A Piece-wise Polynomial Filtering Approach for Graph Neural Networks

Vijay Lingam, C. Ekbote, Manan Sharma, Rahul Ragesh, Arun Shankar Iyer, Sundararajan Sellamanickam

Main figure for A Piece-wise Polynomial Filtering Approach for Graph Neural Networks

Abstract

Graph Neural Networks (GNNs) exploit signals from node features and the input graph topology to improve node classification task performance. However, these models tend to perform poorly on heterophilic graphs, where connected nodes have different labels. Recently proposed GNNs work across graphs having varying levels of homophily. Among these, models relying on polynomial graph filters have shown promise. We observe that solutions to these polynomial graph filter models are also solutions to an overdetermined system of equations. It suggests that in some instances, the model needs to learn a reasonably high order polynomial. On investigation, we find the proposed models ineffective at learning such polynomials due to their designs. To mitigate this issue, we perform an eigendecomposition of the graph and propose to learn multiple adaptive polynomial filters acting on different subsets of the spectrum. We theoretically and empirically show that our proposed model learns a better filter, thereby improving classification accuracy. We study various aspects of our proposed model including, dependency on the number of eigencomponents utilized, latent polynomial filters learned, and performance of the individual polynomials on the node classification task. We further show that our model is scalable by evaluating over large graphs. Our model achieves performance gains of up to 10\

Proposed method: PP-GNN

Benchmark Results

Tested on 3 datasets 2 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
actual #2 vs paper #389 387 places worse
0.9412 ±0.0008
best reported
actual #2 vs paper #389 387 places worse
paper 0.8250 ±0.0123
paper 0.8250 ±0.0123 Δ at pub 0.0535 Δ today 0.1162
3
GAT
0.9398 ±0.0022
8
SAGE
0.9351 ±0.0006
58
APPNP
actual #58 vs paper #403 345 places worse
0.9093 ±0.0018
best reported
actual #58 vs paper #403 345 places worse
paper 0.8203 ±0.0204
126
FAGCN
actual #126 vs paper #399 273 places worse
0.8968 ±0.0097
best reported
actual #126 vs paper #399 273 places worse
paper 0.8216 ±0.0148
paper 0.8216 ±0.0148 Δ today 0.0752
306
PP-GNN
0.8523 ±0.0136
This paper
320
MLP
actual #320 vs paper #479 159 places worse
0.8463
best reported
actual #320 vs paper #479 159 places worse
paper 0.6496 ±0.0357
323
TDGNN
0.8452 ±0.0092
This paper
373
LGC
0.8344 ±0.0177
This paper
381
SuperGAT
0.8304 ±0.0102
This paper
397
GPR-GNN
0.8238 ±0.0160
This paper
425
SGCN
0.8065 ±0.0278
This paper
480
LR
0.6492 ±0.0259
This paper

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
30
GPR-GNN
actual #30 vs paper #218 188 places worse
0.9291 ±0.0132
best reported
actual #30 vs paper #218 188 places worse
paper 0.8135 ±0.0532
paper 0.8135 ±0.0532 Δ at pub 0.0308 Δ today 0.1156
34
MLP
actual #34 vs paper #222 188 places worse
0.9230 ±0.0070
best reported
actual #34 vs paper #222 188 places worse
paper 0.8124 ±0.0635
paper 0.8124 ±0.0635 Δ at pub 0.0206 Δ today 0.1106
40
H2GCN
actual #40 vs paper #148 108 places worse
0.9189 ±0.0393
best reported
actual #40 vs paper #148 108 places worse
paper 0.8486 ±0.0677

Difference within reported uncertainty; not counted as underperformance.

