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August 5, 2025Open Access

Benchmarking DNA Foundation Models for zero-shot variant effect prediction: the role of context, training, and architecture

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Authors

IAIlaria AlfisiFCFrancesca CiapiMBMarta Baragli

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Overview

Benchmarking dna models improves variant predictions using zero-shot scoring, highlighting model architecture's role.

Key Points

  • Large multi-species dna models outperform human-only models in variant effect prediction.
  • Models effectively capture local and extended contextual effects using zero-shot scoring on snvs.
  • The study uses data from Clin-Var to assess the functional consequences of pathogenic, benign, and uncertain variants.
  • Innovations in transformer architecture may enhance modeling of long-range dependencies in genomic sequences.

Cite This Study

Alfisi et al. (2025) studied this question.

synapsesocial.com/papers/689a0f93e6551bb0af8d11afhttps://doi.org/10.21203/rs.3.rs-6988910/v1
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