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References

The (M)ILPs for flow decomposition-like problems at the core of this package appeared in:

  1. Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu, Fast, Flexible, and Exact Minimum Flow Decompositions via ILP, RECOMB 2022 - 26th Annual International Conference on Research in Computational Molecular Biology, Lecture Notes in Computer Science 13278, 230–245, 2022 (preprint)

  2. Fernando H.C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu, Efficient Minimum Flow Decomposition via Integer Linear Programming, Journal of Computational Biology 29(11), 1–16, 2022

The flow decomposition with subpath constraints problem was formalized in:

  1. Lucia Williams, Alexandru I. Tomescu, Brendan Mumey Flow Decomposition with Subpath Constraints, IEEE/ACM Transactions on Computational Biology and Bioinformatics 20(1), 360–370, 2023

The safety optimizations applied to all the path-finding models appeared in:

  1. Andreas Grigorjew, Fernando H. C. Dias, Andrea Cracco, Romeo Rizzi, Alexandru I. Tomescu Accelerating ILP solvers for Minimum Flow Decompositions through search space and dimensionality reductions SEA 2024 - 22nd International Symposium on Experimental Algorithms, Leibniz International Proceedings in Informatics (LIPIcs) 301, 14:1–14:19, 2024

  2. Francisco Sena, Alexandru I. Tomescu Safe Paths and Sequences for Scalable ILPs in RNA Transcript Assembly Problems arXiv, 2024

See the page of each decomposition model for some references to papers introducing them.