ATOM模型可跨分子、跨时长零样本预测分子动力学,速度更快更通用。
ATOM: A Pretrained Neural Operator for Multitask Molecular Dynamics
- 用时序注意力机制实现多状态并行预测,无需依赖分子图结构
- 在超过250万飞秒的80种分子数据上预训练,支持跨化合物泛化
- 首次实现对未见分子在不同时间尺度上的零样本高精度预测
分子动力学模拟是现代药物发现、材料科学和生物化学的核心。现有机器学习模型虽能高效预测,但通常需严格保持对称性且依赖顺序推演,限制了灵活性与效率,且多为单任务,仅针对特定分子和固定时间范围训练,难以推广至新分子和更长时间。为此,我们提出原子级变压器算子(ATOM),一种用于多任务分子动力学的预训练神经算子。ATOM采用准对称设计,无需显式分子图,并引入时序注意力机制,实现多个未来状态的精确并行解码。为支持跨化学种类和时间尺度的算子预训练,我们构建了TG80数据集,包含80种化合物、超250万飞秒的数值稳定轨迹。ATOM在MD17、RMD17和MD22等经典单任务基准上达到领先性能;在TG80上进行多任务预训练后,展现出对未见分子在不同时间跨度下的卓越零样本泛化能力。我们认为,ATOM代表了更准确、高效、可迁移的分子动力学建模的重要进展。
原文摘要 · Abstract (English)
Molecular dynamics (MD) simulations underpin modern computational drug discovery, materials science, and biochemistry. Recent machine learning models provide high-fidelity MD predictions without the need to repeatedly solve quantum mechanical forces, enabling significant speedups over conventional pipelines. Yet many such methods typically enforce strict equivariance and rely on sequential rollouts, thus limiting their flexibility and simulation efficiency. They are also commonly single-task, trained on individual molecules and fixed timeframes, which restricts generalization to unseen compounds and extended timesteps. To address these issues, we propose Atomistic Transformer Operator for Molecules (ATOM), a pretrained transformer neural operator for multitask molecular dynamics. ATOM adopts a quasi-equivariant design that requires no explicit molecular graph and employs a temporal attention mechanism, allowing for the accurate parallel decoding of multiple future states. To support operator pretraining across chemicals and timescales, we curate TG80, a large, diverse, and numerically stable MD dataset with over 2.5 million femtoseconds of trajectories across 80 compounds. ATOM achieves state-of-the-art performance on established single-task benchmarks, such as MD17, RMD17 and MD22. After multitask pretraining on TG80, ATOM shows exceptional zero-shot generalization to unseen molecules across varying time horizons. We believe ATOM represents a significant step toward accurate, efficient, and transferable molecular dynamics models.
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