Learning Relevant Molecular Representations via Self-Attentive Graph Neural Networks

Graph neural networks have been paid a lot attentions in recent years since many real-word data can naturally be represented by graph structures. Graph neural networks such as GCNs and GATs mainly focus on node features while ignoring edge features in graphs. However, in many graph structure data such as knowledge graphs, social networks, edge features are also important as they contain vital information about relations between nodes which are commonly ignored or simplified into binary or scalar values by existing methods. In this work we build a novel learning method on graphs called GNN-EE, i.e. GNN with Edge Enhanced, which takes both the node features and edge features into account while updating representations of graph components and can be applied to most of the common graph neural networks such as GCNs and GATs. Our GNN-EE method fits in the message-passing framework and thus is easy to generalize. In addition, we extend the random-walk-based algorithms on graphs so that they can consider both node and edge features on graphs. We use those random-walk-based algorithms as a pre-training method on graph with few initial features. We demonstrate the effectiveness and flexibility of our GNN-EE method through entity classification tasks and graph classification tasks.

Graph neural networks(GNNs) have been developed to solve challenging resource allocation (RA) problems, which leads to hopeful results in small and simple communication networks. Due to the inevitable heterogeneity of modern networks, it motivated researchers to develop the heterogeneous graph neural networks (HetGNNs) model for the RA problem of heterogeneous networks. However, node features and edge features are usually ignored by the most extant deep models, limited the performance when the size of the hidden layer in the network is larger than that of the node and edge features. In this paper, the power control or beamforming (PC/BF) in heterogeneous device-to-device (D2D) networks is focused, and proposed a HetGNN for the issue. Extensive simulations show that the proposed approach, matching or even outperforming state-of-the-art learning-based benchmarks.

We investigate works under the propagation-based fake news detection domain, which recently seeks to improve performance through the use of Graph Neural Networks (GNNs). Generally, existing works argue that using GNNs can give results superior to what was obtained using classic graph-based methods. We agree with this argument given that GNNs are capable of gaining superior performance by leveraging node features. But we argue that existing works haven't identified the fact that the expressivity of GNNs is limited and bounded by node features. Existing works do not acknowledge that, by utilizing GNNs, they implicitly assume node features are strongly correlated to node labels. There are evidence that node features that have been employed do not necessarily correlate to node label. Instead of having a profound theoretical motivation, they have empirically observed that focusing on nodes features with strong feature-label correlation can increase predictive capability. This is a sub-optimal approach to view this problem, in fact, we argue that finding node features based on correlation is not practical or effective. Our first contribution is shifting readers from a node-level view i.e correlating node features with labels, to a graph-level view. In the graph-level view, we exploit the relationship between graph isomorphism and GNNs' expressivity which can be utilized to well understand and interpret the relation between node features and GNNs' expressivity. We conduct a wide range of experiments on basis of both node-level view and graph-level view and found graph-level view is more interpretable and strongly matches with results. Further, we gained insights on node features that wouldn't be obtainable by a node-level view. In order to have a fair and comprehensive analysis of node features, we built a unified dataset that includes a wide range of node features. Our results indicate, as we improve model accuracy on basis of the graph level view, models' generalizability decreases. We provide our hypothesis for this performance trade-off on the basis of the graph-level view. Our results and insights call for a much broader discussion on whether any sort of filtering method is effective. So, we conclude our work by providing readers with possible solutions that can be helpful to find harmony between node features and GNNs' expressivity.

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.

At present, the urban traffic system is faced with the problems of congestion and low efficiency, and the traditional methods have certain limitations when dealing with the complex urban road network. This paper aims to explore a new method of capacity Optimization of Road Networks in a Smart City environment and proposes a method based on a Graph Neural network, named “Smart City Road optimization Graph Neural Network” (SCRO-GNN). SCRO-GNN first collects and preprocesses multi-source data, including road network data, traffic flow, accident records, environmental factors, etc. The key node and edge features, including the number of lanes at the intersection, the traffic flow of the section, and the adjacency matrix of the road network are defined to characterize the structure of the road network. Then, the graph neural network model is constructed and trained to predict the traffic flow of different sections and evaluate the road capacity by using the graph structure of the road network. This paper tests the performance of SCRO-GNN on real road networks in multiple cities. The results show that, compared with the traditional traffic flow prediction model, SCRO-GNN can significantly improve the prediction accuracy, especially when dealing with the highly complex urban road network structure. Based on these predictions, the proposed optimization strategy performed well in reducing traffic congestion and improving the efficiency of road use. The research in this paper not only demonstrates the potential of graph neural networks in smart city road network optimization, but also provides a new direction for future traffic system research. The successful implementation of the SCRO-GNN approach is expected to provide more efficient and intelligent solutions for urban traffic management and planning.

