797-Quantifying Uncertainty in Protein Representations

Paper Talk · Apr 15, 2026 · 19m

This research introduces the Random Neighbor Score (RNS), a novel, model-agnostic framework designed to measure the reliability of protein language model embeddings. While these computational representations are essential for predicting biological structures and functions, the authors demonstrate that low-quality embeddings often inhabit a "junkyard" of latent space indistinguishable from randomly shuffled sequences. By calculating the proportion of synthetic neighbors surrounding a protein's representation, RNS quantifies uncertainty and identifies segments of the proteome that models fail…