Reusability Report: Pushing adaptive autoregressive diffusion to its limits from antibody humanization to antimicrobial peptide design

AmpDiff, an adaptive autoregressive diffusion model adapted from HuDiff-Nb for antimicrobial peptide (AMP) sequence design. This deposition contains raw training/validation peptide sequence datasets and pretrained plus fine-tuned model checkpoints .These files support computational reproducibility of experiments in the Reusability Report submitted to Nature Machine Intelligence. The checkpoints can be loaded to generate peptide sequences and reproduce loss calculations, evaluation metrics and peptide generation results. Dataset splits, sequence filtering rules and preprocessing scripts are provided in the associated Github repositorie.