Graph, as an important data representation, is ubiquitous in many real world applications ranging from social network analysis to biology. How to correctly and effectively learn and extract information from graph is essential for a large number of machine learning tasks. Graph embedding is a way to transform and encode the data structure in high dimensional and non-euclidean feature space to a low dimensional and structural space, which is easily exploited by other machine learning algorithms. We have witnessed a huge surge of such embedding methods, from statistical approaches to recent deep learning methods such as the graph convolutional networks (GCN). Deep learning approaches usually outperform the traditional methods in most graph learning benchmarks by building an end-to-end learning framework to optimize the loss function directly. However, most of the existing GCN methods can only perform convolution operations with node features, while ignoring the handy information in edge features, such as relations in knowledge graphs. To address this problem, we present CensNet, Convolution with Edge-Node Switching graph neural network, for learning tasks in graph-structured data with both node and edge features. CensNet is a general graph embedding framework, which embeds both nodes and edges to a latent feature space. By using line graph of the original undirected graph, the role of nodes and edges are switched, and two novel graph convolution operations are proposed for feature propagation. Experimental results on real-world academic citation networks and quantum chemistry graphs show that our approach achieves or matches the state-of-the-art performance in four graph learning tasks, including semi-supervised node classification, multi-task graph classification, graph regression, and link prediction.

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.

Molecular machine learning (ML) has proven important for tackling various molecular problems, such as predicting molecular properties based on molecular descriptors or fingerprints. Since relatively recently, graph neural network (GNN) algorithms have been implemented for molecular ML, showing comparable or superior performance to descriptor or fingerprint-based approaches. Although various tools and packages exist to apply GNNs in molecular ML, a new GNN package, named MolGraph, was developed in this work with the motivation to create GNN model pipelines highly compatible with the TensorFlow and Keras application programming interface (API). MolGraph also implements amodule to accommodate the generation of small molecular graphs, which can be passed to a GNN algorithm to solve a molecular ML problem. To validate the GNNs, benchmarking was conducted using the datasets from MoleculeNet, as well as three chromatographic retention time datasets. The benchmarking results demonstrate that the GNNs performed in line with expectations. Additionally, the GNNs proved useful for molecular identification and improved interpretability of chromatographic retention time data. MolGraph is available at https://github.com/akensert/molgraph . Installation, tutorials and implementation details can be found at https://molgraph.readthedocs.io/en/latest/ .

SGNN-T: Space graph neural network coupled transformer for molecular property prediction

PurposeDrug-induced liver injury (DILI) is a significant concern in drug development, often leading to the discontinuation of clinical trials and the withdrawal of drugs from the market. This study explores the application of graph neural networks (GNNs) for DILI prediction, using molecular graph representations as the primary input.MethodsWe evaluated several GNN architectures, including Graph Convolutional Networks (GCNs), Graph Attention Networks (GATs), Graph Sample and Aggregation (GraphSAGE), and Graph Isomorphism Networks (GINs), using the latest FDA DILI dataset and other molecular property prediction datasets. We introduce a novel approach that creates a custom graph dataset, driven by molecular optimisation, that incorporates detailed and realistic chemical features such as bond lengths and partial charges as input into the GNN models. We have named our model approach DILIGeNN.ResultsDILIGeNN achieved an AUC of 0.897 on the DILI dataset, surpassing the current state-of-the-art model in the DILI prediction task. Furthermore, DILIGeNN outperformed the state-of-the-art in other graph-based molecular prediction tasks, achieving an AUC of 0.918 on the Clintox dataset, 0.993 on the BBBP dataset, and 0.953 on the BACE dataset, indicating strong generalisation and performance across different datasets.ConclusionDILIGeNN, utilising a single graph representation as input, outperforms the state-of-the-art methods in DILI prediction that incorporate both molecular fingerprint and graph-structured data. These findings highlight the effectiveness of our molecular graph generation and the GNN training approach as a powerful tool for early-stage drug development and drug repurposing pipeline.Scientific Contribution: DILIGeNN is a GNN framework that extracts graph features from 3D optimised molecular structures as is done in target-based drug discovery and molecular docking simulation. Our method is the first to encode spatial and electrostatic information into a single graph representation, as opposed to other work that require multiple graphs or additional chemical descriptors for feature representation. Our approach, using warm starts following repeated early stopping during training, outperforms the current state-of-the-art methods in liver toxicity (DILI), permeability (BBBP) and activity (BACE) prediction tasks.Graphic

Graph neural networks (GNNs) have demonstrated their effectiveness in various tasks supported by their generalization capabilities. However, the current analysis of GNN generalization relies on the assumption that training and testing data are independent and identically distributed (i.i.d). This imposes limitations on the cases where a model mismatch exists when generating testing data. In this paper, we examine GNNs that operate on geometric graphs generated from manifold models, explicitly focusing on scenarios where there is a mismatch between manifold models generating training and testing data. Our analysis reveals the robustness of the GNN generalization in the presence of such model mismatch. This indicates that GNNs trained on graphs generated from a manifold can still generalize well to unseen nodes and graphs generated from a mismatched manifold. We attribute this mismatch to both node feature perturbations and edge perturbations within the generated graph. Our findings indicate that the generalization gap decreases as the number of nodes grows in the training graph while increasing with larger manifold dimension as well as larger mismatch. Importantly, we observe a trade-off between the generalization of GNNs and the capability to discriminate high-frequency components when facing a model mismatch. The most important practical consequence of this analysis is to shed light on the filter design of generalizable GNNs robust to model mismatch. We verify our theoretical findings with experiments on multiple real-world datasets.

