We introduce Grinch, a new algorithm for large-scale, non-greedy hierarchical clustering with general linkage functions that compute arbitrary similarity between two point sets. The key components of Grinch are its rotate and graft subroutines that efficiently reconfigure the hierarchy as new points arrive, supporting discovery of clusters with complex structure. Grinch is motivated by a new notion of separability for clustering with linkage functions: we prove that when the model is consistent with a ground-truth clustering, Grinch is guaranteed to produce a cluster tree containing the ground-truth, independent of data arrival order. Our empirical results on benchmark and author coreference datasets (with standard and learned linkage functions) show that Grinch is more accurate than other scalable methods, and orders of magnitude faster than hierarchical agglomerative clustering.
Stanford University（斯坦福大学）；Ohio State University（俄亥俄州立大学）；University of Pennsylvania（宾夕法尼亚大学）
This paper characterizes hierarchical clustering methods that abide by two previously introduced axioms -- thus, denominated admissible methods -- and proposes tractable algorithms for their implementation. We leverage the fact that, for asymmetric networks, every admissible method must be contained between reciprocal and nonreciprocal clustering, and describe three families of intermediate methods. Grafting methods exchange branches between dendrograms generated by different admissible methods. The convex combination family combines admissible methods through a convex operation in the space o…
Google（谷歌）；University of Maryland（马里兰大学）；Carnegie Mellon University（卡内基梅隆大学）
As machine learning has become more prevalent, researchers have begun to recognize the necessity of ensuring machine learning systems are fair. Recently, there has been an interest in defining a notion of fairness that mitigates over-representation in traditional clustering. In this paper we extend this notion to hierarchical clustering, where the goal is to recursively partition the data to optimize a specific objective. For various natural objectives, we obtain simple, efficient algorithms to find a provably good fair hierarchical clustering. Empirically, we show that our algorithms can find…
The development of algorithms for hierarchical clustering has been hampered by a shortage of precise objective functions. To help address this situation, we introduce a simple cost function on hierarchies over a set of points, given pairwise similarities between those points. We show that this criterion behaves sensibly in canonical instances and that it admits a top-down construction procedure with a provably good approximation ratio.
FISHDBC is a flexible, incremental, scalable, and hierarchical density-based clustering algorithm. It is flexible because it empowers users to work on arbitrary data, skipping the feature extraction step that usually transforms raw data in numeric arrays letting users define an arbitrary distance function instead. It is incremental and scalable: it avoids the $\mathcal O(n^2)$ performance of other approaches in non-metric spaces and requires only lightweight computation to update the clustering when few items are added. It is hierarchical: it produces a "flat" clustering which can be expanded …
We propose a nearest neighbor based clustering algorithm that results in a naturally defined hierarchy of clusters. In contrast to the agglomerative and divisive hierarchical clustering algorithms, our approach is not dependent on the iterative working of the algorithm, in the sense that the partitions of the hierarchical clusters are purely defined in accordance with the input dataset. Our method is a universal hierarchical clustering approach since it can be implemented as bottom up or top down versions, both of which result in the same clustering. We show that for certain types of datasets,…
There has been a surge in the number of large and flat data sets - data sets containing a large number of features and a relatively small number of observations - due to the growing ability to collect and store information in medical research and other fields. Hierarchical clustering is a widely used clustering tool. In hierarchical clustering, large and flat data sets may allow for a better coverage of clustering features (features that help explain the true underlying clusters) but, such data sets usually include a large fraction of noise features (non-clustering features) that may hide the …
Meila (2018) introduces an optimization based method called the Sublevel Set method, to guarantee that a clustering is nearly optimal and "approximately correct" without relying on any assumptions about the distribution that generated the data. This paper extends the Sublevel Set method to the cost-based hierarchical clustering paradigm proposed by Dasgupta (2016).
