1 Introduction
Graph Neural Networks (GNNs) have been popularly used for analyzing graph data such as social network data and biological data. The basic idea of GNNs such as GraphSAGE [Hamilton et al.2017] is to propagate feature information between neighboring nodes so that nodes can learn feature representations by using locally connected graph structure information.
Although GNNs have achieved great success, one shorting is to tune many parameters of the graph neural architectures. Similar to CNNs that contain many manually setting parameters such as the sizes of filters, the types of pooling layers and residual connections, tuning the parameters of GNNs generally takes heavy manual work which requires domain knowledge as well.
Recently we observe that reinforcement learning has been successfully used to generate accurate neural architectures for CNNs and RNNs. The seminar work NAS [Zoph and Le2016] uses a recurrent network as controller to generate CNN and RNN network descriptions (which are referred to as child networks), and then uses the validation results of the child networks as feedback of the controller to maximize the expected accuracy of the generated architectures of the CNNs and RNNs. According to the experimental reports, the NAS search algorithm can improve CNNs and RNNs on benchmark data by percentage of 0.09 on the CIFAR10 data and 3.6 perplexity on the Penn Treebank data. Inspired by NAS, a large body of advanced neural architecture search algorithms based on reinforcement learning have been proposed to improve its efficient and accuracy, such as the Efficient neural architecture search algorithm (ENAS [Pham et al.2018]) and Stochastic Neural Architecture Search algorithm (SNAS) [Xie et al.2018].
The promising results of using NAS to search neural architectures for CNNs and RNNs motivate us to use reinforcement learning to search graph neural architectures in this work. Our idea is similar to NAS for CNNs and RNNs that first uses a recurrent network as controller to generate the descriptions of GNNs and then compute the rewards of the GNNs as feedback of the controller to maximize the expected accuracy of the generated architectures of the GNNs. However, when using NAS for graph neural architecture search, the following new challenges need to be addressed:

Challenge 1. How to design the search space of GNNs. Different from CNNs for processing regular gridstructural inputs, GNNs for processing graph data that are nonEuclidean and irregularly distributed in a feature space generally contain both spatial and convolutional descriptions [Hamilton et al.2017] and GCN [Kipf and Welling2017] .

Challenge 2. How to design an efficient reinforcement learning search algorithm. The search space of GNNs are generally very large. When generating the descriptions for GNNs by the controller, the training of reinforcement learning converges slowly.

Challenge 3. How to evaluate the performance of the algorithm in both transductive and inductive learning settings is the third challenge.
In this paper, we present an efficient Graph Neural Architecture Search algorithm GraphNAS that can automatically generate neural architecture for GNNs by using reinforcement learning. To solve Challenge 1, GraphNAS designs a search space covering sampling functions, aggregation functions and gated functions. To solve Challenge 2, GraphNAS uses a new parameters sharing and architecture search algorithm that is more efficient than NAS for CNNs and RNNs. To solve Challenge 3, we validate the performance of GraphNAS on node classification tasks in both transductive and inductive learning settings. The results demonstrate that GraphNAS can achieve consistently better performance on the Cora, Citeseer, Pubmed citation network, and proteinprotein network. The contribution of the paper is fourfolder:

We first study the problem of using reinforcement learning to search graph neural architectures, which has the potential to save a lot of manual work for designing graph neural architectures.

We present a new GraphNAS algorithm that can efficiently search the graph neural architectures in a large search space.

We validate the performance of GraphNAS on realworld data sets. The results show that GraphNAS can design a graph neural architecture that rivals the best humaninvented architecture in terms of accuracy and F1 score on test sets.

