Alpha amylase sampling:

Performance comparison between BADASS, EvoProtGrad and GGS (using EvoProtGrad on the Smoothed Seq2Fitness model) using ESM2 and Seq2Fitness models. All approaches are given comparable GPU compute time for the sampling. GGS requires an additional round to evaluate sequences with the original Seq2Fitness model. Metrics include the percentage of sequences better than wild type in the top 10,000 sequences found (or less when a method cannot find enough), the best, best 100th, and best 1,000th sequence scores, and the number of unique mutations and unique mutated sites present in the top 10,000 sequences. The number of mutations per sequence is k. As benchmarks, the reference alpha amylase sequence has an ESM2 score of 0.0, and a Seq2Fitness score of 0.8. BADASS was run for 200 iterations with a batch size of 520 sequences. Missing entries for EvoProtGrad (using T=0.1 for ESM2) are due to the generation of a limited number of unique sequences (on the order of hundreds), as the sampler becomes overly concentrated on a small number of mutations.