Bagging and boosting are proved to be the best methods of building multiple classifiers in classification combination problems. In the area of "flat clustering" problems, it is also recognized that multi-clustering methods based on boosting provide clusterings of an improved quality. In this paper, we introduce a novel multi-clustering method for "hierarchical clusterings" based on boosting theory, which creates a more stable hierarchical clustering of a dataset. The proposed algorithm includes a boosting iteration in which a bootstrap of samples is created by weighted random sampling of eleme…
Université Paul Verlaine-Metz（保罗·魏尔伦-梅斯大学）；Université Paris 1 Panthéon-Sorbonne（巴黎第一大学 先贤祠-索邦）
We introduce in this paper a new way of optimizing the natural extension of the quantization error using in k-means clustering to dissimilarity data. The proposed method is based on hierarchical clustering analysis combined with multi-level heuristic refinement. The method is computationally efficient and achieves better quantization errors than the
University of Copenhagen（哥本哈根大学）；University of Oxford（牛津大学）；The Alan Turing Institute（阿兰·图灵研究所）；École normale supérieure, CNRS, PSL Research University（巴黎高等师范学院，法国国家科学研究中心，巴黎文理研究大学）；Simon Fraser University（西蒙菲莎大学）
Hierarchical clustering is a recursive partitioning of a dataset into clusters at an increasingly finer granularity. Motivated by the fact that most work on hierarchical clustering was based on providing algorithms, rather than optimizing a specific objective, Dasgupta framed similarity-based hierarchical clustering as a combinatorial optimization problem, where a `good' hierarchical clustering is one that minimizes some cost function. He showed that this cost function has certain desirable properties. We take an axiomatic approach to defining `good' objective functions for both similarity and…
Tsinghua University（清华大学）；Microsoft Research（微软研究院）；University of North Carolina at Charlotte（北卡罗来纳大学夏洛特分校）
Hierarchical clustering is an important technique to organize big data for exploratory data analysis. However, existing one-size-fits-all hierarchical clustering methods often fail to meet the diverse needs of different users. To address this challenge, we present an interactive steering method to visually supervise constrained hierarchical clustering by utilizing both public knowledge (e.g., Wikipedia) and private knowledge from users. The novelty of our approach includes 1) automatically constructing constraints for hierarchical clustering using knowledge (knowledge-driven) and intrinsic dat…
Stanford University（斯坦福大学）；Ohio State University（俄亥俄州立大学）；University of Pennsylvania（宾夕法尼亚大学）
This paper introduces hierarchical quasi-clustering methods, a generalization of hierarchical clustering for asymmetric networks where the output structure preserves the asymmetry of the input data. We show that this output structure is equivalent to a finite quasi-ultrametric space and study admissibility with respect to two desirable properties. We prove that a modified version of single linkage is the only admissible quasi-clustering method. Moreover, we show stability of the proposed method and we establish invariance properties fulfilled by it. Algorithms are further developed and the val…
University of Toyama（富山大学）；Institute of Natural Medicine, University of Toyama, Japan（富山大学自然医学研究所）
This paper proposes a new dimensionality reduction algorithm named branching embedding (BE). It converts a dendrogram to a two-dimensional scatter plot, and visualizes the inherent structures of the original high-dimensional data. Since the conversion part is not computationally demanding, the BE algorithm would be beneficial for the case where hierarchical clustering is already performed. Numerical experiments revealed that the outputs of the algorithm moderately preserve the original hierarchical structures.
