Skip to content
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

Jump to bottom

Add pyoptinterface_based_impl.py and integrate it #104

Merged
merged 2 commits into from
Aug 21, 2024
Merged

Add pyoptinterface_based_impl.py and integrate it #104

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
363d560
Add pyoptInterface_based_impl.py and integrate it
KeShih Jul 6, 2024
aba3f19
Rename and improve pyoptinterface_based_impl.py
KeShih Aug 20, 2024
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
66 changes: 15 additions & 51 deletions dingo/MetabolicNetwork.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@

# Copyright (c) 2021 Apostolos Chalkis
# Copyright (c) 2021 Vissarion Fisikopoulos
# Copyright (c) 2024 Ke Shi

# Licensed under GNU LGPL.3, see LICENCE file

Expand All @@ -11,15 +12,7 @@
from typing import Dict
import cobra
from dingo.loading_models import read_json_file, read_mat_file, read_sbml_file, parse_cobra_model
from dingo.fva import slow_fva
from dingo.fba import slow_fba

try:
import gurobipy
from dingo.gurobi_based_implementations import fast_fba, fast_fva, fast_inner_ball
except ImportError as e:
pass

from dingo.pyoptInterface_based_impl import fba,fva,inner_ball,remove_redundant_facets

class MetabolicNetwork:
def __init__(self, tuple_args):
Expand All @@ -28,13 +21,7 @@ def __init__(self, tuple_args):
self._parameters["opt_percentage"] = 100
self._parameters["distribution"] = "uniform"
self._parameters["nullspace_method"] = "sparseQR"

try:
import gurobipy

self._parameters["fast_computations"] = True
except ImportError as e:
self._parameters["fast_computations"] = False
self._parameters["solver"] = None

if len(tuple_args) != 10:
raise Exception(
Expand Down Expand Up @@ -107,30 +94,18 @@ def from_cobra_model(cls, arg):
def fva(self):
"""A member function to apply the FVA method on the metabolic network."""

if self._parameters["fast_computations"]:
return fast_fva(
self._lb,
self._ub,
self._S,
self._objective_function,
self._parameters["opt_percentage"],
)
else:
return slow_fva(
self._lb,
self._ub,
self._S,
self._objective_function,
self._parameters["opt_percentage"],
)
return fva(
self._lb,
self._ub,
self._S,
self._objective_function,
self._parameters["opt_percentage"],
self._parameters["solver"]
)

def fba(self):
"""A member function to apply the FBA method on the metabolic network."""

if self._parameters["fast_computations"]:
return fast_fba(self._lb, self._ub, self._S, self._objective_function)
else:
return slow_fba(self._lb, self._ub, self._S, self._objective_function)
return fba(self._lb, self._ub, self._S, self._objective_function, self._parameters["solver"])

@property
def lb(self):
Expand Down Expand Up @@ -286,20 +261,9 @@ def set_active_bound(reaction: str, reac_index: int, bound: float) -> None:
set_active_bound(
rxn_id, reac_index, min(0.0, -self._lb[reac_index] if is_export else self._ub[reac_index])
)

def set_fast_mode(self):

try:
import gurobipy

self._parameters["fast_computations"] = True
except ImportError as e:
print("You have to install gurobi to use the fast computations.")
self._parameters["fast_computations"] = False

def set_slow_mode(self):

self._parameters["fast_computations"] = False

def set_solver(self, solver: str):
self._parameters["solver"] = solver

def set_nullspace_method(self, value):

Expand Down
108 changes: 25 additions & 83 deletions dingo/PolytopeSampler.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
# dingo is part of GeomScale project

# Copyright (c) 2021 Apostolos Chalkis
# Copyright (c) 2024 Ke Shi

# Licensed under GNU LGPL.3, see LICENCE file

Expand All @@ -10,23 +11,13 @@
import warnings
import math
from dingo.MetabolicNetwork import MetabolicNetwork
from dingo.fva import slow_fva
from dingo.utils import (
map_samples_to_steady_states,
get_matrices_of_low_dim_polytope,
get_matrices_of_full_dim_polytope,
)

try:
import gurobipy
from dingo.gurobi_based_implementations import (
fast_fba,
fast_fva,
fast_inner_ball,
fast_remove_redundant_facets,
)
except ImportError as e:
pass
from dingo.pyoptInterface_based_impl import fba,fva,inner_ball,remove_redundant_facets

from volestipy import HPolytope

Expand All @@ -53,14 +44,8 @@ def __init__(self, metabol_net):
self._parameters["first_run_of_mmcs"] = True
self._parameters["remove_redundant_facets"] = True

try:
import gurobipy

self._parameters["fast_computations"] = True
self._parameters["tol"] = 1e-06
except ImportError as e:
self._parameters["fast_computations"] = False
self._parameters["tol"] = 1e-03
self._parameters["tol"] = 1e-06
self._parameters["solver"] = None

def get_polytope(self):
"""A member function to derive the corresponding full dimensional polytope
Expand All @@ -82,24 +67,18 @@ def get_polytope(self):
) = self._metabolic_network.fba()

if (
self._parameters["fast_computations"]
and self._parameters["remove_redundant_facets"]
self._parameters["remove_redundant_facets"]
):

