Covariance pooling for genomic embeddings

Replaces mean pooling with second-order statistics, achieving large R² and AUC gains on genomic tasks.

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Covariance pooling achieves +52.9% R² improvement over mean pooling on Genomic Track Prediction.Primary empirical result demonstrating practical utility of covariance pooling method.
Covariance pooling compresses gigabytes of activations into compact stable embeddings without large labeled datasetsPractical finding: the method produces compact fixed-length representations from large volumes of token activations without requiring supervised labels.
Gene Ontology prediction: +8.4% AUC improvement with unsupervised autoencoder and covariance pooling embeddingsEmpirical result: covariance pooling combined with unsupervised autoencoder embeddings improves Gene Ontology prediction AUC by 8.4% over mean pooling.

Covariance pooling could generalize beyond genomics as a general-purpose replacement for mean poolingAuthors' suggestion that the second-moment preservation principle applies broadly, not just to genomic foundation models.
Covariance pooling preserves joint activation structure (feature co-occurrence) that mean pooling discardsSpecific interpretive claim about what covariance pooling captures: the pairwise co-activation patterns across features that are invisible to mean pooling.