t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology. Building on recent advances in speeding up t-SNE and obtaining finer-grained structure, we combine the two to create tree-SNE, a hierarchical clustering and visualization algorithm based on stacked one-dimensional t-SNE embeddings. We also introduce alpha-clustering, which recommends the optimal cluster assignment, without foreknowledge of the number of clusters, based off of the cluster stability across multiple scales. We demonstrate the effectiveness of tree-SNE and alpha-clustering …
Hierarchical clustering is a popular unsupervised data analysis method. For many real-world applications, we would like to exploit prior information about the data that imposes constraints on the clustering hierarchy, and is not captured by the set of features available to the algorithm. This gives rise to the problem of "hierarchical clustering with structural constraints". Structural constraints pose major challenges for bottom-up approaches like average/single linkage and even though they can be naturally incorporated into top-down divisive algorithms, no formal guarantees exist on the qual…
Tepper School of Business, Carnegie Mellon University（卡内基梅隆大学泰珀商学院）
This paper explores hierarchical clustering in the case where pairs of points have dissimilarity scores (e.g. distances) as a part of the input. The recently introduced objective for points with dissimilarity scores results in every tree being a 1/2 approximation if the distances form a metric. This shows the objective does not make a significant distinction between a good and poor hierarchical clustering in metric spaces. Motivated by this, the paper develops a new global objective for hierarchical clustering in Euclidean space. The objective captures the criterion that has motivated the use …
Hierarchical clustering with maximum density paths and mixture models
Institute of Computer Science and Campus Institute Data Science, University of Göttingen（计算机科学研究所和校园数据科学研究所，哥廷根大学）；Max Planck Institute for Dynamics and Self-Organization（动态与自组织Max Planck研究所）
Partial orders and directed acyclic graphs are commonly recurring data structures that arise naturally in numerous domains and applications and are used to represent ordered relations between entities in the domains. Examples are task dependencies in a project plan, transaction order in distributed ledgers and execution sequences of tasks in computer programs, just to mention a few. We study the problem of order preserving hierarchical clustering of this kind of ordered data. That is, if we have $a < b$ in the original data and denote their respective clusters by $[a]$ and $[b]$, then we shall…
The information contained in hierarchical topology, intrinsic to many networks, is currently underutilised. A novel architecture is explored which exploits this information through a multiscale decomposition. A dendrogram is produced by a Girvan-Newman hierarchical clustering algorithm. It is segmented and fed through graph convolutional layers, allowing the architecture to learn multiple scale latent space representations of the network, from fine to coarse grained. The architecture is tested on a benchmark citation network, demonstrating competitive performance. Given the abundance of hierar…
College of Information and Computer Sciences, University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校信息与计算机科学学院）
In supervised clustering, standard techniques for learning a pairwise dissimilarity function often suffer from a discrepancy between the training and clustering objectives, leading to poor cluster quality. Rectifying this discrepancy necessitates matching the procedure for training the dissimilarity function to the clustering algorithm. In this paper, we introduce a method for training the dissimilarity function in a way that is tightly coupled with hierarchical clustering, in particular single linkage. However, the appropriate clustering algorithm for a given dataset is often unknown. Thus we…
National Institute of Standards and Technology（美国国家标准与技术研究院）；New York University（纽约大学）；University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）；Google Research（谷歌研究院）
Hierarchical clustering is a critical task in numerous domains. Many approaches are based on heuristics and the properties of the resulting clusterings are studied post hoc. However, in several applications, there is a natural cost function that can be used to characterize the quality of the clustering. In those cases, hierarchical clustering can be seen as a combinatorial optimization problem. To that end, we introduce a new approach based on A* search. We overcome the prohibitively large search space by combining A* with a novel \emph{trellis} data structure. This combination results in an e…
University of Tübingen（图宾根大学）；Max-Planck-Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）
We address the classical problem of hierarchical clustering, but in a framework where one does not have access to a representation of the objects or their pairwise similarities. Instead, we assume that only a set of comparisons between objects is available, that is, statements of the form "objects $i$ and $j$ are more similar than objects $k$ and $l$." Such a scenario is commonly encountered in crowdsourcing applications. The focus of this work is to develop comparison-based hierarchical clustering algorithms that do not rely on the principles of ordinal embedding. We show that single and comp…
Clustering can be used to extract insights from data or to verify some of the assumptions held by the domain experts, namely data segmentation. In the literature, few methods can be applied in clustering qualitative values using the context associated with other variables present in the data, without losing interpretability. Moreover, the metrics for calculating dissimilarity between qualitative values often scale poorly for high dimensional mixed datasets. In this study, we propose a novel method for clustering qualitative values, based on Hierarchical Clustering (HQC), and using Maximum Mean…
Hierarchical clustering is a class of algorithms that seeks to build a hierarchy of clusters. It has been the dominant approach to constructing embedded classification schemes since it outputs dendrograms, which capture the hierarchical relationship among members at all levels of granularity, simultaneously. Being greedy in the algorithmic sense, a hierarchical clustering partitions data at every step solely based on a similarity / dissimilarity measure. The clustering results oftentimes depend on not only the distribution of the underlying data, but also the choice of dissimilarity measure an…
Stanford University（斯坦福大学）；Ohio State University（俄亥俄州立大学）；University of Pennsylvania（宾夕法尼亚大学）
This paper considers networks where relationships between nodes are represented by directed dissimilarities. The goal is to study methods that, based on the dissimilarity structure, output hierarchical clusters, i.e., a family of nested partitions indexed by a connectivity parameter. Our construction of hierarchical clustering methods is built around the concept of admissible methods, which are those that abide by the axioms of value - nodes in a network with two nodes are clustered together at the maximum of the two dissimilarities between them - and transformation - when dissimilarities are …
In the election of a hierarchical clustering method, theoretic properties may give some insight to determine which method is the most suitable to treat a clustering problem. Herein, we study some basic properties of two hierarchical clustering methods: $α$-unchaining single linkage or $SL(α)$ and a modified version of this one, $SL^*(α)$. We compare the results with the properties satisfied by the classical linkage-based hierarchical clustering methods.
