Evaluating Relational Reasoning in LLMs with REL

Authors: Lukas Fesser*, Yasha Ektefaie*, Ada Fang*, Sham M. Kakakde, Marinka Zitnik

* indicates equal contribution

Read our preprint here.

This repository contains the REL benchmarks for chemistry, biology, and algebra. For evaluation scripts please refer to our GitHub repo.

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Algebra (1,000 questions)

All algebra tasks are Raven's Progressive Matrices: complete a 3×3 or 9×9 grid of number tuples by identifying the missing panel from 8 candidates. The matrix sizes differ in context length and difficulty.

Task	RC	RC min	RC max	Size	Questions	Assesses
REL-A1	2	2	2	3×3 and 9×9	125 each	Constant rows — each row is identical; tests whether the model recognizes invariance
REL-A2	2	2	2	3×3 and 9×9	125 each	Arithmetic progression — values shift by a fixed increment across rows; tests detection of linear trends
REL-A3	$n$ where $n\times n$ is the matrix size	3	9	3×3 and 9×9	125 each	Permutation — each row is a cyclic permutation of the same values; tests recognition of reordering patterns
REL-A4	$n$ where $n\times n$ is the matrix size	3	9	3×3 and 9×9	125 each	Row-Sum — the final value in each row is the sum of all other entries in the same row multiplied by either $\pm1$, depending on the column.

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Biology (7,952 questions)

All biology tasks are REL-B1, split across 12 files by phylogenetic tree/alignment instance. Each question presents a multiple sequence alignment (FASTA) and a phylogenetic tree, and asks whether structured homoplasy is present and which taxa are involved.

Task	RC	RC min	RC max	Files	Total questions	Assesses
REL-B1	Number of homoplastic taxa	2	25	001–012	7,952	Homoplasy detection — identifying convergent evolution where distantly related taxa independently share nucleotide motifs across many alignment columns more than expected by chance; tests relational pattern recognition over long biological sequences

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Chemistry (4,016 questions)

Task	RC	RC min	RC max	Questions	Assesses
REL-C1	2	2	2	1,000	Constitutional isomer identification — given a set of SMILES, determine whether all molecules share the same molecular formula (same atoms, different connectivity); tests recognition of molecular equivalence relations
REL-C2	2	2	2	1,016	Maximum common substructure (MCS) — find the largest single connected chemical motif present in every molecule in the set; tests relational reasoning over graph structure
REL-C3	Number of isomers	1	92	1,000	Isomer set completion — given a partial set of constitutional isomers, identify all missing members; tests exhaustive enumeration of a structural equivalence class
REL-C4	Number of molecules	5	50	1,000	Constrained motif extraction — extract one substructure from each of the molecules such that a specified functional group count sums to a target value; tests joint constraint satisfaction over molecular substructures

Citation

@article{fesser2026rel,
  title         = {Evaluating Relational Reasoning in LLMs with REL},
  author        = {Lukas Fesser and Yasha Ektefaie and Ada Fang and Sham M. Kakade and Marinka Zitnik},
  year          = {2026},
  journal       = {arXiv preprint arXiv:2604.12176},
  eprint        = {2604.12176},
  archivePrefix = {arXiv},
  url           = {https://arxiv.org/abs/2604.12176}
}