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We describe a robust, fast, and memory-efficient procedure that can cluster millions of structures derived from molecular dynamics simulations. The essence of the method is based on a peak-picking algorithm applied to three- and…

Biomolecules · Quantitative Biology 2015-12-15 Athanasios S. Baltzis , Panagiotis I. Koukos , Nicholas M. Glykos

Clustering algorithms are fundamental tools across many fields, with density-based methods offering particular advantages in identifying arbitrarily shaped clusters and handling noise. However, their effectiveness is often limited by the…

Machine Learning · Computer Science 2025-12-01 Meysam Shirdel Bilehsavar , Razieh Ghaedi , Samira Seyed Taheri , Xinqi Fan , Christian O'Reilly

There are many cluster analysis methods that can produce quite different clusterings on the same dataset. Cluster validation is about the evaluation of the quality of a clustering; "relative cluster validation" is about using such criteria…

Methodology · Statistics 2020-09-10 Christian Hennig

Deep clustering has exhibited remarkable performance; however, the over confidence problem, i.e., the estimated confidence for a sample belonging to a particular cluster greatly exceeds its actual prediction accuracy, has been over looked…

Computer Vision and Pattern Recognition · Computer Science 2025-04-03 Yuheng Jia , Jianhong Cheng , Hui Liu , Junhui Hou

Ensuring that predicted probabilities align with observed frequencies is critical in high-stakes domains such as clinical decision support, autonomous driving and financial risk assessment. Existing calibration methods typically apply a…

Machine Learning · Computer Science 2026-05-26 Tomer Lavi , Bracha Shapira , Nadav Rappoport

Subspace clustering algorithms are used for understanding the cluster structure that explains the dataset well. These methods are extensively used for data-exploration tasks in various areas of Natural Sciences. However, most of these…

Machine Learning · Computer Science 2022-11-15 Ashutosh Singh , Ashish Singh , Aria Masoomi , Tales Imbiriba , Erik Learned-Miller , Deniz Erdogmus

Sparse linear prediction methods suffer from decreased prediction accuracy when the predictor variables have cluster structure (e.g. there are highly correlated groups of variables). To improve prediction accuracy, various methods have been…

Machine Learning · Statistics 2022-02-03 Rebecca Marion , Johannes Lederer , Bernadette Govaerts , Rainer von Sachs

Clustering is a well-known unsupervised machine learning approach capable of automatically grouping discrete sets of instances with similar characteristics. Constrained clustering is a semi-supervised extension to this process that can be…

Machine Learning · Computer Science 2023-03-02 Germán González-Almagro , Daniel Peralta , Eli De Poorter , José-Ramón Cano , Salvador García

Locating the center of convex objects is important in both image processing and unsupervised machine learning/data clustering fields. The automated analysis of biological images uses both of these fields for locating cell nuclei and for…

Computer Vision and Pattern Recognition · Computer Science 2018-04-12 James Kapaldo , Xu Han , Domingo Mery

We introduce a new method for performing clustering with the aim of fitting clusters with different scatters and weights. It is designed by allowing to handle a proportion $\alpha$ of contaminating data to guarantee the robustness of the…

Statistics Theory · Mathematics 2008-12-18 Luis A. García-Escudero , Alfonso Gordaliza , Carlos Matrán , Agustin Mayo-Iscar

We consider the problem of learning a mixture of Random Utility Models (RUMs). Despite the success of RUMs in various domains and the versatility of mixture RUMs to capture the heterogeneity in preferences, there has been only limited…

Machine Learning · Statistics 2020-04-01 Devavrat Shah , Dogyoon Song

We introduce a method for validation of results obtained by clustering analysis of data. The method is based on resampling the available data. A figure of merit that measures the stability of clustering solutions against resampling is…

Computational Physics · Physics 2007-05-23 Erel Levine , Eytan Domany

The community structure of complex networks reveals both their organization and hidden relationships among their constituents. Most community detection methods currently available are not deterministic, and their results typically depend on…

Physics and Society · Physics 2012-03-29 Andrea Lancichinetti , Santo Fortunato

Bayesian clustering typically relies on mixture models, with each component interpreted as a different cluster. After defining a prior for the component parameters and weights, Markov chain Monte Carlo (MCMC) algorithms are commonly used to…

Methodology · Statistics 2024-07-30 Alexander Dombowsky , David B. Dunson

Cell clustering is crucial for uncovering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data by identifying cell types and marker genes. Despite its importance, benchmarks for scRNA-seq clustering methods remain…

Genomics · Quantitative Biology 2025-12-03 Ping Xu , Zaitian Wang , Zhirui Wang , Pengjiang Li , Jiajia Wang , Ran Zhang , Pengfei Wang , Yuanchun Zhou

Image clustering is a very useful technique that is widely applied to various areas, including remote sensing. Recently, visual representations by self-supervised learning have greatly improved the performance of image clustering. To…

Computer Vision and Pattern Recognition · Computer Science 2022-09-27 Qinglin Li , Guoping Qiu

Clustering algorithms are one of the main analytical methods to detect patterns in unlabeled data. Existing clustering methods typically treat samples in a dataset as points in a metric space and compute distances to group together similar…

Machine Learning · Computer Science 2021-10-12 Tarek Naous , Srinjay Sarkar , Abubakar Abid , James Zou

One basic requirement of many studies is the necessity of classifying data. Clustering is a proposed method for summarizing networks. Clustering methods can be divided into two categories named model-based approaches and algorithmic…

Machine Learning · Computer Science 2013-02-19 Raheleh Namayandeh , Farzad Didehvar , Zahra Shojaei

Face clustering is an essential tool for exploiting the unlabeled face data, and has a wide range of applications including face annotation and retrieval. Recent works show that supervised clustering can result in noticeable performance…

Computer Vision and Pattern Recognition · Computer Science 2020-04-06 Lei Yang , Dapeng Chen , Xiaohang Zhan , Rui Zhao , Chen Change Loy , Dahua Lin

When scholars suspect units are dependent on each other within clusters but independent of each other across clusters, they employ cluster-robust standard errors (CRSEs). Nevertheless, what to cluster over is sometimes unknown. For…

Methodology · Statistics 2025-11-12 Kentaro Fukumoto