Statistical Testing Framework for Clustering Pipelines by Selective Inference

Deep clustering is a powerful approach for discovering meaningful structures in high-dimensional data by learning a low-dimensional latent representation prior to clustering. Despite its empirical success, assessing the statistical reliability of the resulting clusters remains challenging. Testing discovered clusters on the same data induces selection bias and invalidates classical $p$-values. Selective inference (SI) provides a principled framework for correcting this bias, but existing methods focus on clustering performed directly on the observed features. In this work, we develop an SI framework for deep clustering with a fixed pretrained encoder. The key challenge is that cluster assignments are determined through a nonlinear transformation from the original data space to the latent space, resulting in a substantially more complex selection process than in conventional clustering. Our method provides a computationally tractable way to account for this process and enables valid statistical testing of differences between clusters identified in the latent space. Synthetic experiments demonstrate that the proposed method controls the Type I error rate while achieving higher power than valid but conservative baselines, and genomic applications show that it can identify significant cluster differences while appropriately accounting for selection bias. Our framework provides a principled approach to quantifying the statistical reliability of structures discovered by deep clustering.

Selecting the number of clusters remains a fundamental challenge in unsupervised learning. Existing approaches typically focus on identifying a single "optimal" partition, often overlooking statistically meaningful structure present across multiple resolutions. We introduce ElbowSig, a general inferential framework for assessing clustering structure over a range of resolutions. The method formalizes the elbow heuristic by defining a normalized discrete curvature statistic based on the sequence of within-cluster heterogeneity values, and evaluates its significance relative to a null distribution of unstructured data. This yields hypothesis tests across resolutions, enabling simultaneous inference at multiple clustering scales. We derive the asymptotic behavior of the null statistic in both large-sample and high-dimensional regimes, characterizing its limiting form and variability. Because it depends only on the heterogeneity sequence, ElbowSig is compatible with a wide range of clustering algorithms, including hard, fuzzy, and model-based methods. Experiments on synthetic and real datasets show that the procedure controls Type-I error under unstructured data while providing power to detect multiscale organization, revealing structure that is often missed by single-resolution selection criteria.

Unsupervised clustering is widely used to discover underlying group structure, after which researchers often seek to validate these groups via post-hoc hypothesis testing on the population means. However, using the same data both to form clusters and to test for a difference in means inflates the Type I error rate. Recent work in selective inference has proposed solutions when the underlying data are drawn from a multivariate Gaussian distribution with a known covariance matrix or an unknown isotropic covariance matrix. We propose a new selective test for the difference in means between two clusters that provably controls the Type I error rate under an arbitrary unknown covariance matrix. Our test statistic does not require estimating the feature covariance matrix; instead, it leverages a Monte Carlo sampling procedure over the set of orthogonal matrices. We show that this new selective test can be computed efficiently, and we derive closed-form solutions when clusters are formed using k-means or hierarchical clustering. In simulations, we demonstrate that our proposed p-value controls the selective Type I error rate and achieves substantial power, and we illustrate its application on gene expression and drug review data sets.