Graph Processing Research Articles

Multi-relation Graph Summarization

Graph summarization is beneficial in a wide range of applications, such as visualization, interactive and exploratory analysis, approximate query processing, reducing the on-disk storage footprint, and graph processing in modern hardware. However, the bulk of the literature on graph summarization surprisingly overlooks the possibility of having edges of different types. In this article, we study the novel problem of producing summaries of multi-relation networks, i.e., graphs where multiple edges of different types may exist between any pair of nodes. Multi-relation graphs are an expressive model of real-world activities, in which a relation can be a topic in social networks, an interaction type in genetic networks, or a snapshot in temporal graphs. The first approach that we consider for multi-relation graph summarization is a two-step method based on summarizing each relation in isolation, and then aggregating the resulting summaries in some clever way to produce a final unique summary. In doing this, as a side contribution, we provide the first polynomial-time approximation algorithm based on the k -Median clustering for the classic problem of lossless single-relation graph summarization. Then, we demonstrate the shortcomings of these two-step methods, and propose holistic approaches, both approximate and heuristic algorithms, to compute a summary directly for multi-relation graphs. In particular, we prove that the approximation bound of k -Median clustering for the single relation solution can be maintained in a multi-relation graph with proper aggregation operation over adjacency matrices corresponding to its multiple relations. Experimental results and case studies (on co-authorship networks and brain networks) validate the effectiveness and efficiency of the proposed algorithms.

Graph Sequence Neural Network with an Attention Mechanism for Traffic Speed Prediction

Recent years have witnessed the emerging success of Graph Neural Networks (GNNs) for modeling graphical data. A GNN can model the spatial dependencies of nodes in a graph based on message passing through node aggregation. However, in many application scenarios, these spatial dependencies can change over time, and a basic GNN model cannot capture these changes. In this article, we propose a G raph S eq uence neural network with an A tt ention mechanism (GSeqAtt) for processing graph sequences. More specifically, two attention mechanisms are combined: a horizontal mechanism and a vertical mechanism. GTransformer, which is a horizontal attention mechanism for handling time series, is used to capture the correlations between graphs in the input time sequence. The vertical attention mechanism, a Graph Network (GN) block structure with an attention mechanism (GNAtt), acts within the graph structure in each frame of the time series. Experiments show that our proposed model is able to handle information propagation for graph sequences accurately and efficiently. Moreover, results on real-world data from three road intersections show that our GSeqAtt outperforms state-of-the-art baselines on the traffic speed prediction task.

ОПТИМИЗАЦИЯ НОВЫХ ТИПОВ ЭЛЕКТРОМЕХАНИЧЕСКИХ ПРЕОБРАЗОВАТЕЛЕЙ ДЛЯ МЕХАНИЗМОВ С ВЕНТИЛЯТОРНЫМ ХАРАКТЕРОМ НАГРУЗКИ

Abstract. The article considers the main requirements for pumping stations, in particular, for methods of regula¬ting the water supply at the first lift pump unit. A description of the pumping unit and equipment is provided. The artic¬le pro-vides a comparison of the types of the main drive units of pumping stations. It also provides a rationale for the choice of electric drive system between classical asynchronous and synchronous electric drives, as well as a system with a field regulated reluctance machine (FRRM) with a comparison of energy indicators. A description and substantia-tion of the control system work are also given. The articles provide the technical characteristics of the motor parameters and the daily flow rate of the station fluid. The optimal method for regulating the power supply system was chosen based on research. A mathematical model of the device which implements the chosen control method is presented. The results of mathematical modeling are presented in the graphs. A graph of the transient process is given in the case of changing speeds depending on the required fluid supply. Conclusions about the efficiency of the system are drawn and further action plans are outlined.