Many modern clustering methods scale well to a large number of data items, N, but not to a large number of clusters, K. This paper introduces PERCH, a new non-greedy algorithm for online hierarchical clustering that scales to both massive N and K--a problem setting we term extreme clustering. Our algorithm efficiently routes new data points to the leaves of an incrementally-built tree. Motivated by the desire for both accuracy and speed, our approach performs tree rotations for the sake of enhancing subtree purity and encouraging balancedness. We prove that, under a natural separability assump…
The problem of hierarchical clustering items from pairwise similarities is found across various scientific disciplines, from biology to networking. Often, applications of clustering techniques are limited by the cost of obtaining similarities between pairs of items. While prior work has been developed to reconstruct clustering using a significantly reduced set of pairwise similarities via adaptive measurements, these techniques are only applicable when choice of similarities are available to the user. In this paper, we examine reconstructing hierarchical clustering under similarity observation…
Hierarchical clustering is a widely used approach for clustering datasets at multiple levels of granularity. Despite its popularity, existing algorithms such as hierarchical agglomerative clustering (HAC) are limited to the offline setting, and thus require the entire dataset to be available. This prohibits their use on large datasets commonly encountered in modern learning applications. In this paper, we consider hierarchical clustering in the online setting, where points arrive one at a time. We propose two algorithms that seek to optimize the Moseley and Wang (MW) revenue function, a varian…
We initiate a comprehensive experimental study of objective-based hierarchical clustering methods on massive datasets consisting of deep embedding vectors from computer vision and NLP applications. This includes a large variety of image embedding (ImageNet, ImageNetV2, NaBirds), word embedding (Twitter, Wikipedia), and sentence embedding (SST-2) vectors from several popular recent models (e.g. ResNet, ResNext, Inception V3, SBERT). Our study includes datasets with up to $4.5$ million entries with embedding dimensions up to $2048$. In order to address the challenge of scaling up hierarchical cl…
Boston University（波士顿大学）；University of Wisconsin - Madison（威斯康星大学麦迪逊分校）；Carnegie Mellon University（卡内基梅隆大学）
Hierarchical clustering based on pairwise similarities is a common tool used in a broad range of scientific applications. However, in many problems it may be expensive to obtain or compute similarities between the items to be clustered. This paper investigates the hierarchical clustering of N items based on a small subset of pairwise similarities, significantly less than the complete set of N(N-1)/2 similarities. First, we show that if the intracluster similarities exceed intercluster similarities, then it is possible to correctly determine the hierarchical clustering from as few as 3N log N s…
Agglomerative hierarchical clustering (AHC) requires only the similarity between objects to be known. This is attractive when clustering signals of varying length, such as speech, which are not readily represented in fixed-dimensional vector space. However, AHC is characterised by $O(N^2)$ space and time complexity, making it infeasible for partitioning large datasets. This has recently been addressed by an approach based on the iterative re-clustering of independent subsets of the larger dataset. We show that, due to its iterative nature, this procedure can sometimes lead to unchecked growth …
Pohang University of Science and Technology（浦项科技大学）
Bayesian hierarchical clustering (BHC) is an agglomerative clustering method, where a probabilistic model is defined and its marginal likelihoods are evaluated to decide which clusters to merge. While BHC provides a few advantages over traditional distance-based agglomerative clustering algorithms, successive evaluation of marginal likelihoods and careful hyperparameter tuning are cumbersome and limit the scalability. In this paper we relax BHC into a non-probabilistic formulation, exploring small-variance asymptotics in conjugate-exponential models. We develop a novel clustering algorithm, re…
Carnegie Mellon University（卡内基梅隆大学）；Georgia Institute of Technology（佐治亚理工学院）；Google, Inc.（谷歌公司）
One of the most widely used techniques for data clustering is agglomerative clustering. Such algorithms have been long used across many different fields ranging from computational biology to social sciences to computer vision in part because their output is easy to interpret. Unfortunately, it is well known, however, that many of the classic agglomerative clustering algorithms are not robust to noise. In this paper we propose and analyze a new robust algorithm for bottom-up agglomerative clustering. We show that our algorithm can be used to cluster accurately in cases where the data satisfies …
Clustering is a powerful tool in data analysis, but it is often difficult to find a grouping that aligns with a user's needs. To address this, several methods incorporate constraints obtained from users into clustering algorithms, but unfortunately do not apply to hierarchical clustering. We design an interactive Bayesian algorithm that incorporates user interaction into hierarchical clustering while still utilizing the geometry of the data by sampling a constrained posterior distribution over hierarchies. We also suggest several ways to intelligently query a user. The algorithm, along with th…
