On the Token Collapse Phenomenon in Textual Graph Soft Prompting
Organizations: Sapienza University of Rome, Rome, Italy · ISTI-CNR, Pisa, Italy · University of Cambridge, Cambridge, UK · University of Pisa, Pisa, Italy
Abstract
Recent methods for injecting graph structure into LLM prompts include graph soft prompting, in which a graph neural network (GNN) learns graph-specific tokens that capture relational information among entities in textual prompts. G-Retriever combines graph soft prompts with a verbalized description of the same graph to strengthen the textual prompt signal. We conduct an in-depth analysis of G-Retriever and uncover a pathological behavior we term token collapse. Across three benchmarks, three graph encoders, two LLM families, and both frozen and LoRA-adapted models, G-Retriever's graph tokens become almost indistinguishable across inputs. We provide evidence that the same failure is inherited by subsequent methods, even with multi-token pooling. Under the standard setup, swapping a token with the dataset mean, a token from another example, or one derived from a corrupted graph produces no resolved answer-level effect in accuracy. Moreover, a learned constant prompt that never accesses the graph matches or surpasses G-Retriever on all three benchmarks. These findings indicate that, rather than conveying graph content as intended, the collapsed token functions primarily as a generic soft prompt. We also examine conditions linked to this collapse and propose a two-stage procedure that yields non-collapsed tokens while maintaining competitive performance in most cases. However, token variability alone does not prove that the model uses graph information: via interventions and decoding probes, we show that depending on the configuration, a token can reflect the question, an answer prior, or graph-derived content that the LLM may or may not use. Overall, our results offer a practical approach to evaluating graph-token alignment rather than inferring it from task accuracy alone. Code to reproduce our experiments is available at https://github.com/difra100/Token_Collapse_KGQA.
Figures & tables
| Dataset | Model | Score | Encoder cosine | Token cosine |
|---|---|---|---|---|
| ExplaGraphs | G-Retriever (GT) | 85.56 | 0.678 | 0.997 |
| G-Retriever (GAT) | 85.20 | 0.457 | 0.998 | |
| G-Retriever (GCN) | 78.88 | 0.423 | 0.985 | |
| SceneGraphs | G-Retriever (GT) | 81.35 | 0.630 | 0.993 |
| G-Retriever (GAT) | 80.20 | 0.693 | 0.998 | |
| G-Retriever (GCN) | 80.55 | 0.428 | 0.998 |
| Dataset | real | mean | swap | gswap | notxt | notxt-mean | const |
|---|---|---|---|---|---|---|---|
| ExplaGraphs | 85.56 | 66.43 | 85.56 | ||||
| SceneGraphs | 81.35 | † | † | 30.20 | 81.40 | ||
| WebQSP | 70.33 | * | 41.34 | 71.25 |
| Encoder | Projector | Encoder cos. | Step-0 token cos. | Token cos. | Score |
|---|---|---|---|---|---|
| trained end to end | Sigmoid | 0.695 | 1.000 | 0.997 | 85.56 |
| trained end to end | GELU | 0.787 | 0.992 | 0.914 | 73.29 *** |
| frozen after Stage 1 | Sigmoid | 0.024 | 0.987 | 0.992 | 84.48 |
| frozen after Stage 1 | GELU | 0.024 | 0.091 | 0.323 | 57.76 *** |
| Dataset | Model | Score | Token cos. | mean | swap | gswap |
| Llama-2-7B | ||||||
| WebQSP | G-Retriever | 70.33 | 0.996 | * | ||
| Ours | 69.90 | 0.142 | *** | * | † | |
| no entity features | 0.125 | *** | *** | * | ||
| no question | 69.84 | 0.169 | *** | * | ||
| SceneGraphs | G-Retriever | 0.993 | † | † | ||
| Dataset | Model | Q rank | A rank | G rank | Score gswap | NLL S/GS | Diagnosis |
|---|---|---|---|---|---|---|---|
| WebQSP | G-Retriever | 293 | 317 | 369 | soft prompt | ||
| Ours | 65 | 60 | 315 | † | masked | ||
| no entity features | 34 | 51 | 303 | * | prior | ||
| no question | 120 | 134 | 329 | * | used | ||
| SceneGraphs | G-Retriever | 271 | 436 | 248 | † | soft prompt | |
| Ours | 47 | 187 | 427 | *** | used |
Appendix figures & tables72 assets
Supplementary material from the paper’s appendix.