Special issue on big graph data management and processing

Special issue on big graph data management and processing

VeilGraph: incremental graph stream processing

Graphs are found in a plethora of domains, including online social networks, the World Wide Web and the study of epidemics, to name a few. With the advent of greater volumes of information and the need for continuously updated results under temporal constraints, it is necessary to explore alternative approaches that further enable performance improvements. In the scope of stream processing over graphs, we research the trade-offs between result accuracy and the speedup of approximate computation techniques. The relationships between the frequency of graph algorithm execution, the update rate and the type of update play an important role in applying these techniques. Herein we present VeilGraph, through which we conducted our research. We showcase an innovative model for approximate graph processing implemented in Apache Flink. We analyse the feasibility of our model and evaluate it with the case study of the PageRank algorithm, the most famous measure of vertex centrality used to rank websites in search engine results. Our experiments show that VeilGraph can often reduce latency closely to half (speedup of 2.0×), while achieving result quality above 95% when compared to results of the traditional version of PageRank executing in Apache Flink with Gelly (i.e. without any summarization or approximation techniques). In some cases, depending on the workload, speedups against Apache Flink reach up to 3.0x (i.e. yielding a reduction of up to 66% in latency). We have found VeilGraph implementation on Flink to be scalable, as it is able to improve performance up to 10X speedups, when more resources are employed (16 workers), achieving better speedups with scale for larger graphs, which are the most relevant.

Cost Model Based Incremental Processing in Dynamic Graphs

Incremental graph processing has been developed to reduce unnecessary redundant calculations in dynamic graphs. In this paper, we propose an incremental dynamic graph-processing scheme using a cost model to selectively perform incremental processing or static processing. The cost model calculates the predicted values of the detection cost and processing cost of the recalculation region based on the past processing history. If there is a benefit of the cost model, incremental query processing is performed. Otherwise, static query processing is performed because the detection cost and processing cost increase due to the graph change. The proposed incremental scheme reduces the amount of computation by processing only the changed region through incremental processing. Further, it reduces the detection and disk I/O costs of the vertex, which are calculated by reusing the subgraphs from the previous results. The processing structure of the proposed scheme stores the data read from the cache and the adjacent vertices and then performs only memory mapping when processing these graph. It is demonstrated through various performance evaluations that the proposed scheme outperforms the existing schemes.

ℓ $\ell $‐Connectivity and ℓ $\ell $‐edge‐connectivity of random graphs

AbstractFor an integer , the ‐connectivity of a graph is defined to be the minimum number of vertices of whose removal produces a disconnected graph with at least components or a graph with fewer than vertices. The ‐edge‐connectivity of a graph is the minimum number of edges whose removal leaves a graph with at least components if , and if . Given integers and , we investigate and when . Furthermore, our arguments can be used to show that in the random graph process, the hitting times of minimum degree at least and of ‐connectivity (or ‐edge‐connectivity) at least coincide with high probability. These results generalize the work of Bollobás and Thomason on classical connectivity.

Segmentation of Lung Nodules on CT Images Using a Nested Three-Dimensional Fully Connected Convolutional Network.

In computer-aided diagnosis systems for lung cancer, segmentation of lung nodules is important for analyzing image features of lung nodules on computed tomography (CT) images and distinguishing malignant nodules from benign ones. However, it is difficult to accurately and robustly segment lung nodules attached to the chest wall or with ground-glass opacities using conventional image processing methods. Therefore, this study aimed to develop a method for robust and accurate three-dimensional (3D) segmentation of lung nodule regions using deep learning. In this study, a nested 3D fully connected convolutional network with residual unit structures was proposed, and designed a new loss function. Compared with annotated images obtained under the guidance of a radiologist, the Dice similarity coefficient (DS) and intersection over union (IoU) were 0.845 ± 0.008 and 0.738 ± 0.011, respectively, for 332 lung nodules (lung adenocarcinoma) obtained from 332 patients. On the other hand, for 3D U-Net and 3D SegNet, the DS was 0.822 ± 0.009 and 0.786 ± 0.011, respectively, and the IoU was 0.711 ± 0.011 and 0.660 ± 0.012, respectively. These results indicate that the proposed method is significantly superior to well-known deep learning models. Moreover, we compared the results obtained from the proposed method with those obtained from conventional image processing methods, watersheds, and graph cuts. The DS and IoU results for the watershed method were 0.628 ± 0.027 and 0.494 ± 0.025, respectively, and those for the graph cut method were 0.566 ± 0.025 and 0.414 ± 0.021, respectively. These results indicate that the proposed method is significantly superior to conventional image processing methods. The proposed method may be useful for accurate and robust segmentation of lung nodules to assist radiologists in the diagnosis of lung nodules such as lung adenocarcinoma on CT images.

Multimodal reasoning based on knowledge graph embedding for specific diseases.

