Taking the minimum logit can outperform averaging logits when ensembling models for pathogenicity prediction

Summary

Using the minimum logit from an ensemble of models rather than averaging all logits can lead to improved performance on pathogenicity prediction (1). This is particularly effective when distinct models have different levels of confidence.

Figures

Ref (1)

See also

• Averaging logits from multiple sources can improve fitness prediction

1.

Dinh T, Jang S-K, Zaitlen N, Ntranos V. Compressing the collective knowledge of ESM into a single protein language model. Nature Methods. 2026; Available from: https://doi.org/10.1038/s41592-026-03050-9