<SO$ _k$>: One LLM Token for Explicit Graph Structural Understanding

Jingyao Wu, Bin Lu, Zijun Di, Xiaoying Gan, Meng Jin, Luoyi Fu, Xinbing Wang, Cheng Zhou

Main figure for <SO$ _k$>: One LLM Token for Explicit Graph Structural Understanding

Abstract

Large language models show great potential in unstructured data understanding, but still face significant challenges with graphs due to their structural hallucination. Existing approaches mainly either verbalize graphs into natural language, which leads to excessive token consumption and scattered attention, or transform graphs into trainable continuous embeddings (i.e., soft prompt), but exhibit severe misalignment with original text tokens. To solve this problem, we propose to incorporate one special token to fully represent the tructure f raph within a unified token space, facilitating explicit topology input and structural information sharing. Specifically, we propose a topology-aware structural tokenizer that maps each graph topology into a highly selective single token. Afterwards, we construct a set of hybrid structure Question-Answering corpora to align new structural tokens with existing text tokens. With this approach, empowers LLMs to understand, generate, and reason in a concise and accurate manner. Extensive experiments on five graph-level benchmarks demonstrate the superiority of our method, achieving a performance improvement of 9.9–41.4\

Benchmark Results

Tested on 4 datasets

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

MoleculeNet

#ModelROC-AUC ↑Paper
1
HIMP
0.8740 ±0.0050
2
GINE w/ VN
0.8720 ±0.0030
3
NaiveGINe+ K=3 w/ VN
0.8700 ±0.0040
14
GCN
0.8400 ±0.0040
310
Galactica-120B Zero-shot
0.6890
This paper
312
MolCA-GS
0.6850
This paper
316
MolCA-S
0.6660
This paper
317
GPF-AttrMasking
0.6600
This paper
329
GPF-GCL
0.6360
This paper
334
gimlet
actual #334 vs paper #334
0.6120
actual #334 vs paper #334
paper 0.6120
335
LLaMA2-7B LoRA SFT
0.6060 ±0.0340
This paper
336
Deepseek-R1 Zero-shot
0.6010
This paper
340
GPT-4 Zero-shot
0.5520
This paper
341
LLaMA2-7B Few-shot (Morgan Sim)
0.5110 ±0.0250
This paper
342
LLaMA3-3B Few-shot (Morgan Sim)
0.5100 ±0.0870
This paper
343
LLaMA3-3B LoRA SFT
0.5080 ±0.0080
This paper
344
LLaMA2-7B Soft Prompt
0.4980 ±0.0150
This paper
348
LLaMA3-3B Zero-shot
0.4850 ±0.0270
This paper
349
LLaMA2-7B Zero-shot
0.4840 ±0.0330
This paper
350
Llama3-70b zero-shot
0.4490
This paper
351
LLaMA3-3B Soft Prompt
0.3990 ±0.0190
This paper
352
GPT-4o Zero-shot
0.3600
This paper
#ModelROC-AUC ↑Paper
1
ProtoMol
0.9140 ±0.0030
2
MMSG
0.9080 ±0.0050
3
MemGNN
0.9070
43
GIN
0.8646 ±0.0081
284
gimlet
actual #284 vs paper #284
0.6960
actual #284 vs paper #284
paper 0.6960
288
LLaMA3-3B Few-shot (Random)
0.6820 ±0.1750
This paper
296
MolCA-GS
0.6390
This paper
299
MolCA-S
0.6280
This paper
300
GPT-4 Zero-shot
0.6250
This paper
301
GPF-AttrMasking
0.6220
This paper
303
Galactica-120B Zero-shot
0.6170
This paper
304
LLaMA2-7B LoRA SFT
0.6170 ±0.0270
This paper
314
LLaMA2-7B Few-shot (Morgan Sim)
0.5320 ±0.0150
This paper
316
LLaMA3-3B Zero-shot
0.5270 ±0.0180
This paper
315
Deepseek-R1 Zero-shot
0.5270
This paper
317
GPF-GCL
0.5210
This paper
319
Llama3-70b zero-shot
0.5090
This paper
320
LLaMA3-3B LoRA SFT
0.5050 ±0.0290
This paper
321
LLaMA2-7B Zero-shot
0.4990 ±0.0040
This paper
322
LLaMA2-7B Soft Prompt
0.4940 ±0.0230
This paper
324
GPT-4o Zero-shot
0.3850
This paper
325
LLaMA3-3B Soft Prompt
0.2850 ±0.0090
This paper
#ModelROC-AUC ↑Paper
1
MAGPrompt+
0.9432 ±0.0238
2
CamS-LLaMA
0.9420
3
SE(3)-I MPPH
0.9400 ±0.0210
34
GIN
0.8875 ±0.0049
252
Galactica-120B Zero-shot
0.6610
This paper
285
Deepseek-R1 Zero-shot
0.6360
This paper
286
MolCA-GS
0.6360
This paper
294
MolCA-S
0.6250
This paper
297
GPT-4 Zero-shot
0.6150
This paper
302
LLaMA3-3B LoRA SFT
0.6020 ±0.0120
This paper
304
Llama3-70b zero-shot
0.6010
This paper
306
gimlet
actual #306 vs paper #306
0.5940
actual #306 vs paper #306
paper 0.5940
307
GPF-AttrMasking
0.5880
This paper
309
GPT-4o Zero-shot
0.5700
This paper
310
GPF-GCL
0.5650
This paper
312
LLaMA2-7B LoRA SFT
0.5500 ±0.0080
This paper
314
LLaMA2-7B Soft Prompt
0.5370 ±0.0080
This paper
315
LLaMA2-7B Few-shot (Morgan Sim)
0.5130 ±0.0080
This paper
316
LLaMA3-3B Zero-shot
0.5020 ±0.0340
This paper
317
LLaMA2-7B Zero-shot
0.5000
This paper
319
LLaMA3-3B Few-shot (Morgan Sim)
0.4970 ±0.0250
This paper
321
LLaMA3-3B Soft Prompt
0.2790 ±0.0170
This paper
#ModelROC-AUC ↑Paper
1
SE(3)-I MPPH
0.9930 ±0.0040
2
KA-GCN
0.9920 ±0.0050
3
KA-GAT
0.9910 ±0.0050
19
GCN
0.9130 ±0.0170
67
Galactica-120B Zero-shot
0.8260
This paper
209
LLaMA3-3B LoRA SFT
0.6380 ±0.0280
This paper
225
LLaMA2-7B LoRA SFT
0.5930 ±0.0370
This paper
233
LLaMA3-3B Few-shot (Random)
0.5780 ±0.0620
This paper
235
LLaMA2-7B Few-shot (Morgan Sim)
0.5680 ±0.0630
This paper
242
GPT-4o Zero-shot
0.5180
This paper
243
GPT-4 Zero-shot
0.5160
This paper
244
LLaMA3-3B Zero-shot
0.5020 ±0.0250
This paper
245
LLaMA2-7B Soft Prompt
0.4970 ±0.0470
This paper
246
Llama3-70b zero-shot
0.4880
This paper
247
Deepseek-R1 Zero-shot
0.4820
This paper
248
LLaMA2-7B Zero-shot
0.4400 ±0.0260
This paper
249
LLaMA3-3B Soft Prompt
0.3500 ±0.0200
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