This study addresses the issue of predicting the glaucomatous visual field loss from patient disease datasets. Our goal is to accurately predict the progress of the disease in individual patients. As very few measurements are available for each patient, it is difficult to produce good predictors for individuals. A recently proposed clustering-based method enhances the power of prediction using patient data with similar spatiotemporal patterns. Each patient is categorized into a cluster of patients, and a predictive model is constructed using all of the data in the class. Predictions are highly…
Columbia University（哥伦比亚大学）；University of Pennsylvania（宾夕法尼亚大学）
Hierarchical clustering over graphs is a fundamental task in data mining and machine learning with applications in domains such as phylogenetics, social network analysis, and information retrieval. Specifically, we consider the recently popularized objective function for hierarchical clustering due to Dasgupta. Previous algorithms for (approximately) minimizing this objective function require linear time/space complexity. In many applications the underlying graph can be massive in size making it computationally challenging to process the graph even using a linear time/space algorithm. As a res…
Advances in sensing technologies and the growth of the internet have resulted in an explosion in the size of modern datasets, while storage and processing power continue to lag behind. This motivates the need for algorithms that are efficient, both in terms of the number of measurements needed and running time. To combat the challenges associated with large datasets, we propose a general framework for active hierarchical clustering that repeatedly runs an off-the-shelf clustering algorithm on small subsets of the data and comes with guarantees on performance, measurement complexity and runtime…
Convex clustering is a recent stable alternative to hierarchical clustering. It formulates the recovery of progressively coalescing clusters as a regularized convex problem. While convex clustering was originally designed for handling Euclidean distances between data points, in a growing number of applications, the data is directly characterized by a similarity matrix or weighted graph. In this paper, we extend the robust hierarchical clustering approach to these broader classes of similarities. Having defined an appropriate convex objective, the crux of this adaptation lies in our ability to …
We bring together topological data analysis, applied category theory, and machine learning to study multiparameter hierarchical clustering. We begin by introducing a procedure for flattening multiparameter hierarchical clusterings. We demonstrate that this procedure is a functor from a category of multiparameter hierarchical partitions to a category of binary integer programs. We also include empirical results demonstrating its effectiveness. Next, we introduce a Bayesian update algorithm for learning clustering parameters from data. We demonstrate that the composition of this algorithm with o…
University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）；Google LLC（谷歌有限责任公司）；Facebook（脸书）；University of Southern California（南加州大学）
The applicability of agglomerative clustering, for inferring both hierarchical and flat clustering, is limited by its scalability. Existing scalable hierarchical clustering methods sacrifice quality for speed and often lead to over-merging of clusters. In this paper, we present a scalable, agglomerative method for hierarchical clustering that does not sacrifice quality and scales to billions of data points. We perform a detailed theoretical analysis, showing that under mild separability conditions our algorithm can not only recover the optimal flat partition, but also provide a two-approximati…
University of Electronic Science and Technology of China（电子科技大学）；University of Minnesota（明尼苏达大学）
One of the main challenges for hierarchical clustering is how to appropriately identify the representative points in the lower level of the cluster tree, which are going to be utilized as the roots in the higher level of the cluster tree for further aggregation. However, conventional hierarchical clustering approaches have adopted some simple tricks to select the "representative" points which might not be as representative as enough. Thus, the constructed cluster tree is less attractive in terms of its poor robustness and weak reliability. Aiming at this issue, we propose a novel hierarchical …
Comparison of three kind of the clustering and find cost function and loss function and calculate them. Error rate of the clustering methods and how to calculate the error percentage always be one on the important factor for evaluating the clustering methods, so this paper introduce one way to calculate the error rate of clustering methods. Clustering algorithms can be divided into several categories including partitioning clustering algorithms, hierarchical algorithms and density based algorithms. Generally speaking we should compare clustering algorithms by Scalability, Ability to work with …
A hierarchical clustering method is stable if small perturbations on the data set produce small perturbations in the result. These perturbations are measured using the Gromov-Hausdorff metric. We study the problem of stability on linkage-based hierarchical clustering methods. We obtain that, under some basic conditions, standard linkage-based methods are semi-stable. This means that they are stable if the input data is close enough to an ultrametric space. We prove that, apart from exotic examples, introducing any unchaining condition in the algorithm always produces unstable methods.
