Quintina L. Campbell

Quintina L. Campbell, Jonathan Herington, Andrew D. White

Machine learning models have dual-use potential, potentially serving both beneficial and malicious purposes. The development of open-source models in chemistry has specifically surfaced dual-use concerns around toxicological data and chemical warfare agents. We discuss a chain risk framework identifying three misuse pathways and corresponding mitigation strategies: inference-level, model-level, and data-level. At the data level, we introduce a model-agnostic noising method to increase prediction error in specific desired regions (sensitive regions). Our results show that selective noise induces variance and attenuation bias, whereas simply omitting sensitive data fails to prevent extrapolation. These findings hold for both molecular feature multilayer perceptrons and graph neural networks. Thus, noising molecular structures can enable open sharing of potential dual-use molecular data.

Quintina Campbell, Sam Cox, Jorge Medina et al.

Molecular dynamics (MD) simulations are essential for understanding biomolecular systems but remain challenging to automate. Recent advances in large language models (LLM) have demonstrated success in automating complex scientific tasks using LLM-based agents. In this paper, we introduce MDCrow, an agentic LLM assistant capable of automating MD workflows. MDCrow uses chain-of-thought over 40 expert-designed tools for handling and processing files, setting up simulations, analyzing the simulation outputs, and retrieving relevant information from literature and databases. We assess MDCrow's performance across 25 tasks of varying required subtasks and difficulty, and we evaluate the agent's robustness to both difficulty and prompt style. \texttt{gpt-4o} is able to complete complex tasks with low variance, followed closely by \texttt{llama3-405b}, a compelling open-source model. While prompt style does not influence the best models' performance, it has significant effects on smaller models.