MotivationKnowledge Graph (KG) is becoming increasingly important in the biomedical field. Deriving new and reliable knowledge from existing knowledge by KG embedding technology is a cutting-edge method. Some add a variety of additional information to aid reasoning, namely multimodal reasoning. However, few works based on the existing biomedical KGs are focused on specific diseases.ResultsThis work develops a construction and multimodal reasoning process of Specific Disease Knowledge Graphs (SDKGs). We construct SDKG-11, a SDKG set including five cancers, six non-cancer diseases, a combined Cancer5 and a combined Diseases11, aiming to discover new reliable knowledge and provide universal pre-trained knowledge for that specific disease field. SDKG-11 is obtained through original triplet extraction, standard entity set construction, entity linking and relation linking. We implement multimodal reasoning by reverse-hyperplane projection for SDKGs based on structure, category and description embeddings. Multimodal reasoning improves pre-existing models on all SDKGs using entity prediction task as the evaluation protocol. We verify the model’s reliability in discovering new knowledge by manually proofreading predicted drug–gene, gene–disease and disease–drug pairs. Using embedding results as initialization parameters for the biomolecular interaction classification, we demonstrate the universality of embedding models.Availability and implementationThe constructed SDKG-11 and the implementation by TensorFlow are available from https://github.com/ZhuChaoY/SDKG-11.Supplementary information Supplementary data are available at Bioinformatics online.

A novel method for forecasting time series based on directed visibility graph and improved random walk

Recently network-based method for forecasting time series has become a hot research topic. Although some proposed network-based methods achieve good performance in forecasting some series, how to mine more information of time series and make more accurate predictions is still an open question. To address this issue, we propose a novel reconstructing–forecasting method based on directed visibility graph and random walk process. Firstly, the observed time series is reconstructed to explore more information of series. Then, the reconstructed series is converted into a directed visibility graph. Afterwards, the reconstructed series is predicted with the similarity distribution obtained from improved random walk process. Eventually, the prediction of original time series is calculated using the predictions and the similarity distribution of the reconstructed one. To test the forecasting performance, the proposed method is applied to forecast construction cost index (CCI), China’s quarterly total GDP growth (GDP) and China’s tertiary industry quarterly GDP growth (TI). The results of experiments indicate that, with good robustness, the proposed method is of ability to provide more accurate predictions than compared methods.

An effective community-based link prediction model for improving accuracy in social networks

Link prediction plays a predominant role in complex network analysis. It indicates to determine the probability of the presence of future links that depends on available information. The existing standard classical similarity indices-based link prediction models considered the neighbour nodes have a similar effect towards link probability. Nevertheless, the common neighbor nodes residing in different communities may vary in real-world networks. In this paper, a novel community information-based link prediction model has been proposed in which every neighboring node’s community information (community centrality) has been considered to predict the link between the given node pair. In the proposed model, the given social network graph can be divided into different communities and community centrality is calculated for every derived community based on degree, closeness, and betweenness basic graph centrality measures. Afterward, the new community centrality-based similarity indices have been introduced to compute the community centralities which are applied to nine existing basic similarity indices. The empirical analysis on 13 real-world social networks datasets manifests that the proposed model yields better prediction accuracy of 97% rather than existing models. Moreover, the proposed model is parallelized efficiently to work on large complex networks using Spark GraphX Big Data-based parallel Graph processing technique and it attains a lesser execution time of 250 seconds.

Sortledton

Despite the wide adoption of graph processing across many different application domains, there is no underlying data structure that can serve a variety of graph workloads (analytics, traversals, and pattern matching) on dynamic graphs with transactional updates. In this paper, we present Sortledton, a universal graph data structure that addresses the open problem by being carefully optimizing for the most relevant data access patterns used by graph computation kernels. It can support millions of transactional updates per second, while providing competitive performance (1.22x on average) for the most common graph workloads to the best-known baseline for static graphs - CSR. With this, we improve the ingestion throughput over state-of-the-art dynamic graph data structures, while supporting a wider range of graph computations under transactional guarantees, with a much simpler design and significantly smaller memory footprint (2.1x that of CSR).

