Quantum theory has shown its superiority in enhancing machine learning. However, facilitating quantum theory to enhance graph learning is in its infancy. This survey investigates the current advances in quantum graph learning (QGL) from three perspectives, i.e., underlying theories, methods, and prospects. We first look at QGL and discuss the mutualism of quantum theory and graph learning, the specificity of graph-structured data, and the bottleneck of graph learning, respectively. A new taxonomy of QGL is presented, i.e., quantum computing on graphs, quantum graph representation, and quantum circuits for graph neural networks. Pitfall traps are then highlighted and explained. This survey aims to provide a brief but insightful introduction to this emerging field, along with a detailed discussion of frontiers and outlook yet to be investigated.
The inception of spatial transcriptomics has allowed improved comprehension of tissue architectures and the disentanglement of complex underlying biological, physiological, and pathological processes through their positional contexts. Recently, these contexts, and by extension the field, have seen much promise and elucidation with the application of graph learning approaches. In particular, neural operators have risen in regards to learning the mapping between infinite-dimensional function spaces. With basic to deep neural network architectures being data-driven, i.e. dependent on quality data for prediction, neural operators provide robustness by offering generalization among different resolutions despite low quality data. Graph neural operators are a variant that utilize graph networks to learn this mapping between function spaces. The aim of this research is to identify robust machine learning architectures that integrate spatial information to predict tissue types. Under this notion, we propose a study incorporating various graph neural network approaches to validate the efficacy of applying neural operators towards prediction of brain regions in mouse brain tissue samples as a proof of concept towards our purpose. We were able to achieve an F1 score of nearly 72% for the graph neural operator approach which outperformed all baseline and other graph network approaches.
Company financial risk is ubiquitous and early risk assessment for listed companies can avoid considerable losses. Traditional methods mainly focus on the financial statements of companies and lack the complex relationships among them. However, the financial statements are often biased and lagged, making it difficult to identify risks accurately and timely. To address the challenges, we redefine the problem as \textbf{company financial risk assessment on tribe-style graph} by taking each listed company and its shareholders as a tribe and leveraging financial news to build inter-tribe connections. Such tribe-style graphs present different patterns to distinguish risky companies from normal ones. However, most nodes in the tribe-style graph lack attributes, making it difficult to directly adopt existing graph learning methods (e.g., Graph Neural Networks(GNNs)). In this paper, we propose a novel Hierarchical Graph Neural Network (TH-GNN) for Tribe-style graphs via two levels, with the first level to encode the structure pattern of the tribes with contrastive learning, and the second level to diffuse information based on the inter-tribe relations, achieving effective and efficient risk assessment. Extensive experiments on the real-world company dataset show that our method achieves significant improvements on financial risk assessment over previous competing methods. Also, the extensive ablation studies and visualization comprehensively show the effectiveness of our method.
User interaction data in recommender systems is a form of dyadic relation that reflects the preferences of users with items. Learning the representations of these two discrete sets of objects, users and items, is critical for recommendation. Recent multimodal recommendation models leveraging multimodal features (e.g., images and text descriptions) have been demonstrated to be effective in improving recommendation accuracy. However, state-of-the-art models enhance the dyadic relations between users and items by considering either user-user or item-item relations, leaving the high-order relations of the other side (i.e., users or items) unexplored. Furthermore, we experimentally reveal that the current multimodality fusion methods in the state-of-the-art models may degrade their recommendation performance. That is, without tainting the model architectures, these models can achieve even better recommendation accuracy with uni-modal information. On top of the finding, we propose a model that enhances the dyadic relations by learning Dual RepresentAtions of both users and items via constructing homogeneous Graphs for multimOdal recommeNdation. We name our model as DRAGON. Specifically, DRAGON constructs the user-user graph based on the commonly interacted items and the item-item graph from item multimodal features. It then utilizes graph learning on both the user-item heterogeneous graph and the homogeneous graphs (user-user and item-item) to obtain the dual representations of users and items. To capture information from each modality, DRAGON employs a simple yet effective fusion method, attentive concatenation, to derive the representations of users and items. Extensive experiments on three public datasets and seven baselines show that DRAGON can outperform the strongest baseline by 22.03% on average. Various ablation studies are conducted on DRAGON to validate its effectiveness.
Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work (Kim et al., 2022) shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer (Choromanski et al., 2020; Katharopoulos et al., 2020), then MPNN + VN with only O(1) depth and O(1) width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with O(n^d) width and O(1) depth can approximate the self-attention layer arbitrarily well, where d is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with O(1) width and O(n) depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.
