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arXiv 1806.03120stat.ME
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计数数据稀疏网络重构的变分推断

Variational inference for sparse network reconstruction from count data

Julien Chiquet, Mahendra Mariadassou, Stéphane Robin

摘要:

在多元统计中,寻找直接交互作用的问题可以被表述为网络推理或网络重构的问题,高斯图模型(GGM)为这个问题提供了一个规范的框架。不幸的是,高斯假设不适用于在基因组学,社会科学或生态学等领域遇到的计数数据。为了规避这种限制,最先进的方法使用两步策略,首先将计数转换为伪高斯观测,然后应用来自GGM推断的丰富文献的基于(部分)相关性的方法。我们采取不同的立场,依靠一个潜在的模型,我们直接建模计数的泊松分布的条件是潜在的(隐藏的)高斯相关变量。在这个多变量泊松对数正态模型中,依赖结构完全被潜在层捕获。该参数模型能够解释协变量对计数的影响。为了执行网络推理,我们在潜在高斯向量的逆协方差阵上添加稀疏诱导约束。与通常的高斯设置,惩罚的可能性一般是不听话的,而不是我们诉诸于变分近似似然最大化的方法。相应的优化问题是通过交替梯度上升的变分参数和图形的协方差阵上的拉索步骤。我们表明,我们的方法是非常有竞争力的,与现有的方法模拟启发从微生物数据。然后,我们说明了三个不同的数据集如何通过偏移和整合外部协变量(这在现有文献中大多是从来没有做过)的采样努力会计大幅改变推断网络的拓扑结构。

英文摘要:

In multivariate statistics, the question of finding direct interactions can be formulated as a problem of network inference - or network reconstruction - for which the Gaussian graphical model (GGM) provides a canonical framework. Unfortunately, the Gaussian assumption does not apply to count data which are encountered in domains such as genomics, social sciences or ecology. To circumvent this limitation, state-of-the-art approaches use two-step strategies that first transform counts to pseudo Gaussian observations and then apply a (partial) correlation-based approach from the abundant literature of GGM inference. We adopt a different stance by relying on a latent model where we directly model counts by means of Poisson distributions that are conditional to latent (hidden) Gaussian correlated variables. In this multivariate Poisson lognormal-model, the dependency structure is completely captured by the latent layer. This parametric model enables to account for the effects of covariates on the counts. To perform network inference, we add a sparsity inducing constraint on the inverse covariance matrix of the latent Gaussian vector. Unlike the usual Gaussian setting, the penalized likelihood is generally not tractable, and we resort instead to a variational approach for approximate likelihood maximization. The corresponding optimization problem is solved by alternating a gradient ascent on the variational parameters and a graphical-Lasso step on the covariance matrix. We show that our approach is highly competitive with the existing methods on simulation inspired from microbiological data. We then illustrate on three various data sets how accounting for sampling efforts via offsets and integrating external covariates (which is mostly never done in the existing literature) drastically changes the topology of the inferred network.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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