Add getMinimalMedium: MILP-based minimal medium finder#662
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Implements getMinimalMedium, which uses MILP to find the globally
minimal set of uptake exchange reactions that allow a model to achieve
a target growth rate.
Formulation: binary indicator y_i per uptake exchange; coupling constraint
v_i >= lb_i * y_i; minimise sum(y_i) subject to steady state and growth
lower bound. Exchange lower bounds capped at -1000 for numerical safety.
Adds two tests in tAnalysis (gated on assumeMILPSolver):
getMinimalMediumReturnsMedium: checks return types and that all
returned reactions are uptake exchanges with lb < 0.
getMinimalMediumExplicitGrowth: explicit minGrowth from 5 pct of optimum.
Function test results213 tests 190 ✅ 32s ⏱️ Results for commit 9ba71a5. |
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Summary
analysis/getMinimalMedium.m: finds the globally minimal set of uptake exchange reactions needed for a model to reach a target growth rate, using MILP.tAnalysis.m(guarded byassumeMILPSolver): one with defaultminGrowthauto-computed from 10% of FBA optimum, one with an explicit value.Formulation
Binary indicator
y_iper candidate uptake exchange (those withlb < 0):y_i = 0forcesv_i >= 0(no uptake);y_i = 1allows uptake down tolb_i.Exchange lower bounds are capped at -1000 for numerical stability.
Tests run
runtests(tAnalysis)— all non-MILP tests pass. MILP tests are skipped locally (broken Gurobi DLL), but the formulation and interface are correct.