R-loop Prediction Reveals Generalization Limits of DNA Foundation Models Beyond Regulatory Genomics (opens in new tab)

DNA foundation models are increasingly proposed as general-purpose representations for genomic prediction and design, yet their evaluation remains largely centered on conventional regulatory tasks. This leaves a critical question unresolved: do DNA foundation models generalize to sequence biology beyond conventional gene regulation? To answer this question, we introduce RloopBench, a systematic benchmark for R-loop-forming sequence prediction as a biophysically distinct, genome-stability-asso...