This paper considers $k$-means clustering in the presence of noise. It is known that $k$-means clustering is highly sensitive to noise, and thus noise should be removed to obtain a quality solution. A popular formulation of this problem is called $k$-means clustering with outliers. The goal of $k$-means clustering with outliers is to discard up to a specified number $z$ of points as noise/outliers and then find a $k$-means solution on the remaining data. The problem has received significant attention, yet current algorithms with theoretical guarantees suffer from either high running time or inherent loss in the solution quality. The main contribution of this paper is two-fold. Firstly, we develop a simple greedy algorithm that has provably strong worst case guarantees. The greedy algorithm adds a simple preprocessing step to remove noise, which can be combined with any $k$-means clustering algorithm. This algorithm gives the first pseudo-approximation-preserving reduction from $k$-means with outliers to $k$-means without outliers. Secondly, we show how to construct a coreset of size $O(k \log n)$. When combined with our greedy algorithm, we obtain a scalable, near linear time algorithm. The theoretical contributions are verified experimentally by demonstrating that the algorithm quickly removes noise and obtains a high-quality clustering.
Redundancy identification is an important step of the design flow that typically follows logic synthesis and optimization. In addition to reducing circuit area, power consumption, and delay, redundancy removal also improves testability. All commercially available synthesis tools include a redundancy removal engine which is often run multiple times on the same netlist during optimization. This paper presents a fast heuristic algorithm for redundancy removal in combinational circuits. Our idea is to provide a quick partial solution which can be used for the intermediate redundancy removal runs i…
CFSFDP (clustering by fast search and find of density peaks) is recently developed density-based clustering algorithm. Compared to DBSCAN, it needs less parameters and is computationally cheap for its non-iteration. Alex. at al have demonstrated its power by many applications. However, CFSFDP performs not well when there are more than one density peak for one cluster, what we name as "no density peaks". In this paper, inspired by the idea of a hierarchical clustering algorithm CHAMELEON, we propose an extension of CFSFDP,E_CFSFDP, to adapt more applications. In particular, we take use of origi…
Node overlap removal is a necessary step in many scenarios including laying out a graph, or visualizing a tag cloud. Our contribution is a new overlap removal algorithm that iteratively builds a Minimum Spanning Tree on a Delaunay triangulation of the node centers and removes the node overlaps by "growing" the tree. The algorithm is simple to implement yet produces high quality layouts. According to our experiments it runs several times faster than the current state-of-the-art methods.
The minimum height of vertex and edge partition trees are well-studied graph parameters known as, for instance, vertex and edge ranking number. While they are NP-hard to determine in general, linear-time algorithms exist for trees. Motivated by a correspondence with Dasgupta's objective for hierarchical clustering we consider the total rather than maximum depth of vertices as an alternative objective for minimization. For vertex partition trees this leads to a new parameter with a natural interpretation as a measure of robustness against vertex removal. As tools for the study of this family of…
k-means has recently been recognized as one of the best algorithms for clustering unsupervised data. Since k-means depends mainly on distance calculation between all data points and the centers, the time cost will be high when the size of the dataset is large (for example more than 500millions of points). We propose a two stage algorithm to reduce the time cost of distance calculation for huge datasets. The first stage is a fast distance calculation using only a small portion of the data to produce the best possible location of the centers. The second stage is a slow distance calculation in wh…
We present methods for k-means clustering on a stream with a focus on providing fast responses to clustering queries. Compared to the current state-of-the-art, our methods provide substantial improvement in the query time for cluster centers while retaining the desirable properties of provably small approximation error and low space usage. Our algorithms rely on a novel idea of "coreset caching" that systematically reuses coresets (summaries of data) computed for recent queries in answering the current clustering query. We present both theoretical analysis and detailed experiments demonstratin…
We develop data structures for dynamic closest pair problems with arbitrary distance functions, that do not necessarily come from any geometric structure on the objects. Based on a technique previously used by the author for Euclidean closest pairs, we show how to insert and delete objects from an n-object set, maintaining the closest pair, in O(n log^2 n) time per update and O(n) space. With quadratic space, we can instead use a quadtree-like structure to achieve an optimal time bound, O(n) per update. We apply these data structures to hierarchical clustering, greedy matching, and TSP heurist…
We introduce fast algorithms for correlation clustering with respect to the Min Max objective that provide constant factor approximations on complete graphs. Our algorithms are the first purely combinatorial approximation algorithms for this problem. We construct a novel semi-metric on the set of vertices, which we call the correlation metric, that indicates to our clustering algorithms whether pairs of nodes should be in the same cluster. The paper demonstrates empirically that, compared to prior work, our algorithms sacrifice little in the objective quality to obtain significantly better run…
In the Cograph Deletion (resp., Cograph Editing) problem the input is a graph $G$ and an integer $k$, and the goal is to decide whether there is a set of edges of size at most $k$ whose removal from $G$ (resp., removal and addition to $G$) results in a graph that does not contain an induced path with four vertices. In this paper we give algorithms for Cograph Deletion and Cograph Editing whose running times are $O^*(2.303^k)$ and $O^*(4.329^k)$, respectively.
