Graph Structure Research Articles

Research on Smart City Road Network Capacity Optimization Configuration Based on Deep Learning Algorithms

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-based stock prediction with multisource information and relational data fusion

With the application of multisource information in different fields, the combination of different types of information, such as numerical data and text information, has become a favourable choice for performing stock market analyses. Despite the rich information provided by multisource data, building structured relationships remains challenging. In addition, some market relationship-based analysis methods use a predefined graph structure as a stock relationship graph, which makes it impossible to sensitively aggregate attribute features, and these methods cannot dynamically update market relationships or relationship strengths. In this paper, we propose a novel dynamic attribute-driven graph attention network incorporating sentiment (AGATS) information, transaction data, and text data. Inspired by behavioural finance, we separately extract sentiment information as a factor of technical indicators, and further realize the early fusion of technical indicators and textual data through tensor fusion. In particular, real-time intramarket dependencies and key attribute information are captured with graph networks, enabling dynamic relationship and relationship strength updates. Experiments conducted on real datasets show that our model is capable of ourperforming previously developed methods in prediction and trading.

A Method for Single-Phase Ground Fault Section Location in Distribution Networks Based on Improved Empirical Wavelet Transform and Graph Isomorphic Networks

When single-phase ground faults occur in distribution systems, the fault characteristics of zero-sequence current signals are not prominent. They are quickly submerged in noise, leading to difficulties in fault section location. This paper proposes a method for fault section location in distribution networks based on improved empirical wavelet transform (IEWT) and GINs to address this issue. Firstly, based on kurtosis, EWT is optimized using the N-point search method to decompose the zero-sequence current signal into modal components. Noise is filtered out through weighted permutation entropy (WPE), and signal reconstruction is performed to obtain the denoised zero-sequence current signal. Subsequently, GINs are employed for graph classification tasks. According to the topology of the distribution network, the corresponding graph is constructed as the input to the GIN. The denoised zero-sequence current signal is the node input for the GIN. The GIN autonomously explores the features of each graph structure to achieve fault section location. The experimental results demonstrate that this method has strong noise resistance, with a fault section location accuracy of up to 99.95%, effectively completing fault section location in distribution networks.

A Review of Hypergraph Neural Networks

In recent years, Graph Neural Networks (GNNs) have seen notable success in fields such as recommendation systems and natural language processing, largely due to the availability of vast amounts of data and powerful computational resources. GNNs are primarily designed to work with graph data that involve pairwise relationships. However, in many real-world networks, the relationships between entities are complex and go beyond simple pairwise connections, as seen in scientific collaboration networks, protein networks, and similar domains. If these complex relationships are directly represented as pairwise relationships using graph structures, it can lead to information loss. A hypergraph, as a special kind of graph-structured data, can represent higher-order relationships that cannot be fully captured by graphs, thereby addressing the limitations of graphs. In light of this, researchers have begun to focus on how to design neural networks on hypergraphs, leading to the proposal of hypergraph neural network (HGNN) models for downstream tasks. Therefore, this paper reviews the existing hypergraph neural network models. The review is conducted from two perspectives: spectral analysis methods and neural network methods on hypergraphs, discussing both unfolded and non-unfolded methods, and further subdividing them based on their algorithm characteristics and application scenarios. Subsequently, the design concepts of various algorithms are analyzed and compared, and the advantages and disadvantages of each type of algorithm are summarized based on experimental results. Finally, potential future research directions in hypergraph learning are discussed.

A unified framework to analyze transposable element insertion polymorphisms using graph genomes

Transposable elements are ubiquitous mobile DNA sequences generating insertion polymorphisms, contributing to genomic diversity. We present GraffiTE, a flexible pipeline to analyze polymorphic mobile elements insertions. By integrating state-of-the-art structural variant detection algorithms and graph genomes, GraffiTE identifies polymorphic mobile elements from genomic assemblies or long-read sequencing data, and genotypes these variants using short or long read sets. Benchmarking on simulated and real datasets reports high precision and recall rates. GraffiTE is designed to allow non-expert users to perform comprehensive analyses, including in models with limited transposable element knowledge and is compatible with various sequencing technologies. Here, we demonstrate the versatility of GraffiTE by analyzing human, Drosophila melanogaster, maize, and Cannabis sativa pangenome data. These analyses reveal the landscapes of polymorphic mobile elements and their frequency variations across individuals, strains, and cultivars.

