Cluster Trellis: Data Structures & Algorithms for Exact Inference in Hierarchical Clustering

Hierarchical clustering is a fundamental task often used to discover meaningful structures in data. Due to the combinatorial number of possible hierarchical clusterings, approximate algorithms are typically used for inference. In contrast to existing methods, we present novel dynamic-programming algorithms for 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 outperforms greedy and beam search baselines.