# Your Agent Has a Genome: Sequence-Level Behavioral Analysis and Runtime Governance of LLM-Powered Autonomous Agents

arXiv: https://arxiv.org/abs/2606.15579 · HTML: https://mlsanity.com/paper/2606.15579/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Software engineering coding agents, one of 16 directions in LLM agents and tool use.
- Builds on 14 of its 20 references that are in the map.
- First posted on arXiv 5 Apr 2026.

## Placed in

- LLM agents and tool use / [Software engineering coding agents](https://mlsanity.com/agents/software-engineering-coding-agents/)

## Builds on (most cited first, 14 of 14)

- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [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)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [Tree of Thoughts: Deliberate Problem Solving with Large Language Models](https://mlsanity.com/paper/2305.10601/) (2023)
- [Constitutional AI: Harmlessness from AI Feedback](https://mlsanity.com/paper/2212.08073/) (2022)
- [Voyager: An Open-Ended Embodied Agent with Large Language Models](https://mlsanity.com/paper/2305.16291/) (2023)
- [SWE-agent: Agent-Computer Interfaces Enable Automated Software Engineering](https://mlsanity.com/paper/2405.15793/) (2024)
- [AgentBench: Evaluating LLMs as Agents](https://mlsanity.com/paper/2308.03688/) (2023)
- [OpenHands: An Open Platform for AI Software Developers as Generalist Agents](https://mlsanity.com/paper/2407.16741/) (2024)
- [Language Agent Tree Search Unifies Reasoning Acting and Planning in Language Models](https://mlsanity.com/paper/2310.04406/) (2023)
- [Cognitive Architectures for Language Agents](https://mlsanity.com/paper/2309.02427/) (2023)
- [RAGEN: Understanding Self-Evolution in LLM Agents via Multi-Turn Reinforcement Learning](https://mlsanity.com/paper/2504.20073/) (2025)
- [NeMo Guardrails: A Toolkit for Controllable and Safe LLM Applications with Programmable Rails](https://mlsanity.com/paper/2310.10501/) (2023)

## Abstract (arXiv)

We propose Base Sequence Analysis, a framework that encodes the runtime behavior of LLM-powered autonomous agents into compact symbolic sequences using a four-letter alphabet: X (Explore), E (Execute), P (Plan), and V (Verify). Drawing an analogy to genomic sequence analysis, we apply n-gram pattern mining, Markov transition matrices, and point-biserial correlation to 347 real-world execution traces collected from a production ReAct agent system over 8 days. Our analysis reveals that (1) the trigram P-X-P is the only statistically significant high-risk pattern, lowering success rate by 10.4%; (2) P-ratio is the strongest negative predictor of success (r=-0.256, p<0.0001); and (3) the E->V transition probability is only 2.1%, indicating a systemic verification deficit. Based on these findings, we design Governor, a three-layer runtime intervention system comprising a rule engine, a statistical accumulator, and a chi-square-based threshold adaptor. In a natural before/after deployment evaluation (N=101 vs. N=246), Governor achieves a +6.2% absolute increase in task success rate while simultaneously reducing average token consumption by 44%. To validate cross-system generality, we apply the XEPV encoding to 2,000 public SWE-agent trajectories on SWE-bench, confirming that exploration spirals and the E->V verification deficit replicate in an independent system. We outline six research directions including base sequence language models, cross-agent behavioral fingerprinting, and reward shaping, and release an open-source toolkit for reproducibility.