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- W4301455190 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, $k$-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." @default.
- W4301455190 created "2022-10-05" @default.
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- W4301455190 date "2017-06-23" @default.
- W4301455190 modified "2023-09-30" @default.
- W4301455190 title "A practical fpt algorithm for Flow Decomposition and transcript assembly" @default.
- W4301455190 doi "https://doi.org/10.48550/arxiv.1706.07851" @default.
- W4301455190 hasPublicationYear "2017" @default.
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