# Biosecurity-Aware AI: Agentic Risk Auditing of Soft Prompt Attacks on ESM-Based Variant Predictors

arXiv: https://arxiv.org/abs/2512.17146 · HTML: https://mlsanity.com/paper/2512.17146/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Agent threats, guardrails and governance, one of 16 directions in LLM agents and tool use.
- Builds on 6 of its 19 references that are in the map.
- First posted on arXiv 19 Dec 2025.

## Placed in

- LLM agents and tool use / [Agent threats, guardrails and governance](https://mlsanity.com/agents/agent-threats-guardrails-and-governance/)

## Builds on (most cited first, 6 of 6)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [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)
- [A Baseline for Detecting Misclassified and Out-of-Distribution Examples in Neural Networks](https://mlsanity.com/paper/1610.02136/) (2016)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [FIMBA: Evaluating the Robustness of AI in Genomics via Feature Importance Adversarial Attacks](https://mlsanity.com/paper/2401.10657/) (2024)

## Abstract (arXiv)

Genomic Foundation Models (GFMs), such as Evolutionary Scale Modeling (ESM), have demonstrated remarkable success in variant effect prediction. However, their security and robustness under adversarial manipulation remain largely unexplored. To address this gap, we introduce the Secure Agentic Genomic Evaluator (SAGE), an agentic framework for auditing the adversarial vulnerabilities of GFMs. SAGE functions through an interpretable and automated risk auditing loop. It injects soft prompt perturbations, monitors model behavior across training checkpoints, computes risk metrics such as AUROC and AUPR, and generates structured reports with large language model-based narrative explanations. This agentic process enables continuous evaluation of embedding-space robustness without modifying the underlying model. Using SAGE, we find that even state-of-the-art GFMs like ESM2 are sensitive to targeted soft prompt attacks, resulting in measurable performance degradation. These findings reveal critical and previously hidden vulnerabilities in genomic foundation models, showing the importance of agentic risk auditing in securing biomedical applications such as clinical variant interpretation.