Fast, flexible, and exact minimum flow decompositions via ILP

DOI10.1007/978-3-031-04749-7_14zbMath1496.92066arXiv2201.10923OpenAlexW4226237737MaRDI QIDQ2170151

Lucia Williams, Brendan Mumey, Fernando H. C. Dias, Alexandru I. Tomescu

Publication date: 30 August 2022

Full work available at URL: https://arxiv.org/abs/2201.10923

zbMATH Keywords

integer linear programmingnetwork flowflow decompositionRNA assemblymultiassembly

Mathematics Subject Classification ID

Integer programming (90C10) Protein sequences, DNA sequences (92D20)

Related Items (1)

MFD-ILP

Uses Software

• CPLEX
• Gurobi
• Ipopt
• GitHub
• HISAT
• Salmon
• RNASeqReadSimulator
• CLIIQ
• MultiTrans
• Scallop2
• StringTie
• RefShannon
• CIDANE
• SSP
• ShoRAH
• IsoLasso

Cites Work

• Integer programming formulations for the elementary shortest path problem
• Theoretical and computational study of several linearisation techniques for binary quadratic problems
• Simple bounds and greedy algorithms for decomposing a flow into a minimal set of paths
• Compact linearization for binary quadratic problems
• On the implementation of an interior-point filter line-search algorithm for large-scale nonlinear programming
• A practical fpt algorithm for F<scp>low</scp> D<scp>ecomposition</scp> and transcript assembly
• Integer Linear Programming in Computational and Systems Biology
• Flow Decomposition with Subpath Constraints

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