P-tensors: a General Framework for Higher Order Message Passing in Subgraph Neural Networks

Andrew R. Hands, Tianyi Sun, R. Kondor

Main figure for P-tensors: a General Framework for Higher Order Message Passing in Subgraph Neural Networks

Abstract

Several recent papers have proposed increasing the expressive power of graph neural networks by exploiting subgraphs or other topological structures. In parallel, researchers have investigated higher order permutation equivariant networks. In this paper we tie these two threads together by providing a general framework for higher order permutation equivariant message passing in subgraph neural networks. In this paper we introduce a new type of mathematical object called $P$-tensors, which provide a simple way to define the most general form of permutation equivariant message passing in both the above two categories of networks. We show that the P-Tensors paradigm can achieve state-of-the-art performance on benchmark molecular datasets.

Proposed method: MPNNs

Benchmark Results

Tested on 2 datasets

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

Classic

#ModelMAE ↓Paper
1
TIGT
0.0140 ±0.0010
2
FloydNet
0.0160
3
GSSC
0.0190 ±0.0010
7
CIN
actual #7 vs paper #8 1 place worse
0.0210 ±0.0010
best reported
actual #7 vs paper #8 1 place worse
paper 0.0220 ±0.0020

Difference within reported uncertainty; not counted as underperformance.

paper 0.0220 ±0.0020 Δ at pub 0.0010
15
MPNNs
0.0240 ±0.0010
This paper
16
First order P-tensors
0.0240 ±0.0010
This paper
43
HIMP
0.0360 ±0.0020
This paper
63
PNA
actual #63 vs paper #99 36 places worse
0.0670 ±0.0090
best reported
actual #63 vs paper #99 36 places worse
paper 0.3200 ±0.0320
paper 0.3200 ±0.0320 Δ today 0.2530
69
GIN
0.0880 ±0.0020
This paper
70
GINE
0.0880 ±0.0020
This paper
79
GCN
0.1130 ±0.0020

MoleculeNet

#ModelROC-AUC ↑Paper
1
HIMP
actual #1 vs paper #1
0.8740 ±0.0050
best reported
actual #1 vs paper #1
paper 0.8736 ±0.0050

Difference within reported uncertainty; not counted as underperformance.

paper 0.8736 ±0.0050 Δ at pub 0.0004
2
GINE w/ VN
0.8720 ±0.0030
3
NaiveGINe+ K=3 w/ VN
0.8700 ±0.0040
5
GINE
actual #5 vs paper #5
0.8668 ±0.0077
actual #5 vs paper #5
paper 0.8668 ±0.0077
paper 0.8668 ±0.0077 Δ at pub 0.0168
8
MPNNs
0.8495 ±0.0058
This paper
14
GCN
0.8400 ±0.0040
75
RP-NGF
0.7940 ±0.0100
This paper
123
DSS-GNN (EGO+)
0.7795 ±0.0040
This paper
175
DS-GNN (EGO+)
0.7639 ±0.0118
This paper
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere