Language Models as Messengers: Enhancing Message Passing in Heterophilic Graph Learning

Dawei Cheng, Wenjun Wang, Mingjian Guang

Main figure for Language Models as Messengers: Enhancing Message Passing in Heterophilic Graph Learning

Abstract

Graph neural networks (GNNs) have become a standard paradigm for graph representation learning, yet their message passing mechanism implicitly assumes that messages can be represented by source node embeddings, an assumption that fails in heterophilic graphs. While existing methods attempt to address heterophily through graph structure refinement or adaptation of neighbor aggregation, they often overlook the semantic potential of node text, relying on suboptimal message representation for propagation and compromise performance on homophilic graphs. To address these limitations, we propose LEMP4HG, a novel language model (LM)-enhanced message passing approach for heterophilic graph learning. Specifically, for text-attributed graphs (TAG), we leverage a LM to explicitly model inter-node semantic relationships from paired node texts, synthesizing semantically informed messages for propagation. To ensure practical efficiency, we further introduce an active learning–inspired strategy guided by a tailored heuristic, MVRD, which selectively enhances messages for node pairs most affected by message passing. Extensive experiments demonstrate that LEMP4HG consistently outperforms state-of-the-art methods on heterophilic graphs while maintaining robust performance on homophilic graphs under a practical computational budget.

Proposed method: LEMP4HG

Benchmark Results

Tested on 6 datasets 18 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GCN
actual #1 vs paper #15 14 places worse
0.9302 ±0.0011
best reported
actual #1 vs paper #15 14 places worse
paper 0.8700
paper 0.8700 Δ at pub 0.0602
2
RSE + RGCN (70b)
0.8852 ±0.0019
3
LEMP+T
0.8825
This paper
4
RevGAT+T
0.8824
This paper
5
SAGE+T
0.8823
This paper
8
Jacobi
0.8778
This paper
9
SAGE
actual #9 vs paper #9
0.8771
actual #9 vs paper #9
paper 0.8771
paper 0.8771 Δ at pub 0.0815
11
GPR
0.8755
This paper
12
APPNP
actual #12 vs paper #12
0.8754
actual #12 vs paper #12
paper 0.8754
paper 0.8754 Δ at pub 0.0867
14
LEMP
0.8729
This paper
15
GBK
0.8723
This paper
17
OGNN
0.8684
This paper
18
GCNII
actual #18 vs paper #18
0.8674
actual #18 vs paper #18
paper 0.8674
paper 0.8674 Δ at pub 0.0806
19
RevGAT
0.8665
This paper
20
H2GCN
actual #20 vs paper #20
0.8660
actual #20 vs paper #20
paper 0.8660
paper 0.8660 Δ at pub 0.0315
21
FAGCN
0.8655
This paper
22
Disam
0.8651
This paper
23
JKNet
actual #23 vs paper #23
0.8629
actual #23 vs paper #23
paper 0.8629
25
SATA
0.8602
This paper
26
MLP+LLM_features
actual #26 vs paper #26
0.8597
actual #26 vs paper #26
paper 0.8597
27
Cheby
0.8597
This paper
31
GAT
actual #31 vs paper #31
0.8533
actual #31 vs paper #31
paper 0.8533
paper 0.8533 Δ at pub 0.0211
54
GIN
0.8303 ±0.0021
237
MLP
0.7469 ±0.0085

OGB

#ModelAccuracy ↑Paper
1
Jacobi
0.8968
This paper
2
GPR
0.8953
This paper
3
LEMP4HG
0.8939
This paper
4
SAGE
actual #4 vs paper #4
0.8933
actual #4 vs paper #4
paper 0.8933
5
OGNN
0.8908
This paper
6
GCN
actual #6 vs paper #6
0.8868
actual #6 vs paper #6
paper 0.8868
7
JKNet
actual #7 vs paper #7
0.8862
actual #7 vs paper #7
paper 0.8862
paper 0.8862 Δ at pub 0.1492
8
RevGAT
actual #8 vs paper #8
0.8859
actual #8 vs paper #8
paper 0.8859
9
GAT
actual #9 vs paper #9
0.8829
actual #9 vs paper #9
paper 0.8829
13
GCNII
actual #13 vs paper #13
0.8738
actual #13 vs paper #13
paper 0.8738
paper 0.8738 Δ at pub 0.0798
27
MLP+LLM_features
actual #27 vs paper #27
0.8634
actual #27 vs paper #27
paper 0.8634
28
Cheby
0.8634
This paper
29
APPNP
actual #29 vs paper #29
0.8634
actual #29 vs paper #29
paper 0.8634
paper 0.8634 Δ at pub 0.0464
83
GraphSAGE
0.8287
351
MLP
0.6605 ±0.0020