SimGQ+: Simultaneously evaluating iterative point-to-all and point-to-point graph queries

Graph processing frameworks are typically designed to optimize the evaluation of a single graph query. However, in practice, we often need to respond to multiple graph queries, either from different users or from a single user performing a complex analytics task. Therefore in this paper we develop SimGQ+, a system that optimizes simultaneous evaluation of a group of vertex queries that originate at different source vertices (e.g., multiple shortest path queries originating at different source vertices) and delivers substantial speedups over a conventional framework that evaluates and responds to queries one by one. Our work considers both point-to-all and point-to-point queries. The performance benefits are achieved via batching and sharing. Batching fully utilizes system resources to evaluate a batch of queries and amortizes runtime overheads incurred due to fetching vertices and edge lists, synchronizing threads, and maintaining computation frontiers. Sharing dynamically identifies shared queries that substantially represent subcomputations in the evaluation of different queries in a batch, evaluates the shared queries, and then uses their results to accelerate the evaluation of all queries in the batch. With four input power-law graphs and four graph algorithms SimGQ+ achieves speedups of up to 45.67× with batch sizes of up to 512 queries over the baseline implementation that evaluates the queries one by one using the state of the art Ligra system. Moreover, both batching and sharing contribute substantially to the speedups.

Fast datalog evaluation for batch and stream graph processing

Implementing complex algorithms for big data, artificial intelligence, and graph processing requires enormous effort. Succinct, declarative programs to solve complex problems that can be efficiently executed for batching and streaming data are in demand. This paper presents Nexus, a distributed Datalog evaluation system. It evaluates Datalog programs using the semi-naive algorithm for batch and streaming data using incremental and asynchronous iteration. Furthermore, we evaluate Datalog programs with aggregates to determine the advantages of implementing the semi-naive algorithm using incremental iteration on its performance. Our experimental results show that Nexus significantly outperforms acyclic dataflow-based systems.

Uncovering input-sensitive energy bottlenecks in oversubscribed GPU workloads

Graph algorithms are at the core of data-intensive applications in many computational domains. Although accelerator-based implementations have the potential for delivering improved energy efficiency on today’s large-scale graph analytics, there are many challenges to reaching the desired goals. This paper examines the issues of GPU oversubscription and input sensitivity in energy efficient graph processing. We introduce the notion of energy signatures, a collection of runtime events that can determine fluctuations in power consumption as a function of input graph characteristics. The study shows that variations in volume, density, diameter and dispersion in graphs can alter the runtime behavior of GPU applications and these changes in program behavior in turn impact the energy efficiency of the application. Based on the insight gained from our study, we develop three input-aware optimization techniques to mitigate energy bottlenecks. On experiments conducted on a Unified Memory supported GPU, the optimizations yield a 11.97% energy savings on average on Breadth-First Search and Single-Source Shortest Path algorithms.

Benchmarking a New Paradigm: Experimental Analysis and Characterization of a Real Processing-in-Memory System

Many modern workloads, such as neural networks, databases, and graph processing, are fundamentally memory-bound. For such workloads, the data movement between main memory and CPU cores imposes a significant overhead in terms of both latency and energy. A major reason is that this communication happens through a narrow bus with high latency and limited bandwidth, and the low data reuse in memory-bound workloads is insufficient to amortize the cost of main memory access. Fundamentally addressing this data movement bottleneck requires a paradigm where the memory system assumes an active role in computing by integrating processing capabilities. This paradigm is known as processing-in-memory (PIM). Recent research explores different forms of PIM architectures, motivated by the emergence of new 3D-stacked memory technologies that integrate memory with a logic layer where processing elements can be easily placed. Past works evaluate these architectures in simulation or, at best, with simplified hardware prototypes. In contrast, the UPMEM company has designed and manufactured the first publicly-available real-world PIM architecture. The UPMEM PIM architecture combines traditional DRAM memory arrays with general-purpose in-order cores, called DRAM Processing Units (DPUs), integrated in the same chip. This paper provides the first comprehensive analysis of the first publicly-available real-world PIM architecture. We make two key contributions. First, we conduct an experimental characterization of the UPMEM-based PIM system using microbenchmarks to assess various architecture limits such as compute throughput and memory bandwidth, yielding new insights. Second, we present PrIM (Processing-In-Memory benchmarks), a benchmark suite of 16 workloads from different application domains (e.g., dense/sparse linear algebra, databases, data analytics, graph processing, neural networks, bioinformatics, image processing), which we identify as memory-bound. We evaluate the performance and scaling characteristics of PrIM benchmarks on the UPMEM PIM architecture, and compare their performance and energy consumption to their modern CPU and GPU counterparts. Our extensive evaluation conducted on two real UPMEM-based PIM systems with 640 and 2,556 DPUs provides new insights about suitability of different workloads to the PIM system, programming recommendations for software designers, and suggestions and hints for hardware and architecture designers of future PIM systems.