paper 0.8486 ±0.0677 Δ today 0.0703
46
APPNP
actual #46 vs paper #207 161 places worse
0.8189 ±0.0585
actual #46 vs paper #207 161 places worse
paper 0.8189 ±0.0585
53
GraphSAGE
0.9000 ±0.0365
59
PP-GNN
0.8973 ±0.0490
This paper
61
FAGCN
actual #61 vs paper #193 132 places worse
0.8243 ±0.0689
actual #61 vs paper #193 132 places worse
paper 0.8243 ±0.0689

Improvement within reported uncertainty; not highlighted.

paper 0.8243 ±0.0689 Δ at pub 0.0293
185
TDGNN
0.8300 ±0.0450
This paper
219
LR
0.8135 ±0.0633
This paper
240
LGC
0.8020 ±0.0428
This paper
257
GCN
actual #257 vs paper #480 223 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #480 223 places worse
paper 0.6162 ±0.0614
best today: Graph Wave Networks (WWW 2025)
paper 0.6162 ±0.0614 Δ at pub 0.0219 Δ today 0.1771
415
Geom-GCN
actual #415 vs paper #415
0.6760
best reported
actual #415 vs paper #415
paper 0.6757
paper 0.6757 Δ at pub 0.0003
469
SGCN
0.6243 ±0.0443
This paper
490
SuperGAT
actual #490 vs paper #490
0.6108 ±0.0497
actual #490 vs paper #490
paper 0.6108 ±0.0497

Improvement within reported uncertainty; not highlighted.

paper 0.6108 ±0.0497 Δ at pub 0.0248
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
11
GPR-GNN
actual #11 vs paper #197 186 places worse
0.9279 ±0.0312
best reported
actual #11 vs paper #197 186 places worse
paper 0.7811 ±0.0655
paper 0.7811 ±0.0655 Δ at pub 0.0116 Δ today 0.1468
21
APPNP
actual #21 vs paper #158 137 places worse
0.8189 ±0.0625
actual #21 vs paper #158 137 places worse
paper 0.8189 ±0.0625
24
MLP
actual #24 vs paper #118 94 places worse
0.9136 ±0.0070
best reported
actual #24 vs paper #118 94 places worse
paper 0.8378 ±0.0580

Difference within reported uncertainty; not counted as underperformance.

paper 0.8378 ±0.0580 Δ at pub 0.0108 Δ today 0.0758
38
FAGCN
actual #38 vs paper #185 147 places worse
0.8852 ±0.0133
best reported
actual #38 vs paper #185 147 places worse
paper 0.7919 ±0.0979

Difference within reported uncertainty; not counted as underperformance.

paper 0.7919 ±0.0979 Δ today 0.0933
68
H2GCN
actual #68 vs paper #151 83 places worse
0.8623 ±0.0471
best reported
actual #68 vs paper #151 83 places worse
paper 0.8216 ±0.0480

Difference within reported uncertainty; not counted as underperformance.

paper 0.8216 ±0.0480 Δ today 0.0407
128
LR
0.8324 ±0.0564
This paper
135
TDGNN
0.8292 ±0.0661
This paper
138
SAGE
0.8269
144
PP-GNN
0.8243 ±0.0427
This paper
170
GCN
actual #170 vs paper #354 184 places worse
0.6297 ±0.0541
actual #170 vs paper #354 184 places worse
paper 0.6297 ±0.0541

Improvement within reported uncertainty; not highlighted.

paper 0.6297 ±0.0541 Δ at pub 0.0362 Δ today 0.1785
238
LGC
0.7459 ±0.0342
This paper
342
Geom-GCN
actual #342 vs paper #369 27 places worse
0.6412
best reported
actual #342 vs paper #369 27 places worse
paper 0.6081
356
SGCN
actual #356 vs paper #357 1 place worse
0.6252 ±0.0510
best reported
actual #356 vs paper #357 1 place worse
paper 0.6243 ±0.0490

Difference within reported uncertainty; not counted as underperformance.

paper 0.6243 ±0.0490 Δ today 0.0009
416
SuperGAT
0.5730 ±0.0853
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 result worse than the best known when published (best reported in green) Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere