Density-Based Clustering

Clustering is a fundamental data mining technique for pattern recognition through unsupervised learning. Among various clustering methods, hierarchical clustering, density-based clustering, and graph clustering stand out as representative approaches. For hierarchical clustering, it can be categorized into agglomerative and divisive modes to construct clusters in a recursive manner. The key aspect of both modes is the calculation of inter-cluster similarity, which determines whether to merge the sub-clusters into one cluster or divide a current cluster into sub-clusters. Traditionally, the similarity is derived from pairwise distances, often overlooking density variations and structural connectivity in graphs. To address this, we propose a density-aware hierarchical clustering method based on element-categorized connection subgraphs (DHC-ECS), which effectively integrates the hierarchical clustering, density-based clustering, and graph clustering. Particularly, a novel inter-cluster similarity metric is introduced that considers not only distances but also the element categorization in the KNN connection subgraphs, kernel density estimation, and local connectivity within sub-clusters. Extensive evaluations on heterogeneous benchmark datasets demonstrate that DHC-ECS exhibits superior overall performance in terms of clustering accuracy and parameter robustness compared with the baseline methods (including AChameleon, RNN-DBSCAN, McDPC, and G-RMS). The work indicates the great potential of the proposed clustering algorithm for low-dimensional datasets by leveraging local density and graph-structured connectivity (i.e., the duality of vertices and edges), as well as the possibility to determine an intrinsic threshold, reducing the reliance on manual parameter tuning.

In the Big Data era, the scalability of clustering algorithms constitutes a key challenge. Traditional density-based methods (e.g., DBSCAN) offer robustness to noise and the ability to detect non-linear clusters, yet their quadratic time complexity $O(N^2)$ drastically limits their applicability. Conversely, partitional algorithms (e.g., K-Means), with their linear complexity $O(N)$, impose sphericity on the resulting groups and fail in the presence of outliers. This paper presents K-SCAN -- a novel hybrid algorithm that optimizes this trade-off. The method integrates preliminary vector quantization (stochastic Mini-Batch K-Means) to extract a reduced set of weighted micro-clusters, followed by a subsequent density-based structural analysis. Empirical evaluation on datasets of up to $10^6$ samples confirms the linear computational complexity of the proposed solution. K-SCAN achieves more than a 3-fold speed-up over the hierarchical BIRCH algorithm, avoiding the costly management of tree-based structures. The method precisely identifies non-linear manifolds while maintaining structural stability (Adjusted Rand Index > 0.99), even with noise levels reaching 55% of the data volume. The main limitation of the proposed algorithm, which could not be fully eliminated in the present study, remains its susceptibility to over-smoothing and its difficulty in separating clusters with highly heterogeneous local density. In complex visual spaces, this can lead to the loss of the finest topological details.

Clustering is an unsupervised technique for grouping data points by similarity. While explainability methods exist for supervised machine learning, they are not directly applicable to clustering, making it challenging to understand cluster assignments. This interpretability gap is particularly evident in the popular density-based method DBSCAN, which assigns points as inliers (cluster members in dense regions) or outliers (noise points in sparse regions). DBSCAN does not provide insight into why a particular point receives its assignment or whether its assignment is robust to small changes in the data. To address the lack of explainability, we introduce ExDBSCAN, a density-aware, post-hoc explanation method. ExDBSCAN offers actionable counterfactual explanations, with theoretical guarantees for validity. It generates multiple counterfactuals using a density connected weighted graph, adopting a physics-inspired model that repels counterfactual candidates from one another (diversity), while pulling them toward the instance to explain (proximity). Empirical evaluation on 30 tabular datasets comparing against four baselines shows that ExDBSCAN outperforms all baselines while attaining perfect validity and retrieving diverse, proximal counterfactuals.

