Scalable Graph Research Articles

Accurate and Scalable Graph Convolutional Networks for Recommendation Based on Subgraph Propagation

Accurate and Scalable Graph Convolutional Networks for Recommendation Based on Subgraph Propagation

ScGraphformer: unveiling cellular heterogeneity and interactions in scRNA-seq data using a scalable graph transformer network

The precise classification of cell types from single-cell RNA sequencing (scRNA-seq) data is pivotal for dissecting cellular heterogeneity in biological research. Traditional graph neural network (GNN) models are constrained by reliance on predefined graphs, limiting the exploration of complex cell-to-cell relationships. We introduce scGraphformer, a transformer-based GNN that transcends these limitations by learning an all-encompassing cell-cell relational network directly from scRNA-seq data. Through an iterative refinement process, scGraphformer constructs a dense graph structure that captures the full spectrum of cellular interactions. This comprehensive approach enables the identification of subtle and previously obscured cellular patterns and relationships. Evaluated on multiple datasets, scGraphformer demonstrates superior performance in cell type identification compared to existing methods and showcases its scalability with large-scale datasets. Our method not only provides enhanced cell type classification ability but also reveals the underlying cell interactions, offering deeper insights into functional cellular relationships. The scGraphformer thus holds the potential to significantly advance the field of single-cell analysis and contribute to a more nuanced understanding of cellular behavior.

Switch monitoring algorithm for 220 kV terminal substation startup process based on multi time scale graph model

The switch monitoring in the startup process of 220 kV terminal substation is a dynamic and changeable process, which has obvious characteristics of diversified scales in time, so as to solve the problem of switch monitoring under multivariable and multi-scale interference. The switch monitoring framework for the startup process of 220KV terminal substation is built. The process layer uses the graphic configuration software and combines the internal and external models of the substation to build the objective function for the generation of the substation graphic model. The particle swarm optimization algorithm is used to solve it to generate the optimal substation graphic model. Through the online monitoring device, the signals such as sensors, normally open and normally closed contacts are collected in real time, and the status of the switchgear is obtained through processing, the reduced half trapezoidal cloud model multivariable multi-scale sample entropy similarity tolerance criterion is used for softening treatment, and the multivariable multi-scale cloud sample entropy is determined to achieve the extraction of multiple time scale switch fault feature vectors, which are used as the input of the SE-DSCNN fault diagnosis model. Combined with the substation diagram, the switch fault identification during the startup process of the substation is realized, and the fault switch position is located. The experimental results show that the algorithm can accurately generate the substation model, which includes all the equipment in the substation, accurately describes the connection relationship and operation status of the equipment, and has high accuracy, integrity and aesthetics; The algorithm can effectively extract and analyze the MMCES entropy characteristics of different types of switch faults; The algorithm can realize the switch monitoring during the startup of substation C, and determine the fault switch and fault location.

SGFCCDA: Scale Graph Convolutional Networks and Feature Convolution for circRNA-Disease Association Prediction.

Circular RNAs (circRNAs) have emerged as a novel class of non-coding RNAs with regulatory roles in disease pathogenesis. Computational models aimed at predicting circRNA-disease associations offer valuable insights into disease mechanisms, thereby enabling the development of innovative diagnostic and therapeutic approaches while reducing the reliance on costly wet experiments. In this study, SGFCCDA is proposed for predicting potential circRNA-disease associations based on scale graph convolutional networks and feature convolution. Specifically, SGFCCDA integrates multiple measures of circRNA and disease similarity and combines known association information to construct a heterogeneous network. This network is then explored by scale graph convolutional networks to capture both topological and attribute information. Additionally, convolutional neural networks are employed to further learn the features and obtain higher-order feature representations containing richer information about nodes. The Hadamard product is utilized to effectively combine circRNA features with disease features, and a multilayer perceptron is applied to predict the association between each pair of circRNA and disease. Five-fold cross validation experiments conducted on the CircR2Disease dataset demonstrate the accurate prediction capabilities of SGFCCDA in identifying potential circRNA-disease associations. Furthermore, case studies provide further confirmation of SGFCCDA's ability to identify disease-associated circRNAs.