Appendix
| ExplaGraphs | SceneGraphs | WebQSP | |
|---|---|---|---|
| Graphs | 2,766 | 100,000 | 4,737 |
| Average nodes | 5.17 | 19.13 | 1,370.89 |
| Average edges | 4.25 | 68.44 | 4,252.37 |
| Node attributes | commonsense concepts | objects and attributes | Freebase entities |
| Edge attributes | commonsense relations | actions, spatial relations | Freebase relations |
| Task | stance prediction | scene-graph QA | knowledge-graph QA |
| Control | Perturbation | Churn | Accuracy | Exact McNemar |
|---|---|---|---|---|
| Null replicate, same weights, same condition | none at all | 63.2% | .247 | |
| MLPQ, swap | , cosine | 38% | .015 | |
| No entity features, node | zero, features already zeroed | 43% | .415 | |
| CONST, swap | zero, all token rows identical | 0% | 1 |
| information from the original sample retained | |||||
| Condition | What it replaces | question | entities | structure | relations |
| Interventions at fixed weights | |||||
| mean | token training-set mean | ||||
| swap | token another question’s token | ||||
| gswap | graph another question’s graph | ||||
| node | node features resampled features | ||||
| Method | Configuration | Projector | regime | Mean |
|---|---|---|---|---|
| GRAG-PCST ( Hu et al., 2025 ) | released GAT + LoRA | Linear–Sigmoid–Linear | 1.000 | |
| GRETPool ( Grover et al., 2026 ) | TopK ( Gao & Ji, 2019 ) , ratio | Linear–Sigmoid–Linear | 7.848 | |
| – | SAG ( Lee et al., 2019 ) , ratio | Linear–Sigmoid–Linear | 7.848 | |
| – | DiffPool ( Ying et al., 2018 ) | Linear–Sigmoid–Linear | 8.000 | |
| – | DiffPool ( Ying et al., 2018 ) | Linear–Sigmoid–Linear | 100.000 | |
| GraSP-PCST ( Wang et al., 2026 ) | SubgraphGNN ( Alsentzer et al., 2020 ) + Llama | Linear–Tanh–Linear | 16.719 |
| Method | Mean | Hit@1 | Inter cos. | RR | Norm ratio | Within cos. | Eff. rank |
|---|---|---|---|---|---|---|---|
| GRAG-PCST | 1.000 | 74.570 | 0.999171 | 0.028223 | 42.935 | – | 10.300 |
| TopK | 7.848 | 71.437 | 1.000000 | 0.000155 | 28.258 | 1.000000 | – |
| SAG | 7.848 | 72.727 | 1.000000 | 0.000531 | 25.802 | 0.999999 | – |
| DiffPool ( ) | 8.000 | 52.703 | 0.999712 | 0.009284 | 25.477 | 0.999856 | – |
| DiffPool ( ) | 100.000 | 61.364 | 0.999994 | 0.001291 | 27.170 | 1.000000 | – |
| GraSP-PCST | 16.719 | 81.450 | 0.997783 | 0.039442 | 4.271 | 0.999465 | – |
| Dataset | Model | Residual ratio | Norm ratio |
|---|---|---|---|
| ExplaGraphs | G-Retriever (GT) | 0.050 | 21.9 |
| G-Retriever (GAT) | 0.040 | 24.4 | |
| G-Retriever (GCN) | 0.121 | 24.3 | |
| SceneGraphs | G-Retriever (GT) | 0.088 | 84.8 |
| G-Retriever (GAT) | 0.046 | 87.6 | |
| G-Retriever (GCN) | 0.048 | 97.0 |
| Dataset | Model | REAL | MEAN | SWAP | NODE | EDGE | NOTXT-REAL |
|---|---|---|---|---|---|---|---|
| ExplaGraphs | G-Retriever (GAT) | 85.20 | 76.90 | ||||
| G-Retriever (GCN) | 78.88 | 69.86 | |||||
| SceneGraphs | G-Retriever (GAT) | 80.20 | 28.65 | ||||
| G-Retriever (GCN) | 80.55 | † | † | 29.80 |
| Input norm | Token norm | Token cosine | Residual ratio |
|---|---|---|---|
| 1 | 18.4 | 0.9999 | 0.009 |
| 10 | 18.4 | 0.9919 | 0.090 |