Federated learning faces increasing threats from model poisoning attacks, which harms its application to improve privacy. Existing defense methods typically rely on fixed thresholds or perform clustering with a fixed number of clusters to distinguish malicious gradients from benign ones. However, these methods are difficult to adapt to dynamic poisoning strategies of malicious clients, and often result in the loss of benign gradients due to the heterogeneity of clients' local datasets. To address these problems, we propose a novel robust aggregation method that leverages a small number of known benign clients as references, enabling accurate identification and filtering of malicious gradients while retaining as many benign gradients as possible, even when the number of malicious clients is unknown and variable. First, we introduce a density-based low-dimensional gradient clustering method, which projects gradients onto the two most divergent dimensions and applies density-based clustering to identify malicious gradients while retaining clustered benign gradients and potentially benign outliers. Second, we design an enhancing clustering low-dimensional gradient generator model, which learns to generate pseudo-gradients aligned with the boundary of the benign cluster. These pseudo-gradients act as bridges to connect sparse benign gradient outliers. Third, we introduce low-dimensional gradient re-clustering that clusters the generated pseudo-gradients together with real gradients to recover benign gradients misclassified as noise points, enabling more benign gradients to participate in aggregation. Extensive experiments on the MNIST, CIFAR-10, and MIND datasets demonstrate that our method exhibits superior fidelity and robustness under dynamic poisoning scenarios.

We present CluProp, a novel framework that reimagines varied-density clustering in high-dimensional spaces as a label propagation process over neighborhood graphs. Our approach formally bridges the gap between density-based clustering and graph connectivity, leveraging efficient propagation mechanisms from network science to mitigate the parameter sensitivity inherent in traditional density-based methods. Specifically, we introduce a deterministic density-based propagation strategy to ensure scalable neighborhood identification. The framework is agnostic to the choice of distance metric and exhibits superior performance on large-scale data, processing millions of points in minutes while consistently outperforming existing baselines in accuracy.

This paper studies the computational difficulty of clustering problems that are defined directly on a continuous probability density. Rather than working with finite samples, we assume the density is given as a polynomial and ask whether it contains certain cluster structures. Four natural questions are examined. First, do there exist several points with high density that are far apart from each other. Second, do two high density points have a midpoint with low density, creating a valley between them. Third, does the region where the density is above a threshold have at least a given number of separate connected pieces. Fourth, does that same region contain a hole, meaning a loop that cannot be shrunk to a point. We prove that the first two problems, separated points and valley detection, are exactly as hard as the existential theory of the reals, a complexity class that contains NP and is believed to be strictly larger. In contrast, the topological problems of counting connected pieces and detecting holes are at least as hard as the existential theory of the reals, but their exact complexity remains open. Placing them inside that class would need a major advance in real algebraic geometry. These results give the first rigorous classification of exact continuous clustering inside the real polynomial hierarchy. They also show that even basic clustering criteria are not NP complete unless unexpected collapses occur.

Personalized Retrieval-Augmented Generation (RAG) relies on accurately selecting user-relevant documents. In practice, existing RAG approaches often suffer from high retrieval costs and overlook that collaborative signals from similar users can enhance personalized generation for the current user. We propose ClusterRAG, a Cluster-Based Collaborative Filtering for Personalized Retrieval-Augmented Generation. ClusterRAG represents users through their profile documents, organizes users into semantically coherent clusters using density-based clustering, and performs retrieval at both the cluster and document levels via cluster-level similarity and fine-grained ranking. Extensive experiments on the LaMP benchmark demonstrate that jointly leveraging the target user's profile and profiles from top similar users consistently yields the best performance across diverse tasks. Further analysis shows that ClusterRAG integrates seamlessly with different dense retrievers and rankers, and remains effective when paired with both fine-tuned and zero-shot language models.

We introduce Lumbermark, a robust divisive clustering algorithm capable of detecting clusters of varying sizes, densities, and shapes. Lumbermark iteratively chops off large limbs connected by protruding segments of a dataset's mutual reachability minimum spanning tree. The use of mutual reachability distances smoothens the data distribution and decreases the influence of low-density objects, such as noise points between clusters or outliers at their peripheries. The algorithm can be viewed as an alternative to HDBSCAN that produces partitions with user-specified sizes. A fast, easy-to-use implementation of the new method is available in the open-source 'lumbermark' package for Python and R. We show that Lumbermark performs well on benchmark data and hope it will prove useful to data scientists and practitioners across different fields.

