将分子演化动态转化为符号时间语言,让大模型学会预测化学反应过程。
EvoMD-LLM: Learning the Language of Species Evolution in Reactive Molecular Dynamics

- 把分子事件序列化为带持续时间的符号,用大模型建模反应演化过程。
- 在多个时间预测任务中最高达66.14%准确率,优于传统神经网络和语言模型。
- 能自动生成解释性推理,即使未受过成对轨迹-解释训练。
尽管大型语言模型(LLMs)在静态科学推理中表现优异,但在建模动态物理过程的时间结构方面仍存在困难。我们提出EvoMD-LLM(进化分子动力学大语言模型),将物种级分子动力学重构为符号性时间语言建模问题。反应型分子动力学轨迹被离散化为分子事件序列,每个标记代表一个化学物种及其持续时间,使标准自回归大模型可通过高效微调学习随时间的组合演化。EvoMD-LLM的关键组件是时间支架机制,将事件持续时间作为显式语言标记,提供结构化归纳偏置,显著降低传统序列建模方法产生的无效或幻觉分子输出。我们在多个时间预测任务上评估了EvoMD-LLM,最高达到66.14%的准确率,并持续优于序列神经网络和基于语言的基线模型。除了定量提升外,我们还定性观察到,该模型能够在未接受成对轨迹-解释数据监督的情况下,结合相关化学知识生成对其预测的解释。这些结果表明,符号时间语言建模为大模型在动态物理模拟中的落地提供了有效框架。
原文摘要 · Abstract (English)
While large language models (LLMs) excel at static scientific reasoning, they struggle to model the temporal structure of dynamic physical processes. We present EvoMD-LLM (Evolutionary Molecular Dynamics Large Language Model), a framework that reformulates species-level molecular dynamics as a symbolic temporal language modeling problem. Reactive MD trajectories are discretized into sequences of molecular events, where each token represents a chemical species augmented with its persistence duration, enabling standard autoregressive LLMs to learn compositional evolution over time through efficient fine-tuning. A key component of EvoMD-LLM is temporal scaffolding, which treats event duration as an explicit linguistic token and serves as a structured inductive bias, significantly reducing invalid or hallucinated molecular outputs compared to conventional sequence modeling approaches. We evaluate EvoMD-LLM on multiple temporal prediction tasks, achieving up to 66.14% accuracy and consistently outperforming sequential neural networks and language-based baselines. Beyond quantitative improvements, we qualitatively observe that the model is capable of generating interpretations for its own predictions by incorporating relevant chemical knowledge, even though it was not explicitly supervised with paired trajectory-explanation data. These results demonstrate that symbolic temporal language modeling provides an effective framework for grounding LLMs in dynamic physical simulations.
Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。