We publish the Python codes based on Pytorch for future comparisons at:
https://github.com/GraphNAS/GraphNASsimple
2 Related work
Graph Neural Networks. The notation of graph neural networks was firstly outlined in the work [Gori et al.2005]
. Inspired by the convolutional networks in computer vision, a large number of methods that redefine the notation of convolution filter for graph data have been proposed recently. convolution filters for graph data fall into two categories, spectralbased and spatialbased.
As spectral methods usually handle the whole graph simultaneously and are difficult to parallel or scale to large graphs, spatialbased graph convolutional networks have rapidly developed recently [Hamilton et al.2017, Monti et al.2017, Niepert et al.2016, Gao et al.2018, Velickovic et al.2017]. These methods directly perform the convolution in the graph domain by aggregating the neighbor nodes’ information. Together with sampling strategies, the computation can be performed in a batch of nodes instead of the whole graph [Hamilton et al.2017, Gao et al.2018].
Recent graph neural architectures follow the neighborhood aggregation scheme that consists of three types of functions, i.e., neighbor sampling, correlation measurement, and information aggregation. Each layer of GNNs includes the combination of the three types of functions. For example, each layer of semiGCN [Kipf and Welling2017] consists of the firstorder neighbor sampling, correlation measured by node’s degree and the aggregate function.
In this paper, we use reinforcement learning to search the best combination of these types of functions on each layer of GNNs, instead of manual settings in the previous work.
Neural architecture search. Neural architecture search (NAS) has been popularly used to design convolutional architectures for classification tasks with image and text streaming as input [Zoph and Le2016, Pham et al.2018, Xie et al.2018, Zoph et al.2018, Bello et al.2017].
The seminal work of using reinforcement learning for neural architecture search aims to automatically design deep neural architecture by using a recurrent network to generate structure description of CNNs and RNNs. Following the NAS, Evolutionbased NAS such as work in [Real et al.2017, Real et al.2018] employs evolution algorithm to simultaneously optimize topology alongside with parameters. However, evolutionbased methods take enormous computational time and could not leverage the efficient gradient backpropagation. To achieve the stateoftheart performance as humandesigned architectures, the work [Real et al.2018] takes 3150 GPU days for the whole evolution.
In comparison, the work ENAS [Pham et al.2018] is endtoend for gradient backpropagation. To get rid of the architecture sampling process, DARTS [Liu et al.2018a] replace the feedback triggered by constant rewards in reinforcement learning with more efficient gradient feedback from generic loss.
3 Methods
In this section, we first introduce the problem of searching graph neural architectures with reinforcement learning. Then, we establish the search space and we discuss an efficient search algorithm based on policy gradient descent and the parameter sharing method during training.
3.1 Problem formulation
Given the search space of a graph neural architecture , we aim to find the best architecture that maximizes the accuracy of the network on a validation set . Here we use reinforcement learning to obtain by sampling from feasible architectures in the space based on the rewards observed on .
Figure 1 shows the entire reinforcement learning framework. First, the recurrent network generates network descriptions of GNNs. Then, the generated GNNs are tested on the given validate set and the test results are used as feedback of the recurrent network. The iteration maximizes the expected accuracy of the generated GNNs on the set .
Formally, during the learning process, the recurrent network as the controller maximizes the expected accuracy on the validation set , where is the distribution of parameterized by the choice of controller , and the shared weights describing the architecture. The learning is to minimize the training loss which can be represented as a bilevel optimization problem listed below,
(1) 
The training process of Eq.(1) will be discussed in the remaining parts of this section. The goal of GraphNAS is to find that maximizes the expected validation accuracy .
3.2 Search Space
In GraphNAS, we use a controller network to generate the descriptions of GNNs. The controller network used in GraphNAS is implemented as a recurrent neural network which requires a state space. In order to define the search space, we introduce a generalized framework of GNNs, where each layer can be described as follows,
Attention  Formula 

const  
gcn  
gat  
symgat  
cos  
linear  
genelinear 

Feature transform functions. The hidden embedding ( represents the initial input) is multiplied by a weight matrix , which is used to extract features and reduce feature dimensions. For each layer of GNNs, the output dimension is required.

Sampling functions. Select the receptive field for a given target node. Many GNNs samples the firstorder neighbors iteratively and collect messages globally. GraphSAGE and PinSAGE sample a fixed size neighbor to speed up for large graphs. FastGCN uses importance sampling while maintaining the performance of the algorithm. LGCN sorts the firstorder neighbors’ features and selects top features. For each layer, one of the sampling methods is required.

Correlation measure functions. Calculate the correlation of node with its neighbors . GAT assigns neighborhood importance by using attention layers. SemiGCN assigns neighborhood importance according to the degree of nodes. More choices are listed in Table 1. For each layer, we choose one correlation measurement method and repeat times .

