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Keyword: protein sequence databases ×Clear all

3 claims from 1 paper

1. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Protein language models are biased by unequal sequence sampling across the tree of life

   Ding and Steinhardt · bioRxiv (Cold Spring Harbor Laboratory) · 2024

   The paper finds that protein language models are biased towards certain species because of uneven species representation in training databases, and that this can hamper some protein design tasks such as thermostability.

   Unchecked3 claims
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   1. UncheckedProtein language model likelihoods appear to carry a species bias: sequences from some species score systematically higher, whatever the protein.“In this work we find that pLM likelihoods unintentionally encode a species bias: likelihoods of protein sequences from certain species are systematically higher, independent of the protein in question.”
   2. UncheckedProtein language models score sequences from some species higher regardless of the protein, largely because databases sample species unevenly.“We quantify this bias and show that it arises in large part because of unequal species representation in popular protein sequence databases.”
   3. UncheckedThe paper says species bias in protein language models can harm some protein design tasks, such as making proteins more heat-stable.“We further show that the bias can be detrimental for some protein design applications, such as enhancing thermostability.”