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
34
MLP
0.9230 ±0.0070
40
H2GCN
actual #40 vs paper #364 324 places worse
0.9189 ±0.0393
best reported
actual #40 vs paper #364 324 places worse
paper 0.7244
paper 0.7244 Δ at pub 0.1945
46
APPNP
actual #46 vs paper #438 392 places worse
0.9131 ±0.0197
best reported
actual #46 vs paper #438 392 places worse
paper 0.6538
paper 0.6538 Δ at pub 0.2593
53
GraphSAGE
0.9000 ±0.0365
61
FAGCN
actual #61 vs paper #252 191 places worse
0.8961 ±0.0152
best reported
actual #61 vs paper #252 191 places worse
paper 0.7949
paper 0.7949 Δ at pub 0.1012
70
GCNII
actual #70 vs paper #240 170 places worse
0.8918 ±0.0443
best reported
actual #70 vs paper #240 170 places worse
paper 0.8013
paper 0.8013 Δ at pub 0.0905
111
OGNN
actual #111 vs paper #168 57 places worse
0.8622 ±0.0412
best reported
actual #111 vs paper #168 57 places worse
paper 0.8397

Difference within reported uncertainty; not counted as underperformance.

paper 0.8397 Δ at pub 0.0225
127
SEGSL
0.8590
This paper
128
RevGAT+T
0.8590
This paper
129
LEMP+T
0.8590
This paper
140
SAGE+T
0.8526
This paper
156
MLP+LLM_features
0.8462
This paper
157
Cheby
0.8462
This paper
169
GBK
0.8397
This paper
174
LLM4HeG
0.8362
This paper
178
GPR
0.8333
This paper
189
SAGE
actual #189 vs paper #189
0.8269
actual #189 vs paper #189
paper 0.8269
paper 0.8269 Δ at pub 0.0339
190
LEMP
0.8269
This paper
207
RevGAT
0.8205
This paper
211
GAT
actual #211 vs paper #509 298 places worse
0.8162 ±0.0645
best reported
actual #211 vs paper #509 298 places worse
paper 0.5962
paper 0.5962 Δ at pub 0.2120 Δ today 0.2200
216
Disam
0.8141
This paper
234
SATA
0.8077
This paper
257
GCN
actual #257 vs paper #499 242 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #499 242 places worse
paper 0.6026
best at pub: Graph Wave Networks (WWW 2025)
paper 0.6026 Δ at pub 0.1907
292
Jacobi
0.7692
This paper
392
JKNet
actual #392 vs paper #449 57 places worse
0.6410
actual #392 vs paper #449 57 places worse
paper 0.6410

Improvement within reported uncertainty; not highlighted.

paper 0.6410 Δ at pub 0.0032
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
21
APPNP
actual #21 vs paper #334 313 places worse
0.9181 ±0.0196
best reported
actual #21 vs paper #334 313 places worse
paper 0.6474
paper 0.6474 Δ at pub 0.2707
24
MLP
0.9136 ±0.0070
35
GCNII
actual #35 vs paper #177 142 places worse
0.8918 ±0.0396
best reported
actual #35 vs paper #177 142 places worse
paper 0.8013
paper 0.8013 Δ at pub 0.0413 Δ today 0.0905
38
FAGCN
actual #38 vs paper #280 242 places worse
0.8852 ±0.0133
best reported
actual #38 vs paper #280 242 places worse
paper 0.7051
paper 0.7051 Δ at pub 0.1801
39
RevGAT+T
0.8846
This paper
50
SAGE+T
0.8718
This paper
51
OGNN
actual #51 vs paper #99 48 places worse
0.8703 ±0.0473
best reported
actual #51 vs paper #99 48 places worse
paper 0.8462

Difference within reported uncertainty; not counted as underperformance.