Aggregation functions. Aggregate data from neighbors to generate an embedding for each node . Most GNNs use the sum aggregator, Mean aggregator, LSTM aggregator and pooling aggregator. MLP aggregator are described in the work [Xu et al.2018]. For each layer, one of the aggregation functions is required.

Residual functions.
Merge historical hidden representation
as a part of the current embedding after a transform function. The merge function includes concatenation and adding. For each layer of GNNs, a previous layer’s indexand the activation function
of the current layer are required to build a residual layer. 
Gated functions. As in GeniePath [Liu et al.2018b], the attention procedure learns the importance of neighbors with different sizes. Gated procedure extracts and filters signals aggregated from neighbors of distant hops.
To sum up, we define the search space of GNNs as follows: the sampling dimension , the correlation measure dimension , the aggregation dimension , the numbers of multiheads , the output hidden embedding , the previous layers’ index and the activation function . As a result, GraphNAS can generate the architecture descriptions as a sequence of tokens. Each token represents one of the functions in the architecture space .
Note that we do not predict training parameters such as the learning rates of GNNs and we also assume that the architectures without gated procedures bring large computation and improvement during the initial stage of training. It is possible to add those actions as one of the predictions. In our experiments, the process of generating an architecture stops if the number of layers exceeds a preset value.
action  operators 

sample method  ”firstorder” 
attention type  listed in Table 1 
aggregation type  ”sum”, ”meanpooling”, ”max pooling”, 
”mlp”  
activation type  ”sigmoid”, ”tanh”, ”relu”, ”linear”, 
”softplus”, ”leaky_relu”, ”relu6”, ”elu”  
number of heads  1,2,4,6,8,16 
hidden units  4, 8, 16, 32, 64, 128,256 
3.3 Search Algorithm
Training the controller parameters . In order to maximize the objective function given in Eq.(1), we describe a policy gradient method to update parameters so that the controller network generates better architectures over time.
The architecture descriptions (hyperparameters) of GNNs that the controller predicts can be viewed as a list of actions
. GNNs will achieve an accuracy of on a heldout dataset at convergence. We use the accuracy as reward signal and use reinforcement learning to train the controller. Since the reward signal is nondifferentiable, we use a policy gradient method to iteratively updatewith a moving average baseline for reward to reduce variance
[Williams1992] as follows,(2)  
Training the shared parameters .
In this step, we use stochastic gradient descent (SGD) with respect to
to minimize the training loss , where is the standard crossentropy loss in node classification, obtained from a minibatch of training data with a model sampled by the controller.3.4 Parameters Sharing
In most previous neural architecture search algorithms, generated models are trained from the scratch. However, training models from scratch to convergence brings heavy computation. Recently, ENAS [Pham et al.2018] forces all child models to share weights in order to improve the efficiency. Similarly, we introduce parameters sharing for GraphNAS.
Parameters sharing in ENAS are without conditions, ignoring the performance of the child models. This strategy does not suit for GNNs. As we found in experiments, parameters sharing between different GNNs does not work immediately, but can be observed after several iterations. Therefore we use a new strategy to share weights between different GNNs.
Sharing strategy. Figure 2 shows the parameters from one layer. Solid arrows represent the transform weights in GNNs which are shared between different GNNs including , , and . However, GNNs constraints search dimensions such as the attention and aggregation dimensions. For instance, , listed in Table 1 are used to form correlation measures for the attention functions. In GraphNAS, we allow different GNNs sharing the transform weights. Parameters are only shared for specific combinations of attention and aggregation functions
Update strategy. The parameters are trained and updated during training child models. The parameter update is also different from ENAS. Parameters shared by GNNs stored in the form of dictionary. When training, GNNs obtain a copy of shared parameters. After training, the parameters of the current child model are merged into the shared parameters when the reward is positive.
Reward generation. In ENAS [Pham et al.2018], the reward is generated according to the shared parameters without training child models. Since there may be parameters untrained, the strategy may cause deviation during reward generation. In GraphNAS, we train the child models with shared parameters to obtain more precise reward. After then, we apply a moving average on rewards to generate the final reward.
Exploration for shared parameters. Models with updated sharing parameters generally have large reward. Therefore, the controller has the potential to choose structures appearing at the beginning. In order to avoid this bias, we allow the GraphNAS to do exploration. During exploration, the parameters of the controller are fixed, while the shared parameters are trained with novel structures.
Deriving architectures. We derive novel architectures from a trained GraphNAS model. We first sample several models under the distribution of . For each sampled model, we compute its reward on a single minibatch sampled from the validation set after a few iterations. We then take only the model with the highest reward to retrain from scratch. It is possible to improve the results by training all the sampled models from scratch and select the model with the highest accuracy on a separated validation set [Zoph and Le2016, Zoph et al.2018].
4 Experiments
We test the performance of GraphNAS on both transductive and inductive learning scenarios. We use citation networks including Cora, Citeseer, and Pubmed for the transductive learning, and PPI for the inductive learning. On each dataset, we have a separated heldout validation set used to generate reward to compute the reward signal. The reported performance on the test set is computed only once for the network that achieves the best result on the heldout validation set.
4.1 Datasets
Transductive Learning Task
We classify academic papers into different subjects using the Cora, Citeseer and Pubmed datasets. The data obtained from semiGCN
[Kipf and Welling2017] has been preprocessed. We follow the same setting used in semiGCN that allows 20 nodes per class for training, 500 nodes for validation and 1,000 nodes for testing.Inductive Learning Task We use the proteinprotein interaction (PPI) dataset, which contains 20 graphs for training, two graphs for validation, and two graphs for testing. Since the graphs for validation and testing are separated, the training process does not use them. There are 2,372 nodes in each graph on average. Each node has 50 features including positional, motif genes and signatures. Each node has multiple labels from 121 classes.
4.2 Baseline Methods
In order to evaluate the GNNs searched by GraphNAS, we choose the stateoftheart GNNs for comparisons,