Image clustering is one of the crucial techniques in multimedia analytics and knowledge discovery. Recently, the Deep clustering method (DC), characterized by its ability to perform feature learning and cluster assignment jointly, surpasses the performance of traditional ones on image data. However, existing methods rarely consider the role of model learning strategies in improving the robustness and performance of clustering complex image data. Furthermore, most approaches rely solely on point-to-point distances to cluster centers for partitioning the latent representations, resulting in error accumulation throughout the iterative process. In this paper, we propose a robust image clustering method (IDCL) which, to our knowledge for the first time, introduces a model training strategy using density information into image clustering. Specifically, we design a curriculum learning scheme grounded in the density information of input data, with a more reasonable learning pace. Moreover, we employ the density core rather than the individual cluster center to guide the cluster assignment. Finally, extensive comparisons with state-of-the-art clustering approaches on benchmark datasets demonstrate the superiority of the proposed method, including robustness, rapid convergence, and flexibility in terms of data scale, number of clusters, and image context.

We propose a novel clustering approach for point-cloud segmentation based on supervised contrastive metric learning (CML). Rather than predicting cluster assignments or object-centric variables, the method learns a latent representation in which points belonging to the same object are embedded nearby while unrelated points are separated. Clusters are then reconstructed using a density-based readout in the learned metric space, decoupling representation learning from cluster formation and enabling flexible inference. The approach is evaluated on simulated data from a highly granular calorimeter, where the task is to separate highly overlapping particle showers represented as sets of calorimeter hits. A direct comparison with object condensation (OC) is performed using identical graph neural network backbones and equal latent dimensionality, isolating the effect of the learning objective. The CML method produces a more stable and separable embedding geometry for both electromagnetic and hadronic particle showers, leading to improved local neighbourhood consistency, a more reliable separation of overlapping showers, and better generalization when extrapolating to unseen multiplicities and energies. This translates directly into higher reconstruction efficiency and purity, particularly in high-multiplicity regimes, as well as improved energy resolution. In mixed-particle environments, CML maintains strong performance, suggesting robust learning of the shower topology, while OC exhibits significant degradation. These results demonstrate that similarity-based representation learning combined with density-based aggregation is a promising alternative to object-centric approaches for point cloud segmentation in highly granular detectors.

We report the discovery of bimodal structure in the drift rate distribution of upward-drifting burst clusters from the hyperactive repeating fast radio burst FRB 20240114A. Using unsupervised machine learning (UMAP dimensionality reduction combined with HDBSCAN density-based clustering) applied to 233 upward-drifting burst clusters from the FAST telescope dataset, we identify a distinct subpopulation of 45 burst clusters (Cluster C1) with mean drift rates 2.5x higher than typical upward-drifting burst clusters (245.6 vs 98.1 MHz/ms). Gaussian mixture modeling reveals strong evidence for bimodality (delta-BIC = 296.6), with clearly separated modes (Ashman's D = 2.70 > 2) and a statistically significant gap in the distribution (11.3 sigma). Crucially, we demonstrate that this bimodality persists when restricting the analysis to single-component (U1) burst clusters only (delta-BIC = 19.9, Ashman's D = 2.71), confirming that the result is not an artifact of combining single- and multi-component burst clusters with different drift rate definitions. The extreme-drift subpopulation also exhibits systematically lower peak frequencies (-7%), shorter durations (-29%), and distinct clustering in multi-dimensional feature space. These findings are suggestive of two spatially separated emission regions in the magnetosphere, each producing upward-drifting burst clusters with distinct physical characteristics, although confirmation requires observations from additional epochs and sources.

