简单、注意力机制与空间特征结合,提升分子性质预测效果。
Optimal message passing for molecular prediction is simple, attentive and spatial
- 用简化消息传递+注意力机制,替代复杂模型设计。
- 在多数数据集上超越复杂模型,且计算成本降低50%以上。
- 2D图配3D描述符即可,适合高通量筛选场景。
为提升分子性质预测的图神经网络性能,本文通过简化消息传递方式并引入多维度分子图描述符,设计出达到当前最优表现的模型架构,优于许多在外部数据库预训练的复杂模型。我们评估了数据集多样性,发现结构多样性影响对额外组件的需求。在多数数据集中,最佳架构采用双向消息传递与注意力机制,配合不包含自感知的极简消息形式,显著提升类别可分性。而卷积归一化因子在所有测试数据集中未带来性能增益。同时分析表明,加入空间特征并使用3D图并非必要;当搭配合适3D描述符时,仅用2D分子图即可保持预测性能,且计算成本降低超过50%,特别适用于高通量筛选任务。
原文摘要 · Abstract (English)
Strategies to improve the predicting performance of Message-Passing Neural-Networks for molecular property predictions can be achieved by simplifying how the message is passed and by using descriptors that capture multiple aspects of molecular graphs. In this work, we designed model architectures that achieved state-of-the-art performance, surpassing more complex models such as those pre-trained on external databases. We assessed dataset diversity to complement our performance results, finding that structural diversity influences the need for additional components in our MPNNs and feature sets. In most datasets, our best architecture employs bidirectional message-passing with an attention mechanism, applied to a minimalist message formulation that excludes self-perception, highlighting that relatively simpler models, compared to classical MPNNs, yield higher class separability. In contrast, we found that convolution normalization factors do not benefit the predictive power in all the datasets tested. This was corroborated in both global and node-level outputs. Additionally, we analyzed the influence of both adding spatial features and working with 3D graphs, finding that 2D molecular graphs are sufficient when complemented with appropriately chosen 3D descriptors. This approach not only preserves predictive performance but also reduces computational cost by over 50%, making it particularly advantageous for high-throughput screening campaigns.
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