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| Main Authors: | , |
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| Format: | Preprint |
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2026
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| Online Access: | https://arxiv.org/abs/2604.27209 |
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| _version_ | 1866910182699696128 |
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| author | Young, Halley Björner, Nikolaj |
| author_facet | Young, Halley Björner, Nikolaj |
| contents | Large language models can now generate substantial code and draft research text, but research-software projects require more than either artifact alone. The mathematical thesis, executable system, benchmark surface, and public claims must mature together, yet often drift apart. We identify two LM-specific failure modes: hallucination accumulation, in which claims exceed what code or theory supports and unsupported assertions propagate across sessions; and desynchronization, in which code, theory, or the model's own world model fall out of alignment.
We propose Comet-H, an iterative prompt automaton that orchestrates ideation, implementation, evaluation, grounding, and paper-writing as coupled coordinates of a single workspace state. At each step, a controller selects the next prompt by scoring it against what the workspace currently lacks, carries unfinished follow-up work forward with a half-life, and re-checks the paper and README against the code and benchmarks whenever documentation changes. We frame prompt selection as a small contextual bandit problem over prompt families, with prompts as arms, workspace deficits as context, and a hand-weighted linear score. This transparent scorer, paired with a fading record of unfinished work, bounds long-horizon follow-ups, requires no learned policy, and makes each prompt choice legible from the workspace.
We created a portfolio of 46 research-software repositories across two dozen domains. We study A3 in depth, a Python static-analysis tool built entirely within the loop, which reaches (F1 = 0.768) on a 90-case benchmark, compared with a next-best baseline of 0.364. Across approximately 400 commits, we find that audit-and-contraction passes dominate the later phases of every successful trajectory. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2604_27209 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Theory Under Construction: Orchestrating Language Models for Research Software Where the Specification Evolves Young, Halley Björner, Nikolaj Software Engineering Artificial Intelligence Large language models can now generate substantial code and draft research text, but research-software projects require more than either artifact alone. The mathematical thesis, executable system, benchmark surface, and public claims must mature together, yet often drift apart. We identify two LM-specific failure modes: hallucination accumulation, in which claims exceed what code or theory supports and unsupported assertions propagate across sessions; and desynchronization, in which code, theory, or the model's own world model fall out of alignment. We propose Comet-H, an iterative prompt automaton that orchestrates ideation, implementation, evaluation, grounding, and paper-writing as coupled coordinates of a single workspace state. At each step, a controller selects the next prompt by scoring it against what the workspace currently lacks, carries unfinished follow-up work forward with a half-life, and re-checks the paper and README against the code and benchmarks whenever documentation changes. We frame prompt selection as a small contextual bandit problem over prompt families, with prompts as arms, workspace deficits as context, and a hand-weighted linear score. This transparent scorer, paired with a fading record of unfinished work, bounds long-horizon follow-ups, requires no learned policy, and makes each prompt choice legible from the workspace. We created a portfolio of 46 research-software repositories across two dozen domains. We study A3 in depth, a Python static-analysis tool built entirely within the loop, which reaches (F1 = 0.768) on a 90-case benchmark, compared with a next-best baseline of 0.364. Across approximately 400 commits, we find that audit-and-contraction passes dominate the later phases of every successful trajectory. |
| title | Theory Under Construction: Orchestrating Language Models for Research Software Where the Specification Evolves |
| topic | Software Engineering Artificial Intelligence |
| url | https://arxiv.org/abs/2604.27209 |