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Hierarchical clustering is a fundamental task often used to discover meaningful structures in data, such as phylogenetic trees, taxonomies of concepts, subtypes of cancer, and cascades of particle decays in particle physics. Typically approximate algorithms are used for inference due to the combinatorial number of possible hierarchical clusterings. In contrast to existing methods, we present novel dynamic-programming algorithms for emph{exact} inference in hierarchical clustering based on a novel trellis data structure, and we prove that we can exactly compute the partition function, maximum likelihood hierarchy, and marginal probabilities of sub-hierarchies and clusters. Our algorithms scale in time and space proportional to the powerset of $N$ elements which is super-exponentially more efficient than explicitly considering each of the (2N-3)!! possible hierarchies. Also, for larger datasets where our exact algorithms become infeasible, we introduce an approximate algorithm based on a sparse trellis that compares well to other benchmarks. Exact methods are relevant to data analyses in particle physics and for finding correlations among gene expression in cancer genomics, and we give examples in both areas, where our algorithms outperform greedy and beam search baselines. In addition, we consider Dasguptas cost with synthetic data.
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
Recent works on Hierarchical Clustering (HC), a well-studied problem in exploratory data analysis, have focused on optimizing various objective functions for this problem under arbitrary similarity measures. In this paper we take the first step and g
In the past few years powerful generalizations to the Euclidean k-means problem have been made, such as Bregman clustering [7], co-clustering (i.e., simultaneous clustering of rows and columns of an input matrix) [9,18], and tensor clustering [8,34].
We present an $(e^{O(p)} frac{log ell}{loglogell})$-approximation algorithm for socially fair clustering with the $ell_p$-objective. In this problem, we are given a set of points in a metric space. Each point belongs to one (or several) of $ell$ grou
In this paper we present novel algorithms for several multidimensional data processing problems. We consider problems related to the computation of restricted clusters and of the diameter of a set of points using a new distance function. We also cons