Tootfinder

Fully-Dynamic Parallel Algorithms for Single-Linkage Clustering
Quinten De Man, Laxman Dhulipala, Kishen N Gowda
https://arxiv.org/abs/2506.18384 https://

Fully-Dynamic Parallel Algorithms for Single-Linkage Clustering
Single-linkage clustering is a popular form of hierarchical agglomerative clustering (HAC) where the distance between two clusters is defined as the minimum distance between any pair of points across the two clusters. In single-linkage HAC, the output is typically the single-linkage dendrogram (SLD), which is the binary tree representing the hierarchy of clusters formed by iteratively contracting the two closest clusters. In the dynamic setting, prior work has only studied maintaining a minimum…

Covariance Decomposition for Distance Based Species Tree Estimation
Georgios Aliatimis, Ruriko Yoshida, Burak Boyak, James Grant
https://arxiv.org/abs/2506.16425

Covariance Decomposition for Distance Based Species Tree Estimation
In phylogenomics, species-tree methods must contend with two major sources of noise; stochastic gene-tree variation under the multispecies coalescent model (MSC) and finite-sequence substitutional noise. Fast agglomerative methods such as GLASS, STEAC, and METAL combine multi-locus information via distance-based clustering. We derive the exact covariance matrix of these pairwise distance estimates under a joint MSC-plus-substitution model and leverage it for reliable confidence estimation, and …