POEMS通过稀疏解码实现多组学数据的可解释集成,兼顾预测性能与生物标志物发现。
POEMS: Product of Experts for Interpretable Multi-omic Integration using Sparse Decoding
- 用稀疏连接映射特征到潜在因子,直接支持生物标志物挖掘。
- 通过专家产品模型共享潜空间,捕捉跨组学关联,保持非线性表达能力。
- 门控网络自适应计算各组学贡献,适合需要可解释性的癌症研究者。
整合不同分子层(即多组学数据)对揭示疾病复杂性至关重要;然而,大多数深度生成模型要么牺牲可解释性以追求预测性能,要么通过线性化解码器来强制可解释性,从而削弱了网络的非线性表达能力。为克服这一权衡,我们提出POEMS:基于稀疏解码的可解释多组学集成方法,一种无监督概率框架,在保持预测性能的同时提供可解释性。POEMS通过以下方式实现可解释性且不线性化网络任何部分:1)利用稀疏连接将特征映射至潜在因子,直接对应生物标志物发现;2)通过专家产品模型在共享潜空间中建立跨组学关联;3)通过门控网络自适应计算各组学在表示学习中的影响。此外,我们设计了一种高效的稀疏解码器。在癌症亚型分类案例研究中,POEMS实现了具有竞争力的聚类与分类性能,同时提供了新颖的解释视角,证明了基于生物标志物的洞见与预测准确性可在多组学表征学习中共存。
原文摘要 · Abstract (English)
Integrating different molecular layers, i.e., multiomics data, is crucial for unraveling the complexity of diseases; yet, most deep generative models either prioritize predictive performance at the expense of interpretability or enforce interpretability by linearizing the decoder, thereby weakening the network's nonlinear expressiveness. To overcome this tradeoff, we introduce POEMS: Product Of Experts for Interpretable Multiomics Integration using Sparse Decoding, an unsupervised probabilistic framework that preserves predictive performance while providing interpretability. POEMS provides interpretability without linearizing any part of the network by 1) mapping features to latent factors using sparse connections, which directly translates to biomarker discovery, 2) allowing for cross-omic associations through a shared latent space using product of experts model, and 3) reporting contributions of each omic by a gating network that adaptively computes their influence in the representation learning. Additionally, we present an efficient sparse decoder. In a cancer subtyping case study, POEMS achieves competitive clustering and classification performance while offering our novel set of interpretations, demonstrating that biomarker based insight and predictive accuracy can coexist in multiomics representation learning.
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