Graph-GIC: A smart and parallelized geomagnetically induced current modelling algorithm based on graph theory for space weather applications

Geomagnetically Induced Current (GIC) refers to the electromagnetic response of the Earth and its conductive modern infrastructures to space weather and would pose a significant threat to high-voltage power grids designed for the alternative current operation. To assess the impact of space weather on the power grid, one needs to calculate the GIC on a national or continental scale. In this study, we developed a smart and parallelized GIC modelling algorithm, Graph GIC. This algorithm deploys a graph representing a power grid in a single-line diagram, in which substations/transformers act as nodes and transmission lines as edges. With these denotations, a power grid and its electric parameters are mathematically represented with an adjacency matrix and an admittance matrix. We used sparse matrix and parallelisation techniques to expedite the intensive computation in cases of large-scale power grids. The Graph GIC was validated with a benchmark grid, applied to the GIC calculation of the 500 kV power grid of Guangdong, China, and conducted preliminary analysis on the grid’s susceptibility to geomagnetic storms. The Graph GIC algorithm has the advantage of an intuitive and highly scalable graph representation of a power grid at any scale. It achieves high-accuracy calculation and a speedup of about 18 times after parallelisation. This algorithm could be applied to assess the impact of space weather on a power grid up to continental scales and could be incorporated into global space weather modelling frameworks.

A Survey on Efficient and Scalable Graph processing Frameworks and Architectures

A Survey on Efficient and Scalable Graph processing Frameworks and Architectures

Node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking.

Computational methods in biology can infer large molecular interaction networks from multiple data sources and at different resolutions, creating unprecedented opportunities to explore the mechanisms driving complex biological phenomena. Networks can be built to represent distinct conditions and compared to uncover graph-level differences-such as when comparing patterns of gene-gene interactions that change between biological states. Given the importance of the graph comparison problem, there is a clear and growing need for robust and scalable methods that can identify meaningful differences. We introduce node2vec2rank (n2v2r), a method for graph differential analysis that ranks nodes according to the disparities of their representations in joint latent embedding spaces. Improving upon previous bag-of-features approaches, we take advantage of recent advances in machine learning and statistics to compare graphs in higher-order structures and in a data-driven manner. Formulated as a multi-layer spectral embedding algorithm, n2v2r is computationally efficient, incorporates stability as a key feature, and can provably identify the correct ranking of differences between graphs in an overall procedure that adheres to veridical data science principles. By better adapting to the data, node2vec2rank clearly outperformed the commonly used node degree in finding complex differences in simulated data. In the real-world applications of breast cancer subtype characterization, analysis of cell cycle in single-cell data, and searching for sex differences in lung adenocarcinoma, node2vec2rank found meaningful biological differences enabling the hypothesis generation for therapeutic candidates. Software and analysis pipelines implementing n2v2r and used for the analyses presented here are publicly available.

Poligras: Policy-Based Graph Summarization

Large graphs are ubiquitous. Their sizes, rates of growth, and complexity, however, have significantly outpaced human capabilities to ingest and make sense of them. As a cost-effective graph simplification technique, graph summarization is aimed to reduce large graphs into concise, structure-preserving, and quality-enhanced summaries readily available for efficient graph storage, processing, and visualization. Concretely, given a graph G , graph summarization condenses G into a succinct representation comprising (1) a supergraph with supernodes representing disjoint sets of vertices of G and superedges depicting aggregate-level connections between supernodes, and (2) a set of correction edges that help reconstruct G losslessly from the supergraph. Existing graph summarization solutions offer non-optimal graph summaries and are time-demanding in real-world large graphs. In this paper, we propose a learning-enhanced graph summarization approach, Poligras ( Poli cy-based gra ph summarization), to model the most critical computational component in graph summarization: supernode selection and merging. Specifically, we design a probabilistic policy learned and optimized by neural networks for efficient optimal supernode pair selection. As the first learning-enhanced, scalable graph summarization method, Poligras achieves significantly improved performance over state-of-the-art graph summarization solutions in real-world large graphs.

