From bd0ccaeb0e3b93c02ad7b164f8c3014ca1367d5d Mon Sep 17 00:00:00 2001
From: Peter Schubert <Peter.Schubert@hhu.de>
Date: Wed, 14 Sep 2022 12:00:54 +0200
Subject: [PATCH] in GBA_problem - density constraint with scaled density
---
xbanalysis/problems/gba_problem.py | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/xbanalysis/problems/gba_problem.py b/xbanalysis/problems/gba_problem.py
index acafcc8..dee8097 100644
--- a/xbanalysis/problems/gba_problem.py
+++ b/xbanalysis/problems/gba_problem.py
@@ -26,6 +26,7 @@ def cache_last(func):
# TODO: call get_reaction_rates from solver ?
# TODO: split get_reaction_rates, get_reaction_jacs, get_reaction_hesses
+# TODO: variable transformation x = exp(y) and solve for unbounded y. start with vector y = log(x)
class GbaProblem:
@@ -40,7 +41,9 @@ class GbaProblem:
:type xba_model: XbaModel
"""
self.xba_model = xba_model
- # self.cache = True
+
+ # check to scale density constraint to improve convergence
+ self.scale_density = 1e-4
# metabolites and enzymes in the model
metab_sids = [s.id for s in xba_model.species.values() if s.sboterm.is_in_branch('SBO:0000247')]
@@ -713,7 +716,7 @@ class GbaProblem:
density = self.model_params['mws'][self.var_mask_enz].dot(ce)
else:
density = self.model_params['mws'].dot(x)
- return np.array([self.model_params['rho'] - density])
+ return np.array([self.model_params['rho'] - density]) * self.scale_density
@cache_last
def heq_density_jac(self, x):
@@ -733,7 +736,7 @@ class GbaProblem:
density_grad[self.var_mask_enz] = -self.model_params['mws'][self.var_mask_enz]
else:
density_grad = -self.model_params['mws']
- return density_grad
+ return density_grad * self.scale_density
# noinspection PyUnusedLocal
@cache_last
@@ -746,4 +749,4 @@ class GbaProblem:
:rtype: numpy.ndarray (3D), shape [1,x,x]
"""
hess = np.zeros((1, self.n_vars, self.n_vars))
- return np.tril(hess)
+ return np.tril(hess) * self.scale_density
--
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