AcetylBench: a Deduplicated Benchmark Dataset Reveals Systematic Performance Inflation and Cross-Database Generalisation Failure in Lysine Acetylation Site Prediction

Lysine acetylation is a pervasive post-translational modification with critical regulatory roles, yet computational prediction of acetylation sites remains hampered by unreliable benchmarking practices including dataset redundancy and non-independent test set evaluation. We report a systematic investigation demonstrating that three independent sources of metric inflation, including near-ubiquitous sequence redundancy, non-independent test sets, and distribution-locked dimensionality reduction collectively reduced an apparent accuracy of 99.38