<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
Benchmark Results
Tested on 4 datasets
Tables show presented results in global context (best 3 papers + GCN + MLP).
MoleculeNet
| # | Model | ROC-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 | 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 |
| # | Model | ROC-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 | 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 |
| # | Model | ROC-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 | 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 |
| # | Model | ROC-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 |
