新矩阵分解方法自动选参数,提升网络缺链预测准确率
Matrix Factorization for Inferring Associations and Missing Links
- 用加权、布尔、推荐三类新分解法自动确定隐藏特征数
- 在蛋白质互作网络上比传统方法更准,尤其小样本时优势明显
- 自带置信度评估,可拒绝不确定预测,适合安全等高风险场景
缺链预测广泛应用于推荐系统、生物网络、网络安全等领域。现有非负矩阵分解(NMF)和逻辑矩阵分解(LMF)需手动设定隐特征数k,易过拟合或欠拟合。本文提出加权(WNMFk)、布尔(BNMFk)和推荐(RNMFk)三种新方法,并引入集成版本融合逻辑分解。通过改进的自助法与不确定性量化(UQ),实现自动选择最优秩k,评估预测可靠性。采用Otsu阈值和k-means聚类优化布尔分解,对比坐标下降法。实验在三个合成数据集及五个真实蛋白-蛋白互作网络上验证,结果表明:秩选择影响显著,小测试集下性能更优;结合弃权策略的UQ可提升预测可信度。
原文摘要 · Abstract (English)
Missing link prediction is a method for network analysis, with applications in recommender systems, biology, social sciences, cybersecurity, information retrieval, and Artificial Intelligence (AI) reasoning in Knowledge Graphs. Missing link prediction identifies unseen but potentially existing connections in a network by analyzing the observed patterns and relationships. In proliferation detection, this supports efforts to identify and characterize attempts by state and non-state actors to acquire nuclear weapons or associated technology - a notoriously challenging but vital mission for global security. Dimensionality reduction techniques like Non-Negative Matrix Factorization (NMF) and Logistic Matrix Factorization (LMF) are effective but require selection of the matrix rank parameter, that is, of the number of hidden features, k, to avoid over/under-fitting. We introduce novel Weighted (WNMFk), Boolean (BNMFk), and Recommender (RNMFk) matrix factorization methods, along with ensemble variants incorporating logistic factorization, for link prediction. Our methods integrate automatic model determination for rank estimation by evaluating stability and accuracy using a modified bootstrap methodology and uncertainty quantification (UQ), assessing prediction reliability under random perturbations. We incorporate Otsu threshold selection and k-means clustering for Boolean matrix factorization, comparing them to coordinate descent-based Boolean thresholding. Our experiments highlight the impact of rank k selection, evaluate model performance under varying test-set sizes, and demonstrate the benefits of UQ for reliable predictions using abstention. We validate our methods on three synthetic datasets (Boolean and uniformly distributed) and benchmark them against LMF and symmetric LMF (symLMF) on five real-world protein-protein interaction networks, showcasing an improved prediction performance.
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