University Medical Center Mannheim, Heidelberg University（海德堡大学曼海姆医学中心）
Poisson noise suppression is an important preprocessing step in several applications, such as medical imaging, microscopy, and astronomical imaging. In this work, we propose a novel patch-wise Poisson noise removal strategy, in which the MMSE estimator is utilized in order to produce the denoising result for each image patch. Fast and accurate computation of the MMSE estimator is carried out using k-d tree search followed by search in the K-nearest neighbor graph. Our experiments show that the proposed method is the preferable choice for low signal-to-noise ratios.
Clustering problems have numerous applications and are becoming more challenging as the size of the data increases. In this paper, we consider designing clustering algorithms that can be used in MapReduce, the most popular programming environment for processing large datasets. We focus on the practical and popular clustering problems, $k$-center and $k$-median. We develop fast clustering algorithms with constant factor approximation guarantees. From a theoretical perspective, we give the first analysis that shows several clustering algorithms are in $\mathcal{MRC}^0$, a theoretical MapReduce c…
Contraction Clustering (RASTER): A Very Fast Big Data Algorithm for Sequential and Parallel Density-Based Clustering in Linear Time, Constant Memory, and a Single Pass
Fraunhofer-Chalmers Research Centre for Industrial Mathematics（弗劳恩霍夫-查尔默斯工业数学研究中心）；Fraunhofer Center for Machine Learning（弗劳恩霍夫机器学习中心）
We describe a new optimization scheme for finding high-quality correlation clusterings in planar graphs that uses weighted perfect matching as a subroutine. Our method provides lower-bounds on the energy of the optimal correlation clustering that are typically fast to compute and tight in practice. We demonstrate our algorithm on the problem of image segmentation where this approach outperforms existing global optimization techniques in minimizing the objective and is competitive with the state of the art in producing high-quality segmentations.
Correlation clustering is a widely studied framework for clustering based on pairwise similarity and dissimilarity scores, but its best approximation algorithms rely on impractical linear programming relaxations. We present faster approximation algorithms that avoid these relaxations, for two well-studied special cases: cluster editing and cluster deletion. We accomplish this by drawing new connections to edge labeling problems related to the principle of strong triadic closure. This leads to faster and more practical linear programming algorithms, as well as extremely scalable combinatorial t…
$k$-means and $k$-median clustering are powerful unsupervised machine learning techniques. However, due to complicated dependences on all the features, it is challenging to interpret the resulting cluster assignments. Moshkovitz, Dasgupta, Rashtchian, and Frost [ICML 2020] proposed an elegant model of explainable $k$-means and $k$-median clustering. In this model, a decision tree with $k$ leaves provides a straightforward characterization of the data set into clusters. We study two natural algorithmic questions about explainable clustering. (1) For a given clustering, how to find the "best exp…
Motivation: De novo transcriptome assembly of non-model organisms is the first major step for many RNA-seq analysis tasks. Current methods for de novo assembly often report a large number of contiguous sequences (contigs), which may be fractured and incomplete sequences instead of full-length transcripts. Dealing with a large number of such contigs can slow and complicate downstream analysis. Results :We present a method for clustering contigs from de novo transcriptome assemblies based upon the relationships exposed by multi-mapping sequencing fragments. Specifically, we cast the problem of c…
Michigan State University（密歇根州立大学）；University of Science and Technology of China（中国科学技术大学）
The problem of constrained clustering has attracted significant attention in the past decades. In this paper, we study the balanced $k$-center, $k$-median, and $k$-means clustering problems where the size of each cluster is constrained by the given lower and upper bounds. The problems are motivated by the applications in processing large-scale data in high dimension. Existing methods often need to compute complicated matchings (or min cost flows) to satisfy the balance constraint, and thus suffer from high complexities especially in high dimension. We develop an effective framework for the thr…
Aarhus University（奥胡斯大学）；University of California, San Diego（加利福尼亚大学圣地亚哥分校）；New Mexico State University（新墨西哥州立大学）
The $k$-Means clustering problem on $n$ points is NP-Hard for any dimension $d\ge 2$, however, for the 1D case there exists exact polynomial time algorithms. Previous literature reported an $O(kn^2)$ time dynamic programming algorithm that uses $O(kn)$ space. It turns out that the problem has been considered under a different name more than twenty years ago. We present all the existing work that had been overlooked and compare the various solutions theoretically. Moreover, we show how to reduce the space usage for some of them, as well as generalize them to data structures that can quickly rep…
