# Toward Reliable, Safe, and Secure LLMs for Scientific Applications

arXiv: https://arxiv.org/abs/2603.18235 · HTML: https://mlsanity.com/paper/2603.18235/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Agent threats, guardrails and governance, one of 16 directions in LLM agents and tool use.
- Builds on 62 of its 92 references that are in the map.
- First posted on arXiv 18 Mar 2026.

## 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, 30 of 62)

- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Generative Agents: Interactive Simulacra of Human Behavior](https://mlsanity.com/paper/2304.03442/) (2023)
- [Universal and Transferable Adversarial Attacks on Aligned Language Models](https://mlsanity.com/paper/2307.15043/) (2023)
- [TruthfulQA: Measuring How Models Mimic Human Falsehoods](https://mlsanity.com/paper/2109.07958/) (2021)
- [Jailbroken: How Does LLM Safety Training Fail?](https://mlsanity.com/paper/2307.02483/) (2023)
- [Not what you've signed up for: Compromising Real-World LLM-Integrated Applications with Indirect Prompt Injection](https://mlsanity.com/paper/2302.12173/) (2023)
- [FEVER: a large-scale dataset for Fact Extraction and VERification](https://mlsanity.com/paper/1803.05355/) (2018)
- [RealToxicityPrompts: Evaluating Neural Toxic Degeneration in Language Models](https://mlsanity.com/paper/2009.11462/) (2020)
- [Llama Guard: LLM-based Input-Output Safeguard for Human-AI Conversations](https://mlsanity.com/paper/2312.06674/) (2023)
- [Fine-tuning Aligned Language Models Compromises Safety, Even When Users Do Not Intend To!](https://mlsanity.com/paper/2310.03693/) (2023)
- [Red Teaming Language Models with Language Models](https://mlsanity.com/paper/2202.03286/) (2022)
- [Red Teaming Language Models to Reduce Harms: Methods, Scaling Behaviors, and Lessons Learned](https://mlsanity.com/paper/2209.07858/) (2022)
- [BBQ: A Hand-Built Bias Benchmark for Question Answering](https://mlsanity.com/paper/2110.08193/) (2021)
- [Safe RLHF: Safe Reinforcement Learning from Human Feedback](https://mlsanity.com/paper/2310.12773/) (2023)
- [Baseline Defenses for Adversarial Attacks Against Aligned Language Models](https://mlsanity.com/paper/2309.00614/) (2023)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Fact or Fiction: Verifying Scientific Claims](https://mlsanity.com/paper/2004.14974/) (2020)
- [ToxiGen: A Large-Scale Machine-Generated Dataset for Adversarial and Implicit Hate Speech Detection](https://mlsanity.com/paper/2203.09509/) (2022)
- [HaluEval: A Large-Scale Hallucination Evaluation Benchmark for Large Language Models](https://mlsanity.com/paper/2305.11747/) (2023)
- [Benchmarking Large Language Models in Retrieval-Augmented Generation](https://mlsanity.com/paper/2309.01431/) (2023)
- [PoisonedRAG: Knowledge Corruption Attacks to Retrieval-Augmented Generation of Large Language Models](https://mlsanity.com/paper/2402.07867/) (2024)
- [Do Membership Inference Attacks Work on Large Language Models?](https://mlsanity.com/paper/2402.07841/) (2024)
- [FEVEROUS: Fact Extraction and VERification Over Unstructured and Structured information](https://mlsanity.com/paper/2106.05707/) (2021)
- [Witches' Brew: Industrial Scale Data Poisoning via Gradient Matching](https://mlsanity.com/paper/2009.02276/) (2020)
- [ProPILE: Probing Privacy Leakage in Large Language Models](https://mlsanity.com/paper/2307.01881/) (2023)
- [Empowering Biomedical Discovery with AI Agents](https://mlsanity.com/paper/2404.02831/) (2024)
- [A Review of Large Language Models and Autonomous Agents in Chemistry](https://mlsanity.com/paper/2407.01603/) (2024)
- [CVE-Bench: A Benchmark for AI Agents' Ability to Exploit Real-World Web Application Vulnerabilities](https://mlsanity.com/paper/2503.17332/) (2025)
- [SciFact-Open: Towards open-domain scientific claim verification](https://mlsanity.com/paper/2210.13777/) (2022)
- [Benchmarking large language models for biomedical natural language processing applications and recommendations](https://mlsanity.com/paper/2305.16326/) (2023)

## Built on by (most cited first, 1 of 1)

- [Eta Given Delta: Defining LLM Tool Efficiency With Marginal Tool Utility](https://mlsanity.com/paper/2607.14108/) (2026)

## Abstract (arXiv)

As large language models (LLMs) evolve into autonomous "AI scientists," they promise transformative advances but introduce novel vulnerabilities, from potential "biosafety risks" to "dangerous explosions." Ensuring trustworthy deployment in science requires a new paradigm centered on reliability (ensuring factual accuracy and reproducibility), safety (preventing unintentional physical or biological harm), and security (preventing malicious misuse). Existing general-purpose safety benchmarks are poorly suited for this purpose, suffering from a fundamental domain mismatch, limited threat coverage of science-specific vectors, and benchmark overfitting, which create a critical gap in vulnerability evaluation for scientific applications. This paper examines the unique security and safety landscape of LLM agents in science. We begin by synthesizing a detailed taxonomy of LLM threats contextualized for scientific research, to better understand the unique risks associated with LLMs in science. Next, we conceptualize a mechanism to address the evaluation gap by utilizing dedicated multi-agent systems for the automated generation of domain-specific adversarial security benchmarks. Based on our analysis, we outline how existing safety methods can be brought together and integrated into a conceptual multilayered defense framework designed to combine a red-teaming exercise and external boundary controls with a proactive internal Safety LLM Agent. Together, these conceptual elements provide a necessary structure for defining, evaluating, and creating comprehensive defense strategies for trustworthy LLM agent deployment in scientific disciplines.