TensorFlow GNN（TF-GNN）是张量曲线的图形神经网络的可扩展库。它是从自下而上设计的，以支持当今信息生态系统中发生的丰富的异质图数据。Google的许多生产模型都使用TF-GNN，最近已作为开源项目发布。在本文中，我们描述了TF-GNN数据模型，其KERAS建模API以及相关功能，例如图形采样，分布式训练和加速器支持。

图形神经网络（GNN）已被证明是分析非欧国人图数据的强大工具。但是，缺乏有效的分布图学习（GL）系统极大地阻碍了GNN的应用，尤其是当图形大且GNN相对深时。本文中，我们提出了GraphTheta，这是一种以顶点为中心的图形编程模型实现的新颖分布式和可扩展的GL系统。 GraphTheta是第一个基于分布式图处理的GL系统，其神经网络运算符以用户定义的功能实现。该系统支持多种培训策略，并在分布式（虚拟）机器上启用高度可扩展的大图学习。为了促进图形卷积实现，GraphTheta提出了一个名为NN-Tgar的新的GL抽象，以弥合图形处理和图形深度学习之间的差距。提出了分布式图引擎，以通过混合平行执行进行随机梯度下降优化。此外，除了全球批次和迷你批次外，我们还为新的集群批次培训策略提供了支持。我们使用许多网络大小的数据集评估GraphTheta，范围从小，适度到大规模。实验结果表明，GraphTheta可以很好地扩展到1,024名工人，用于培训内部开发的GNN，该工业尺度的Aripay数据集为14亿个节点和41亿个属性边缘，并带有CPU虚拟机（Dockers）群的小群。 （5 $ \ sim $ 12GB）。此外，GraphTheta比最先进的GNN实现获得了可比或更好的预测结果，证明其学习GNN和现有框架的能力，并且可以超过多达$ 2.02 \ tims $ $ 2.02 \ times $，具有更好的可扩展性。据我们所知，这项工作介绍了文献中最大的边缘属性GNN学习任务。

TensorFlow is a machine learning system that operates at large scale and in heterogeneous environments. Tensor-Flow uses dataflow graphs to represent computation, shared state, and the operations that mutate that state. It maps the nodes of a dataflow graph across many machines in a cluster, and within a machine across multiple computational devices, including multicore CPUs, generalpurpose GPUs, and custom-designed ASICs known as Tensor Processing Units (TPUs). This architecture gives flexibility to the application developer: whereas in previous "parameter server" designs the management of shared state is built into the system, TensorFlow enables developers to experiment with novel optimizations and training algorithms. TensorFlow supports a variety of applications, with a focus on training and inference on deep neural networks. Several Google services use TensorFlow in production, we have released it as an open-source project, and it has become widely used for machine learning research. In this paper, we describe the TensorFlow dataflow model and demonstrate the compelling performance that Tensor-Flow achieves for several real-world applications.

Graphs are ubiquitous in nature and can therefore serve as models for many practical but also theoretical problems. For this purpose, they can be defined as many different types which suitably reflect the individual contexts of the represented problem. To address cutting-edge problems based on graph data, the research field of Graph Neural Networks (GNNs) has emerged. Despite the field's youth and the speed at which new models are developed, many recent surveys have been published to keep track of them. Nevertheless, it has not yet been gathered which GNN can process what kind of graph types. In this survey, we give a detailed overview of already existing GNNs and, unlike previous surveys, categorize them according to their ability to handle different graph types and properties. We consider GNNs operating on static and dynamic graphs of different structural constitutions, with or without node or edge attributes. Moreover, we distinguish between GNN models for discrete-time or continuous-time dynamic graphs and group the models according to their architecture. We find that there are still graph types that are not or only rarely covered by existing GNN models. We point out where models are missing and give potential reasons for their absence.

最近，作为基于图形机器学习的骨干的图形神经网络（GNN）展示了各个域（例如，电子商务）的巨大成功。然而，由于基于高稀疏和不规则的图形操作，GNN的性能通常不令人满意。为此，我们提出，TC-GNN，基于GNN加速框架的第一个GPU张量核心单元（TCU）。核心思想是将“稀疏”GNN计算与“密集”TCU进行调和。具体地，我们对主流GNN计算框架中的稀疏操作进行了深入的分析。我们介绍了一种新颖的稀疏图翻译技术，便于TCU处理稀疏GNN工作量。我们还实现了一个有效的CUDA核心和TCU协作设计，以充分利用GPU资源。我们将TC-GNN与Pytorch框架完全集成，以便于编程。严格的实验在各种GNN型号和数据集设置的最先进的深图库框架上平均显示了1.70倍的加速。

