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 Clustering


Fast estimation of Gaussian mixture components via centering and singular value thresholding

Qing, Huan

arXiv.org Machine Learning

Estimating the number of components is a fundamental challenge in unsupervised learning, particularly when dealing with high-dimensional data with many components or severely imbalanced component sizes. This paper addresses this challenge for classical Gaussian mixture models. The proposed estimator is simple: center the data, compute the singular values of the centered matrix, and count those above a threshold. No iterative fitting, no likelihood calculation, and no prior knowledge of the number of components are required. We prove that, under a mild separation condition on the component centers, the estimator consistently recovers the true number of components. The result holds in high-dimensional settings where the dimension can be much larger than the sample size. It also holds when the number of components grows to the smaller of the dimension and the sample size, even under severe imbalance among component sizes. Computationally, the method is extremely fast: for example, it processes ten million samples in one hundred dimensions within one minute. Extensive experimental studies confirm its accuracy in challenging settings such as high dimensionality, many components, and severe class imbalance.


A proposal for PU classification under Non-SCAR using clustering and logistic model

Furmanczyk, Konrad, Paczutkowski, Kacper

arXiv.org Machine Learning

The present study aims to investigate a cluster cleaning algorithm that is both computationally simple and capable of solving the PU classification when the SCAR condition is unsatisfied. A secondary objective of this study is to determine the robustness of the LassoJoint method to perturbations of the SCAR condition. In the first step of our algorithm, we obtain cleaning labels from 2-means clustering. Subsequently, we perform logistic regression on the cleaned data, assigning positive labels from the cleaning algorithm with additional true positive observations. The remaining observations are assigned the negative label. The proposed algorithm is evaluated by comparing 11 real data sets from machine learning repositories and a synthetic set. The findings obtained from this study demonstrate the efficacy of the clustering algorithm in scenarios where the SCAR condition is violated and further underscore the moderate robustness of the LassoJoint algorithm in this context.


Scalable Model-Based Clustering with Sequential Monte Carlo

Trojan, Connie, Myshkov, Pavel, Fearnhead, Paul, Hensman, James, Minka, Tom, Nemeth, Christopher

arXiv.org Machine Learning

In online clustering problems, there is often a large amount of uncertainty over possible cluster assignments that cannot be resolved until more data are observed. This difficulty is compounded when clusters follow complex distributions, as is the case with text data. Sequential Monte Carlo (SMC) methods give a natural way of representing and updating this uncertainty over time, but have prohibitive memory requirements for large-scale problems. We propose a novel SMC algorithm that decomposes clustering problems into approximately independent subproblems, allowing a more compact representation of the algorithm state. Our approach is motivated by the knowledge base construction problem, and we show that our method is able to accurately and efficiently solve clustering problems in this setting and others where traditional SMC struggles.


Joint Representation Learning and Clustering via Gradient-Based Manifold Optimization

Liu, Sida, Guo, Yangzi, Wang, Mingyuan

arXiv.org Machine Learning

Clustering and dimensionality reduction have been crucial topics in machine learning and computer vision. Clustering high-dimensional data has been challenging for a long time due to the curse of dimensionality. For that reason, a more promising direction is the joint learning of dimension reduction and clustering. In this work, we propose a Manifold Learning Framework that learns dimensionality reduction and clustering simultaneously. The proposed framework is able to jointly learn the parameters of a dimension reduction technique (e.g. linear projection or a neural network) and cluster the data based on the resulting features (e.g. under a Gaussian Mixture Model framework). The framework searches for the dimension reduction parameters and the optimal clusters by traversing a manifold,using Gradient Manifold Optimization. The obtained The proposed framework is exemplified with a Gaussian Mixture Model as one simple but efficient example, in a process that is somehow similar to unsupervised Linear Discriminant Analysis (LDA). We apply the proposed method to the unsupervised training of simulated data as well as a benchmark image dataset (i.e. MNIST). The experimental results indicate that our algorithm has better performance than popular clustering algorithms from the literature.


Forecasting Multivariate Time Series under Predictive Heterogeneity: A Validation-Driven Clustering Framework

Ma, Ziling, Oriona, Ángel López, Ombao, Hernando, Sun, Ying

arXiv.org Machine Learning

We study adaptive pooling under predictive heterogeneity in high-dimensional multivariate time series forecasting, where global models improve statistical efficiency but may fail to capture heterogeneous predictive structure, while naive specialization can induce negative transfer. We formulate adaptive pooling as a statistical decision problem and propose a validation-driven framework that determines when and how specialization should be applied. Rather than grouping series based on representation similarity, we define partitions through out-of-sample predictive performance, thereby aligning data organization with predictive risk, defined as expected out-of-sample loss and approximated via validation error. Cluster assignments are iteratively updated using validation losses for both point (Huber) and probabilistic (pinball) forecasting, improving robustness to heavy-tailed errors and local anomalies. To ensure reliability, we introduce a leakage-free fallback mechanism that reverts to a global model whenever specialization fails to improve validation performance, providing a safeguard against performance degradation under a strict training-validation-test protocol. Experiments on large-scale traffic datasets demonstrate consistent improvements over strong baselines while avoiding degradation when heterogeneity is weak. Overall, the proposed framework provides a principled and practically reliable approach to adaptive pooling in high-dimensional forecasting problems.


