量子核学习提升小分子药物活性分类,可定位关键分子的预测变化
QBioFusion-QSAR: Morgan-Anchored Quantum Multiple Kernel Learning for Small-Data Ligand Classification
- 融合摩根指纹与量子保真度核,用支持向量机构建多核模型
- 在54分子基准上准确率提升至0.833,活动悬崖子集的MCC达0.22
- 可追溯量子核对特定分子预测的影响,适合小数据药物发现研究
小样本定量结构-活性关系(QSAR)研究中,结构相近却活性不同的分子难以区分。本文探索量子核能否为摩根/Tanimoto指纹模型补充相似性信息,并识别关键分子。QBioFusion-QSAR采用量子多核学习(QMKL):支持向量机结合摩根/Tanimoto核、基于RDKit和Mordred描述符及Deep-PK特征的折叠局部成分构建的量子保真度核,以及线性和径向基函数描述符核作为经典对照。在54分子PsychLight-A基准上,摩根/Tanimoto为最强单一表示。主分层五折评估中,QMKL将准确率从0.815提升至0.833,马修斯相关系数(MCC)从0.613升至0.645。匹配正则化审计显示,预测变化主要来自N-Me-5-HT和N-Me-tryptamine由假阴性转为真阳性;活动悬崖子集的MCC从0.07升至0.22。十次随机划分五折重复实验表明,学习到的QMKL平均MCC未超越摩根/Tanimoto;配对留出自助区间亦包含零。结果支持QBioFusion-QSAR作为可审计的QMKL框架,用于小数据、活动悬崖敏感的配体分类中定位局域量子核贡献。
原文摘要 · Abstract (English)
Small quantitative structure-activity relationship (QSAR) studies are difficult when close molecular analogues have different activity labels. This paper asks whether a quantum kernel can add similarity information to a Morgan/Tanimoto fingerprint model, and which molecules account for the change. QBioFusion-QSAR uses quantum multiple kernel learning (QMKL): a support vector machine combines a Morgan/Tanimoto kernel with a quantum fidelity kernel constructed from fold-local components derived from RDKit and Mordred descriptors and Deep-PK features. Linear and radial basis function descriptor kernels are included as classical controls. On the 54-molecule PsychLight-A benchmark, Morgan/Tanimoto was the strongest single representation. In the primary stratified five-fold evaluation, QMKL increased accuracy from 0.815 to 0.833 and Matthews correlation coefficient (MCC) from 0.613 to 0.645. Matched-regularization auditing attributed the change to N-Me-5-HT and N-Me-tryptamine changing from false-negative to true-positive predictions; activity-cliff subset MCC increased from 0.07 to 0.22. Repeating the five-fold protocol over ten random partitionings showed that learned QMKL did not exceed Morgan/Tanimoto on mean MCC; paired held-out bootstrap intervals for the matched comparison also span zero. These results support QBioFusion-QSAR as an auditable QMKL framework for identifying localized residual quantum-kernel contributions in small-data, activity-cliff-aware ligand classification.
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