Turtle shell clustering: A mixture approach to discriminative clustering with applications to flow cytometry and other data
Authors: Mackenzie R. Neal, Paul D. McNicholas, Arthur White
Organizations: Department of Mathematics & Statistics, McMaster University, Ontario, Canada · School of Computer Science & Statistics, Trinity College Dublin, Ireland
Generative approaches to clustering provide information on geometric properties of clusters, whereas discriminative approaches provide boundaries between clusters. Ideas from both approaches are incorporated to present a fully unsupervised, probabilistic, and discriminative clustering method via a regularized mutual information objective function, wherein a mixture of mixtures of Gaussian and uniform distributions is used for formulation of the conditional model. Automatic selection of the number of components is established with the introduction of the regularizing term and a merge step, similar to those applied in reversible jump Markov chain Monte Carlo methods used in Bayesian clustering. Consequently, the turtle shell method -- a fully unsupervised clustering method capable of estimating non-linear boundary lines, automatically selecting the number of components, and capturing intuitive clusters in the presence of data abnormalities such as noise and/or irregular cluster shapes -- is introduced. We test this method on various simulated and real datasets commonly explored in clustering research, and extend the analysis to datasets arising from flow cytometry experiments.
The manifold hypothesis suggests a natural criterion for clustering: partition data according to the manifold component from which each point is drawn. Whether two components are separable depends on a geometric tradeoff: the ambient separation between components versus the largest gap in sampling. In practice, this tradeoff is rarely assessed explicitly, leading standard methods to over-commit to a single clustering assignment even when the data do not support a unique answer. We formalize this tradeoff by combining intrinsic manifold geometry (volume growth and reach) with sample-level quantities (fill distance and density), yielding a threshold phenomenon for mutual-k-nearest-neighbor graphs: when the offset-to-fill ratio exceeds a conservative upper threshold, component separation is preserved; below a lower threshold, components fuse. The gap between these thresholds defines a geometric uncertainty zone in which the number of clusters is not identifiable from the data. Nevertheless, conventional approaches still seek one: sweeping parameters (an engineering approach) or fitting a generative mixture model (a model-based approach). Rather than forcing a single estimate of the number of clusters, we propose Manifold-Based Clustering (MBC), which returns an explicit bracket interval to quantify the underlying data uncertainty. This bracket acts as an empirically calibrated diagnostic: it narrows when a single resolution is supported, widens when multiple resolutions coexist, and collapses to one when no separated structure is detectable. Empirically, we find that many real datasets lie within the uncertainty zone rather than admitting one clear answer. Our results suggest that ambiguity in cluster number is often intrinsic, and should be quantified rather than resolved.
Existing granular-ball generation methods are still mainly driven by handcrafted quality measures and heuristic splitting or stopping criteria, which may weaken the transparency of local generation decisions in clustering. To address this issue, this paper proposes Minimum Description Length based Granular-Ball Generation (MDL-GBG), a non-parametric and interpretable granular-ball generation method for clustering. MDL-GBG reformulates granular-ball generation as a local model selection problem under the Minimum Description Length principle. For each granular ball, three candidate explanations are compared, namely a single-ball model, a two-ball model, and a core-ball-plus-residual model, and the model with the shortest description length is selected. In this way, ball retention, splitting, and residual peeling are unified within a common coding-theoretic framework. A residual reassignment mechanism is further introduced to re-evaluate peeled-off boundary samples after stable granular-balls are formed. Experiments on 20 UCI datasets show that the stable granular-balls generated by MDL-GBG provide an effective upstream representation for clustering. In particular, MDL-GBG+AC achieves the best average ranks in ARI, ACC, and NMI among the compared methods. These results indicate that MDL-GBG offers a principled and interpretable alternative to heuristic granular-ball generation strategies.
Clustering is widely used across the sciences as the foundation for downstream data-driven scientific discoveries. However, clustering results are highly sensitive to the choice of algorithm, preprocessing, and the number of clusters k, producing scientific claims that are often not reproducible. The current state of the art for validating clustering solutions consists of clustering validation indices (CVIs) such as Silhouette, Davies-Bouldin, and Calinski-Harabasz, which rely on geometric assumptions that break down on the heavy-tailed, high-dimensional, and nonlinearly structured data encountered in biomedical research. Resampling-based alternatives - grounded in the ideas of clustering stability and generalizability - have been proposed but remain scattered across specialized tools with no unified, accessible software. We fill this gap with CARVE (Cluster Analysis with Resampling for Validation and Exploration), an open-source Python and R package that jointly evaluates multiple clustering algorithms and hyperparameters, returning stability and generalizability diagnostics at the global, cluster, and sample level together with principled selection rules and consensus-based cluster labels. Across six synthetic benchmarks CARVE consistently recovers near-optimal clusterings where classical indices degrade substantially. On experimental genomics and proteomics data sets, CARVE recovers finer biological structure when classical CVIs collapse entirely. CARVE is available with a scikit-learn-compatible Python API and an analogous R interface compatible with Seurat workflows.