Link prediction on graphs is a fundamental problem. Subgraph representation learning approaches (SGRLs), by transforming link prediction to graph classification on the subgraphs around the links, have achieved state-of-the-art performance in link prediction. However, SGRLs are computationally expensive, and not scalable to large-scale graphs due to expensive subgraph-level operations. To unlock the scalability of SGRLs, we propose a new class of SGRLs, that we call Scalable Simplified SGRL (S3GRL). Aimed at faster training and inference, S3GRL simplifies the message passing and aggregation operations in each link's subgraph. S3GRL, as a scalability framework, accommodates various subgraph sampling strategies and diffusion operators to emulate computationally-expensive SGRLs. We propose multiple instances of S3GRL and empirically study them on small to large-scale graphs. Our extensive experiments demonstrate that the proposed S3GRL models scale up SGRLs without significant performance compromise (even with considerable gains in some cases), while offering substantially lower computational footprints (e.g., multi-fold inference and training speedup).
Weather forecasting is an essential task to tackle global climate change. Weather forecasting requires the analysis of multivariate data generated by heterogeneous meteorological sensors. These sensors comprise of ground-based sensors, radiosonde, and sensors mounted on satellites, etc., To analyze the data generated by these sensors we use Graph Neural Networks (GNNs) based weather forecasting model. GNNs are graph learning-based models which show strong empirical performance in many machine learning approaches. In this research, we investigate the performance of weather forecasting using GNNs and traditional Machine learning-based models.
LiDAR (Light Detection and Ranging) is an advanced active remote sensing technique working on the principle of time of travel (ToT) for capturing highly accurate 3D information of the surroundings. LiDAR has gained wide attention in research and development with the LiDAR industry expected to reach 2.8 billion $ by 2025. Although the LiDAR dataset is of rich density and high spatial resolution, it is challenging to process LiDAR data due to its inherent 3D geometry and massive volume. But such a high-resolution dataset possesses immense potential in many applications and has great potential in 3D object detection and recognition. In this research we propose Graph Neural Network (GNN) based framework to learn and identify the objects in the 3D LiDAR point clouds. GNNs are class of deep learning which learns the patterns and objects based on the principle of graph learning which have shown success in various 3D computer vision tasks.
The surging demand for high-definition video streaming services and large neural network models (e.g., Generative Pre-trained Transformer, GPT) implies a tremendous explosion of Internet traffic. To mitigate the traffic pressure, architectures with in-network storage have been proposed to cache popular contents at devices in closer proximity to users. Correspondingly, in order to maximize caching utilization, it becomes essential to devise an effective popularity prediction method. In that regard, predicting popularity with dynamic graph neural network (DGNN) models achieve remarkable performance. However, DGNN models still suffer from tackling sparse datasets where most users are inactive. Therefore, we propose a reformative temporal graph network, named semantics-enhanced temporal graph network (STGN), which attaches extra semantic information into the user-content bipartite graph and could better leverage implicit relationships behind the superficial topology structure. On top of that, we customize its temporal and structural learning modules to further boost the prediction performance. Specifically, in order to efficiently aggregate the diversified semantics that a content might possess, we design a user-specific attention (UsAttn) mechanism for temporal learning module. Unlike the attention mechanism that only analyzes the influence of genres on content, UsAttn also considers the attraction of semantic information to a specific user. Meanwhile, as for the structural learning, we introduce the concept of positional encoding into our attention-based graph learning and adopt a semantic positional encoding (SPE) function to facilitate the analysis of content-oriented user-association analysis. Finally, extensive simulations verify the superiority of our STGN models and demonstrate the effectiveness in content caching.
Research on continual learning (CL) mainly focuses on data represented in the Euclidean space, while research on graph-structured data is scarce. Furthermore, most graph learning models are tailored for static graphs. However, graphs usually evolve continually in the real world. Catastrophic forgetting also emerges in graph learning models when being trained incrementally. This leads to the need to develop robust, effective and efficient continual graph learning approaches. Continual graph learning (CGL) is an emerging area aiming to realize continual learning on graph-structured data. This survey is written to shed light on this emerging area. It introduces the basic concepts of CGL and highlights two unique challenges brought by graphs. Then it reviews and categorizes recent state-of-the-art approaches, analyzing their strategies to tackle the unique challenges in CGL. Besides, it discusses the main concerns in each family of CGL methods, offering potential solutions. Finally, it explores the open issues and potential applications of CGL.
We study the causal bandit problem when the causal graph is unknown and develop an efficient algorithm for finding the parent node of the reward node using atomic interventions. We derive the exact equation for the expected number of interventions performed by the algorithm and show that under certain graphical conditions it could perform either logarithmically fast or, under more general assumptions, slower but still sublinearly in the number of variables. We formally show that our algorithm is optimal as it meets the universal lower bound we establish for any algorithm that performs atomic interventions. Finally, we extend our algorithm to the case when the reward node has multiple parents. Using this algorithm together with a standard algorithm from bandit literature leads to improved regret bounds.