| 100 | 21.4 | 0.7346 | 0.600 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 85.56 | – | – |
| MEAN | 85.38 | 0.18 | 1 |
| SWAP | 84.30 | 1.26 | 0.118 |
| 85.20 | 0.36 | 0.727 | |
| 84.48 | 1.08 | 0.146 | |
| NODE (real rows) | 84.66 | 0.90 | 0.227 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 86.28 | – | – |
| MEAN | 84.84 | 1.44 | 0.134 |
| SWAP | 85.02 | 1.26 | 0.265 |
| 84.84 | 1.44 | 0.134 | |
| 83.57 | 2.71 *** | 0.000275 | |
| NODE (real rows) | 86.10 | 0.18 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 87.91 | – | – |
| MEAN | 87.18 | 0.72 | 0.219 |
| SWAP | 87.73 | 0.18 | 1 |
| 87.73 | 0.18 | 1 | |
| 87.91 | 0.00 | 1 | |
| NODE (real rows) | 88.09 | 0.18 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 89.71 | – | – |
| MEAN | 89.71 | 0.00 | 1 |
| SWAP | 90.07 | 0.36 | 0.625 |
| 89.71 | 0.00 | 1 | |
| 90.07 | 0.36 | 0.5 | |
| NODE (real rows) | 89.71 | 0.00 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 85.20 | – | – |
| MEAN | 84.84 | 0.36 | 0.754 |
| SWAP | 85.20 | 0.00 | 1 |
| 85.02 | 0.18 | 1 | |
| 85.20 | 0.00 | 1 | |
| NODE (real rows) | 85.02 | 0.18 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 78.88 | – | – |
| MEAN | 79.78 | 0.90 | 0.405 |
| SWAP | 79.24 | 0.36 | 0.86 |
| 80.14 | 1.26 | 0.23 | |
| 77.44 | 1.44 | 0.215 | |
| NODE (real rows) | 79.96 | 1.08 | 0.345 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 85.56 | – | – |
| MEAN | 85.02 | 0.54 | 0.375 |
| SWAP | 85.56 | 0.00 | 1 |
| 85.02 | 0.54 | 0.375 | |
| 84.84 | 0.72 | 0.125 | |
| NODE (real rows) | 85.56 | 0.00 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 85.56 | – | – |
| MEAN | 85.02 | 0.54 | 0.25 |
| SWAP | 85.56 | 0.00 | 1 |
| 85.02 | 0.54 | 0.25 | |
| 85.56 | 0.00 | 1 | |
| NODE (real rows) | 85.56 | 0.00 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 84.84 | – | – |
| MEAN | 85.02 | 0.18 | 1 |
| SWAP | 85.20 | 0.36 | 0.688 |
| 85.02 | 0.18 | 1 | |
| 85.20 | 0.36 | 0.5 | |
| NODE (real rows) | 84.84 | 0.00 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 73.29 | – | – |
| SWAP | 72.20 | 1.08 | 0.631 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 84.48 | – | – |
| MEAN | 84.48 | 0.00 | 1 |
| SWAP | 84.66 | 0.18 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 57.76 | – | – |
| MEAN | 58.84 | 1.08 | 0.735 |
| SWAP | 51.08 | 6.68 * | 0.0167 |
| NODE (real rows) | 56.50 | 1.26 | 0.685 |
| NODE (Gaussian) | 48.56 | 9.21 *** | 0.000616 |
| EDGE (rewired) | 51.62 | 6.14 * | 0.02 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 85.74 | – | – |
| MEAN | 86.10 | 0.36 | 0.832 |
| SWAP | 85.20 | 0.54 | 0.749 |
| 86.10 | 0.36 | 0.832 | |
| NODE (real rows) | 85.20 | 0.54 | 0.648 |
| NODE (Gaussian) | 86.10 | 0.36 | 0.824 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 76.35 | – | – |
| MEAN | 72.74 | 3.61 * | 0.0265 |
| SWAP | 77.44 | 1.08 | 0.545 |
| 72.92 | 3.43 * | 0.037 | |
| NODE (real rows) | 77.08 | 0.72 | 0.636 |
| NODE (Gaussian) | 75.45 | 0.90 | 0.511 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 84.48 | – | – |
| MEAN | 87.55 | 3.07 ** | 0.00232 |
| SWAP | 84.48 | 0.00 | 1 |
