
Split and Aggregation Sensitivity in the ProteinGym Supervised Benchmark
NeurIPS 2026, AI for Science workshop · AcceptedProteinGym is the standard supervised benchmark for predicting how mutations change a protein's fitness, and leaderboards on it decide which models get used. This paper shows that the ranking of methods depends on choices that are rarely reported: how the data is split and how per-assay scores are aggregated. Under different but equally defensible protocols the same set of models reorders, so a claimed state of the art can be an artefact of the evaluation rather than of the model. Accepted at the NeurIPS 2026 AI for Science workshop at a 22.5% acceptance rate.



