From aaae4ae63f432da45eb0f4363a92767ba537a074 Mon Sep 17 00:00:00 2001 From: Nitish Malang <71919457+nitishmalang@users.noreply.github.com> Date: Thu, 12 Oct 2023 01:12:06 +0530 Subject: [PATCH] Create redundant_facet_removal_backup.py (#81) * Create redundant_facet_removal_backup.py * Update redundant_facet_removal_backup.py * Create update_gurobi_model_backup.py * Update redundant_facet_removal_backup.py * Update redundant_facet_removal_backup.py * Update redundant_facet_removal_backup.py * Rename redundant_facet_removal_backup.py to redundant_facet_removal_experimental.py * Rename update_gurobi_model_backup.py to update_gurobi_model_experiment.py * Create redundant_facet_removal_experiment.py * Delete dingo/backup directory * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py * Delete dingo/experimental_gurobi_functions/update_gurobi_model_experiment.py * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py * Update redundant_facet_removal_experiment.py --- .../redundant_facet_removal_experiment.py | 306 ++++++++++++++++++ 1 file changed, 306 insertions(+) create mode 100644 dingo/experimental_gurobi_functions/redundant_facet_removal_experiment.py diff --git a/dingo/experimental_gurobi_functions/redundant_facet_removal_experiment.py b/dingo/experimental_gurobi_functions/redundant_facet_removal_experiment.py new file mode 100644 index 00000000..6c26c349 --- /dev/null +++ b/dingo/experimental_gurobi_functions/redundant_facet_removal_experiment.py @@ -0,0 +1,306 @@ +# dingo : a python library for metabolic networks sampling and analysis +# dingo is part of GeomScale project + +# Copyright (c) 2021 Apostolos Chalkis + +# Licensed under GNU LGPL.3, see LICENCE file + +import sys +import numpy as np +import scipy.sparse as sp +import gurobipy as gp +from gurobipy import GRB +import math + +def update_model_constraints_and_bounds(model, Aeq_sparse=None, beq=None, A_sparse=None, b=None, + new_lower_bounds=None, new_upper_bounds=None): + if Aeq_sparse is not None and beq is not None: + # Remove the old equality constraints + model.remove("c") + + # Add new equality constraints + model.addMConstr(sp.csr_matrix(Aeq_sparse), model.getVars(), "=", np.array(beq), name="c") + + if A_sparse is not None and b is not None: + # Remove the old inequality constraints + model.remove("d") + + # Add new inequality constraints + model.addMConstr(sp.csr_matrix(A_sparse), model.getVars(), "<", np.array(b), name="d") + + if new_lower_bounds is not None or new_upper_bounds is not None: + # Retrieve the variable objects + x_vars = model.getVars() + + # Update variable bounds if specified + if new_lower_bounds is not None: + for i, x_var in enumerate(x_vars): + x_var.lb = new_lower_bounds[i] + + if new_upper_bounds is not None: + for i, x_var in enumerate(x_vars): + x_var.ub = new_upper_bounds[i] + + # Update the model to apply the changes + model.update() + +# Usage example: +# Assuming you have a Gurobi model 'model' and new constraint matrices/vectors and bounds +# Call the function to update the model +# update_model_constraints_and_bounds(model, Aeq_sparse_new, beq_new, A_sparse_new, b_new, new_lower_bounds, new_upper_bounds) + + +def solve_lp_with_different_objectives(model, new_objective_coeffs): + """ + Solve a linear program with a different objective function. + + Parameters: + model (gurobipy.Model): The Gurobi model with the original constraints. + new_objective_coeffs (list or numpy.ndarray): List or array of new objective coefficients for the variables. + + Returns: + gurobipy.Model: The updated Gurobi model with the new objective function. + """ + # Clear the existing objective function + model.setObjective(0, clear=True) + + # TODO: Optimization opportunity - You could pass a numpy array here (instead of a list of coefficients) + # and update the objective in one call without a for loop. + # For example, you can use: + # model.setObjective(new_objective_coeffs, GRB.MINIMIZE) + + # Update the objective function with the new coefficients + for i, var in enumerate(model.getVars()): + var.setAttr(GRB.Attr.Obj, new_objective_coeffs[i]) + + # Optimize the updated model + model.optimize() + + return model + + +def fast_remove_redundant_facets(lb, ub, S, c, opt_percentage=100): + if lb.size != S.shape[1] or ub.size != S.shape[1]: + raise Exception( + "The number of reactions must be equal to the number of given flux bounds." + ) + + redundant_facet_tol = 1e-07 + tol = 1e-06 + + m = S.shape[0] + n = S.shape[1] + beq = np.zeros(m) + Aeq_res = S + + A = np.zeros((2 * n, n), dtype="float") + A[0:n] = np.eye(n) + A[n:] -= np.eye(n, n, dtype="float") + + b = np.concatenate((ub, -lb), axis=0) + b = np.asarray(b, dtype="float") + b = np.ascontiguousarray(b, dtype="float") + + max_biomass_flux_vector, max_biomass_objective = fast_fba(lb, ub, S, c) + val = -np.floor(max_biomass_objective / tol) * tol * opt_percentage / 100 + + b_res = [] + A_res = np.empty((0, n), float) + beq_res = np.array(beq) + + try: + with gp.Env(empty=True) as env: + env.setParam("OutputFlag", 0) + env.start() + + with gp.Model(env=env) as model: + x = model.addMVar( + shape=n, + vtype=GRB.CONTINUOUS, + name="x", + lb=lb, + ub=ub, + ) + + Aeq_sparse = sp.csr_matrix(S) + A_sparse = sp.csr_matrix(np.array(-c)) + b_sparse = np.array(val) + + b = np.array(b) + beq = np.array(beq) + + model.addMConstr(Aeq_sparse, x, "=", beq, name="c") + model.update() + model.addMConstr(A_sparse, x, "<", [val], name="d") + model.update() + + model_iter = model.copy() + + indices_iter = range(n) + removed = 1 + offset = 1 + facet_left_removed = np.zeros((1, n), dtype=bool) + facet_right_removed = np.zeros((1, n), dtype=bool) + + while removed > 0 or offset > 0: + removed = 0 + offset = 0 + indices = indices_iter + indices_iter = [] + + Aeq_sparse = sp.csr_matrix(Aeq_res) + beq = np.array(beq_res) + + b_res = [] + A_res = np.empty((0, n), float) + + update_model_constraints_and_bounds(model_iter, Aeq_sparse, beq, A_sparse, [val], lb, ub) + + + for i in indices: + objective_function = A[i] + + redundant_facet_right = True + redundant_facet_left = True + + objective_function_max = np.asarray( + [-x for x in objective_function] + ) + + model_iter = solve_lp_with_different_objectives( + model_iter.copy(), objective_function_max + ) + + + status = model_iter.status + if status == GRB.OPTIMAL: + max_objective = -model_iter.objVal + else: + max_objective = ub[i] + + if not facet_right_removed[0, i]: + ub_iter = ub.copy() + ub_iter[i] = ub_iter[i] + 1 + + # Call solve_lp_with_different_objectives to solve LP + model_iter = solve_lp_with_different_objectives( + model_iter.copy(), objective_function + ) + + status = model_iter.status + if status == GRB.OPTIMAL: + max_objective2 = -model_iter.objVal + if ( + np.abs(max_objective2 - max_objective) + > redundant_facet_tol + ): + redundant_facet_right = False + else: + removed += 1 + facet_right_removed[0, i] = True + + model_iter.reset() + x = model_iter.getVars() + for j in range(n): + x[j].LB = lb[j] + x[j].UB = ub[j] + x[j].obj = objective_function[j] + + model_iter.optimize() + + status = model_iter.status + if status == GRB.OPTIMAL: + min_objective = model_iter.objVal + else: + min_objective = lb[i] + + if not facet_left_removed[0, i]: + lb_iter = lb.copy() + lb_iter[i] = lb_iter[i] - 1 + + # Call solve_lp_with_different_objectives to solve LP + model_iter = solve_lp_with_different_objectives( + model_iter.copy(), objective_function + ) + + + status = model_iter.status + if status == GRB.OPTIMAL: + min_objective2 = model_iter.objVal + if ( + np.abs(min_objective2 - min_objective) + > redundant_facet_tol + ): + redundant_facet_left = False + else: + removed += 1 + facet_left_removed[0, i] = True + + if (not redundant_facet_left) or (not redundant_facet_right): + width = abs(max_objective - min_objective) + + if width < redundant_facet_tol: + offset += 1 + Aeq_res = np.vstack( + ( + Aeq_res, + A[ + i, + ], + ) + ) + beq_res = np.append( + beq_res, min(max_objective, min_objective) + ) + ub[i] = sys.float_info.max + lb[i] = -sys.float_info.max + else: + indices_iter.append(i) + + if not redundant_facet_left: + A_res = np.append( + A_res, + np.array( + [ + A[ + n + i, + ] + ] + ), + axis=0, + ) + b_res.append(b[n + i]) + else: + lb[i] = -sys.float_info.max + + if not redundant_facet_right: + A_res = np.append( + A_res, + np.array( + [ + A[ + i, + ] + ] + ), + axis=0, + ) + b_res.append(b[i]) + else: + ub[i] = sys.float_info.max + else: + ub[i] = sys.float_info.max + lb[i] = -sys.float_info.max + + b_res = np.asarray(b_res) + A_res = np.asarray(A_res, dtype="float") + A_res = np.ascontiguousarray(A_res, dtype="float") + + return A_res, b_res, Aeq_res, beq_res + + except gp.GurobiError as e: + print("Error code " + str(e.errno) + ": " + str(e)) + except AttributeError: + print("Gurobi solver failed.") + +