# Aleena: Alignment Agent for Research Software Engineering Collaborations

arXiv: https://arxiv.org/abs/2607.08043 · HTML: https://mlsanity.com/paper/2607.08043/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 15 of its 52 references that are in the map.
- First posted on arXiv 9 Jul 2026.

## Builds on (most cited first, 15 of 15)

- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [SWE-bench: Can Language Models Resolve Real-World GitHub Issues?](https://mlsanity.com/paper/2310.06770/) (2023)
- [A Survey on Large Language Model based Autonomous Agents](https://mlsanity.com/paper/2308.11432/) (2023)
- [LLMs Get Lost In Multi-Turn Conversation](https://mlsanity.com/paper/2505.06120/) (2025)
- [Small Language Models are the Future of Agentic AI](https://mlsanity.com/paper/2506.02153/) (2025)
- [Is Stack Overflow Obsolete? An Empirical Study of the Characteristics of ChatGPT Answers to Stack Overflow Questions](https://mlsanity.com/paper/2308.02312/) (2023)
- [LLMRouterBench: A Massive Benchmark and Unified Framework for LLM Routing](https://mlsanity.com/paper/2601.07206/) (2026)
- [RAG-MCP: Mitigating Prompt Bloat in LLM Tool Selection via Retrieval-Augmented Generation](https://mlsanity.com/paper/2505.03275/) (2025)
- [How Scientists Use Large Language Models to Program](https://mlsanity.com/paper/2502.17348/) (2025)
- [From Technical Debt to Cognitive and Intent Debt: Rethinking Software Health in the Age of AI](https://mlsanity.com/paper/2603.22106/) (2026)
- [GitHub Discussions: An Exploratory Study of Early Adoption](https://mlsanity.com/paper/2102.05230/) (2021)
- [Ten Simple Rules for AI-Assisted Coding in Science](https://mlsanity.com/paper/2510.22254/) (2025)
- [A survey of generative AI adoption and perceived productivity among scientists who program](https://mlsanity.com/paper/2512.19644/) (2025)
- [Action-Item-Driven Summarization of Long Meeting Transcripts](https://mlsanity.com/paper/2312.17581/) (2023)
- [Requirements Engineering for Research Software: A Vision](https://mlsanity.com/paper/2405.07781/) (2024)

## Abstract (arXiv)

Research software collaborations span meetings, informal chats, pull requests, and GitHub issues. A decision surfaced in a Slack thread, refined in a meeting, and implemented in a pull request can lose its original rationale across these artifacts, leaving domain researchers and research software engineers with divergent mental models of project intent, ownership, and scientific assumptions. We argue that alignment in research software engineering is a continuous lifecycle problem, and that agentic AI can support stakeholder alignment and project-state tracking without replacing human decision-making. We present Aleena, an open-source lifecycle alignment agent that uses GitHub as a shared collaboration surface, transforming multi-modal stakeholder interactions into structured project records that surface risks, track open questions, and preserve decision continuity. Grounded in university-based research software engineering center experiences, this paper presents the motivating problem, system design, prototype, and illustrative lifecycle scenarios for Aleena.