A practical fpt algorithm for Flow Decomposition and transcript assembly
Abstract
The Flow Decomposition problem, which asks for the smallest set of weighted paths that "covers" a flow on a DAG, has recently been used as an important computational step in transcript assembly. We prove the problem is in FPT when parameterized by the number of paths by giving a practical linear fpt algorithm. Further, we implement and engineer a Flow Decomposition solver based on this algorithm, and evaluate its performance on RNA-sequence data. Crucially, our solver finds exact solutions while achieving runtimes competitive with a state-of-the-art heuristic. Finally, we contextualize our design choices with two hardness results related to preprocessing and weight recovery. Specifically, -Flow Decomposition does not admit polynomial kernels under standard complexity assumptions, and the related problem of assigning (known) weights to a given set of paths is NP-hard.
Cite
@article{arxiv.1706.07851,
title = {A practical fpt algorithm for Flow Decomposition and transcript assembly},
author = {Kyle Kloster and Philipp Kuinke and Michael P. O'Brien and Felix Reidl and Fernando Sánchez Villaamil and Blair D. Sullivan and Andrew van der Poel},
journal= {arXiv preprint arXiv:1706.07851},
year = {2017}
}
Comments
Introduces software package Toboggan: Version 1.0. http://dx.doi.org/10.5281/zenodo.821634