GraMeR: Graph Meta Reinforcement learning for multi-objective influence maximization

Influence maximization (IM) is a combinatorial problem of identifying a subset of seed nodes in a network (graph), which when activated, provide a maximal spread of influence in the network for a given diffusion model and a budget for seed set size. IM has numerous applications such as viral marketing, epidemic control, sensor placement and other network-related tasks. However, its practical uses are limited due to the computational complexity of current algorithms. Recently, deep reinforcement learning has been leveraged to solve IM in order to ease the computational burden. However, there are serious limitations in current approaches, including narrow IM formulation that only consider influence via spread and ignore self activation, low scalability to large graphs, and lack of generalizability across graph families leading to a large running time for every test network. In this work, we address these limitations through a unique approach that involves: (1) Formulating a generic IM problem as a Markov decision process that handles both intrinsic and influence activations; (2) incorporating generalizability via meta-learning across graph families. There are previous works that combine deep reinforcement learning with graph neural network but this work solves a more realistic IM problem and incorporates generalizability across graphs via meta reinforcement learning. Extensive experiments are carried out in various standard networks to validate performance of the proposed Graph Meta Reinforcement learning (GraMeR) framework. The results indicate that GraMeR is multiple orders faster and generic than conventional approaches when applied on small to medium scale graphs.

Multi-Scale Dense Graph Attention Network for Hyperspectral Classification

In recent years, numerous deep learning-based methods have gained increasing attention in hyperspectral classification, particularly the Graph Neural Network, which exhibits superior capabilities in structural description. However, a single graph structure is not suitable for hyperspectral feature representation. Therefore, we propose a novel Multiple-Scale graph network structure, known as the Multi-Scale Dense Graph Attention network for hyperspectral classification. Firstly, semi-supervised local Fisher discriminant analysis and superpixel segmentation were employed for dimensionality reduction and multi-scale graph construction, respectively. Secondly, Spectral-Spatial convolution is applied to extract shallow features from the image. Subsequently, an improved graph self-attention network is sequentially applied to each scale graph, and the different scale graphs are densely connected through spatial feature alignment modules, designed using twice matrix multiplication. Finally, the combined pixel-level feature map from multiple graph spaces is derived, and Spectral-Spatial convolution is employed to fuse the abundant feature maps for hyperspectral classification. Experimental results on various hyperspectral datasets demonstrate the superiority of our MSDesGATnet over many state-of-the-art methods. The code is available at https://github.com/l7170/MSDesGAT.git.

AFSDCGN: Adaptive Feature Scaling and Dynamic Contextual Graph Networks for image captioning with unseen relationship detection

AFSDCGN: Adaptive Feature Scaling and Dynamic Contextual Graph Networks for image captioning with unseen relationship detection

Distributed Graph Processing in Cloud Computing: A Review of Large-Scale Graph Analytics

The rapid growth of graph data in various domains has propelled the need for efficient distributed graph processing techniques in cloud computing environments. This paper presents a comprehensive review of distributed graph processing for graph analytics of massive size in the context of cloud computing. The paper begins by highlighting the challenges associated with distributed graph processing, including load balancing, communication overhead, scalability, and partitioning strategies. It provides an overview of existing frameworks and tools specifically designed for distributed graph processing in cloud environments. Furthermore, the review encompasses various techniques and algorithms employed in distributed graph processing. The paper also reviews recent research advancements in optimizing distributed graph processing in cloud computing. To provide practical insights, the paper presents a comparative analysis of representative large-scale graph analytics applications implemented on different cloud computing platforms. Performance, scalability, and efficiency metrics are evaluated under varying workload sizes and graph characteristics. Overall, this comprehensive review paper serves as a highly prized asset for researchers and large-scale graph analytics professionals who are practitioners in the field. It provides a holistic understanding of the state-of-the-art distributed graph processing techniques in cloud computing and guides future research efforts towards more efficient and scalable graph processing in cloud environments.

ScaleGCN: Efficient and Effective Graph Convolution via Channel-Wise Scale Transformation.

Graph convolutional networks (GCNs) have shown success in many graph-based applications as they can combine node features and graph topology to obtain expressive embeddings. While there exist numerous GCN variants, a typical graph convolution layer uses neighborhood aggregation and fully-connected (FC) layers to extract topological and node-wise features, respectively. However, when the receptive field of GCNs becomes larger, the tight coupling between the number of neighborhood aggregation and FC layers can increase the risk of over-fitting. Also, the FC layer between two successive aggregation operations will mix and pollute features in different channels, bringing noise and making node features hard to converge at each channel. In this article, we explore graph convolution without FC layers. We propose scale graph convolution, a new graph convolution using channel-wise scale transformation to extract node features. We provide empirical evidence that our new method has lower over-fitting risk and needs fewer layers to converge. We show from both theoretical and empirical perspectives that models with scale graph convolution have lower computational and memory costs than traditional GCN models. Experimental results on various datasets show that our method can achieve state-of-the-art results, in a cost-effective fashion.