即使机器学习算法已经在数据科学中发挥了重要作用，但许多当前方法对输入数据提出了不现实的假设。由于不兼容的数据格式，或数据集中的异质，分层或完全缺少的数据片段，因此很难应用此类方法。作为解决方案，我们提出了一个用于样本表示，模型定义和培训的多功能，统一的框架，称为“ Hmill”。我们深入审查框架构建和扩展的机器学习的多个范围范式。从理论上讲，为HMILL的关键组件的设计合理，我们将通用近似定理的扩展显示到框架中实现的模型所实现的所有功能的集合。本文还包含有关我们实施中技术和绩效改进的详细讨论，该讨论将在MIT许可下发布供下载。该框架的主要资产是其灵活性，它可以通过相同的工具对不同的现实世界数据源进行建模。除了单独观察到每个对象的一组属性的标准设置外，我们解释了如何在框架中实现表示整个对象系统的图表中的消息推断。为了支持我们的主张，我们使用框架解决了网络安全域的三个不同问题。第一种用例涉及来自原始网络观察结果的IoT设备识别。在第二个问题中，我们研究了如何使用以有向图表示的操作系统的快照可以对恶意二进制文件进行分类。最后提供的示例是通过网络中实体之间建模域黑名单扩展的任务。在所有三个问题中，基于建议的框架的解决方案可实现与专业方法相当的性能。

While many systems have been developed to train Graph Neural Networks (GNNs), efficient model inference and evaluation remain to be addressed. For instance, using the widely adopted node-wise approach, model evaluation can account for up to 94% of the time in the end-to-end training process due to neighbor explosion, which means that a node accesses its multi-hop neighbors. On the other hand, layer-wise inference avoids the neighbor explosion problem by conducting inference layer by layer such that the nodes only need their one-hop neighbors in each layer. However, implementing layer-wise inference requires substantial engineering efforts because users need to manually decompose a GNN model into layers for computation and split workload into batches to fit into device memory. In this paper, we develop Deep Graph Inference (DGI) -- a system for easy and efficient GNN model inference, which automatically translates the training code of a GNN model for layer-wise execution. DGI is general for various GNN models and different kinds of inference requests, and supports out-of-core execution on large graphs that cannot fit in CPU memory. Experimental results show that DGI consistently outperforms layer-wise inference across different datasets and hardware settings, and the speedup can be over 1,000x.

Graph neural networks (GNNs) have been demonstrated to be a powerful algorithmic model in broad application fields for their effectiveness in learning over graphs. To scale GNN training up for large-scale and ever-growing graphs, the most promising solution is distributed training which distributes the workload of training across multiple computing nodes. However, the workflows, computational patterns, communication patterns, and optimization techniques of distributed GNN training remain preliminarily understood. In this paper, we provide a comprehensive survey of distributed GNN training by investigating various optimization techniques used in distributed GNN training. First, distributed GNN training is classified into several categories according to their workflows. In addition, their computational patterns and communication patterns, as well as the optimization techniques proposed by recent work are introduced. Second, the software frameworks and hardware platforms of distributed GNN training are also introduced for a deeper understanding. Third, distributed GNN training is compared with distributed training of deep neural networks, emphasizing the uniqueness of distributed GNN training. Finally, interesting issues and opportunities in this field are discussed.

事实证明，分子机器学习（ML）对于解决各种分子问题很重要，包括预测蛋白质 - 药物相互作用和血液脑性渗透性。自最近以来，已经为分子ML实施了所谓的图神经网络（GNN），显示出与基于描述符的方法相当或出色的性能。尽管存在各种工具和包装用于将GNN用于分子ML，但新的GNN包装，名为Molgraph（https://github.com/akensert/molgraph），在这项工作中开发了，以创建GNNS与TensorFlow高度兼容的动力和KERAS应用程序编程接口（API）。由于Molgraph专门关注分子ML，因此实施了化学模块，以适应分子图的产生$ \ unicode {x2014} $，然后可以将其输入到GNNS中以用于分子ML。为了验证GNN，它们针对分子数据集以及三个色谱保留时间数据集进行了基准测试。这些基准测试的结果表明，GNN按预期进行。此外，GNN被证明可用于分子识别和改善色谱保留数据的可解释性。

Pre-publication draft of a book to be published byMorgan & Claypool publishers. Unedited version released with permission. All relevant copyrights held by the author and publisher extend to this pre-publication draft.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