| NODE (real rows) | 84.66 | 0.18 | 1 |
| EDGE (rewired) | 84.66 | 0.18 | 1 |
| GSWAP (other graph) | 84.12 | 0.36 | 0.754 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 81.35 | – | – |
| MEAN | 81.00 | 0.35 | 0.614 |
| SWAP | 80.15 | 1.20 † | 0.0566 |
| 80.30 | 1.05 | 0.119 | |
| 82.05 | 0.70 | 0.338 | |
| NODE (real rows) | 81.55 | 0.20 | 0.699 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 80.20 | – | – |
| MEAN | 80.80 | 0.60 | 0.213 |
| SWAP | 80.40 | 0.20 | 0.781 |
| 80.60 | 0.40 | 0.434 | |
| 80.15 | 0.05 | 1 | |
| NODE (real rows) | 80.00 | 0.20 | 0.757 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 80.55 | – | – |
| MEAN | 80.45 | 0.10 | 0.921 |
| SWAP | 79.50 | 1.05 | 0.137 |
| 80.35 | 0.20 | 0.752 | |
| 79.00 | 1.55 * | 0.0178 | |
| NODE (real rows) | 79.30 | 1.25 † | 0.0725 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 81.40 | – | – |
| MEAN | 81.25 | 0.15 | 0.25 |
| SWAP | 81.40 | 0.00 | 1 |
| 81.25 | 0.15 | 0.25 | |
| 80.95 | 0.45 ** | 0.00391 | |
| NODE (real rows) | 81.40 | 0.00 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 69.15 | – | – |
| MEAN | 48.95 | 20.20 *** | |
| SWAP | 34.10 | 35.05 *** | |
| 49.05 | 20.10 *** | ||
| 38.85 | 30.30 *** | ||
| NODE (real rows) | 60.25 | 8.90 *** |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| real | 72.50 | – | – |
| mean | 71.10 | .182 | |
| swap | 69.10 | *** | |
| swap (permutation 2) | 67.85 | *** | |
| swap (permutation 3) | 67.85 | *** | |
| 70.50 | * | .0481 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 77.40 | – | – |
| MEAN | 77.30 | 0.10 | 0.918 |
| SWAP | 77.20 | 0.20 | 0.801 |
| 77.35 | 0.05 | 1 | |
| NODE (real rows) | 77.50 | 0.10 | 0.856 |
| NODE (Gaussian) | 77.35 | 0.05 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 76.90 | – | – |
| MEAN | 75.40 | 1.50 † | 0.0829 |
| SWAP | 72.45 | 4.45 *** | |
| 74.95 | 1.95 * | 0.0242 | |
| NODE (real rows) | 75.85 | 1.05 | 0.158 |
| NODE (Gaussian) | 76.10 | 0.80 | 0.323 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 77.55 | – | – |
| MEAN | 76.45 | 1.10 | 0.191 |
| SWAP | 75.10 | 2.45 ** | 0.00146 |
| 76.50 | 1.05 | 0.214 | |
| NODE (real rows) | 78.55 | 1.00 | 0.116 |
| NODE (Gaussian) | 78.15 | 0.60 | 0.366 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 79.65 | – | – |
| MEAN | 73.90 | 5.75 *** | |
| SWAP | 70.05 | 9.60 *** | |
| NODE (real rows) | 79.75 | 0.10 | 0.73 |
| EDGE (rewired) | 80.05 | 0.40 | 0.56 |
| GSWAP (other graph) | 80.00 | 0.35 | 0.54 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 70.33 | – | – |
| MEAN | 68.49 | 1.84 * | 0.0285 |
| SWAP | 69.41 | 0.92 | 0.311 |
| 70.70 | 0.37 | 0.687 | |
| 70.95 | 0.61 | 0.495 | |
| NODE (real rows) | 70.39 | 0.06 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 74.32 | – | – |
| MEAN | 73.89 | 0.43 | 0.634 |
| SWAP | 73.59 | 0.74 | 0.382 |
| 73.89 | 0.43 | 0.636 | |
| NODE (real rows) | 73.34 | 0.98 | 0.224 |
| NODE (Gaussian) | 73.59 | 0.74 | 0.359 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 55.47 | – | – |
| MEAN | 54.98 | 0.49 | 0.48 |
| SWAP | 54.79 | 0.68 | 0.428 |
| 54.98 | 0.49 | 0.48 | |