Towards Automated RISC-V Microarchitecture Design with Reinforcement Learning

Microarchitecture determines the implementation of a microprocessor. Designing a microarchitecture to achieve better performance, power, and area (PPA) trade-off has been increasingly difficult. Previous data-driven methodologies hold inappropriate assumptions and lack more tightly coupling with expert knowledge. This paper proposes a novel reinforcement learning-based (RL) solution that addresses these limitations. With the integration of microarchitecture scaling graph, PPA preference space embedding, and proposed lightweight environment in RL, experiments using commercial electronic design automation (EDA) tools show that our method achieves an average PPA trade-off improvement of 16.03% than previous state-of-the-art approaches with 4.07× higher efficiency. The solution qualities outperform human implementations by at most 2.03× in the PPA trade-off.

Generating scalable graph states in an atom-nanophotonic interface

Scalable graph states are essential for measurement-based quantum computation and many entanglement-assisted applications in quantum technologies. Generation of these multipartite entangled states requires a controllable and efficient quantum device with delicate design of generation protocol. Here we propose to prepare high-fidelity and scalable graph states in one and two dimensions, which can be tailored in an atom-nanophotonic cavity via state carving technique. We propose a systematic protocol to carve out unwanted state components, which facilitates scalable graph states generations via adiabatic transport of a definite number of atoms in optical tweezers. An analysis of state fidelity is also presented, and the state preparation probability can be optimized via multiqubit state carvings and sequential single-photon probes. Our results showcase the capability of an atom-nanophotonic interface for creating graph states and pave the way toward novel problem-specific applications using scalable high-dimensional graph states with stationary qubits.

Energy Efficient Graph-Based Hybrid Learning for Speech Emotion Recognition on Humanoid Robot

This paper presents a novel deep graph-based learning technique for speech emotion recognition which has been specifically tailored for energy efficient deployment within humanoid robots. Our methodology represents a fusion of scalable graph representations, rooted in the foundational principles of graph signal processing theories. By delving into the utilization of cycle or line graphs as fundamental constituents shaping a robust Graph Convolution Network (GCN)-based architecture, we propose an approach which allows the capture of relationships between speech signals to decode intricate emotional patterns and responses. Our methodology is validated and benchmarked against established databases such as IEMOCAP and MSP-IMPROV. Our model outperforms standard GCNs and prevalent deep graph architectures, demonstrating performance levels that align with state-of-the-art methodologies. Notably, our model achieves this feat while significantly reducing the number of learnable parameters, thereby increasing computational efficiency and bolstering its suitability for resource-constrained environments. This proposed energy-efficient graph-based hybrid learning methodology is applied towards multimodal emotion recognition within humanoid robots. Its capacity to deliver competitive performance while streamlining computational complexity and energy efficiency represents a novel approach in evolving emotion recognition systems, catering to diverse real-world applications where precision in emotion recognition within humanoid robots stands as a pivotal requisite.

GraphScale: Scalable Processing on FPGAs for HBM and Large Graphs

Recent advances in graph processing on FPGAs promise to alleviate performance bottlenecks with irregular memory access patterns. Such bottlenecks challenge performance for a growing number of important application areas like machine learning and data analytics. While FPGAs denote a promising solution through flexible memory hierarchies and massive parallelism, we argue that current graph processing accelerators either use the off-chip memory bandwidth inefficiently or do not scale well across memory channels. In this work, we propose GraphScale, a scalable graph processing framework for FPGAs. GraphScale combines multi-channel memory with asynchronous graph processing (i.e., for fast convergence on results) and a compressed graph representation (i.e., for efficient usage of memory bandwidth and reduced memory footprint). GraphScale solves common graph problems like breadth-first search, PageRank, and weakly connected components through modular user-defined functions, a novel two-dimensional partitioning scheme, and a high-performance two-level crossbar design. Additionally, we extend GraphScale to scale to modern high-bandwidth memory (HBM) and reduce partitioning overhead of large graphs with binary packing.