Chebyshev [Defferrard et al.2016]. The method approximates the graph spectral convolutions by a truncated expansion in terms of Chebyshev polynomials up to Tth order. This method needs the graph Laplacian in advance, so that it only works in the transductive setting.

SemiGCN [Kipf and Welling2017] is the same as Chebyshev, it works only in the transductive setting.

GraphSAGE [Hamilton et al.2017] consists of a group of inductive graph representations with different aggregation functions. The GCNmean with residual connections is equivalent to GraphSAGE using mean pooling.

GAT [Velickovic et al.2017] introduces attention into GNN. Therefore, GAT archives good results in both transductive and inductive learning.

LGCN [Gao et al.2018] enables regular convolutional operations on generic graphs which archives good results in both transductive and inductive learning.
All the tasks in transductive learning are singlelabel classification. We use accuracy as the measure for comparison. On the other hand, tasks in transductive learning are multilabel classification, and we use F1 score as the measure.
4.3 Architecture on Transductive learning
Search space. Our search space consists of the functions listed in Section 3.2. For each layer of GNNs, the controller has to sample actions which do not contain previous layer index for skip connection. In experiments on the citation dataset, there are usually two layers for GNNs.
Training details. The controller is a onelayer LSTM with 100 hidden units. It is trained with the ADAM optimizer [Kingma and Ba2015]
with a learning rate of 0.0035. The weights of the controller are initialized uniformly between 0.1 and 0.1. To prevent premature convergence, we also use a tanh of 2.5 and a temperature of 5.0 for the sampling logits
[Bello et al.2017, Bello et al.2016], and add the controller’s sample entropy to the reward, weighted by 0.0001.Once the controller samples an architecture, a child model is constructed and trained for 200 epochs without parameter sharing. During training, we apply L2 regularization with
= 0.0005 for Cora and Citeseer. Furthermore, dropout with = 0.6 is applied to both layers’ inputs, as well as to the normalized attention coefficients. For Pubmed, we set L2 regularization to = 0.001.In all experiments, child models are initialized using the Glorot initialization [Glorot and Bengio2010] and trained to minimize crossentropy loss on the training nodes using the Adam SGD optimizer [Kingma and Ba2015] with an initial learning rate of 0.01 for Pubmed, and 0.005 for all the other datasets. In both cases we use an early stopping strategy according to the crossentropy loss and accuracy on the validation nodes, with a patience of 100 epochs.
During training the controller, we fix the number of child network layers to be two, because many GNNs obtain the best performance on these dataset with two layers. Besides, we do not force GNNs sharing parameters, because training GNNs to convergence are fast on these datasets and models are easy to overfitting in a semisupervision task.
Results. After the controller trains 1,000 architectures, we collect the top 5 architectures that achieve the best validation accuracy. Then, we compute the test accuracy and time for each epoch of such models and summarize their results in Table 3. The time reported here is the training time for running one epoch using a single 1080Ti GPU. As can be seen from the table, GraphNAS can design several promising architectures that perform as well as some of the best models on this dataset. Other experiments results on citation network are listed in Table 4.
Random Search. Besides reinforcement learning, one can use random search to find the network. Although this baseline seems simple, it is often very hard to surpass. We report the number of GNNs model which has accuracy over 0.81 on validation set during search in Figure 3. And we list the best structure found by random search in Table3. The results show that GraphNAS trends to find better GNNs.
Models  Depth  Params  Time(s)  Accuracy 
Chebyshev  2  92K  0.49  81.2% 
GCN  2  23K  0.08  81.5% 
GAT  2  237K  0.62  83.00.7% 
LGCN  2  56K  0.14  83.30.5% 
random  2  364K  1.29  82.00.6% 
GraphNAS  2  188K  0.13  84.21.0% 
Models  Citeseer  Pubmed 