图形神经网络（GNNS）在学习从图形结构数据中展示了成功，其中包含欺诈检测，推荐和知识图形推理。然而，培训GNN有效地具有挑战性，因为：1）GPU存储器容量有限，对于大型数据集可能不足，而2）基于图形的数据结构导致不规则的数据访问模式。在这项工作中，我们提供了一种统计分析的方法，并确定了GNN培训前更频繁地访问的数据。我们的数据分层方法不仅利用输入图的结构，而且还从实际GNN训练过程中获得了洞察力，以实现更高的预测结果。通过我们的数据分层方法，我们还提供了一种新的数据放置和访问策略，以进一步最大限度地减少CPU-GPU通信开销。我们还考虑了多GPU GNN培训，我们也展示了我们在多GPU系统中的策略的有效性。评估结果表明，我们的工作将CPU-GPU流量降低了87-95％，并通过数亿节点和数十亿边缘的图表提高了现有解决方案的GNN训练速度。

Graph neural networks (GNNs) have received great attention due to their success in various graph-related learning tasks. Several GNN frameworks have then been developed for fast and easy implementation of GNN models. Despite their popularity, they are not well documented, and their implementations and system performance have not been well understood. In particular, unlike the traditional GNNs that are trained based on the entire graph in a full-batch manner, recent GNNs have been developed with different graph sampling techniques for mini-batch training of GNNs on large graphs. While they improve the scalability, their training times still depend on the implementations in the frameworks as sampling and its associated operations can introduce non-negligible overhead and computational cost. In addition, it is unknown how much the frameworks are 'eco-friendly' from a green computing perspective. In this paper, we provide an in-depth study of two mainstream GNN frameworks along with three state-of-the-art GNNs to analyze their performance in terms of runtime and power/energy consumption. We conduct extensive benchmark experiments at several different levels and present detailed analysis results and observations, which could be helpful for further improvement and optimization.

Graph classification is an important area in both modern research and industry. Multiple applications, especially in chemistry and novel drug discovery, encourage rapid development of machine learning models in this area. To keep up with the pace of new research, proper experimental design, fair evaluation, and independent benchmarks are essential. Design of strong baselines is an indispensable element of such works. In this thesis, we explore multiple approaches to graph classification. We focus on Graph Neural Networks (GNNs), which emerged as a de facto standard deep learning technique for graph representation learning. Classical approaches, such as graph descriptors and molecular fingerprints, are also addressed. We design fair evaluation experimental protocol and choose proper datasets collection. This allows us to perform numerous experiments and rigorously analyze modern approaches. We arrive to many conclusions, which shed new light on performance and quality of novel algorithms. We investigate application of Jumping Knowledge GNN architecture to graph classification, which proves to be an efficient tool for improving base graph neural network architectures. Multiple improvements to baseline models are also proposed and experimentally verified, which constitutes an important contribution to the field of fair model comparison.

图形神经网络（GNNS）将深度神经网络（DNN）的成功扩展到非欧几里德图数据，实现了各种任务的接地性能，例如节点分类和图形属性预测。尽管如此，现有系统效率低，培训数十亿节点和GPU的节点和边缘训练大图。主要瓶颈是准备GPU数据的过程 - 子图采样和特征检索。本文提出了一个分布式GNN培训系统的BGL，旨在解决一些关键思想的瓶颈。首先，我们提出了一种动态缓存引擎，以最小化特征检索流量。通过协同设计缓存政策和抽样顺序，我们发现低开销和高缓存命中率的精美斑点。其次，我们改善了曲线图分区算法，以减少子图采样期间的交叉分区通信。最后，仔细资源隔离减少了不同数据预处理阶段之间的争用。关于各种GNN模型和大图数据集的广泛实验表明，BGL平均明显优于现有的GNN训练系统20.68倍。

深度学习的快速进步正在导致一系列快速变化的模型，对计算的需求急剧增长。但是，随着框架将性能优化专门针对流行网络的模式，它们隐含地限制了推动研究进展的新颖和多样化的模型。我们通过定义灵活和用户可定制的管道来优化基于数据运动最小化的任意深神经网络的培训来赋予深度学习研究人员的能力。管道始于Pytorch或ONNX中的标准网络，并通过逐步降低转换计算。我们定义了四个级别的通用转换级别，从局部操作员优化到全球数据运动减少。这些在以数据为中心的图形中间表示上运行，该表示在各个级别的抽象级别表达计算和数据移动，包括扩展基本运算符，例如其基础计算的卷积。设计的核心是管道的互动性和内省性质。每个部分都可以通过Python API扩展，并且可以使用GUI进行交互调整。我们在十个不同的网络上展示了竞争性能或加速性，交互式优化发现了高效网络中的新机会。

