Tootfinder

Accelerating Deterministic Global Optimization via GPU-parallel Interval Arithmetic
Hongzhen Zhang (Department of Chemical Engineering, KU Leuven, Leuven, Belgium), Tim Kerkenhoff (Institute of Climate and Energy Systems - Energy Systems Engineering), Neil Kichler (Software and Tools for Computational Engineering), Manuel Dahmen (Institute of Climate and Energy Systems - Energy Systems Engineering), Alexander Mitsos (JARA-CSD, Aachen, Germany, Process Systems Enginering, Institute of C…

Accelerating Deterministic Global Optimization via GPU-parallel Interval Arithmetic
Spatial Branch and Bound (B&B) algorithms are widely used for solving nonconvex problems to global optimality, yet they remain computationally expensive. Though some works have been carried out to speed up B&B via CPU parallelization, GPU parallelization is much less explored. In this work, we investigate the design of a spatial B&B algorithm that involves an interval-based GPU-parallel lower bounding solver: The domain of each B&B node is temporarily partitioned into numerous subdomains, then …

phylo2vec: a library for vector-based phylogenetic tree manipulation
Neil Scheidwasser, Ayush Nag, Matthew J Penn, Anthony MV Jakob, Frederik M{\o}lkj{\ae}r Andersen, Mark P Khurana, Landung Setiawan, Madeline Gordon, David A Duch\^ene, Samir Bhatt
https://arxiv.org/abs/2506.19490

phylo2vec: a library for vector-based phylogenetic tree manipulation
Phylogenetics is a fundamental component of many analysis frameworks in biology as well as linguistics to study the evolutionary relationships of different entities. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has underscored the necessity for phylogenetic software to handle large datasets of genomes or phylogenetic trees. While significant efforts have focused on scaling optimisation algorithms, visualization, and lineage identification, an emerging body of researc…