GASCOM: Graph-based Attentive Semantic Context Modeling for Online Conversation Understanding

Online conversation understanding is an important yet challenging NLP problem which has many useful applications (e.g., hate speech detection). However, online conversations typically unfold over a series of posts and replies to those posts, forming a tree structure within which individual posts may refer to semantic context from elsewhere in the tree. Such semantic cross-referencing makes it difficult to understand a single post by itself; yet considering the entire conversation tree is not only difficult to scale but can also be misleading as a single conversation may have several distinct threads or points, not all of which are relevant to the post being considered. In this paper, we propose a Graph-based Attentive Semantic COntext Modeling (GASCOM) framework for online conversation understanding. Specifically, we design two novel algorithms that utilize both the graph structure of the online conversation as well as the semantic information from individual posts for retrieving relevant context nodes from the whole conversation. We further design a token-level multi-head graph attention mechanism to pay different attentions to different tokens from different selected context utterances for fine-grained conversation context modelling. Using this semantic conversational context, we re-examine two well-studied problems: polarity prediction and hate speech detection. Our proposed framework significantly outperforms state-of-the-art methods on both tasks, improving macro-F1 scores by 4.5% for polarity prediction and by 5% for hate speech detection. The GASCOM context weights also enhance interpretability.

GeoEntity-type constrained knowledge graph embedding for predicting natural-language spatial relations

Natural-language spatial relations between geographic entities (geoentities) reflect diverse perceptions influenced by factors like location, culture, and linguistic conventions. These relations play a crucial role in supporting geospatial tasks, such as question answering and cognitive reasoning. While prior studies focused on a limited set of human-selected spatial terms and geometric attributes, they often overlooked essential semantic attributes. To overcome this limitation, we developed a Spatial Relation-based Knowledge Graph Embedding framework, SR-KGE, with new KG fusion functions to predict spatial relation terms among distinct geoentities. This method not only considers graph structures and the diversity of natural language expressions in the embedding and learning process, but also incorporates geoentity types as a constraint to capture spatial and semantic relations more accurately. Our experiments on two knowledge graph datasets, one small-scale and one large-scale, have both shown its superior performance in spatial relation inference compared to popular KGE models, including TransE, RotatE, and HAKE. We hope our research will advance the classic study of natural language described spatial relations in a more automated and intelligent way.

DGSIST: Clustering spatial transcriptome data based on deep graph structure Infomax

Although spatial transcriptomics data provide valuable insights into gene expression profiles and the spatial structure of tissues, most studies rely solely on gene expression information, underutilizing the spatial data. To fully leverage the potential of spatial transcriptomics and graph neural networks, the DGSI (Deep Graph Structure Infomax) model is proposed. This innovative graph data processing model uses graph convolutional neural networks and employs an unsupervised learning approach. It maximizes the mutual information between graph-level and node-level representations, emphasizing flexible sampling and aggregation of nodes and their neighbors. This effectively captures and incorporates local information from nodes into the overall graph structure. Additionally, this paper developed the DGSIST framework, an unsupervised cell clustering method that integrates the DGSI model, SVD dimensionality reduction algorithm, and k-means++ clustering algorithm. This aims to identify cell types accurately. DGSIST fully uses spatial transcriptomics data and outperforms existing methods in accuracy. Demonstrations of DGSIST’s capability across various tissue types and technological platforms have shown its effectiveness in accurately identifying spatial domains in multiple tissue sections. Compared to other spatial clustering methods, DGSIST excels in cell clustering and effectively eliminates batch effects without needing batch correction. DGSIST excels in spatial clustering analysis, spatial variation identification, and differential gene expression detection and directly applies to graph analysis tasks, such as node classification, link prediction, or graph clustering. Anticipation lies in the contribution of the DGSIST framework to a deeper understanding of the spatial organizational structures of diseases such as cancer.

Identifying shader sub-patterns for GPU performance tuning and architecture design

GPUs are increasingly playing vital roles in the modern technology industry. Improving the GPU performance involves optimizing its architectural design and fine-tuning its software code. However, to achieve this, engineers must investigate codes from as many GPU-related applications as possible to identify code portions that need fine-tuning. Moreover, this effort requires engineers to have good domain knowledge, and their work is made more arduous because the source codes of applications are normally confidential. To this end, we introduce ShaderAnalyzer, a solution leveraging graph mining and machine learning to analyze GPU-executed low-level machine codes and identify their fine-tuning opportunities. Our approach includes representing machine code with graph structure and subsequently identifying frequently occurring substructures within the codes. Optimizing the execution of these substructures can enhance the overall performance of the GPU. In addition, our model leverages these frequent patterns to further facilitate engineers’ tasks by selecting representative patterns to predict and investigate low-efficiency ones. We conduct comprehensive experiments to evaluate the performance of our solution, and the results have been validated by our industry partners. ShaderAnalyzer is an end-to-end framework that helps engineers identify code segments with the highest potential for performance gains after fine-tuning and offers valuable insights for hardware architects in future products design.

