PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space.

Abstract excerpt

BACKGROUND: Protein language models (PLMs) have revolutionized protein fitness prediction, yet their application to rapidly evolving viral pathogens is often confounded by extreme sequence homology. This homology leads to "data leakage" in standard random validation splits, yielding inflated performance metrics that fail to translate into real-world biosurveillance utility. RESULTS: We present Protein...

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