As the interest to Graph Neural Networks (GNNs) is growing, the importance of benchmarking and performance characterization studies of GNNs is increasing. So far, we have seen many studies that investigate and present the performance and computational efficiency of GNNs. However, the work done so far has been carried out using a few high-level GNN frameworks. Although these frameworks provide ease of use, they contain too many dependencies to other existing libraries. The layers of implementation details and the dependencies complicate the performance analysis of GNN models that are built on top of these frameworks, especially while using architectural simulators. Furthermore, different approaches on GNN computation are generally overlooked in prior characterization studies, and merely one of the common computational models is evaluated. Based on these shortcomings and needs that we observed, we developed a benchmark suite that is framework independent, supporting versatile computational models, easily configurable and can be used with architectural simulators without additional effort. Our benchmark suite, which we call gSuite, makes use of only hardware vendor's libraries and therefore it is independent of any other frameworks. gSuite enables performing detailed performance characterization studies on GNN Inference using both contemporary GPU profilers and architectural GPU simulators. To illustrate the benefits of our new benchmark suite, we perform a detailed characterization study with a set of well-known GNN models with various datasets; running gSuite both on a real GPU card and a timing-detailed GPU simulator. We also implicate the effect of computational models on performance. We use several evaluation metrics to rigorously measure the performance of GNN computation.

我们呈现GSPMD，一种用于公共机器学习计算的自动，基于编译的并行化系统。它允许用户以与单个设备的方式相同的方式编写程序，然后通过关于如何分发Tensors的一些注释来提供提示，基于哪个GSPMD将并行化计算。其分区的表示简单尚不一般，允许它在各种模型上表达并行性的不同或混合范式。GSPMD基于有限的用户注释为每个运算符的分区Inventing，使得缩放现有的单设备程序方便。它解决了生产使用的几种技术挑战，允许GSPMD实现50％至62％的计算利用率，用于高达2048个云TPUv3核心，适用于高达1万亿参数的模型。

学术界和工业广泛研究了图形机器学习。然而，作为图表学习繁荣的文献，具有大量的新兴方法和技术，它越来越难以手动设计用于不同的图形相关任务的最佳机器学习算法。为了解决挑战，自动化图形机器学习，目的是在没有手动设计的不同图表任务/数据中发现最好的图形任务/数据的最佳超参数和神经架构配置，正在增加研究界的越来越多的关注。在本文中，我们广泛地讨论了自动化图形机方法，涵盖了用于图形机学习的超参数优化（HPO）和神经架构搜索（NAS）。我们简要概述了专为Traph Machine学习或自动化机器学习而设计的现有库，进一步深入介绍AutoGL，我们的专用和世界上第一个用于自动图形机器学习的开放源库。最后但并非最不重要的是，我们分享了对自动图形机学习的未来研究方向的见解。本文是对自动图形机学习的方法，图书馆以及方向的第一个系统和全面讨论。

Graph Neural Networks (GNNs), originally proposed for node classification, have also motivated many recent works on edge prediction (a.k.a., link prediction). However, existing methods lack elaborate design regarding the distinctions between two tasks that have been frequently overlooked: (i) edges only constitute the topology in the node classification task but can be used as both the topology and the supervisions (i.e., labels) in the edge prediction task; (ii) the node classification makes prediction over each individual node, while the edge prediction is determinated by each pair of nodes. To this end, we propose a novel edge prediction paradigm named Edge-aware Message PassIng neuRal nEtworks (EMPIRE). Concretely, we first introduce an edge splitting technique to specify use of each edge where each edge is solely used as either the topology or the supervision (named as topology edge or supervision edge). We then develop a new message passing mechanism that generates the messages to source nodes (through topology edges) being aware of target nodes (through supervision edges). In order to emphasize the differences between pairs connected by supervision edges and pairs unconnected, we further weight the messages to highlight the relative ones that can reflect the differences. In addition, we design a novel negative node-pair sampling trick that efficiently samples 'hard' negative instances in the supervision instances, and can significantly improve the performance. Experimental results verify that the proposed method can significantly outperform existing state-of-the-art models regarding the edge prediction task on multiple homogeneous and heterogeneous graph datasets.