Measurement error and information bias in causal diagrams: mapping epidemiological concepts and graphical structures.

Measurement error and information bias are ubiquitous in epidemiology, yet directed acyclic graphs (DAGs) are infrequently used to represent them, in contrast with confounding and selection bias. This represents a missed opportunity to leverage the full utility of DAGs to depict associations between the variables we actually analyse in practice: empirically measured variables, which are necessarily measured with error. In this article, we focus on applying causal diagrams to depict the data-generating mechanisms that give rise to the data we analyse, including measurement error. We begin by considering empirical data considerations using a general example, and then build up to a specific worked example from the clinical epidemiology of hearing health. Throughout, our goal is to highlight both the challenges and the benefits of using DAGs to depict measurement error. In addition to the application of DAGs to conceptual causal questions (which pertain to unmeasured constructs free from measurement error), which is common, we highlight the advantages associated with applying DAGs to also include empirically measured variables and-potentially-information bias. We also highlight the implications implied by this use of DAGs, particularly regarding the unblocked backdoor path causal structure. Ultimately, we seek to help increase the clarity with which epidemiologists can map traditional epidemiological concepts (such as information bias and confounding) onto causal graphical structures.

A Graph-Refinement Algorithm to Minimize Squared Delivery Delays Using Parcel Robots

In recent years, parcel volumes have reached record highs, prompting the logistics industry to explore innovative solutions to meet growing demand. In densely populated areas, delivery robots offer a promising alternative to traditional truck-based delivery systems. These autonomous electric robots operate on sidewalks and deliver time-sensitive goods, such as express parcels, medicine and meals. However, their limited cargo capacity and battery life require a return to a depot after each delivery. This challenge can be modeled as an electric vehicle-routing problem with soft time windows and single-unit capacity constraints. The objective is to serve all customers while minimizing the quadratic sum of delivery delays and ensuring each vehicle operates within its battery limitations. To address this problem, we propose a mixed-integer quadratic programming model and introduce an enhanced formulation using a layered graph structure. For this layered graph, we present two solution approaches based on relaxations that reduce the number of nodes and arcs compared to the expanded formulation. The first approach, Iterative Refinement, solves the current relaxation to optimality and refines the graph when the solution is infeasible for the expanded formulation. This process continues until a proven optimal solution is obtained. The second approach, Branch and Refine, integrates graph refinement into a branch-and-bound framework, eliminating the need for restarts. Computational experiments on modified Solomon instances demonstrate the effectiveness of our solution approaches, with Branch and Refine consistently outperforming Iterative Refinement across all tested parameter configurations.

Predictions on new Cu-based ABO3 (A=Cu and B=Lu, Y) oxide-perovskite for energy storage and optoelectronic applications: A DFT study

Cu-based novel oxide-perovskite ABO3(A = Cu and B=Lu, Y) compounds have been investigated for their physical properties using the Generalized Gradient Approximation and Revised-Perdew-Burke-Ernzerhof (GGA-RPBE) exchanging correlation-functional within the density functional theory (DFT). The calculations show that both compounds comprise a cubic structure with the space group of Pm3m. The calculations also indicate that the results we have discovered represent unique compounds. Formation enthalpy computations have been used to assess the overall structural stability of both compounds. The density of states and band structure graphs for both perovskite compounds provide strong evidence of their semiconducting behavior. In-depth research is also done on optical properties such as the refractive index, extinction coefficient, absorption, reflectivity, electrical conductivity, and the energy loss function. At high-energy photons, both compounds CuLuO3 and CuYO3 show outstanding conductivity and absorption. While, at lower incident photon energy intervals, they both exhibit transparency. Based on our electronic and optical properties investigations, we have found that CuLuO3 and CuYO3 are potential candidates for use in high-energy UV, and optoelectronic technologies.

Knowledge Graph Completion for High-Speed Railway Turnout Switch Machine Maintenance Based on the Multi-Level KBGC Model

The incompleteness of the existing knowledge graphs in the railway domain creates information gaps, impacting their quality and effectiveness in the operation and maintenance of high-speed railway turnout switch machines. To address this, we propose a multi-layer model (KBGC) that combines KG-BERT, graph attention network (GAT), and Convolutional Embedding Network (ConvE) for knowledge graph completion in railway maintenance. KG-BERT fine-tunes a pre-trained BERT model to extract deep semantic features from entities and relationships, converting them into graph structures. GAT captures key structural relationships between nodes using an attention mechanism, producing enriched semantic and structural embeddings. Finally, ConvE reshapes and convolves these embeddings to learn complex entity interactions, enabling accurate link prediction. Extensive experiments on the HRTOM dataset, containing triplet data from high-speed railway turnout switch machines, demonstrate the model’s effectiveness, achieving an MRR of 50.8% and a Hits@10 of 60.7%. These findings show that the KBGC model significantly improves knowledge graph completion, aiding railway maintenance personnel in decision making and preventive maintenance, and providing new tools for railway maintenance applications.