| NODE (real rows) | 54.85 | 0.61 | 0.378 |
| NODE (Gaussian) | 54.67 | 0.80 | 0.232 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 64.62 | – | – |
| MEAN | 49.88 | 14.74 *** | |
| SWAP | 54.73 | 9.89 *** | |
| 49.88 | 14.74 *** | ||
| 37.65 | 26.97 *** | ||
| NODE (real rows) | 62.22 | 2.40 * | 0.0289 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 69.90 | – | – |
| MEAN | 66.77 | 3.13 *** | 0.000865 |
| SWAP | 67.75 | 2.15 * | 0.0387 |
| 67.38 | 2.52 ** | 0.00807 | |
| NODE (real rows) | 68.67 | 1.23 | 0.216 |
| NODE (Gaussian) | 68.55 | 1.35 | 0.157 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 74.57 | – | – |
| MEAN | 73.46 | 1.11 | 0.195 |
| SWAP | 72.24 | 2.33 ** | 0.00839 |
| 72.60 | 1.97 * | 0.0192 | |
| NODE (real rows) | 73.77 | 0.80 | 0.332 |
| NODE (Gaussian) | 73.40 | 1.17 | 0.161 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 71.25 | – | – |
| MEAN | 71.44 | 0.18 | 0.69 |
| SWAP | 71.25 | 0.00 | 1 |
| 71.44 | 0.18 | 0.69 | |
| NODE (real rows) | 71.25 | 0.00 | 1 |
| NODE (Gaussian) | 71.25 | 0.00 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 70.70 | – | – |
| MEAN | 70.21 | 0.49 | 0.115 |
| SWAP | 68.98 | 1.72 * | 0.015 |
| 70.21 | 0.49 | 0.115 | |
| NODE (real rows) | 70.70 | 0.00 | 1 |
| NODE (Gaussian) | 70.70 | 0.00 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 65.79 | – | – |
| MEAN | 63.70 | 2.09 ** | 0.00187 |
| SWAP | 63.88 | 1.90 ** | 0.00573 |
| 63.70 | 2.09 ** | 0.00187 | |
| NODE (real rows) | 64.99 | 0.80 | 0.25 |
| NODE (Gaussian) | 65.17 | 0.61 | 0.373 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 57.13 | – | – |
| MEAN | 56.57 | 0.55 | 0.478 |
| SWAP | 55.71 | 1.41 | 0.104 |
| 56.70 | 0.43 | 0.595 | |
| NODE (real rows) | 56.82 | 0.31 | 0.704 |
| NODE (Gaussian) | 56.57 | 0.55 | 0.452 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 70.58 | – | – |
| MEAN | 70.02 | 0.55 | 0.538 |
| SWAP | 70.15 | 0.43 | 0.654 |
| 69.90 | 0.68 | 0.46 | |
| NODE (real rows) | 70.33 | 0.25 | 0.784 |
| NODE (Gaussian) | 70.58 | 0.00 | 1 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 67.75 | – | – |
| MEAN | 67.69 | 0.06 | 1 |
| SWAP | 67.26 | 0.49 | 0.614 |
| 67.57 | 0.18 | 0.89 | |
| NODE (real rows) | 67.26 | 0.49 | 0.598 |
| NODE (Gaussian) | 67.63 | 0.12 | 0.942 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 70.02 | – | – |
| MEAN | 70.02 | 0.00 | 1 |
| SWAP | 69.78 | 0.25 | 0.836 |
| 68.86 | 1.17 | 0.22 | |
| NODE (real rows) | 69.16 | 0.86 | 0.356 |
| NODE (Gaussian) | 70.52 | 0.49 | 0.617 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 63.14 | – | – |
| MEAN | 59.71 | 3.44 ** | 0.00341 |
| SWAP | 57.80 | 5.34 *** | |
| 60.01 | 3.13 ** | 0.0045 | |
| NODE (real rows) | 61.49 | 1.66 | 0.127 |
| NODE (Gaussian) | 62.16 | 0.98 | 0.385 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 63.64 | – | – |
| MEAN | 60.69 | 2.95 ** | 0.0075 |
| SWAP | 58.42 | 5.22 *** | |
| 59.28 | 4.36 *** | ||
| NODE (real rows) | 60.87 | 2.76 ** | 0.00953 |
| NODE (Gaussian) | 62.59 | 1.04 | 0.324 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 64.56 | – | – |
