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artifact:covariance-based-sequence-pooling-2026

Covariance-based Sequence Pooling (2026)

Goodfire research post introducing covariance pooling as a replacement for mean pooling in genomic foundation models; shows +52.9% R² lift on genomic track prediction.

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Papers (1)

paper

Thinkers (3)

thinker

Concepts (5)

concept
  • Genomic Foundation Models
    mentions
    Large pretrained models for genomic sequences; subject of this work's pooling improvements.
  • Genomic Track Prediction
    about
    Downstream task evaluated in the paper; shows +52.9% R² improvement with covariance pooling.
  • Sequence pooling
    mentions
    General technique for aggregating variable-length token embedding sequences into fixed-length representations; mean pooling and covariance pooling are instances.
  • Gene Ontology Prediction
    about
    Second evaluated task showing +8.4% AUC improvement with covariance pooling and unsupervised autoencoder embeddings.
  • Token embeddings
    mentions
    Vector representations of individual tokens from genomic foundation models; the raw inputs to sequence pooling methods.

Artifacts (2)

artifact
  • EVEE
    cites
    Interpretable prediction tool for explaining genetic variant effects across the human genome.
  • Mayo
    cites
    Goodfire project; covariance pooling emerged as a methodological side-product of the EVEE/Mayo work.