Graph neural network, as a powerful data processing tool for graph structure, provides a new perspective for the optimization and modular design of electronic information engineering course structure. This paper integrates the graph convolutional neural network model into the electronic information course knowledge map and constructs a graph convolutional network recommendation algorithm based on the knowledge map. By designing an online learning platform to optimize the structure of the electronic information course, the modular teaching mode of the course is designed in this way. The recommendation model constructed in this paper converges to about 0.89 and 0.13 in precision and recall of training data and validation data after 40 rounds of iteration, and the recommendation performance of the model in this paper is better than the basic model. When the number of recommendations is 40, the model of this paper still shows better recommendation performance; its recommendation performance is best when the learning rate is 0.005, the embedding dimension is 64, and the aggregation method is bi-interaction. After the experiment, the average level of EE knowledge in the experimental class increased by 7.56 points compared to the control class, which showed a significant difference. And the student’s satisfaction with the teaching method of this paper is high. This paper provides key technical support for optimizing and modularizing the structure of electronic information engineering courses using graph neural networks.

Network modeling is a critical component for building self-driving Software-Defined Networks, particularly to find optimal routing schemes that meet the goals set by administrators. However, existing modeling techniques do not meet the requirements to provide accurate estimations of relevant performance metrics such as delay and jitter. In this paper we propose a novel Graph Neural Network (GNN) model able to understand the complex relationship between topology, routing and input traffic to produce accurate estimates of the per-source/destination pair mean delay and jitter. GNN are tailored to learn and model information structured as graphs and as a result, our model is able to generalize over arbitrary topologies, routing schemes and variable traffic intensity. In the paper we show that our model provides accurate estimates of delay and jitter (worst case R2 = 0.86) when testing against topologies, routing and traffic not seen during training. In addition, we present the potential of the model for network operation by presenting several use-cases that show its effective use in per-source/destination pair delay/jitter routing optimization and its generalization capabilities by reasoning in topologies and routing schemes not seen during training.

Graph Neural Networks (GNNs) have demonstrated significant success in various graph-related tasks. However, their performance is highly dependent on the availability of sufficient, class-balanced annotated data and an accurate graph structure. GNNs are vulnerable to substantial performance degradation when confronted with limited annotated samples, class imbalance, or noisy graph structures. First, a Dual GNN learning framework is introduced for semi-supervised node classification under limited supervision. The framework comprises two GNN-based node prediction modules: a primary module, which uses the input graph structure to induce standard node embeddings and predictions, and an auxiliary module, which leverages spectral clustering to construct a new graph structure and learn new node embeddings and predictions. These modules collaborate to enable end-to-end learning of discriminative node representations. Next, a graph augmentation method called Graph Dual Mixup (GDM) is proposed for graph classification with scarce labels. GDM employs a graph structural auto-encoder to learn structural embeddings, applying mixup in the learned structural embedding space to generate new graph structures. Additionally, mixup is applied to input node features, generating node features for new graph instances. Together, these generated node features and graph structures contribute new graphs that increase the size and diversity of the labeled dataset, improving classification performance. To enhance robustness against adversarial attacks on graph structures, an Efficient Low-Rank GNN is introduced. This approach learns robust low-rank sparse graph structures through a two-stage process. In the first stage, Singular Value Decomposition is used to estimate a low-rank approximation of the graph structure. This estimate is refined in the second stage by jointly learning a low-rank sparse graph structure alongside the GNN model, resulting in enhanced robustness. Finally, to address class-imbalanced node classification, a Unified GNN Learning (Uni-GNN) framework is proposed. Uni-GNN integrates structural and semantic connectivity representations to extend the propagation of embeddings to non-adjacent structural neighbors and semantically similar nodes, facilitating the diffusion of discriminative information. Additionally, it incorporates a balanced pseudo-label generation mechanism to improve the representations of minority classes. Comprehensive evaluations on benchmark datasets demonstrate that these methods outperform state-of-the-art approaches and hold significant potential for advancing GNN learning with limited supervision.

Temporal link prediction based on graph neural networks has become a hot spot in the field of complex networks. To solve the problems of the existing temporal link prediction methods based on graph neural networks do not consider the future time-domain features and spatial-domain features are limited used, this paper proposes a novel temporal link prediction method based on two streams adaptive graph neural networks. Firstly, the network topology features are extracted from the micro, meso, and middle perspectives. Combined with the adaptive mechanism of convolution and self-attention, the preprocessing of the feature extraction is more effective; Secondly, an extended bi-directional long short-term memory network is proposed, which uses graph convolution to process topological features, and recursively learns the state vectors of the target snapshot by using the future time-domain information and the past historical information; Thirdly, the location coding is replaced by the time-coding for the transformer mechanism, so that past information and future information can be learned from each other, and the time-domain information of the network can be further mined; Finally, a novel two-stream network framework is proposed, which combines the processing results of point features and edge features. The experimental results on 9 data sets show that the proposed method has a better prediction effect and better robustness than the classical graph neural network methods.