-based aggregated node representations but also transform achieved node embeddings into noise-reduced and task-driven friendly embedding space. Extensive experiments in benchmark heterogeneous networked datasets for node classification task showed the effectiveness of our proposed AGSE model in comparing with state-of-the-art network embedding baselines.

Graph neural network, as a powerful graph representation technique based on deep learning, has shown superior performance and attracted considerable research interest. However, it has not been fully considered in graph neural network for heterogeneous graph which contains different types of nodes and links. The heterogeneity and rich semantic information bring great challenges for designing a graph neural network for heterogeneous graph. Recently, one of the most exciting advancements in deep learning is the attention mechanism, whose great potential has been well demonstrated in various areas. In this paper, we first propose a novel heterogeneous graph neural network based on the hierarchical attention, including node-level and semantic-level attentions. Specifically, the node-level attention aims to learn the importance between a node and its metapath based neighbors, while the semantic-level attention is able to learn the importance of different meta-paths. With the learned importance from both node-level and semantic-level attention, the importance of node and meta-path can be fully considered. Then the proposed model can generate node embedding by aggregating features from meta-path based neighbors in a hierarchical manner. Extensive experimental results on three real-world heterogeneous graphs not only show the superior performance of our proposed model over the state-of-the-arts, but also demonstrate its potentially good interpretability for graph analysis.

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.

This study proposes a user influence propagation model based on dynamic heterogeneous network representation learning. The model combines multi-type nodes and semantic edge types, and adopts a learnable temporal embedding strategy to construct a dynamic heterogeneous graph, so as to realize the time-aware representation of nodes. In the representation learning stage, a multi-head attention mechanism is introduced to enhance context modeling and propagation path awareness. Meanwhile, structural contrastive learning is used as an auxiliary task to improve the discriminability of node representation, and a joint training strategy of node classification and edge prediction is adopted to enhance the generalization ability of the model. In the experimental evaluation, the proposed model is compared with several representative Graph Neural Network (GNN) models, including Graph Convolutional Network (GCN), Temporal Graph Attention Network (TGAT), and Heterogeneous Graph Transformer (HGT). In the overall prediction task, the proposed model achieves a Mean Squared Error (MSE) of 0.1214, a Mean Absolute Error (MAE) of 0.2398, and an R² of 0.701. All these metrics are significantly better than those of TGAT (MSE: 0.1597, MAE: 0.2785, R²: 0.603) and HGT (MSE: 0.1429, MAE: 0.2652, R²: 0.642). Within a 14-day prediction window, the model maintains an error rate of 0.1390, demonstrating superior temporal generalization capability. For identifying high-influence user groups, the model achieves an MSE of 0.1268, significantly better than HGT’s 0.1456, indicating higher sensitivity in modeling strong propagation nodes. This shows that the combination of these methods enables the proposed model to demonstrate stronger temporal modeling capability and heterogeneous relationship understanding capability compared with TGAT and HGT, in terms of capturing users’ historical behaviors and predicting future influence.

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.

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;

Predicting the next interaction of a short-term interaction session is a challenging task in session-based recommendation. Almost all existing works rely on item transition patterns, and neglect the impact of user historical sessions while modeling user preference, which often leads to non-personalized recommendation. Additionally, existing personalized session-based recommenders capture user preference only based on the sessions of the current user, but ignore the useful item-transition patterns from other user's historical sessions. To address these issues, we propose a novel Heterogeneous Global Graph Neural Networks (HG-GNN) to exploit the item transitions over all sessions in a subtle manner for better inferring user preference from the current and historical sessions. To effectively exploit the item transitions over all sessions from users, we propose a novel heterogeneous global graph that contains item transitions of sessions, user-item interactions and global co-occurrence items. Moreover, to capture user preference from sessions comprehensively, we propose to learn two levels of user representations from the global graph via two graph augmented preference encoders. Specifically, we design a novel heterogeneous graph neural network (HGNN) on the heterogeneous global graph to learn the long-term user preference and item representations with rich semantics. Based on the HGNN, we propose the Current Preference Encoder and the Historical Preference Encoder to capture the different levels of user preference from the current and historical sessions, respectively. To achieve personalized recommendation, we integrate the representations of the user current preference and historical interests to generate the final user preference representation. Extensive experimental results on three real-world datasets show that our model outperforms other state-of-the-art methods.