| MEAN | 60.32 | 4.24 *** | |
| SWAP | 60.87 | 3.69 *** | 0.000608 |
| 61.86 | 2.70 ** | 0.00801 | |
| NODE (real rows) | 63.27 | 1.29 | 0.216 |
| NODE (Gaussian) | 63.21 | 1.35 | 0.196 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 67.20 | – | – |
| MEAN | 68.55 | 1.35 | 0.143 |
| SWAP | 66.89 | 0.31 | 0.794 |
| 68.92 | 1.72 † | 0.0511 | |
| NODE (real rows) | 69.23 | 2.03 * | 0.0281 |
| NODE (Gaussian) | 68.49 | 1.29 | 0.172 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 69.53 | – | – |
| MEAN | 68.00 | 1.54 † | 0.0967 |
| SWAP | 66.34 | 3.19 ** | 0.00151 |
| 67.87 | 1.66 † | 0.0732 | |
| NODE (real rows) | 66.28 | 3.26 *** | 0.000443 |
| NODE (Gaussian) | 68.24 | 1.29 | 0.174 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 66.89 | – | – |
| MEAN | 65.11 | 1.78 † | 0.0888 |
| SWAP | 65.85 | 1.04 | 0.322 |
| 63.70 | 3.19 ** | 0.00139 | |
| NODE (real rows) | 64.68 | 2.21 * | 0.0298 |
| NODE (Gaussian) | 65.29 | 1.60 | 0.101 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 68.43 | – | – |
| MEAN | 68.18 | 0.25 | 0.848 |
| SWAP | 68.30 | 0.12 | 0.948 |
| 68.73 | 0.31 | 0.797 | |
| NODE (real rows) | 68.37 | 0.06 | 1 |
| NODE (Gaussian) | 68.80 | 0.37 | 0.737 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 70.95 | – | – |
| MEAN | 69.78 | 1.17 | 0.166 |
| SWAP | 70.02 | 0.92 | 0.279 |
| 69.53 | 1.41 † | 0.0845 | |
| NODE (real rows) | 69.47 | 1.47 † | 0.0669 |
| NODE (Gaussian) | 69.59 | 1.35 † | 0.0945 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 72.17 | – | – |
| MEAN | 71.93 | 0.25 | 0.805 |
| SWAP | 71.99 | 0.18 | 0.859 |
| 70.82 | 1.35 † | 0.0882 | |
| NODE (real rows) | 71.87 | 0.31 | 0.738 |
| NODE (Gaussian) | 71.56 | 0.61 | 0.456 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 72.73 | – | – |
| MEAN | 66.58 | 6.14 *** | |
| SWAP | 67.08 | 5.65 *** | |
| NODE (real rows) | 72.11 | 0.61 | 0.415 |
| EDGE (rewired) | 72.30 | 0.43 | 0.664 |
| GSWAP (other graph) | 70.76 | 1.97 * | 0.0347 |
| Condition | Accuracy | Difference | |
|---|---|---|---|
| REAL | 69.84 | – | – |
| MEAN | 69.78 | 0.06 | 1 |
| SWAP | 66.15 | 3.69 *** | 0.000365 |
| NODE (real rows) | 67.75 | 2.09 * | 0.0367 |
| EDGE (rewired) | 69.35 | 0.49 | 0.636 |
| GSWAP (other graph) | 67.51 | 2.33 * | 0.0247 |
| Dataset | Model | REAL | zero token | norm word | ||
|---|---|---|---|---|---|---|
| ExplaGraphs | G-Retriever (GT) | 85.56 | *** | *** | *** | *** |
| CONST | 85.56 | *** | *** | *** | † | |
| CONST at word norm | 85.56 | *** | *** | *** | ||
| SceneGraphs | G-Retriever (GT) | 81.35 | *** | *** | *** | |
| CONST | 81.40 | *** | *** | *** | ** | |
| WebQSP | G-Retriever (GT) | 70.33 | *** | *** | *** | *** |
| Model | Trainable parameters | ExplaGraphs | SceneGraphs | WebQSP |
|---|---|---|---|---|
| G-Retriever | 31,492,099 | 85.56 | 81.35 | 70.33 |
| const | 10,492,928 | 85.56 | 81.40 | 71.25 |
| mlpq | 14,690,304 | 84.84 | – | 70.70 |
| pt | 40,960 | 60.60 | 70.22 | 52.21 |
| ours, Stage 2 | 20,990,979 | 85.74 | 72.50 | 69.90 |
| Dataset | Model | REAL | MEAN | SWAP | GSWAP |
|---|---|---|---|---|---|
| WebQSP | G-Retriever | 0.7558 | |||
