Source code for the paper "Efficient Sparse Flow Decomposition Methods for RNA Multi-Assembly", Mathieu Besançon, ECAI 2025 (https://arxiv.org/abs/2501.14662).
The code cannot run without the data files which were not added for a size concern but are available at this zenodo entry. The datasets are expected in the "imperfect_flow_dataset" folder, with the same subfolder structure as in the Zenodo entry.
- functions.jl contains most of the logic functions, builds the different objective functions and integer optimization models. It is imported by all experiments.
- run_xyz.jl files correspond to an experiment running on all instances and writing result files.
- consolidate_xyz files gather the corresponding JSON result files and produces plots and printed table results which were used in the paper.
- single_poisson_case.jl corresponds to a single hard salmon instance used to display the numerical difficulties associated with the Poisson model.
Cite the code specifically using the Zenodo DOI: https://doi.org/10.5281/zenodo.16033781