Chebyshev  69.8%  74.4% 
GCN  70.3%  79.0% 
GAT  72.50.7%  79.00.3% 
LGCN  73.00.6%  79.50.2% 
GraphNAS  73.10.9%  79.60.4% 
4.4 Architecture on Inductive Learning
Search space. We use the full search space defined in Section 3.2 . For skipconnection, we perform two sets of experiments, where one fixes the input of residual layer with output of the last hidden layer and the other allows the controller to predict previous layer index to build skipconnection.
Training details. The setting of training and the controller are the same as in transductive learning. We use parameter sharing to solve the huge computational resource requirements. The shared parameters of the child models are trained using the Adam SGD optimizer with a learning rate of 0.005. Before training the controller, the exploration process is executed at the first 20 epochs. After that the controller is trained for 50 epochs. During training of the child model, we apply no L2 regularization and dropout. During the process, each GNN model sampled by the controller is trained for five epochs with shared parameters.
During the training of the controller, we fix the number of child networks layers at three, because most GNNs obtain the best performance on this dataset are with three layers.
Results. After the controller trained for 1,000 time, we let the controller to output the best model from 200 sampled GNNs. And we then compute the microf1 score and the time for each epoch of the model and summarize the results in Table 5. The time reported here is the training time for running one epoch using a single 1080Ti GPU. As can be seen from the table, GraphNAS can design several promising architectures that perform as well as the best models on this dataset.
Models  Depth  Params  microF1(%) 

