用图谱模式融合生成药物不良反应,突破传统分类限制。
From Classification to Generation: An Open-Ended Paradigm for Adverse Drug Reaction Prediction Based on Graph-Motif Feature Fusion
- 构建原子-局部-全局三层次图结构,融合分子片段特征。
- 将多标签预测转为生成任务,预测空间从200扩至超1万种。
- 支持开放标签生成,适合新药研发中的风险预警场景。
计算生物学有望通过药物不良反应(ADR)预测降低新药研发的成本与周期。然而现有方法受限于数据稀缺导致的冷启动问题、封闭标签集及标签依赖建模不足。本文提出基于图谱模式融合与多标签生成的开放式预测范式(GM-MLG)。利用分子结构作为内在特征,构建跨越原子级、局部分子级(通过BRICS算法动态提取细粒度片段并结合额外断裂规则)和全局分子级的双图表示架构。创新性地将多标签分类转化为基于Transformer解码器的多标签生成任务,将ADR标签视为离散序列,通过位置嵌入显式建模大规模标签空间内的依赖与共现关系,采用自回归解码动态扩展预测空间。实验表明,GM-MLG最高提升38%,平均提升20%,预测类型数从200增至超10,000种。此外,通过逆合成片段分析揭示了非线性的结构-活性关系,为药物安全系统性降险提供可解释的新视角。
原文摘要 · Abstract (English)
Computational biology offers immense potential for reducing the high costs and protracted cycles of new drug development through adverse drug reaction (ADR) prediction. However, current methods remain impeded by drug data scarcity-induced cold-start challenge, closed label sets, and inadequate modeling of label dependencies. Here we propose an open-ended ADR prediction paradigm based on Graph-Motif feature fusion and Multi-Label Generation (GM-MLG). Leveraging molecular structure as an intrinsic and inherent feature, GM-MLG constructs a dual-graph representation architecture spanning the atomic level, the local molecular level (utilizing fine-grained motifs dynamically extracted via the BRICS algorithm combined with additional fragmentation rules), and the global molecular level. Uniquely, GM-MLG pioneers transforming ADR prediction from multi-label classification into Transformer Decoder-based multi-label generation. By treating ADR labels as discrete token sequences, it employs positional embeddings to explicitly capture dependencies and co-occurrence relationships within large-scale label spaces, generating predictions via autoregressive decoding to dynamically expand the prediction space. Experiments demonstrate GM-MLG achieves up to 38% improvement and an average gain of 20%, expanding the prediction space from 200 to over 10,000 types. Furthermore, it elucidates non-linear structure-activity relationships between ADRs and motifs via retrosynthetic motif analysis, providing interpretable and innovative support for systematic risk reduction in drug safety.
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