sparseFBA¶
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sparseFBA
(model, osenseStr, checkMinimalSet, checkEssentialSet, zeroNormApprox, printLevel)[source]¶ Finds the minimal set of reactions subject to a LP objective
\[\begin{split}min ~&~ ||v||_0 \\ s.t ~&~ S v \leq, = or \geq b \\ ~&~ c^T v = f* \\ ~&~ l \leq v \leq u\end{split}\]where \(f*\) is the optimal value of objective (default is \(max c^T v\)).
Usage
[vSparse, sparseRxnBool, essentialRxnBool] = sparseFBA(model, osenseStr, checkMinimalSet, checkEssentialSet, zeroNormApprox, printLevel)Input
- model – (the following fields are required - others can be supplied): * S - Stoichiometric matrix * b - Right hand side = dx/dt * c - Objective coefficients * lb - Lower bounds * ub - Upper bounds
Optional inputs
model – (optional for C*v<=d): * C - Stoichiometric matrix * d - Right hand side = dx/dt
osenseStr – (default = ‘max’)
- max: \(f* = argmax \{max\ c^T v: Sv \leq, = or \geq b, l \leq v \leq u\}\)
- min: \(f* = argmin \{min\ c^T v: Sv \leq, = or \geq b, l \leq v \leq u\}\)
- none: ignore the constraint \(c^T v = f*\)
checkMinimalSet – {0,(1)} Heuristically check if the selected set of reactions is minimal by removing one by one the predicted active reaction
- true = check (default value)
- false = do not check
checkEssentialSet – {0,(1)} Heuristically check if the selected set of reactions is essential
zeroNormApprox – appoximation type of zero-norm (only available when minNorm = ‘zero’) (default = ‘cappedL1’)
- ‘cappedL1’ : Capped-L1 norm
- ‘exp’ : Exponential function
- ‘log’ : Logarithmic function
- ‘SCAD’ : SCAD function
- ‘lp-‘ : \(L_p\) norm with \(p < 0\)
- ‘lp+’ : \(L_p\) norm with \(0 < p < 1\)
- ‘l1’ : L1 norm
- ‘all’ : try all approximations and return the best result
printLevel – Printing level
- 0 - Silent (Default)
- 1 - Summary information
Outputs
- vSparse – Depends on the set of reactions
- sparseRxnBool – Returns a vector with 1 and 0’s, where 1 means sparse
- essentialRxnBool – Returns a vector with 1 and 0’s, where 1 means essential
Authors: - Hoai Minh Le, Ronan Fleming