融合分子图、SMILES和理化参数的多模态模型,提升药物分子性质预测效率
GLACIER: A Multimodal Student-Teacher Foundation Model for Molecular Property Prediction

- 三模态学生编码器分别处理分子图、SMILES串和理化描述符
- 在10万种类药分子上预训练,对比学习蒸馏大模型知识
- 轻量级模型实现高精度与低计算开销,适合药物研发场景
深度学习模型助力在数十亿候选化合物中发现具有特定性质的分子。然而,开发和部署先进模型的计算成本持续上升,限制了其可扩展性。现有大规模模型多为单模态,未能充分利用互补的分子数据模态。为此,本文提出一种名为GLACIER的多模态师生框架,整合分子图、SMILES字符串和理化描述符以学习丰富的分子嵌入。该框架包含三个阶段:(1) 在10万种类药分子上预训练三个学生编码器——基于消息传递的神经网络处理分子图,基于Transformer的编码器处理SMILES字符串,多层感知机处理理化描述符;(2) 使用新颖的弗因斯勒几何感知模块融合三类模态信息;(3) 通过对比学习将MiniMol和MolFormer等大型教师模型中的互补知识蒸馏至一个轻量级模型。实验表明,GLACIER在复杂分子性质预测任务中兼具高预测性能与计算效率。代码已公开于https://github.com/eemokey/glacier。
原文摘要 · Abstract (English)
Deep learning models facilitate the discovery of molecules with tailored properties among billions of candidate compounds. However, the computational burden to develop and deploy state-of-the-art models continuously increases, limiting their scalability. Most large-scale models are unimodal in nature and overlook the potential to leverage complementary molecular data modalities. To address these shortcomings, this paper introduces the Graph-Language Alignment for Chemical Inference and Exploration using Representations (GLACIER) model, a student-teacher framework that integrates molecular graphs, SMILES strings, and physicochemical descriptors to learn rich molecular embeddings. Our framework consists of three stages: (1) we pretrain three student encoders on 100,000 drug-like molecules: a message-passing neural network for molecular graphs, a transformer-based encoder for SMILES strings, and a multilayer perceptron for physicochemical descriptors, (2) we fuse these student modalities using a novel Finsler geometry-aware module, and (3) distill complementary knowledge from large teacher models, including MiniMol and MolFormer, into a single lightweight model via contrastive learning. We demonstrate that GLACIER is a robust framework that delivers high predictive performance and computational efficiency in complex molecular property prediction tasks. Our code is publicly available at https://github.com/eemokey/glacier.
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