Author

Jordan F. Safer

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Open access Aug 2026

EmmaEmb: A quantitative framework for analyzing embedding spaces in molecular biology

EmmaEmb is introduced, a quantitative, model-agnostic framework for geometric correction, direct analysis, and comparison of embedding spaces that encompasses local and global analysis methods to quantify data distribution within an embedding space and enable comparisons of representations across spaces in relation to...

Pia Francesca Rissom, Vít Škrhák, Paulo Yanez Sarmiento et al. · Patterns · 0 citations

Preprint Aug 2026

Interpreting Protein Language Model Embeddings via Orthogonal Projection for Protein Fitness Prediction

It is shown that PLM embeddings encode patterns correlated with biochemical properties and quantify their contribution to predicting protein fitness, and this technique is readily transferable to problem settings beyond protein fitness prediction.

Paulo Yanez Sarmiento, Pia Francesca Rissom, Manuel Pfeuffer et al. · 0 citations