| ours | 0.8540 | ||||
| ours, no entity features | 0.8213 | ||||
| ours, no question | 0.8517 | ||||
| G-Retriever, Qwen2.5-3B | 1.0367 | ||||
| ours, Qwen2.5-3B | 1.0553 |
| Dataset | Model | Q rank | A rank | G rank | Score gswap | NLL S/GS | Diagnosis |
| Llama-2-7B | |||||||
| WebQSP | G-Retriever | 293 | 317 | 369 | soft prompt | ||
| mlpq | 407 | 407 | 407 | – | – | – | |
| Ours | 65 | 60 | 315 | † | masked | ||
| no entity features | 34 | 51 | 303 | * | prior | ||
| no question | 120 | 134 | 329 | * | used | ||
| Run | Target | Validation top-1 | Graph gap |
|---|---|---|---|
| SceneGraphs , with question | full answer sentence | 0.433 | |
| SceneGraphs , without question | full answer sentence | 0.084 | Same embeddings, N/A |
| SceneGraphs , scene-disjoint halves | full answer sentence | 0.376 | |
| WebQSP , half split | gold answers | 0.469 | N/A |
| ExplaGraphs , half split | verbalised graph | 0.501 | N/A |
| Variant | Hit@1 | Token cosine | MEAN | SWAP | NODE |
|---|---|---|---|---|---|
| Joint Stage 2, as used in the paper | 69.53 | 0.1778 | † | ** | *** |
| Projector only | 63.14 | 0.5700 | *** | *** | |
| Prompt token added after the projector | 63.64 | 0.5700 | *** | *** | *** |
| Dropout 0.5 on the projector | 64.56 | 0.7563 | *** | *** | |
| 40% of verbalised edges hidden in training | 67.20 | 0.1847 | ** |
| Dataset | Model | real | Token cos. | mean | swap | node | edge | gswap |
| Llama-2-7B | ||||||||
| WebQSP | projector only | 64.62 | 0.543 | *** | *** | * | – | |
| Ours | 69.90 | 0.142 | *** | * | † | |||
| no entity features | 72.73 | 0.125 | *** | *** | * | |||
| no question | 69.84 | 0.169 | *** | * | * | |||
| cross-fitted | 69.53 | 0.178 | † | ** | *** | ** | ||
| Dataset | Model | notxt | mean | swap | gswap | With text |
|---|---|---|---|---|---|---|
| WebQSP | G-Retriever | 41.34 | 70.33 | |||
| Ours | 28.75 | * | * | * | 69.90 | |
| no entity features | 28.38 | *** | – | – | 72.73 | |
| no question | 30.90 | – | – | 69.84 | ||
| SceneGraphs | G-Retriever | 30.20 | – | 81.35 | ||
| Ours | 32.60 | *** | *** | ** | 72.50 |
| Dataset | Model | notxt | mean | swap | gswap | With text |
|---|---|---|---|---|---|---|
| WebQSP | G-Retriever | 29.30 | † | † | 57.13 | |
| Ours | 34.34 | 65.79 | ||||
| no entity features | 30.10 | * | – | – | 58.54 | |
| no question | 32.74 | – | – | 60.14 | ||
| SceneGraphs | G-Retriever | 39.50 | * | – | – | 76.05 |
| Ours | 43.90 | *** | – | – | 72.65 |
| Dataset | Stage 2 | Accuracy | Baseline | MEAN | SWAP | NODE | EDGE |
|---|---|---|---|---|---|---|---|
| WebQSP | projector only | 63.14 | 70.52 | *** | *** | ||
| WebQSP | projector + prompt | 69.53 | 70.58 | † | ** | *** | |
| SceneGraphs | projector + prompt, run 1 | 76.90 | 78.57 | † | *** | *** | |
| SceneGraphs | projector + prompt, run 2 | 77.55 | 78.57 | ** | |||
| ExplaGraphs | projector + prompt | 76.35 | 80.87 | * |
| Model | Run 1 | Run 2 | Run 3 | Mean sd | MEAN | SWAP | NODE |
|---|---|---|---|---|---|---|---|
| G-Retriever | 70.58 | 67.75 | 70.02 | ||||
| Ours, joint | 69.53 | 66.89 | 68.43 | ** | ** | *** |