gpuGEM: GPU-based linear optimisation of genome-scale metabolic models

Abstract

Summary: Genome-scale metabolic models increasingly challenge CPU linear-programming solvers in repeated optimisation. We present gpuGEM, an open-source Python library for GPU-based optimisation using NVIDIA cuOpt, with size-adaptive settings validated against HiGHS and Gurobi. Across ten models spanning four orders of magnitude, gpuGEM achieved 1.1x to 94x speed-ups over the faster HiGHS method (dual simplex or interior point), and outperformed Gurobi on three models (1.6x to 2.5x). In candidate-gene prioritisation, gpuGEM reduced end-to-end query time from 41 s to 21 s. Availability and Implementation: gpuGEM is released under the MIT licence at https://github.com/Digital-Metabolic-Twin-Centre/gpuGEM and on PyPI (pip install gpugem); release v0.1.3 is archived at https://zenodo.org/records/23422813. It requires an NVIDIA GPU of compute capability 7.0 or newer (Volta onward), Python 3.11 or later, CUDA 12 and cuOpt 26.6 or later. Contact: ronan.mt.fleming@gmail.com Supplementary information: Supplementary data are available as an ancillary file on arXiv.