Graph-based self-supervised learning for repeat detection in metagenomic assembly.

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, in which genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and nonrepetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudolabels for a small proportion of the nodes. We then use those pseudolabels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with predefined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic data sets. The results on the simulated data highlight GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, experiments with synthetic metagenomic data sets reveal that incorporating the graph structure and the GNN enhances the detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.

CBRec: A causal way balancing multidimensional attraction effect in POI recommendations

In the next Point-of-Interest recommendation, sparse and uneven location data generate biases, resulting in homogeneous recommendation outcomes that fail to reflect user preferences. Although there are many related unbiased studies, they still exhibit limitations. They lack a unified debiasing paradigm and typically employ different methods to address various biases, resulting in complex and incompatible debiasing models. Additionally, they often overlook the potential advantages of biases, thus harming the quality of location features. To address these challenges, we propose a unified debiasing paradigm by intervening in location attraction to balance the positive and negative effects of bias. By analyzing the structural causal graph, we identify attraction as a feature influenced by bias. By comparing observational results affected by attraction with counterfactual results unaffected by it, we derive a unified debiasing paradigm that eliminates the effects of bias. Additionally, through feature fusion, we embed multidimensional attraction into user features, leveraging the advantages of bias to preserve the quality of location features. Finally, experimental results on five real-world datasets demonstrate that our proposed model outperforms recent sequential recommendation models.

MVD-HG: multigranularity smart contract vulnerability detection method based on heterogeneous graphs

Smart contracts have significant losses due to various types of vulnerabilities. However, traditional vulnerability detection methods rely extensively on expert rules, resulting in low detection accuracy and poor adaptability to novel attacks. To address these problems, in this paper, deep learning methods are combined with smart contract vulnerability code detection approaches. syntax trees (ASTs), which are special isomorphic graph structures, are an important bridge between source code and graph neural networks. By learning the AST, the model can understand the semantics of the source code. Moreover, graph neural networks have an increasing ability to address complex heterogeneous graphs. Therefore, control flow graphs are fused with data flow graphs on the basis of the ASTs to build heterogeneous graphs with richer code semantics. Furthermore, multigranularity analysis of the vulnerability detection results is performed, including coarse-grained contract-level vulnerability detection and fine-grained line-level vulnerability detection. Through this multigranularity detection approach, vulnerabilities in contracts can be identified and analysed more comprehensively, providing a richer perspective and more solutions for vulnerability detection. The experimental results show that the proposed multigranularity vulnerability detection method based on heterogeneous graphs (MVD-HG) improves both the accuracy and range of the detected vulnerability types in contract-level vulnerability detection tasks; moreover, in the line-level vulnerability detection task, the MVD-HG model achieves significant results and addresses the shortcomings of existing methods. In addition, based on code generation methods used in related fields, a data enhancement method based on the source code is developed, which effectively expands the experimental dataset to address the reduced credibility of the results due to insufficient amounts of data.

Hierarchical graph contrastive learning framework based on quantum neural networks for sentiment analysis

Existing multi-modal sentiment analysis (MSA) methods typically achieve interaction by connecting different layers or designing special structures, but rarely consider the synergistic effects among data. Moreover, most sentiment analysis research tends to focus solely on single sentiment polarity analysis, without considering the intensity and directional attributes of emotions. Addressing these issues, we propose a framework called Hierarchical Graph Contrastive Learning based on Quantum Neural Network (HGCL-QNN) to remedy these shortcomings. Specifically, a graph structure is established within and between modalities. In the quantum fuzzy neural network module, fuzzy quantum encoding is implemented by using complex-valued, then quantum superposition and entanglement are utilized to consider the intensity and directional attributes of emotions while analyzing emotional polarity. In the quantum multi-modal fusion neural network module, methods such as amplitude encoding and quantum entanglement are employed to further integrate information from different modalities, thereby enhancing the model's power to express emotional information. To enhance the model's understanding of fine-grained and global features, and to better align and integrate features from different modalities, hierarchical graph contrastive learning is employed on different levels. The experimental results demonstrate that HGCL-QNN outperforms the existing baseline methods on MOSI and MOSEI datasets, achieving significant efficacy improvements.