GraphSAGE(lstm)  2  0.26M  61.2 
GeniePath  3  1.81M  97.9 
GAT  3  3.64M  97.30.2 
LGCN      77.20.2 
GraphNAS( no sc)  3  3.95M  98.60.1 
GraphNAS with sc  3  2.11M  97.70.2 
NASlike search  3  0.95M  95.70.2 
ENASlike search  3  1.38M  96.50.2 
Effectiveness of parameters sharing. To evaluate the effectiveness of parameter sharing strategy during search, we compare the F1 score of the best structure designed by GraphNAS with parameters sharing and trained from scratch in Figure 4. Both of them are trained for five epochs.
Comparison against Search strategy. We compare GraphNAS with other search strategies including random search, reinforcement learning without parameter sharing (NASlike), and GraphNAS without iterations of GNNs during training the controller (ENASlike). Each sampled GNN is trained for two epochs. We show the model’s validation F1score during training in Figure 5. The performance of the found best model are listed in Table5. The results show that GraphNAS trends to find a better GNN model.
5 Conclusions
In this paper, we study a new problem of graph neural architecture search with reinforcement learning. We present a GraphNAS algorithm that can design accurate graph neural network architectures that rival the best humaninvented architectures in terms of test set accuracy. Experiments on node classification tasks in both transductive and inductive learning settings demonstrate that GraphNAS can achieve consistently better performance on citation networks, and proteinprotein interaction network. Comparisons with existing search strategies show that the new parameters sharing and search strategy used in GraphNAS are effective.
References
 [Bello et al.2016] Irwan Bello, Hieu Pham, Quoc V. Le, Mohammad Norouzi, and Samy Bengio. Neural combinatorial optimization with reinforcement learning. CoRR, abs/1611.09940, 2016.
 [Bello et al.2017] Irwan Bello, Barret Zoph, Vijay Vasudevan, and Quoc V. Le. Neural optimizer search with reinforcement learning. In ICML, 2017.
 [Defferrard et al.2016] Michaël Defferrard, Xavier Bresson, and Pierre Vandergheynst. Convolutional neural networks on graphs with fast localized spectral filtering. In NIPS, 2016.
 [Gao et al.2018] Hongyang Gao, Zhengyang Wang, and Shuiwang Ji. Largescale learnable graph convolutional networks. In KDD, 2018.
 [Glorot and Bengio2010] Xavier Glorot and Yoshua Bengio. Understanding the difficulty of training deep feedforward neural networks. In AISTATS, 2010.
 [Gori et al.2005] M. Gori, G. Monfardini, and F. Scarselli. A new model for learning in graph domains. In IEEE International Joint Conference on Neural Networks, 2005.
 [Hamilton et al.2017] William L. Hamilton, Zhitao Ying, and Jure Leskovec. Inductive representation learning on large graphs. In NIPS, 2017.
 [Kingma and Ba2015] Diederik P. Kingma and Jimmy Ba. Adam: A method for stochastic optimization. CoRR, abs/1412.6980, 2015.
 [Kipf and Welling2017] Thomas N. Kipf and Max Welling. Semisupervised classification with graph convolutional networks. In International Conference on Learning Representations (ICLR), 2017.
 [Liu et al.2018a] Hanxiao Liu, Karen Simonyan, and Yiming Yang. Darts: Differentiable architecture search. CoRR, abs/1806.09055, 2018.
 [Liu et al.2018b] Ziqi Liu, Chaochao Chen, Longfei Li, Jun Zhou, Xiaolong Li, and Le Song. Geniepath: Graph neural networks with adaptive receptive paths. CoRR, abs/1802.00910, 2018.

[Monti et al.2017]
Federico Monti, Davide Boscaini, Jonathan Masci, Emanuele Rodolà, Jan
Svoboda, and Michael M. Bronstein.
Geometric deep learning on graphs and manifolds using mixture model cnns.
2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR)
, pages 5425–5434, 2017.  [Niepert et al.2016] Mathias Niepert, Mohamed Ahmed, and Konstantin Kutzkov. Learning convolutional neural networks for graphs. In ICML, 2016.
 [Pham et al.2018] Hieu Pham, Melody Y. Guan, Barret Zoph, Quoc V. Le, and Jeff Dean. Efficient neural architecture search via parameter sharing. In ICML, 2018.
 [Real et al.2017] Esteban Real, Sherry Moore, Andrew Selle, Saurabh Saxena, Yutaka Leon Suematsu, Quoc V. Le, and Alexey Kurakin. Largescale evolution of image classifiers. In ICML, 2017.
 [Real et al.2018] Esteban Real, Alok Aggarwal, Yanping Huang, and Quoc V. Le. Regularized evolution for image classifier architecture search. CoRR, abs/1802.01548, 2018.
 [Velickovic et al.2017] Petar Velickovic, Guillem Cucurull, Arantxa Casanova, Adriana Romero, Pietro Liò, and Yoshua Bengio. Graph attention networks. CoRR, abs/1710.10903, 2017.
 [Williams1992] Ronald J. Williams. Simple statistical gradientfollowing algorithms for connectionist reinforcement learning. Machine Learning, 8(34):229–256, 1992.
 [Xie et al.2018] Sirui Xie, H P Zheng, Chunxiao Liu, and Liang Lin. Snas: Stochastic neural architecture search. CoRR, abs/1812.09926, 2018.
 [Xu et al.2018] Keyulu Xu, Weihua Hu, Jure Leskovec, and Stefanie Jegelka. How powerful are graph neural networks? CoRR, abs/1810.00826, 2018.
 [Zoph and Le2016] Barret Zoph and Quoc V. Le. Neural architecture search with reinforcement learning. CoRR, abs/1611.01578, 2016.
 [Zoph et al.2018] Barret Zoph, Vijay Vasudevan, Jonathon Shlens, and Quoc V. Le. Learning transferable architectures for scalable image recognition. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, pages 8697–8710, 2018.
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