×

Speedy colorful subtrees. (English) Zbl 1467.92078

Xu, Dachuan (ed.) et al., Computing and combinatorics. 21st international conference, COCOON 2015, Beijing, China, August 4–6, 2015. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 9198, 310-322 (2015).
Summary: Fragmentation trees are a technique for identifying molecular formulas and deriving some chemical properties of metabolites – small organic molecules – solely from mass spectral data. Computing these trees involves finding exact solutions to the NP-hard maximum colorful subtree problem. Existing solvers struggle to solve the large instances involved fast enough to keep up with instrument throughput, and their performance remains a hindrance to adoption in practice.
We attack this problem on two fronts: by combining fast and effective reduction algorithms with a strong integer linear program (ILP) formulation of the problem, we achieve overall speedups of 9.4 fold and 8.8 fold on two sets of real-world problems – without sacrificing optimality. Both approaches are, to our knowledge, the first of their kind for this problem. We also evaluate the strategy of solving global problem instances, instead of first subdividing them into many candidate instances as has been done in the past. Software (C++ source for our reduction program and our CPLEX/Gurobi driver program) available under LGPL at https://github.com/wtwhite/speedy_colorful_subtrees/.
For the entire collection see [Zbl 1316.68028].

MSC:

92C40 Biochemistry, molecular biology
90C10 Integer programming
PDF BibTeX XML Cite
Full Text: DOI