Evee outperforms existing methods for variant pathogenicity prediction

Interpretive claim supported by the high AUROC findings.

Source paper

extracted_from

(2026) · Pearce, Michael · Dooms, Thomas · Yamamoto, Ryo · Meehl, Joshua +18

paper

finding

0.997 AUROC on pathogenicity prediction for 839k ClinVar variants
supports
EVEE achieves state-of-the-art performance on variant pathogenicity classification, outperforming existing methods.
0.991 AUROC zero-shot on insertions/deletions
supports
EVEE demonstrates strong generalization to indels without explicit training, indicating learned mechanistic principles.

community

Mechanistic interpretability & model evaluation
members_of
Spans attention head decomposition, benchmark awareness, and genomic pathogenicity prediction via neural models.
Mechanistic explanation of genetic variant pathogenicity
members_of
Using genomic foundation model internals to generate disruption profiles that explain variant effects mechanistically, achieving 0.997 AUROC on ClinVar pathogenicity prediction.
Mechanistic variant pathogenicity prediction
members_of
EVEE tool predicts and mechanistically explains effects of 4.2M human genome variants using model internals.

cosine ≥ 0.65 · no typed edge

Entities in the same semantic neighborhood but without a typed relation to this one — candidates for new edges or unrecognized duplicates.

Evee variant effect prediction methodmethod0.869
The method that predicts and explains variant pathogenicity using Evo 2, producing disruption profiles.
EVEE provides mechanistic explanations for variant effects derived from model internals, not just pathogenicity calls.claim0.839
Core interpretability claim distinguishing EVEE from black-box prediction tools; applies interpretability for science.
Variant pathogenicity predictionconcept0.822
Core task of predicting whether genetic variants cause disease, central to clinical genomics.
Evee provides predictions and mechanistic explanations for 4.2 million genetic variants across the whole human genomeclaim0.800
Scale claim, demonstrating whole-genome applicability.
variant pathogenicityconcept0.751
The property of a genetic variant being disease-causing or benign; the main prediction target.
Evolution makes problem-solving agents, not solutions; commitment to mutation and uncontrollable environments as ratchet for intelligenceclaim0.698
Causal emergence is widespread across measures of causation, not just EI.claim0.695
Claim by Comolatti & Hoel (2022) endorsed by this survey.
Self-evaluated emotionality and textual evaluation of SAE features predict persistence in opposite directions.claim0.692
Surprising finding that the two evaluation methods diverge in their relationship with persistence