Spatiotemporal learning, which aims at extracting spatiotemporal correlations from the collected spatiotemporal data, is a research hotspot in recent years. And considering the inherent graph structure of spatiotemporal data, recent works focus on capturing spatial dependencies by utilizing Graph Convolutional Networks (GCNs) to aggregate vertex features with the guidance of adjacency matrices. In this paper, with extensive and deep-going experiments, we comprehensively analyze existing spatiotemporal graph learning models and reveal that extracting adjacency matrices with carefully design strategies, which are viewed as the key of enhancing performance on graph learning, are largely ineffective. Meanwhile, based on these experiments, we also discover that the aggregation itself is more important than the way that how vertices are aggregated. With these preliminary, a novel efficient Graph-Free Spatial (GFS) learning module based on layer normalization for capturing spatial correlations in spatiotemporal graph learning. The proposed GFS module can be easily plugged into existing models for replacing all graph convolution components. Rigorous theoretical proof demonstrates that the time complexity of GFS is significantly better than that of graph convolution operation. Extensive experiments verify the superiority of GFS in both the perspectives of efficiency and learning effect in processing graph-structured data especially extreme large scale graph data.
Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.
In the field of skeleton-based action recognition, current top-performing graph convolutional networks (GCNs) exploit intra-sequence context to construct adaptive graphs for feature aggregation. However, we argue that such context is still \textit{local} since the rich cross-sequence relations have not been explicitly investigated. In this paper, we propose a graph contrastive learning framework for skeleton-based action recognition (\textit{SkeletonGCL}) to explore the \textit{global} context across all sequences. In specific, SkeletonGCL associates graph learning across sequences by enforcing graphs to be class-discriminative, \emph{i.e.,} intra-class compact and inter-class dispersed, which improves the GCN capacity to distinguish various action patterns. Besides, two memory banks are designed to enrich cross-sequence context from two complementary levels, \emph{i.e.,} instance and semantic levels, enabling graph contrastive learning in multiple context scales. Consequently, SkeletonGCL establishes a new training paradigm, and it can be seamlessly incorporated into current GCNs. Without loss of generality, we combine SkeletonGCL with three GCNs (2S-ACGN, CTR-GCN, and InfoGCN), and achieve consistent improvements on NTU60, NTU120, and NW-UCLA benchmarks. The source code will be available at \url{https://github.com/OliverHxh/SkeletonGCL}.
The identification of cancer genes is a critical yet challenging problem in cancer genomics research. Existing computational methods, including deep graph neural networks, fail to exploit the multilayered gene-gene interactions or provide limited explanation for their predictions. These methods are restricted to a single biological network, which cannot capture the full complexity of tumorigenesis. Models trained on different biological networks often yield different and even opposite cancer gene predictions, hindering their trustworthy adaptation. Here, we introduce an Explainable Multilayer Graph Neural Network (EMGNN) approach to identify cancer genes by leveraging multiple genegene interaction networks and pan-cancer multi-omics data. Unlike conventional graph learning on a single biological network, EMGNN uses a multilayered graph neural network to learn from multiple biological networks for accurate cancer gene prediction. Our method consistently outperforms all existing methods, with an average 7.15% improvement in area under the precision-recall curve (AUPR) over the current state-of-the-art method. Importantly, EMGNN integrated multiple graphs to prioritize newly predicted cancer genes with conflicting predictions from single biological networks. For each prediction, EMGNN provided valuable biological insights via both model-level feature importance explanations and molecular-level gene set enrichment analysis. Overall, EMGNN offers a powerful new paradigm of graph learning through modeling the multilayered topological gene relationships and provides a valuable tool for cancer genomics research.
Graph neural networks (GNNs) have been widely used in graph-structured data computation, showing promising performance in various applications such as node classification, link prediction, and network recommendation. Existing works mainly focus on node-wise correlation when doing weighted aggregation of neighboring nodes based on attention, such as dot product by the dense vectors of two nodes. This may cause conflicting noise in nodes to be propagated when doing information propagation. To solve this problem, we propose a General Information Propagation Algorithm (GIPA in short), which exploits more fine-grained information fusion including bit-wise and feature-wise correlations based on edge features in their propagation. Specifically, the bit-wise correlation calculates the element-wise attention weight through a multi-layer perceptron (MLP) based on the dense representations of two nodes and their edge; The feature-wise correlation is based on the one-hot representations of node attribute features for feature selection. We evaluate the performance of GIPA on the Open Graph Benchmark proteins (OGBN-proteins for short) dataset and the Alipay dataset of Alibaba. Experimental results reveal that GIPA outperforms the state-of-the-art models in terms of prediction accuracy, e.g., GIPA achieves an average ROC-AUC of $0.8901\pm 0.0011$, which is better than that of all the existing methods listed in the OGBN-proteins leaderboard.
