Skip to content

fix: inverted allowExcretion constraint sense in ftINITInternalAlg #675

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
edkerk merged 1 commit into from
Jul 17, 2026
Merged

fix: inverted allowExcretion constraint sense in ftINITInternalAlg #675

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 9 additions & 2 deletions INIT/ftINITInternalAlg.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -392,10 +392,17 @@
metVarInd = (1:nMetabolMets) + (length(prob.vartype) - nMetVars);

if allowExcretion
prob.csense = [repmat('L', 1, length(milpModel.mets)), ...
%S*v >= 0: a metabolite may be produced in excess of what is consumed,
%and the surplus is implicitly excreted. 'L' would say S*v <= 0, which
%lets a metabolite be consumed without ever being produced -- free
%uptake, the opposite of excretion, and enough for the MILP to switch a
%reaction on by conjuring its substrates out of nothing.
prob.csense = [repmat('G', 1, length(milpModel.mets)), ...
repmat('E', 1, length(prob.b) - length(milpModel.mets))];
else
prob.csense = '=';
%One character per row: optimizeProb maps csense elementwise for glpk and
%cobra, so a scalar '=' only happens to work on gurobi.
prob.csense = repmat('E', 1, length(prob.b));
end

params.intTol = 10^-7; %This value is very important. If set too low
Expand Down
26 changes: 26 additions & 0 deletions testing/function_tests/tINIT.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -259,6 +259,32 @@ function ftINITFullVsThreeStepRuns(testCase)
testCase.verifyTrue(all(contains(mres2.rxns, expResult)));
end

function ftINITSeriesVariantsRun(testCase)
% Only '1+1' and 'full' were ever exercised, so the 2-step series
% from the paper -- and the allowExcretion constraint they lean on
% -- had no coverage at all.
testCase.assumeMILPSolver();
testModel = getTstModel();
testParams = struct();
evalc('prepData = prepINITModel(testModel, {}, {}, false, {}, ''s'');');
arrayData.genes = testModel.genes;
arrayData.tissues = {'a'};
arrayData.levels = getExprForRxnScore(getTstModelRxnScores());
arrayData.threshold = 1;

steps = getINITSteps([], '2+1');
evalc(['resModel = ftINIT(prepData,arrayData.tissues{1},[],[],' ...
'arrayData,[],steps,true,true,testParams,false);']);
% Same answer as the '1+1' series in ftINITPipelineRuns.
testCase.verifyEqual(resModel.rxns, {'R1';'R4';'R6';'R8';'R9';'R10'});

steps = getINITSteps([], '2+0');
evalc(['resModel = ftINIT(prepData,arrayData.tissues{1},[],[],' ...
'arrayData,[],steps,true,true,testParams,false);']);
% '2+0' skips step 3, so the GPR-less transport R2 survives.
testCase.verifyEqual(resModel.rxns, {'R1';'R2';'R4';'R6';'R8';'R9';'R10'});
end

end
end

Expand Down