# Theory Under Construction: Orchestrating Language Models for Research Software Where the Specification Evolves

arXiv: https://arxiv.org/abs/2604.27209 · HTML: https://mlsanity.com/paper/2604.27209/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 64 references that are in the map.
- First posted on arXiv 29 Apr 2026.

## Builds on (most cited first, 13 of 13)

- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Reflexion: Language Agents with Verbal Reinforcement Learning](https://mlsanity.com/paper/2303.11366/) (2023)
- [Voyager: An Open-Ended Embodied Agent with Large Language Models](https://mlsanity.com/paper/2305.16291/) (2023)
- [MetaGPT: Meta Programming for A Multi-Agent Collaborative Framework](https://mlsanity.com/paper/2308.00352/) (2023)
- [SWE-agent: Agent-Computer Interfaces Enable Automated Software Engineering](https://mlsanity.com/paper/2405.15793/) (2024)
- [The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery](https://mlsanity.com/paper/2408.06292/) (2024)
- [OpenHands: An Open Platform for AI Software Developers as Generalist Agents](https://mlsanity.com/paper/2407.16741/) (2024)
- [ChatDev: Communicative Agents for Software Development](https://mlsanity.com/paper/2307.07924/) (2023)
- [AlphaEvolve: A coding agent for scientific and algorithmic discovery](https://mlsanity.com/paper/2506.13131/) (2025)
- [Darwin Godel Machine: Open-Ended Evolution of Self-Improving Agents](https://mlsanity.com/paper/2505.22954/) (2025)
- [SciAgents: Automating scientific discovery through multi-agent intelligent graph reasoning](https://mlsanity.com/paper/2409.05556/) (2024)
- [Efficient Prompt Optimization Through the Lens of Best Arm Identification](https://mlsanity.com/paper/2402.09723/) (2024)
- [SMT-based Model Checking for Recursive Programs](https://mlsanity.com/paper/1405.4028/) (2014)

## Abstract (arXiv)

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.