Robert M. Vernon

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 early-layer embeddings, secondary structure from subsequent layers, and domain-level semantics from middle layers.