860-Quantifying Uncertainty in Protein Sequence Embeddings

Paper Talk · Apr 26, 2026 · 26m

The article introduces the Random Neighbor Score (RNS), a model-agnostic framework designed to measure the reliability of protein language model (pLM) embeddings. While these computational representations are vital for predicting biological functions and structures, the authors argue that embedding uncertainty often goes unquantified, leading to erroneous downstream scientific insights. To address this, RNS calculates the proportion of non-biological, synthetic sequences that cluster near a specific protein within a model's latent space. High-uncertainty embeddings, which closely resemble…