Filter-Informed Spectral Graph Wavelet Networks for Multiscale Feature Extraction and Intelligent Fault Diagnosis.

Intelligent fault diagnosis has been increasingly improved with the evolution of deep learning (DL) approaches. Recently, the emerging graph neural networks (GNNs) have also been introduced in the field of fault diagnosis with the goal to make better use of the inductive bias of the interdependencies between the different sensor measurements. However, there are some limitations with these GNN-based fault diagnosis methods. First, they lack the ability to realize multiscale feature extraction due to the fixed receptive field of GNNs. Second, they eventually encounter the over-smoothing problem with increase of model depth. Finally, the extracted features of these GNNs are hard to understand due to the black-box nature of GNNs. To address these issues, a filter-informed spectral graph wavelet network (SGWN) is proposed in this article. In SGWN, the spectral graph wavelet convolutional (SGWConv) layer is established upon the spectral graph wavelet transform, which can decompose a graph signal into scaling function coefficients and spectral graph wavelet coefficients. With the help of SGWConv, SGWN is able to prevent the over-smoothing problem caused by long-range low-pass filtering, by simultaneously extracting low-pass and band-pass features. Furthermore, to speed up the computation of SGWN, the scaling kernel function and graph wavelet kernel function in SGWConv are approximated by the Chebyshev polynomials. The effectiveness of the proposed SGWN is evaluated on the collected solenoid valve dataset and aero-engine intershaft bearing dataset. The experimental results show that SGWN can outperform the comparative methods in both diagnostic accuracy and the ability to prevent over-smoothing. Moreover, its extracted features are also interpretable with domain knowledge.

Enhanced Scalable Graph Neural Network via Knowledge Distillation.

Graph neural networks (GNNs) have achieved state-of-the-art performance in various graph representation learning scenarios. However, when applied to graph data in real world, GNNs have encountered scalability issues. Existing GNNs often have high computational load in both training and inference stages, making them incapable of meeting the performance needs of large-scale scenarios with a large number of nodes. Although several studies on scalable GNNs have developed, they either merely improve GNNs with limited scalability or come at the expense of reduced effectiveness. Inspired by knowledge distillation's (KDs) achievement in preserving performances while balancing scalability in computer vision and natural language processing, we propose an enhanced scalable GNN via KD (KD-SGNN) to improve the scalability and effectiveness of GNNs. On the one hand, KD-SGNN adopts the idea of decoupled GNNs, which decouples feature transformation and feature propagation in GNNs and leverages preprocessing techniques to improve the scalability of GNNs. On the other hand, KD-SGNN proposes two KD mechanisms (i.e., soft-target (ST) distillation and shallow imitation (SI) distillation) to improve the expressiveness. The scalability and effectiveness of KD-SGNN are evaluated on multiple real datasets. Besides, the effectiveness of the proposed KD mechanisms is also verified through comprehensive analyses.

A novel spatial electric load forecasting method based on LDTW and GCN

AbstractSpatial power load forecasting is crucial for power grid planning, generation planning, dispatching, efficient power utilization, and sustainable development. The integration of new energy sources and electric vehicles has significantly altered grid loads, increasing the complexity of spatial load forecasting. However, existing techniques fail to fully consider the temporal and spatial correlation characteristics of data, leading to challenges in data identification and summarization. This reduces load forecasting accuracy and prolongs prediction time. To address these issues, a spatial electric load forecasting method based on improved scale limited dynamic time warping (LDTW) and graph convolutional network (GCN) are proposed. Firstly, the improved scale LDTW is used to improve the clustering effect of K‐Mediods++, refine the type of load data, and make the subsequent model training more targeted. Secondly, the interconnections and distances of substations in a real network structure is used to build a graph model to capture the power load distribution. Finally, based on the clustering results and the graph model, GCN‐LSTM is used to construct the spatio‐temporal forecasting algorithm. The proposed algorithm is tested using load data from a region in Shanghai and compared with other advanced algorithms. Results show that the algorithm achieves higher prediction accuracy and efficiency.