Musab Hamed Saeed

Sequence models for oral resistome proteins lacked an evaluation that rules out homology-driven memorization. The study clustered 26,324 proteins into 1,437 clusters at 40% sequence identity, trained eight causal architectures under one protocol, and validated externally on CARD and NCBI AMRFinderPlus. Hyena reached the lowest held-out perplexity at 14.93, but only four of eight architectures beat the residue-composition baseline of 17.99 externally, where parameter-matched MoR led at 17.40 and the Transformer degraded by 27%.

Sequence models for oral resistome proteins lacked an evaluation that rules out homology-driven memorization. The study clustered 26,324 proteins into 1,437 clusters at 40% sequence identity, trained eight causal architectures under one protocol, and validated externally on CARD and NCBI AMRFinderPlus. Hyena reached the lowest held-out perplexity at 14.93, but only four of eight architectures beat the residue-composition baseline of 17.99 externally, where parameter-matched MoR led at 17.40 and the Transformer degraded by 27%.