Driven by the multi-level structure of human intracranial electroencephalogram (iEEG) recordings of epileptic seizures, we introduce a new variant of a hierarchical Dirichlet Process---the multi-level clustering hierarchical Dirichlet Process (MLC-HDP)---that simultaneously clusters datasets on multiple levels. Our seizure dataset contains brain activity recorded in typically more than a hundred individual channels for each seizure of each patient. The MLC-HDP model clusters over channels-types, seizure-types, and patient-types simultaneously. We describe this model and its implementation in d…
We propose a new anytime hierarchical clustering method that iteratively transforms an arbitrary initial hierarchy on the configuration of measurements along a sequence of trees we prove for a fixed data set must terminate in a chain of nested partitions that satisfies a natural homogeneity requirement. Each recursive step re-edits the tree so as to improve a local measure of cluster homogeneity that is compatible with a number of commonly used (e.g., single, average, complete) linkage functions. As an alternative to the standard batch algorithms, we present numerical evidence to suggest that …
Stanford University（斯坦福大学）；Ohio State University（俄亥俄州立大学）；Rice University（莱斯大学）
We provide a complete taxonomic characterization of robust hierarchical clustering methods for directed networks following an axiomatic approach. We begin by introducing three practical properties associated with the notion of robustness in hierarchical clustering: linear scale preservation, stability, and excisiveness. Linear scale preservation enforces imperviousness to change in units of measure whereas stability ensures that a bounded perturbation in the input network entails a bounded perturbation in the clustering output. Excisiveness refers to the local consistency of the clustering out…
Simon Fraser University（西蒙弗雷泽大学）；Ulsan National Institute of Science and Technology（蔚山科学技术院）；University of British Columbia（不列颠哥伦比亚大学）；Disney Research（迪士尼研究院）
We present a hierarchical maximum-margin clustering method for unsupervised data analysis. Our method extends beyond flat maximum-margin clustering, and performs clustering recursively in a top-down manner. We propose an effective greedy splitting criteria for selecting which cluster to split next, and employ regularizers that enforce feature sharing/competition for capturing data semantics. Experimental results obtained on four standard datasets show that our method outperforms flat and hierarchical clustering baselines, while forming clean and semantically meaningful cluster hierarchies.
University of Electronic Science and Technology of China（电子科技大学）；Tencent Inc.（腾讯公司）；Harbin Institute of Technology, Shenzhen（哈尔滨工业大学（深圳））；Peng Cheng National Lab（鹏城国家实验室）
Hierarchical clustering recursively partitions data at an increasingly finer granularity. In real-world applications, multi-view data have become increasingly important. This raises a less investigated problem, i.e., multi-view hierarchical clustering, to better understand the hierarchical structure of multi-view data. To this end, we propose a novel neural network-based model, namely Contrastive Multi-view Hyperbolic Hierarchical Clustering (CMHHC). It consists of three components, i.e., multi-view alignment learning, aligned feature similarity learning, and continuous hyperbolic hierarchical…
