通过构建包含链结构拓扑的图模型,显著提升聚合物性质预测精度。
It's All Connected: Topology-Aware Structural Graph Encoding Improves Performance on Polymer Prediction

- 基于分子量分布采样链结构,构建包含拓扑信息的大规模图表示
- 自监督预训练结合大图结构使误差降低5.1%,达24.76K RMSE
- 适用于多种GNN架构,对化学特征敏感,适合材料设计研究者
图神经网络在分子性质预测中表现优异,但聚合物面临标签数据稀缺(通常仅数百种)和链结构复杂性影响性能的挑战。现有方法仅用重复单元图表示聚合物,忽略了决定玻璃化转变温度(Tg)等关键性质的链尺度形貌。本文提出一种系统性图构建方法:基于分子量分布(MMD)从Schulz-Zimm分布中采样代表性链,构建编码链级拓扑的大规模图,使用丰富化学描述符对原子和键进行表征。进一步在10万条未标注PSMILES字符串上进行自监督预训练,再微调至381种聚合物数据集(180种均聚物,201种共聚物)。结果表明,图构建与预训练协同必要:无预训练时,大图方法性能与重复单元基线相当(28.40 K vs. 28.36 K RMSE);有预训练时,误差降至24.76 K ± 3.30 K,较预训练重复单元基线(26.08 K ± 4.20 K,p < 0.001,30次运行)降低5.1%。移除化学特征后性能降为36.65 K,证明两组件均关键。结果对GINE与GATv2架构均成立。
原文摘要 · Abstract (English)
Graph Neural Networks (GNNs) have achieved strong results in molecular property prediction, but polymers present distinct challenges: labeled datasets are scarce and small (typically in the order of hundreds of polymers) due to the need for expensive experimentation, and complex polymer chain distributions influence polymer properties. Established practice in polymer prediction represents polymers solely by graphs of their repeat units, discarding the chain-scale morphology that governs key properties such as the glass transition temperature ($T_g$). In this work, we propose a principled graph construction that addresses this gap. Given a polymer's molecular mass distribution (MMD), we sample representative chains from the Schulz-Zimm distribution and construct representative sets of large graphs encoding chain-scale topology directly, with atoms and bonds featurized using rich chemical descriptors. We further pretrain GNN encoders via masked graph modeling on 100,000 unlabeled PSMILES strings before fine-tuning on labeled data. On a dataset of 381 polymers (180 homopolymers and 201 copolymers), we show that graph construction and self-supervised pretraining are jointly necessary: without pretraining, the large graph method matches the repeat-unit baseline (28.40 K vs. 28.36 K RMSE); with pretraining, it achieves 24.76 K +/- 3.30 K, a 5.1% reduction in mean error over the pretrained repeat-unit baseline (26.08 K +/- 4.20 K, p < 0.001, 30 runs). An ablation removing chemical features degrades performance to 36.65 K, confirming both components are essential. Results are architecture-agnostic, holding for both GINE and GATv2 encoders.
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