Density-based clustering algorithms like DBSCAN and HDBSCAN are foundational tools for discovering arbitrarily shaped clusters, yet their practical utility is undermined by acute hyperparameter sensitivity -- parameters tuned on one dataset frequently fail to transfer to others, requiring expensive re-optimization for each deployment. We introduce AdaBox (Adaptive Density-Based Box Clustering), a grid-based density clustering algorithm designed for robustness across diverse data geometries. AdaBox features a six-parameter design where parameters capture cluster structure rather than pairwise point relationships. Four parameters are inherently scale-invariant, one self-corrects for sampling bias, and one is adjusted via a density scaling stage, enabling reliable parameter transfer across 30-200x scale factors. AdaBox processes data through five stages: adaptive grid construction, liberal seed initialization, iterative growth with graduation, statistical cluster merging, and Gaussian boundary refinement. Comprehensive evaluation across 111 datasets demonstrates three key findings: (1) AdaBox significantly outperforms DBSCAN and HDBSCAN across five evaluation metrics, achieving the best score on 78% of datasets with p < 0.05; (2) AdaBox uniquely exhibits parameter generalization. Protocol A (direct transfer to 30-100x larger datasets) shows AdaBox maintains performance while baselines collapse. (3) Ablation studies confirm the necessity of all five architectural stages for maintaining robustness.

We introduce a novel framework for uncertainty quantification in clustering that combines martingale posterior distributions with density-based clustering. Unlike classical model-based approaches, which define clusters at the latent level of a mixture model, we treat clusters as explicit functionals of the data-generating density, without assuming any specific parametric form. To characterize density uncertainty, we obtain martingale posterior samples via a predictive resampling scheme driven by model score evaluations. This allows us to leverage state-of-the-art differentiable density estimators, such as normalizing flows, making density resampling efficient in large-scale settings and fully parallelizable on modern GPU hardware. Martingale posterior samples of the clustering structure are then obtained by applying density-based clustering to the density draws, enabling principled inference on any clustering-related quantity. Casting the inference target as a density functional further enables a rigorous theoretical analysis of the procedure's convergence properties. We apply our methodology to image and single-cell RNA sequencing data, demonstrating the computational efficiency afforded by its GPU compatibility as well as its ability to recover meaningful clustering structures, with associated uncertainty, across diverse domains.

Standard Mean-Shift algorithms are notoriously sensitive to the bandwidth hyperparameter, particularly in data-scarce regimes where fixed-scale density estimation leads to fragmentation and spurious modes. In this paper, we propose Doubly Stochastic Mean-Shift (DSMS), a novel extension that introduces randomness not only in the trajectory updates but also in the kernel bandwidth itself. By drawing both the data samples and the radius from a continuous uniform distribution at each iteration, DSMS effectively performs a better exploration of the density landscape. We show that this randomized bandwidth policy acts as an implicit regularization mechanism, and provide convergence theoretical results. Comparative experiments on synthetic Gaussian mixtures reveal that DSMS significantly outperforms standard and stochastic Mean-Shift baselines, exhibiting remarkable stability and preventing over-segmentation in sparse clustering scenarios without other performance degradation.

Clustering is a cornerstone of modern data analysis. Detecting clusters in exploratory data analyses (EDA) requires algorithms that make few assumptions about the data. Density-based clustering algorithms are particularly well-suited for EDA because they describe high-density regions, assuming only that a density exists. Applying density-based clustering algorithms in practice, however, requires selecting appropriate hyperparameters, which is difficult without prior knowledge of the data distribution. For example, DBSCAN requires selecting a density threshold, and HDBSCAN* relies on a minimum cluster size parameter. In this work, we propose Persistent Leaves Spatial Clustering for Applications with Noise (PLSCAN), a multiscale density-based clustering algorithm that replaces HDBSCAN*'s fixed minimum cluster size pruning of a mutual-reachability linkage hierarchy with a persistence-based cluster selection procedure. Effectively, PLSCAN identifies all minimum cluster sizes for which HDBSCAN* produces stable (leaf) clusters. In concept, PLSCAN applies scale-space clustering principles and is equivalent to persistent homology on a novel metric space. We compare its performance to HDBSCAN* on several real-world datasets, demonstrating that it achieves a higher median ARI, is less sensitive to changes in the number of mutual reachability neighbours, and has higher stability under resampling. Additionally, we compare PLSCAN's computational costs to $k$-Means++, demonstrating competitive run-times on low-dimensional datasets. At higher dimensions, run times scale more similarly to HDBSCAN*.