Graphs have a superior ability to represent relational data, like chemical compounds, proteins, and social networks. Hence, graph-level learning, which takes a set of graphs as input, has been applied to many tasks including comparison, regression, classification, and more. Traditional approaches to learning a set of graphs heavily rely on hand-crafted features, such as substructures. But while these methods benefit from good interpretability, they often suffer from computational bottlenecks as they cannot skirt the graph isomorphism problem. Conversely, deep learning has helped graph-level learning adapt to the growing scale of graphs by extracting features automatically and encoding graphs into low-dimensional representations. As a result, these deep graph learning methods have been responsible for many successes. Yet, there is no comprehensive survey that reviews graph-level learning starting with traditional learning and moving through to the deep learning approaches. This article fills this gap and frames the representative algorithms into a systematic taxonomy covering traditional learning, graph-level deep neural networks, graph-level graph neural networks, and graph pooling. To ensure a thoroughly comprehensive survey, the evolutions, interactions, and communications between methods from four different branches of development are also examined. This is followed by a brief review of the benchmark data sets, evaluation metrics, and common downstream applications. The survey concludes with a broad overview of 12 current and future directions in this booming field.
Understanding and accurately predicting protein-ligand binding affinity are essential in the drug design and discovery process. At present, machine learning-based methodologies are gaining popularity as a means of predicting binding affinity due to their efficiency and accuracy, as well as the increasing availability of structural and binding affinity data for protein-ligand complexes. In biomolecular studies, graph theory has been widely applied since graphs can be used to model molecules or molecular complexes in a natural manner. In the present work, we upgrade the graph-based learners for the study of protein-ligand interactions by integrating extensive atom types such as SYBYL and extended connectivity interactive features (ECIF) into multiscale weighted colored graphs (MWCG). By pairing with the gradient boosting decision tree (GBDT) machine learning algorithm, our approach results in two different methods, namely $^\text{sybyl}\text{GGL}$-Score and $^\text{ecif}\text{GGL}$-Score. Both of our models are extensively validated in their scoring power using three commonly used benchmark datasets in the drug design area, namely CASF-2007, CASF-2013, and CASF-2016. The performance of our best model $^\text{sybyl}\text{GGL}$-Score is compared with other state-of-the-art models in the binding affinity prediction for each benchmark. While both of our models achieve state-of-the-art results, the SYBYL atom-type model $^\text{sybyl}\text{GGL}$-Score outperforms other methods by a wide margin in all benchmarks.
We consider the problem of inferring graph topology from smooth graph signals in a novel but practical scenario where data are located in distributed clients and prohibited from leaving local clients due to factors such as privacy concerns. The main difficulty in this task is how to exploit the potentially heterogeneous data of all clients under data silos. To this end, we first propose an auto-weighted multiple graph learning model to jointly learn a personalized graph for each local client and a single consensus graph for all clients. The personalized graphs match local data distributions, thereby mitigating data heterogeneity, while the consensus graph captures the global information. Moreover, the model can automatically assign appropriate contribution weights to local graphs based on their similarity to the consensus graph. We next devise a tailored algorithm to solve the induced problem, where all raw data are processed locally without leaving clients. Theoretically, we establish a provable estimation error bound and convergence analysis for the proposed model and algorithm. Finally, extensive experiments on synthetic and real data are carried out, and the results illustrate that our approach can learn graphs effectively in the target scenario.
Finding the optimal pass sequence of compilation can lead to a significant reduction in program size and/or improvement in program efficiency. Prior works on compilation pass ordering have two major drawbacks. They either require an excessive budget (in terms of compilation steps) at compile time or fail to generalize to unseen programs. In this paper, for code-size reduction tasks, we propose a novel pipeline to find program-dependent pass sequences within 45 compilation calls. It first identifies a coreset of 50 pass sequences via greedy optimization of a submodular function, and then learns a policy with Graph Neural Network (GNN) to pick the optimal sequence by predicting the normalized values of the pass sequences in the coreset. Despite its simplicity, our pipeline outperforms the default -Oz flag by an average of 4.7% over a large collection (4683) of unseen code repositories from diverse domains across 14 datasets. In comparison, previous approaches like reinforcement learning on the raw pass sequence space may take days to train due to sparse reward, and may not generalize well in held-out ones from different domains. Our results demonstrate that existing human-designed compiler flags can be improved with a simple yet effective technique that transforms the raw action space into a small one with denser rewards.