NeurIPS 2024

Towards Graph Foundation Models: Training on Knowledge Graphs Enables Transferability to General Graphs

Kai Wang, Siqiang Luo, Caihua Shan, Yifei Shen

Main figure for Towards Graph Foundation Models: Training on Knowledge Graphs Enables Transferability to General Graphs

Abstract

Inspired by the success of large language models, there is a trend toward developing graph foundation models to conduct diverse downstream tasks in various domains. However, current models often require extra fine-tuning to apply their learned structural and semantic representations to new graphs, which limits their versatility. Recent breakthroughs in zero-shot inductive reasoning on knowledge graphs (KGs), offer us a new perspective on extending KG reasoning to general graph applications. In this paper, we introduce SCR, a unified graph reasoning framework designed to train on knowledge graphs and effectively generalize across a wide range of graph tasks and domains. We begin by designing the task-specific KG structures to establish a unified topology for different task formats. Then we propose semantic-conditioned message passing, a novel mechanism addressing the inherent semantic isolation in traditional KG reasoning, by jointly modeling structural and semantic invariance patterns in graph representations. To demonstrate the effectiveness, we evaluate the inductive reasoning capability of SCR using 38 diverse graph datasets, covering node-level, link-level, and graph-level tasks across multiple domains. Our results show substantial performance gains over existing foundation models and supervised baselines, highlighting the efficacy and adaptability of our approach.

Benchmark Results

Tested on 1 dataset

Tables show presented results in global context (best 3 papers + GCN + MLP).

Knowledge Graphs

#ModelMRR ↑Paper
1
FedSage
0.8426 ±0.0026
2
FED-PUB
0.8348 ±0.0025
3
FedAvg
0.8252 ±0.0023
7
GCN
0.8171 ±0.0030
18
Supervised SOTA
actual #18 vs paper #18
0.6400
actual #18 vs paper #18
paper 0.6400
paper 0.6400 Δ at pub 0.0890
22
SCR-MPNet
0.5780
This paper
23
SCR(3g)
0.5760
This paper
24
SCR-MiniLM
0.5760
This paper
25
SCR-DistilBert
0.5760
This paper
26
SCR-Ontology
0.5700
This paper
27
SCR-One
0.5690
This paper
28
ULTRA(4g)
0.5670
This paper
31
ProLINK(3g)
0.5530
This paper
SOTA performance (not significantly different from the best) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported value improved over the best known when published