Interpretable variant effect prediction from genomic foundation model embeddings
Michael T. Pearce, Thomas Dooms, Ryo Yamamoto, Shant Ayanian, Alexander J. Ryu, Joshua Meehl, Carl Molnar, Tuomo Kiiskinen, Mark Bissell, Dron Hazra, Ching Fang, Nam Nguyen, Michael Anderson, Collin Osborne, Patrick Emmet Duffy, , Nicholas K. Wang
A low-rank covariance probe on Evo 2 embeddings predicts ClinVar pathogenicity across SNVs and indels, while annotation probes plus an LLM produce mechanistic hypotheses; scores released for 4.2 million variants.
bioRxiv · Jul 11, 2026 · PreprintGenomics✦ In-depth digest