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William L. Hamilton; Rex Ying; Jure Leskovec

Abstract
Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.
Code Repositories
Benchmarks
| Benchmark | Methodology | Metrics |
|---|---|---|
| graph-classification-on-cifar10-100k | GraphSage | Accuracy (%): 66.08 |
| graph-regression-on-zinc-500k | GraphSage | MAE: 0.398 |
| graph-regression-on-zinc-full | GraphSAGE | Test MAE: 0.126±0.003 |
| link-property-prediction-on-ogbl-citation2 | NeighborSampling (SAGE aggr) | Ext. data: No Number of params: 460289 Test MRR: 0.8044 ± 0.0010 Validation MRR: 0.8054 ± 0.0009 |
| link-property-prediction-on-ogbl-citation2 | Full-batch GraphSAGE | Ext. data: No Number of params: 460289 Test MRR: 0.8260 ± 0.0036 Validation MRR: 0.8263 ± 0.0033 |
| link-property-prediction-on-ogbl-collab | GraphSAGE (val as input) | Ext. data: No Number of params: 460289 Test Hits@50: 0.5463 ± 0.0112 Validation Hits@50: 0.5688 ± 0.0077 |
| link-property-prediction-on-ogbl-collab | GraphSAGE | Ext. data: No Number of params: 460289 Test Hits@50: 0.4810 ± 0.0081 Validation Hits@50: 0.5688 ± 0.0077 |
| link-property-prediction-on-ogbl-collab | GraphSAGE (val as input) | Number of params: 460289 |
| link-property-prediction-on-ogbl-ddi | GraphSAGE | Ext. data: No Number of params: 1421057 Test Hits@20: 0.5390 ± 0.0474 Validation Hits@20: 0.6262 ± 0.0037 |
| link-property-prediction-on-ogbl-ppa | GraphSAGE | Ext. data: No Number of params: 424449 Test Hits@100: 0.1655 ± 0.0240 Validation Hits@100: 0.1724 ± 0.0264 |
| node-classification-on-brazil-air-traffic | GraphSAGE (Hamilton et al., [2017a]) | Accuracy: 0.404 |
| node-classification-on-chameleon-60-20-20 | GraphSAGE | 1:1 Accuracy: 62.15 ± 0.42 |
| node-classification-on-citeseer-05 | GraphSAGE | Accuracy: 33.8% |
| node-classification-on-citeseer-1 | GraphSAGE | Accuracy: 51.0% |
| node-classification-on-citeseer-60-20-20 | GraphSAGE | 1:1 Accuracy: 78.24 ± 0.30 |
| node-classification-on-citeseer-full | GraphSAGE | Accuracy: 71.40% |
| node-classification-on-citeseer-with-public | GraphSAGE | Accuracy: 67.2 |
| node-classification-on-cora-05 | GraphSAGE | Accuracy: 37.5% |
| node-classification-on-cora-1 | GraphSAGE | Accuracy: 49.0% |
| node-classification-on-cora-3 | GraphSAGE | Accuracy: 64.2% |
| node-classification-on-cora-60-20-20-random | GraphSAGE | 1:1 Accuracy: 86.58 ± 0.26 |
| node-classification-on-cora-full-supervised | GraphSAGE | Accuracy: 82.2% |
| node-classification-on-cora-with-public-split | GraphSAGE | Accuracy: 74.5% |
| node-classification-on-cornell-60-20-20 | GraphSAGE | 1:1 Accuracy: 71.41 ± 1.24 |
| node-classification-on-europe-air-traffic | GraphSAGE (Hamilton et al., [2017a]) | Accuracy: 27.2 |
| node-classification-on-facebook | GraphSAGE (Hamilton et al., [2017a]) | Accuracy: 38.9 |
| node-classification-on-film-60-20-20-random | GraphSAGE | 1:1 Accuracy: 36.37 ± 0.21 |
| node-classification-on-flickr | GraphSAGE (Hamilton et al., [2017a]) | Accuracy: 0.641 |
| node-classification-on-non-homophilic | GraphSAGE | 1:1 Accuracy: 71.41 ± 1.24 |
| node-classification-on-non-homophilic-1 | GraphSAGE | 1:1 Accuracy: 64.85 ± 5.14 |
| node-classification-on-non-homophilic-2 | GraphSAGE | 1:1 Accuracy: 79.03 ± 1.20 |
| node-classification-on-non-homophilic-4 | GraphSAGE | 1:1 Accuracy: 62.15 ± 0.42 |
| node-classification-on-pattern-100k | GraphSage | Accuracy (%): 50.516 |
| node-classification-on-ppi | GraphSAGE | F1: 61.2 |
| node-classification-on-pubmed-003 | GraphSAGE | Accuracy: 45.4% |
| node-classification-on-pubmed-005 | GraphSAGE | Accuracy: 53.0% |
| node-classification-on-pubmed-01 | GraphSAGE | Accuracy: 65.4% |
| node-classification-on-pubmed-60-20-20-random | GraphSAGE | 1:1 Accuracy: 86.85 ± 0.11 |
| node-classification-on-pubmed-full-supervised | GraphSAGE | Accuracy: 87.1% |
| node-classification-on-pubmed-with-public | GraphSAGE | Accuracy: 76.8% |
| node-classification-on-reddit | GraphSAGE | Accuracy: 94.32% |
| node-classification-on-squirrel-60-20-20 | GraphSAGE | 1:1 Accuracy: 41.26 ± 0.26 |
| node-classification-on-texas-60-20-20-random | GraphSAGE | 1:1 Accuracy: 79.03 ± 1.20 |
| node-classification-on-usa-air-traffic | GraphSAGE (Hamilton et al., [2017a]) | Accuracy: 31.6 |
| node-classification-on-wiki-vote | GraphSAGE (Hamilton et al., [2017a]) | Accuracy: 24.5 |
| node-classification-on-wisconsin-60-20-20 | GraphSAGE | 1:1 Accuracy: 64.85 ± 5.14 |
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