arXiv AI By Rome Thorstenson

Protein contacts are already in the attention: a single-forward-pass alternative to the Categorical Jacobian

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arXiv:2606. 21876v2 Announce Type: replace-cross Abstract: The Categorical Jacobian of Zhang et al.

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arXiv AI
Sep 24

ProteinJEPA: Latent prediction improves protein language model pretraining

ProteinJEPA introduces a joint‑embedding predictive architecture that supplements masked language modeling (MLM) with a cosine loss to predict latent representations of a teacher model. On 19 protein tasks, MLM+JEPA outperforms compute‑matched and step‑matched MLM‑only training across 78 and 76 of 114 comparisons, achieving notable gains on structure‑ and homology‑sensitive tasks such as SCOPe‑40 retrieval and remote homology. Ablation studies show the cosine loss is superior to mean squared error and that latent prediction complements rather than replaces MLM.

By Dan Ofer, Dafna Shahaf, Michal Linial