From DNA Design to DNA Slimming: Auditable Agentic Discovery of a Deletion-Only Designer
ERA found a deletion-only DNA “slimming” program that beat greedy baselines in most held-out tests.
The paper defines sequence slimming as keeping an exact-length, order-preserving subsequence while preserving predicted regulatory activity. Its benchmark requires slimmed sequences to include source indices, making compliance auditable. Starting from a substitution-only designer, the ERA coding agent produced GRADASLIM and tested it on five transcription-factor binding targets at 400 bp and 100 bp. ERA led the mean score in 9 of 10 settings, with clearer gains over greedy at 400 bp than at 100 bp. ArXiv · AI/CL/LG's note
The paper defines sequence slimming as keeping an exact-length, order-preserving subsequence while preserving predicted regulatory activity. Its benchmark requires slimmed sequences to include source indices, making compliance auditable. Starting from a substitution-only designer, the ERA coding agent produced GRADASLIM and tested it on five transcription-factor binding targets at 400 bp and 100 bp. ERA led the mean score in 9 of 10 settings, with clearer gains over greedy at 400 bp than at 100 bp. ArXiv · AI/CL/LG's note
score 4