Explainable cluster analysis: a bagging approach

Clustering is widely used for exploratory analysis and scientific discovery, driving insights from market segmentation to biological data analysis, but its outputs can be difficult to interpret, audit, and reproduce as modern datasets become increasingly large and complex. Reliable use of clustering requires understanding which features drive the discovered structure, yet feature-level explanations for clustering remain scarce compared with methods in supervised learning. Furthermore, existing clustering feature importance scores are often tied to specific algorithms and data assumptions. To address these challenges, we propose Cluster LOCO (Leave-One-Covariate-Out), a family of model-agnostic feature importance scores for clustering. Cluster LOCO is built on feature occlusion and clustering generalizability, defined as whether cluster labels learned on one subset of the data can be accurately predicted on held-out samples. For any chosen clustering algorithm, Cluster LOCO quantifies a feature's importance by measuring how much its removal degrades generalizability. We first introduce Cluster LOCO-Split, which relies on data splitting, and then extend it to Cluster LOCO-MP, a minipatch ensemble-based version designed for large-scale data. Across synthetic simulations and an application to cell-type discovery in single-cell transcriptomics, we show that Cluster LOCO more reliably recovers informative features than existing clustering feature importance methods.

Interpreting clustering outcomes remains a fundamental challenge in data analysis, particularly in domains such as healthcare where meaningful patterns must be extracted from high-dimensional data. While numerous explainability techniques exist, they are primarily designed to assess feature importance or provide local instance-level explanations rather than to identify structured patterns present within clusters. This work presents a comparative evaluation of commonly used post-hoc analysis methods for pattern detection in clustering results. To enable controlled evaluation, we introduce a suite of synthetic datasets in which predefined patterns are systematically injected. Three widely used techniques are evaluated: a Random Forest surrogate model with permutation feature importance, LIME (Local Interpretable Model-agnostic Explanations), and principal component analysis. Results demonstrate that although each method can successfully recover relevant features, none consistently detects all injected pattern types. These findings high- light a critical gap between existing explainability tools and the requirements of pattern-level cluster interpretation, motivating the development of dedicated pattern detection methodologies.

Clustering mixed-type tabular data is fundamental for exploratory analysis, yet remains challenging due to misaligned numerical-categorical representations, uneven and context-dependent feature relevance, and disconnected and post-hoc explanation from the clustering process. We propose WISE, a Weight-Informed Self-Explaining framework that unifies representation, feature weighting, clustering, and interpretation in a fully unsupervised and transparent pipeline. WISE introduces Binary Encoding with Padding (BEP) to align heterogeneous features in a unified sparse space, a Leave-One-Feature-Out (LOFO) strategy to sense multiple high-quality and diverse feature-weighting views, and a two-stage weight-aware clustering procedure to aggregate alternative semantic partitions. To ensure intrinsic interpretability, we further develop Discriminative FreqItems (DFI), which yields feature-level explanations that are consistent from instances to clusters with an additive decomposition guarantee. Extensive experiments on six real-world datasets demonstrate that WISE consistently outperforms classical and neural baselines in clustering quality while remaining efficient, and produces faithful, human-interpretable explanations grounded in the same primitives that drive clustering.