Learning to Extrapolate Knowledge:
Transductive Few-shot Out-of-Graph Link Prediction

Official Code Repository for the paper "Learning to Extrapolate Knowledge: Transductive Few-shot Out-of-Graph Link Prediction" (NeurIPS 2020) : https://arxiv.org/abs/2006.06648.

In this repository, we implement Graph Extrapolation Network (GEN) with both inductive and transductive schemes, proposed in our paper.

Abstract

Many practical graph problems, such as knowledge graph construction and drug-drug interaction prediction, require to handle multi-relational graphs. However, handling real-world multi-relational graphs with Graph Neural Networks (GNNs) is often challenging due to their evolving nature, where new entities (nodes) can emerge over time. Moreover, newly emerged entities often have few links, which makes the learning even more difficult. Motivated by this challenge, we introduce a realistic problem of few-shot out-of-graph link prediction, where we not only predict the links between the seen and unseen nodes as in a conventional out-of-knowledge link prediction but also between the unseen nodes, with only few edges per node. We tackle this problem with a novel transductive meta-learning framework which we refer to as Graph Extrapolation Networks (GEN). GEN meta-learns both the node embedding network for inductive inference (seen-to-unseen) and the link prediction network for transductive inference (unseen-to-unseen). For transductive link prediction, we further propose a stochastic embedding layer to model uncertainty in the link prediction between unseen entities. We validate our model on multiple benchmark datasets for knowledge graph completion and drug-drug interaction prediction. The results show that our model significantly outperforms relevant baselines for out-of-graph link prediction tasks.

Contribution of this work

• We tackle a realistic problem setting of few-shot out-of-graph link prediction, aiming to perform link prediction not only between seen and unseen entities but also among unseen entities for multi-relational graphs that exhibit long-tail distributions, where each entity has only few triplets.
• To tackle this problem, we propose a novel meta-learning framework, Graph Extrapolation Network (GEN), which meta-learns the node embeddings for unseen entities, to obtain low error on link prediction for both seen-to-unseen (inductive) and unseen-to-unseen (transductive) cases.
• We validate GEN for few-shot out-of-graph link prediction tasks on five benchmark datasets for knowledge graph completion and drug-drug interaction prediction, on which it significantly outperforms relevant baselines, even when baseline models are re-trained with the unseen entities.

Dependencies

• Python 3.7
• PyTorch 1.4
• PyTorch Geometric 1.4.3

Training

To train models in the paper, run following commands:

• (GEN-KG) FB15k-237 - Inductive (I-GEN)

python trainer_induc.py --data FB15k-237 --gpu -1 --few 3 --pre-train --fine-tune --model InducGEN --pre-train-model DistMult --score-function DistMult --margin 1 --seed 42 --evaluate-every 500 --pre-train-emb-size 100 --negative-sample 32 --model-tail log --max-few 10

• (GEN-KG) FB15k-237 - Transductive (T-GEN)

python trainer_trans.py --data FB15k-237 --gpu -1 --few 3 --pre-train --fine-tune --model TransGEN --pre-train-model DistMult --score-function DistMult --margin 1 --seed 42 --evaluate-every 500 --pre-train-emb-size 100 --negative-sample 32 --model-tail log --max-few 10

• (GEN-DDI) DeepDDI - Inductive (I-GEN)

python trainer_induc.py --data DeepDDI --pre-train --fine-tune --pre-train-model MPNN --n-epochs 5000 --evaluate-every 100 --model InducGEN --seed 42 --gpu -1 --few 3 --bases 200

• (GEN-DDI) DeepDDI - Transductive (T-GEN)

python trainer_trans.py --data DeepDDI --pre-train --fine-tune --pre-train-model MPNN --n-epochs 5000 --evaluate-every 100 --model TransGEN --seed 42 --gpu -1 --few 3 --bases 200

Evaluation

To evaluate models, run following commands:

• (GEN-KG) FB15k-237 - Inductive (I-GEN)

python eval_induc.py --data FB15k-237 --gpu -1 --few 3 --pre-train --fine-tune --model InducGEN --pre-train-model DistMult --score-function DistMult --margin 1 --pre-train-emb-size 100 --negative-sample 32 --exp-name FB15k-237_Induc

• (GEN-KG) FB15k-237 - Transductive (T-GEN)

python eval_trans.py --data FB15k-237 --gpu -1 --few 3 --pre-train --fine-tune --model TransGEN --pre-train-model DistMult --score-function DistMult --margin 1 --pre-train-emb-size 100 --negative-sample 32 --exp-name FB15k-237_Trans --mc-times 10

• (GEN-DDI) DeepDDI - Inductive (I-GEN)

python eval_induc.py --data DeepDDI --gpu -1 --few 3 --pre-train --fine-tune --model InducGEN --pre-train-model MPNN --exp-name Deep-DDI_Induc --bases 200

• (GEN-DDI) DeepDDI - Transductive (T-GEN)

python eval_trans.py --data DeepDDI --gpu -1 --few 3 --pre-train --fine-tune --model TransGEN --pre-train-model MPNN --exp-name Deep-DDI_Trans --bases 200 --mc-times 10

Pre-trained Models

You can see the pre-trained models in a Pretraining folder for each task (GEN-KG or GEN-DDI).

Results

We demonstrate our Graph Extrapolation Networks on two types of link prediction task: entity prediction for knowledge graph completion and relation prediction for drug-drug interaction prediction.

Citation

If you found the provided code with our paper useful in your work, we kindly request that you cite our work.

@inproceedings{baek2020gen,
 author = {Baek, Jinheon and Lee, Dong Bok and Hwang, Sung Ju},
 booktitle = {Advances in Neural Information Processing Systems},
 editor = {H. Larochelle and M. Ranzato and R. Hadsell and M. F. Balcan and H. Lin},
 pages = {546--560},
 publisher = {Curran Associates, Inc.},
 title = {Learning to Extrapolate Knowledge: Transductive Few-shot Out-of-Graph Link Prediction},
 url = {https://proceedings.neurips.cc/paper/2020/file/0663a4ddceacb40b095eda264a85f15c-Paper.pdf},
 volume = {33},
 year = {2020}
}