Self-improving LLM agents edit their own harness, the prompts and rules around a fixed model, and keep an edit only if an acceptance gate scores it higher on a batch of tasks. Such a gate sees what the harness does under the current model, not what it would still prevent if one safeguard failed. When safeguards overlap, deleting one is masked: the others still block the harm, so the gate decides on task success alone and redundancy erodes unseen. We measure harm for every subset of four written safeguards in two agent environments and run 411 improvement loops under ten gate rules, mostly as controlled deletion experiments, plus three runs of the GEPA optimizer. A deletion behind another working safeguard adds almost no observable harm. A paired significance test blocks deletions that pass by chance but not deletions that genuinely raise task success, and a larger evaluation batch lets it delete cheaper safeguards: at the same cost, 20-task batches kept every harness protected while 40-task batches lost all six. Large harm audits prevent exposure but not the loss of depth, which turns into harm when the harness is reused with a weaker model. GEPA kept every safety rule verbatim, yet two of its three final harnesses misused credentials under a weaker model. A statistical model frozen before the runs predicts where each gate's protection breaks as safeguard cost and batch size change, and freezing safety text or auditing one-layer ablations preserves depth.
Weicai Long, Yusen Hou The Hong Kong University of Science and Technology (Guangzhou), Junning Feng, Houcheng su Hong Kong University of Science and Technology, Shuo Yang, Donglin Xie, Yanlin Zhang The Hong Kong University of Science and Technology (Guangzhou)
Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However, existing benchmarks either focus on specialized DNA models trained for sequence prediction or evaluate biological knowledge using text-only questions, leaving the behavior of general-purpose LLMs when directly exposed to raw genome sequences underexplored. We introduce GenomeQA, a benchmark designed to provide a controlled evaluation setting for general-purpose LLMs on sequence-based genome inference tasks. GenomeQA comprises 5,200 samples drawn from multiple biological databases, with sequence lengths ranging from 6 to 1,000 base pairs (bp), spanning six task families: Enhancer and Promoter Identification, Splice Site Identification, Taxonomic Classification, Histone Mark Prediction, Transcription Factor Binding Site Prediction, and TF Motif Prediction. Across six frontier LLMs, we find that models often outperform random baselines, particularly on tasks driven by local sequence cues such as GC content and short motifs, while performance degrades on tasks that require more indirect or multi-step inference over sequence patterns. GenomeQA establishes a diagnostic benchmark for studying and improving the use of general-purpose LLMs on raw genomic sequences.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表