Accelerating Graph Processing With Lightweight Learning-Based Data Reordering

Graph processing is a vital component in various application domains. However, a good graph processing performance is hard to achieve due to its intensive irregular data accesses. Noticing that in real-world graphs, a small portion of vertices occupy most connections, several techniques are proposed to reorder vertices based on their access frequency for better data access locality. However, these approaches can be further improved by identifying reordered data more effectively, which will reduce reordering overhead and improve overall performance. In this letter, we propose <i>Learning-Based Reordering (LBR)</i>, a novel lightweight framework that identifies and reorders hot data adaptively for given graphs, algorithms, and threads. Our experimental evaluation indicates that <i>LBR</i> decreases reordering overhead by 24.7&#x0025; while improves performance by 9.9&#x0025; compared to the best-performing existing scheme.

Analyzing GCN Aggregation on GPU

Graph convolutional neural networks (GCNs) are emerging neural networks for graph structures that include large features associated with each vertex. The operations of GCN can be divided into two phases - aggregation and combination. While the combination just performs matrix multiplications using trained weights and aggregated features, the aggregation phase requires graph traversal to collect features from adjacent vertices. Even though neural network applications rely on GPU’s massively parallel processing, GCN aggregation kernels exhibit rather low performance since graph processing using compressed graph structures provokes frequent irregular accesses in GPUs. In order to investigate the performance hurdles of GCN aggregation on GPU, we perform an in-depth analysis of the aggregation kernels using real GPU hardware and a cycle-accurate GPU simulator. We first analyze the characteristics of the popular graph datasets used for GCN studies. We reveal the fractions of non-zero elements in feature vectors are diverse among datasets. Based on the observation, we build two types of aggregation kernels that handle uncompressed and compressed feature vectors. Our evaluation exhibits the performance of aggregation can be significantly influenced by kernel design approaches and feature density. We also analyze the individual loads that access the data arrays of the aggregation kernels to specify critical loads. Our analysis reveals the performance of GPU memory hierarchy is influenced by access patterns and feature size of graph datasets. Based on our observations we discuss possible kernel design approaches and architectural ideas that can improve the performance of GCN aggregation.

Multifeature Fusion Keyword Extraction Algorithm Based on TextRank

Keyword extraction is the predecessor of many tasks, and its results directly affect search, recommendation, classification, and other tasks. In this study, we take Chinese text as the research object and propose a multi-feature fusion keyword extraction algorithm combined with BERT semantics and K-Truss graph(BSKT). The BSKT algorithm is based on the TextRank algorithm, which combines BERT semantic features, K-Truss features, and other features. First, the BSKT algorithm obtains the word vectors from the BERT pretraining model to calculate the semantic difference, which is used to optimize the iterative process of the TextRank word graph. Then, the BSKT algorithm obtains its K-Truss graph by decomposing the TextRank word graph and obtains the truss level feature of the word. Finally, by combining the word IDF and truss level features, the BSKT algorithm scores the words to extract keywords. Experimental results show that the BSKT algorithm achieves better performance than the latest keyword extraction algorithm SCTR in the task of extracting 1&#x2013;10 keywords. Furthermore, the increment in F1 increased by 11.2&#x0025; when the BSKT algorithm was used to extract three keywords from the Sensor dataset.

Graph Computing Systems and Partitioning Techniques: A Survey

Graphs are a tremendously suitable data representation that models the relationships of entities in many application domains, such as recommendation systems, machine learning, computational biology, social network analysis, and other application domains. Graphs with many vertices and edges have become quite prevalent in recent years. Therefore, graph computing systems with integrated various graph partitioning techniques have been envisioned as a promising paradigm to handle large-scale graph analytics in these application domains. However, scalable processing of large-scale graphs is challenging due to their high volume and inherent irregular structure of the real-world graphs. Hence, industry and academia have recently proposed graph partitioning and computing systems to efficiently process and analyze large-scale graphs. The graph partitioning and computing systems have been designed to improve scalability issues and reduce processing time complexity. This paper presents an overview, classification, and investigation of the most popular graph partitioning and computing systems. The various methods and approaches of graph partitioning and diverse categories of graph computing systems are presented. Finally, we discuss future challenges and research directions in graph partitioning and computing systems.