paper 0.8462 Δ at pub 0.0241
57
MLP+LLM_features
0.8654
This paper
58
Cheby
0.8654
This paper
59
LEMP+T
0.8654
This paper
68
H2GCN
actual #68 vs paper #301 233 places worse
0.8623 ±0.0471
best reported
actual #68 vs paper #301 233 places worse
paper 0.6795
best at pub: Heterophily-informed Message Passing (TMLR 2025)
paper 0.6795 Δ at pub 0.1825 Δ today 0.1828
86
LEMP
0.8526
This paper
87
LLM4HeG
0.8524
This paper
100
Disam
0.8462
This paper
115
RevGAT
0.8397
This paper
125
GBK
0.8333
This paper
126
SEGSL
0.8333
This paper
138
SAGE
actual #138 vs paper #138
0.8269
actual #138 vs paper #138
paper 0.8269
paper 0.8269 Δ at pub 0.1129
139
GPR
0.8269
This paper
157
GraphSAGE
0.8196 ±0.0739
158
GAT
actual #158 vs paper #507 349 places worse
0.8190 ±0.0540
best reported
actual #158 vs paper #507 349 places worse
paper 0.4808
paper 0.4808 Δ at pub 0.3382
162
SATA
0.8141
This paper
170
GCN
actual #170 vs paper #348 178 places worse
0.8082 ±0.0360
best reported
actual #170 vs paper #348 178 places worse
paper 0.6346
paper 0.6346 Δ at pub 0.1669 Δ today 0.1736
210
Jacobi
0.7756
This paper
241
JKNet
actual #241 vs paper #320 79 places worse
0.6603
actual #241 vs paper #320 79 places worse
paper 0.6603

Heterophily Benchmark

#ModelROC-AUC ↑Paper
1
Polynormer-r
0.8591 ±0.0074
2
DC-GNN
0.8588 ±0.0081
3
TANGO-GPS
0.8566 ±0.0101
28
GAT
actual #28 vs paper #110 82 places worse
0.8443 ±0.0100
best reported
actual #28 vs paper #110 82 places worse
paper 0.7821
paper 0.7821 Δ at pub 0.0622
50
GCN
actual #50 vs paper #110 60 places worse
0.8364 ±0.0067
best reported
actual #50 vs paper #110 60 places worse
paper 0.7820
76
SAGE
actual #76 vs paper #102 26 places worse
0.8243 ±0.0044
best reported
actual #76 vs paper #102 26 places worse
paper 0.7885
77
GraphSAGE
0.8243 ±0.0044
97
RevGAT+T
0.7991
This paper
99
RevGAT
0.7968
This paper
102
LEMP+T
0.7897
This paper
105
LEMP
0.7867
This paper
106
GCNII
0.7861
This paper
107
SAGE+T
0.7848
This paper
108
JKNet
0.7838
This paper
109
Disam
0.7835
This paper
112
Jacobi
0.7817
This paper
113
H2GCN
actual #113 vs paper #113
0.7815
actual #113 vs paper #113
paper 0.7815
paper 0.7815 Δ at pub 0.0480
114
SATA
0.7815
This paper
115
GPR
0.7813
This paper
116
FAGCN
actual #116 vs paper #116
0.7812
actual #116 vs paper #116
paper 0.7812
prev best: Evolving Computation Graphs (ICML 2023)

Improvement within reported uncertainty; not highlighted.

paper 0.7812 Δ at pub 0.0037
118
APPNP
0.7809
This paper
119
OGNN
0.7803
This paper
120
GBK
0.7799
This paper
121
MLP+LLM_features
0.7793
This paper
122
Cheby
0.7793
This paper
139
MLP
0.7362 ±0.0020

Other Graph Benchmarks

#ModelAccuracy ↑Paper
1
MA-GCL
0.8883 ±0.0030
2
CCA-SSG
0.8842 ±0.0030
3
ARIEL
0.8827 ±0.0020
9
GAT
actual #9 vs paper #46 37 places worse
0.8693 ±0.0030
best reported
actual #9 vs paper #46 37 places worse
paper 0.4520
paper 0.4520 Δ at pub 0.4173
10
GCN
actual #10 vs paper #42 32 places worse
0.8651 ±0.0050
best reported
actual #10 vs paper #42 32 places worse
paper 0.4558
paper 0.4558 Δ at pub 0.4093
33
GIN
0.4916 ±0.0102
36
RevGAT+T
0.4722
This paper
37
LEMP+T
0.4675
This paper
38
SAGE
0.4648
This paper
39
SAGE+T
0.4639
This paper
40
RevGAT
0.4590
This paper
41
LEMP
0.4590
This paper
43
GPR
0.4554
This paper
44
Jacobi
0.4554
This paper
45
JKNet
0.4551
This paper
46
APPNP
0.4534
This paper
50
GCNII
0.4429
This paper
51
Disam
0.4410
This paper
52
OGNN
0.4366
This paper
53
FAGCN
0.4319
This paper
55
MLP+LLM_features
0.4275
This paper
56
Cheby
0.4275
This paper
57
GBK
0.4274
This paper
58
SATA
0.4237
This paper
61
H2GCN
actual #61 vs paper #61
0.4071
actual #61 vs paper #61
paper 0.4071
paper 0.4071 Δ at pub 0.0424
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) Best at pub — reported value improved over the best known when published