GGAS2SN: Gated Graph and SmilesToSeq Network for Solubility Prediction.

Aqueous solubility is a critical physicochemical property of drug discovery. Solubility is a key issue in pharmaceutical development because it can limit a drug's absorption capacity. Accurate solubility prediction is crucial for pharmacological, environmental, and drug development studies. This research introduces a novel method for solubility prediction by combining gated graph neural networks (GGNNs) and graph attention neural networks (GATs) with Smiles2Seq encoding. Our methodology involves converting chemical compounds into graph structures with nodes representing atoms and edges indicating chemical bonds. These graphs are then processed by using a specialized graph neural network (GNN) architecture. Incorporating attention mechanisms into GNN allows for capturing subtle structural dependencies, fostering improved solubility predictions. Furthermore, we utilized the Smiles2Seq encoding technique to bridge the semantic gap between molecular structures and their textual representations. Smiles2Seq seamlessly converts chemical notations into numeric sequences, facilitating the efficient transfer of information into our model. We demonstrate the efficacy of our approach through comprehensive experiments on benchmark solubility data sets, showcasing superior predictive performance compared to traditional methods. Our model outperforms existing solubility prediction models and provides interpretable insights into the molecular features driving solubility behavior. This research signifies an important advancement in solubility prediction, offering potent tools for drug discovery, formulation development, and environmental assessments. The fusion of GGNN and Smiles2Seq encoding establishes a robust framework for accurately forecasting solubility across various chemical compounds, fostering innovation in various domains reliant on solubility data.

GSSCL: A framework for Graph Self-Supervised Curriculum Learning based on clustering label smoothing

Graph self-supervised learning is an effective technique for learning common knowledge from unlabeled graph data through pretext tasks. To capture the interrelationships between nodes and their essential roles globally, existing methods use clustering labels as self-supervised signals. However, in some cases, these methods may introduce noise, leading to over-fitting of the model and a reduction in performance. To address these issues, a novel framework for Graph Self-Supervised Curriculum Learning based on clustering label smoothing called GSSCL has been proposed. GSSCL clusters knowledge in an easy-to-difficult manner, reducing the heavy dependence on the reliability of clustering and improving the generalizability of the model. Moreover, the Silhouette Coefficient is employed to evaluate the clustering confident scores for all nodes. Some nodes are selected based on high confident scores to perform self-supervised learning. To account for the possibility of complex heterophilous information in graphs (e.g., noisy links), clustering pseudo-label smoothing is performed on K-nearest neighbor graphs built upon the similarities between node features instead of the original graph structures. The obtained multi-scale knowledge is then applied to curriculum learning. Finally, comprehensive experiments conducted across diverse public graph benchmarks demonstrate the superior performance of the proposed framework. It exhibits comparable results to state-of-the-art methods across semi-supervised node classification and clustering tasks.

Bayesian inference of frequency-specific functional connectivity in MEG imaging using a spectral graph model

Abstract Understanding the relationship between structural connectivity (SC) and functional connectivity (FC) of the human brain is an important goal of neuroscience. Highly detailed mathematical models of neural masses exist that can simulate the interactions between functional activity and structural wiring. These models are often complex and require intensive computation. Most importantly, they do not provide a direct or intuitive interpretation of this structure–function relationship. In this study, we employ the emerging concepts of spectral graph theory to obtain this mapping in terms of graph harmonics, which are eigenvectors of the structural graph’s Laplacian matrix. In order to imbue these harmonics with biophysical underpinnings, we leverage recent advances in parsimonious spectral graph modeling (SGM) of brain activity. Here, we show that such a model can indeed be cast in terms of graph harmonics, and can provide a closed-form prediction of FC in an arbitrary frequency band. The model requires only three global, spatially invariant parameters, yet is capable of generating rich FC patterns in different frequency bands. Only a few harmonics are sufficient to reproduce realistic FC patterns. We applied the method to predict FC obtained from pairwise magnitude coherence of source-reconstructed resting-state magnetoencephalography (MEG) recordings of 36 healthy subjects. To enable efficient model inference, we adopted a deep neural network-based Bayesian procedure called simulation-based inference. Using this tool, we were able to speedily infer not only the single most likely model parameters, but also their full posterior distributions. We also implemented several other benchmark methods relating SC to FC, including graph diffusion and coupled neural mass models. The present method was shown to give the best performance overall. Notably, we discovered that a single biophysical parameterization is capable of fitting FCs from all relevant frequency bands simultaneously, an aspect that did not receive adequate attention in prior computational studies.