Author

Robert M. Vernon

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Open access Jul 2026

pLM representations unlock metagenomic space beyond homology

Residue Embedding Diversity (RED), a metric for protein quality assessment orders of magnitude cheaper than likelihood, and a calibration task that measures model alignment with natural evolutionary distributions are introduced.

Lola Le Breton, David Heurtel-Depeiges, Douglas C. Millar et al. · bioRxiv · 1 citation

Open access Jul 2026

High-resolution dissection of concept acquisition in different families of protein language models

A high-resolution layer-by-layer interpretability analysis of 8 models from the ESM2 and AMPLIFY families on 22 concepts from human proteome annotations found that these models encode concepts of increasing levels of complexity along their depth: basic physicochemical properties and linear motifs are best captured by e...

Shawn T. Whitfield, Tom Marty, Robert M. Vernon et al. · bioRxiv · 0 citations