Evaluating Relational Reasoning in LLMs with REL
Organizations: Harvard University · Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard
Abstract
Relational reasoning is the ability to infer relations that jointly bind multiple entities, attributes, or variables. This ability is central to scientific reasoning, but existing evaluations of relational reasoning in large language models often focus on structured inputs such as tables, graphs, or synthetic tasks, and do not isolate the difficulty introduced by higher-arity relational binding. We study this problem through the lens of Relational Complexity (RC), which we define as the minimum number of independent entities or operands that must be simultaneously bound to apply a relation. RC provides a principled way to vary reasoning difficulty while controlling for confounders such as input size, vocabulary, and representational choices. Building on RC, we introduce REL, a generative benchmark framework spanning algebra, chemistry, and biology that varies RC within each domain. Across frontier LLMs, performance degrades consistently and monotonically as RC increases, even when the total number of entities is held fixed. This failure mode persists with increased test-time compute and in-context learning, suggesting a limitation tied to the arity of the required relational binding rather than to insufficient inference steps or lack of exposure to examples. Our results identify a regime of higher-arity reasoning in which current models struggle, and motivate re-examining benchmarks through the lens of relational complexity.
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Appendix
| Dataset | RC-2 | RC-3 | RC-4 | RC-5 | RC-6 |
|---|---|---|---|---|---|
| GFP | 81.4% | 27.5% | 46.3% | 13.2% | 11.8% |
| HA | 81.4% | 34.3% | 47.1% | 16.2% | 8.0% |
| HA2 | 83.3% | 35.3% | 40.4% | 14.0% | 6.6% |
| GB1 | 78.4% | 15.7% | – | – | – |
| TrpB | 76.5% | 21.6% | – | – | – |
| Chance | 33% | 25% | 25% | 25% | 25% |
| 5 | 10 | 15 | 20 | 25 | 30 | 35 | 40 | 45 | 50 | |
|---|---|---|---|---|---|---|---|---|---|---|
| # Questions | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
| Avg. Atoms | 5.75 | 5.78 | 5.94 | 6.10 | 6.20 | 6.10 | 6.34 | 6.21 | 6.15 | 6.32 |
| Avg. DBE | 4.31 | 4.54 | 4.61 | 4.68 | 4.78 | 4.80 | 4.79 | 5.35 | 5.31 | 5.47 |
| 5 | 10 | 15 | 20 | 25 | 30 | 35 | 40 | 45 | 50 | |
|---|---|---|---|---|---|---|---|---|---|---|
| # Questions | 120 | 120 | 120 | 120 | 120 | 120 | 120 | 76 | 53 | 47 |
| Avg. atoms | 30.74 | 30.75 | 27.28 | 28.18 | 27.25 | 27.39 | 26.46 | 27.42 | 27.42 | 28.45 |
| Avg. elements | 3.32 | 3.34 | 3.29 | 3.34 | 3.30 | 3.25 | 3.14 | 3.02 | 2.96 | 2.83 |
| Avg. DBE | 24.55 | 24.59 | 22.11 | 22.55 | 22.09 | 22.12 | 21.79 | 23.08 | 23.27 | 24.08 |
| Avg. rings | 3.03 | 2.97 | 2.98 | 3.00 | 3.09 | 3.07 | 3.13 | 3.32 | 3.42 | 3.81 |
| Motif (SMILES) | Count |
|---|---|
| COc1ccccc1 | 180 |
| CCc1ccccc1 | 114 |
| O=SHc1ccccc1 | 50 |
| CCOc1ccccc1 | 17 |
| CC12C=CC(=O)C=C1CCC1C2CCC2(C)C(C=O)CCC12 | 13 |
| CC(C)NCC(O)COc1ccccc1 | 9 |
| 5 | 10 | 15 | 20 | 25 | 30 | 35 | 40 | 45 | 50 | |
|---|---|---|---|---|---|---|---|---|---|---|
| # Questions | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
| # Missing Isomers | 36.41 | 32.92 | 29.93 | 30.39 | 24.13 | 27.28 | 24.17 | 33.24 | 28.16 | 26.44 |
| Avg. atoms | 5.91 | 5.83 | 5.84 | 6.22 | 6.23 | 6.19 | 6.42 | 6.18 | 6.22 | 6.31 |
| Avg. DBE | 4.56 | 4.69 | 4.73 | 4.74 | 4.59 | 4.78 | 4.66 | 5.39 | 5.34 | 5.40 |
| Model | Count | Recall | Precision | F1 | |
|---|---|---|---|---|---|
| Claude Opus 4.5 | 300 | 0.341 (0.013) | 0.569 (0.016) | 0.386 (0.011) | |
| 400 | 20–40 | 0.313 (0.011) | 0.390 (0.013) | 0.299 (0.008) | |
| 300 | 0.253 (0.009) | 0.398 (0.015) | 0.289 (0.009) | ||
| Gemini 3 Pro | 300 | 0.417 (0.014) | 0.472 (0.015) | 0.403 (0.012) | |
| 400 | 20–40 | 0.362 (0.012) | 0.275 (0.011) | 0.260 (0.009) | |
| 300 | 0.259 (0.010) | 0.256 (0.012) | 0.234 (0.010) |
| Model | Rule Type (RC) | 3x3 | 9x9 | 15x15 | 30x30 |
|---|---|---|---|---|---|
| Llama 3.1-70b | Progression (2) | 0.912 | 0.864 | 0.856 | 0.816 |
| Llama 3.1-70b | Permutation (n) | 0.648 | 0.552 | 0.296 | 0.144 |
| Qwen3-4B | Progression (2) | 0.616 | 0.568 | 0.528 | 0.504 |
| Qwen3-4B | Permutation (n) | 0.552 | 0.216 | 0.184 | 0.104 |
| Digits | GPT REL -A5 ( ) | Claude REL -A5 ( ) | GPT REL -A4 ( ) | Claude REL -A4 ( ) |
|---|---|---|---|---|
| 4096 Tokens | ||||
| 8192 Tokens | ||||
| 16384 Tokens |
| Digits | GPT REL-A3 ( ) | Claude REL-A3 ( ) | GPT REL-A4 ( ) | Claude REL-A4 ( ) |
|---|---|---|---|---|
| 5 Digits | ||||
| 10 Digits | ||||
| 20 Digits |
| Motif Ratio | Gemini | GPT | Claude |
|---|---|---|---|
| 0–5% | 2.6% | 0.8% | 0.0% |
| 5–10% | 9.2% | 10.2% | 1.8% |
| 10–12.5% | 13.5% | 18.6% | 2.1% |
| 12.5–15% | 22.6% | 29.0% | 12.9% |
| 15–17.5% | 19.6% | 17.6% | 17.6% |
| 17.5–20% | 34.2% | 23.7% | 28.9% |
| Relational Complexity (RC) | ||||
| Method | 4 | 10 | 20 | 25 |
| Baseline | 45% | 15% | 5% | 5% |
| Structured | 65% | 25% | 10% | 5% |
| +20 | +10 | +5 | 0 | |
Relational Reasoning
Relational reasoning studies how AI systems represent and infer relationships among objects, entities, events, and facts.
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