diff --git a/README.md b/README.md index 2ce6b2f..5f489dd 100644 --- a/README.md +++ b/README.md @@ -101,7 +101,7 @@ You can always check which modules are installed/available to you by running `ge ### Composite / Ensemble Utilities 1. `ZScoreRescaledScorer` - - Wraps any per-variant scorer and rescales its log-ratios within an amino-acid group (destination residue or substitution type) — the z-score ("Z") ranking from the [MULTI-evolve](https://www.science.org/doi/10.1126/science.adr8628) ensemble. Behaves as a single scikit-learn transformer (`fit`/`transform`), and `score_table` returns the per-mutation DataFrame. + - Wraps any per-variant scorer and rescales its log-ratios within an amino-acid group (destination residue or substitution type) — the z-score ("Z") ranking from the [MULTI-evolve](https://www.science.org/doi/10.1126/science.aea1820) ensemble. Behaves as a single scikit-learn transformer (`fit`/`transform`), and `score_table` returns the per-mutation DataFrame. - See the "Ensemble Variant Nomination" user guide for a full structure + sequence first-round scan. Lower-level primitives (`per_variant_mutation_info`, `zscore_by_aa_group`) live in `aide_predict.utils.scoring`. ### Embeddings for Downstream ML diff --git a/docs/user_guide/multi_evolve_ensemble.md b/docs/user_guide/multi_evolve_ensemble.md index c8beff9..63cc793 100644 --- a/docs/user_guide/multi_evolve_ensemble.md +++ b/docs/user_guide/multi_evolve_ensemble.md @@ -6,7 +6,7 @@ title: Ensemble Variant Nomination ## Overview -This guide reproduces the first round of the [MULTI-evolve](https://www.science.org/doi/10.1126/science.adr8628) zero-shot nomination workflow using AIDE primitives. The idea is to score a full saturation-mutagenesis (SSM) library along two complementary tracks and combine them: +This guide reproduces the first round of the [MULTI-evolve](https://www.science.org/doi/10.1126/science.aea1820) zero-shot nomination workflow using AIDE primitives. The idea is to score a full saturation-mutagenesis (SSM) library along two complementary tracks and combine them: - a **structure track** — `ESMIFLikelihoodWrapper` (ESM-IF1), conditioned on the backbone; - a **sequence track** — an ensemble of sequence PLMs (`ESM2LikelihoodWrapper` loading the ESM-1v / ESM-2 checkpoints), averaged.