Asymptotic Theory for Graphical SLOPE: Precision Estimation and Pattern Convergence

Hejný, Ivan, Bonaccolto, Giovanni, Kremer, Philipp, Paterlini, Sandra, Bogdan, Małgorzata, Wallin, Jonas

arXiv.org Machine Learning

This paper studies Graphical SLOPE for precision matrix estimation, with emphasis on its ability to recover both sparsity and clusters of edges with equal or similar strength. In a fixed-dimensional regime, we establish that the root-$n$ scaled estimation error converges to the unique minimizer of a strictly convex optimization problem defined through the directional derivative of the SLOPE penalty. We also establish convergence of the induced SLOPE pattern, thereby obtaining an asymptotic characterization of the clustering structure selected by the estimator. A comparison with GLASSO shows that the grouping property of SLOPE can substantially improve estimation accuracy when the precision matrix exhibits structured edge patterns. To assess the effect of departures from Gaussianity, we then analyze Gaussian-loss precision matrix estimation under elliptical distributions. In this setting, we derive the limiting distribution and quantify the inflation in variability induced by heavy tails relative to the Gaussian benchmark. We also study TSLOPE, based on the multivariate $t$-loss, and derive its limiting distribution. The results show that TSLOPE offers clear advantages over GSLOPE under heavy-tailed data-generating mechanisms. Simulation evidence suggests that these qualitative conclusions persist in high-dimensional settings, and an empirical application shows that SLOPE-based estimators, especially TSLOPE, can uncover economically meaningful clustered dependence structures.


Distributionally Robust K-Means Clustering

Malik, Vikrant, Kargin, Taylan, Hassibi, Babak

arXiv.org Machine Learning

In recent years, the widespreadavailability of large-scale, high-dimensionaldatasets has driven significant interest in clustering algorithms that are both computationally efficient and robust to distributional shifts and outliers. The classical clustering method, K-means, can be seen as an application of the Lloyd-Max quantization algorithm, in which the distribution being quantized is the empirical distribution of the points to be clustered. This empirical distribution generally differs from the true underlying distribution, especially when the number of points to be clustered is small. This induces a distributional shift, which can also arise in many real-world settings, such as image segmentation, biological data analysis, and sensor networks, due to noise variations, sensor inaccuracies, or environmental changes. Distributional shifts can severely impact the performance of clustering algorithms, leading to degraded cluster assignments and unreliable downstream analysis. The field of clustering has a rich history. One of the most popular algorithms in this field is theK-means (KM) algorithm, introduced by [1], which computes centroids by iteratively updating the conditional mean of the data in the Voronoi regions induced by the centroids. However, standardK-means is sensitive to initialization and, in general, converges only to a local minimum.


Nested Atoms Model with Application to Clustering Big Population-Scale Single-Cell Data

Chakrabarti, Arhit, Ni, Yang, Jiang, Yuchao, Mallick, Bani K.

arXiv.org Machine Learning

We consider the problem of clustering nested or hierarchical data, where observations are grouped and there are both group-level and observation-level variables. In our motivating OneK1K dataset, observations consist of single-cell RNA-sequencing (scRNA-seq) data from 982 individuals (groups), totaling 1.27 million cells (observations), along with individual-specific genotype data. This type of data would enable the identification of cell types and the investigation of how genetic variations among individuals influence differences in cell-type profiles. Our goal, therefore, is to jointly cluster cells and individuals to capture the heterogeneity across both levels using cell-specific gene expressions as well as individual-specific genotypes. However, existing grouped clustering methods do not incorporate group-level variables, thereby limiting their ability to capture the heterogeneity of genotypes in our motivating application. To address this, we propose the Nested Atoms Model (NAM), a new Bayesian nonparametric approach that enables the desired two-layered clustering, accounting for both group-level and observation-level variables. To scale NAM for high-dimensional data, we develop a fast variational Bayesian inference algorithm. Simulations show that NAM outperforms existing methods that ignore group-level variables. Applied to the OneK1K dataset, NAM identifies clusters of genetically similar individuals with homogeneous cell-type profiles. The resulting cell clusters align with known immune cell types based on differential gene expression, underscoring the ability of NAM to capture nested heterogeneity and provide biologically meaningful insights.


The Condition-Number Principle for Prototype Clustering

Li, Romano, Cao, Jianfei

arXiv.org Machine Learning

We develop a geometric framework that links objective accuracy to structural recovery in prototype-based clustering. The analysis is algorithm-agnostic and applies to a broad class of admissible loss functions. We define a clustering condition number that compares within-cluster scale to the minimum loss increase required to move a point across a cluster boundary. When this quantity is small, any solution with a small suboptimality gap must also have a small misclassification error relative to a benchmark partition. The framework also clarifies a fundamental trade-off between robustness and sensitivity to cluster imbalance, leading to sharp phase transitions for exact recovery under different objectives. The guarantees are deterministic and non-asymptotic, and they separate the role of algorithmic accuracy from the intrinsic geometric difficulty of the instance. We further show that errors concentrate near cluster boundaries and that sufficiently deep cluster cores are recovered exactly under strengthened local margins. Together, these results provide a geometric principle for interpreting low objective values as reliable evidence of meaningful clustering structure.


Lumbermark: Resistant Clustering by Chopping Up Mutual Reachability Minimum Spanning Trees

Gagolewski, Marek

arXiv.org Machine Learning

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.