arXiv:2605.24742cs.LG2026-05

让分子图解释与化学身份一致,解决同分异构体导致的模型不一致问题。

Aligning Molecular Graph Explanations with Chemical Identity via InChIfied Invariants

论文配图:Aligning Molecular Graph Explanations with Chemical Identity via InChIfied Invariants
图 1 · 摘自论文原文
  • 基于InChI设计不变特征,确保同一分子不同画法输出相同表示。
  • 99.62%情况下对等价分子图生成一致表示,远超传统方法的0.35%。
  • 可直接替换现有特征,提升模型预测与解释的一致性,适合药物发现研究者。

机器学习在分子图上的可解释性依赖于预测与化学身份的一致性。然而,同一分子的不同画法可能产生不同表示,导致预测和解释不一致。本文提出InChIfied Invariants,一类基于国际化学标识符(InChI)的节点、边和图级特征,对保持化学身份的变换具有不变性。在来自PubChem Substances的一百万个分子图上,InChIfied Invariants在99.62%的情况下对等价分子图生成相同表示,而标准Daylight不变量仅在0.35%的情况下做到。在MoleculeNet任务中,InChIfied Invariants保持了预测性能,同时显著提升了同一分子不同图表示下的预测一致性。定量归因分析表明,传统特征方法在等价分子图上解释差异大,而InChIfied Invariants通过构造实现一致归因。我们开源了实现代码,可作为标准分子图特征的即插即用替代品。

原文摘要 · Abstract (English)

Obtaining consistent explanations for machine learning on molecular graphs requires predictions and attributions to be aligned with chemical identity. However, chemically equivalent drawings of the same molecule can induce different molecular representations, leading to inconsistent predictions and explanations. Here, we introduce InChIfied Invariants, a class of node, edge, and graph features based on the International Chemical Identifier (InChI) and designed to be invariant under transformations that preserve chemical identity. Using one million molecular graphs from PubChem Substances, we show that InChIfied Invariants produce identical representations for chemically equivalent graphs in 99.62% of cases, whereas standard Daylight invariants do so in only 0.35% of cases. Across MoleculeNet tasks, InChIfied Invariants preserve predictive performance while significantly improving prediction consistency across alternative graph depictions of the same molecules. We further perform a quantitative attribution analysis and show that explanations produced with standard molecular featurization methods vary substantially across chemically equivalent graphs, while InChIfied Invariants enforce consistent attributions by construction. We release open-source software implementing InChIfied Invariants, which can be used as a drop-in replacement for standard molecular graph features.

分子图可解释性化学信息学不变特征

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