A, b, Aeq, beq = fast_remove_redundant_facets(
A, b, Aeq, beq = remove_redundant_facets(
self._metabolic_network.lb,
self._metabolic_network.ub,
self._metabolic_network.S,
self._metabolic_network.objective_function,
self._parameters["opt_percentage"],
self._parameters["solver"],
)
else:
if (not self._parameters["fast_computations"]) and self._parameters[
"remove_redundant_facets"
]:
warnings.warn(
"We continue without redundancy removal (slow mode is ON)"
)

(
min_fluxes,
Expand Down Expand Up @@ -162,14 +141,9 @@ def generate_steady_states(

P = HPolytope(self._A, self._b)

if self._parameters["fast_computations"]:
self._A, self._b, Tr, Tr_shift, samples = P.fast_mmcs(
ess, psrf, parallel_mmcs, num_threads
)
else:
self._A, self._b, Tr, Tr_shift, samples = P.slow_mmcs(
ess, psrf, parallel_mmcs, num_threads
)
self._A, self._b, Tr, Tr_shift, samples = P.mmcs(
ess, psrf, parallel_mmcs, num_threads, self._parameters["solver"]
)

if self._parameters["first_run_of_mmcs"]:
steady_states = map_samples_to_steady_states(
Expand Down Expand Up @@ -207,7 +181,7 @@ def generate_steady_states_no_multiphase(
else:
bias_vector = bias_vector.astype('float64')

samples = P.generate_samples(method, n, burn_in, thinning, self._parameters["fast_computations"], variance, bias_vector)
samples = P.generate_samples(method, n, burn_in, thinning, variance, bias_vector, self._parameters["solver"])
samples_T = samples.T

steady_states = map_samples_to_steady_states(
Expand All @@ -218,7 +192,7 @@ def generate_steady_states_no_multiphase(

@staticmethod
def sample_from_polytope(
A, b, ess=1000, psrf=False, parallel_mmcs=False, num_threads=1
A, b, ess=1000, psrf=False, parallel_mmcs=False, num_threads=1, solver=None
):
"""A static function to sample from a full dimensional polytope.
Expand All @@ -233,22 +207,16 @@ def sample_from_polytope(

P = HPolytope(A, b)

try:
import gurobipy
A, b, Tr, Tr_shift, samples = P.mmcs(
ess, psrf, parallel_mmcs, num_threads, solver
)

A, b, Tr, Tr_shift, samples = P.fast_mmcs(
ess, psrf, parallel_mmcs, num_threads
)
except ImportError as e:
A, b, Tr, Tr_shift, samples = P.slow_mmcs(
ess, psrf, parallel_mmcs, num_threads
)

return samples

@staticmethod
def sample_from_polytope_no_multiphase(
A, b, method = 'billiard_walk', n=1000, burn_in=0, thinning=1, variance=1.0, bias_vector=None
A, b, method = 'billiard_walk', n=1000, burn_in=0, thinning=1, variance=1.0, bias_vector=None, solver=None
):
"""A static function to sample from a full dimensional polytope with an MCMC method.
Expand All @@ -267,25 +235,17 @@ def sample_from_polytope_no_multiphase(

P = HPolytope(A, b)

try:
import gurobipy
samples = P.generate_samples(method, n, burn_in, thinning, True, variance, bias_vector)
except ImportError as e:
samples = P.generate_samples(method, n, burn_in, thinning, False, variance, bias_vector)
samples = P.generate_samples(method, n, burn_in, thinning, variance, bias_vector, solver)

samples_T = samples.T
return samples_T

@staticmethod
def round_polytope(
A, b, method = "john_position"
A, b, method = "john_position", solver = None
):
P = HPolytope(A, b)
try:
import gurobipy
A, b, Tr, Tr_shift, round_value = P.rounding(method, True)
except ImportError as e:
A, b, Tr, Tr_shift, round_value = P.rounding(method, False)
A, b, Tr, Tr_shift, round_value = P.rounding(method, solver)

return A, b, Tr, Tr_shift

Expand All @@ -301,6 +261,7 @@ def sample_from_fva_output(
psrf=False,
parallel_mmcs=False,
num_threads=1,
solver = None
):
"""A static function to sample steady states when the output of FVA is given.
Expand Down Expand Up @@ -335,16 +296,9 @@ def sample_from_fva_output(

P = HPolytope(A, b)

try:
import gurobipy

A, b, Tr, Tr_shift, samples = P.fast_mmcs(
ess, psrf, parallel_mmcs, num_threads
)
except ImportError as e:
A, b, Tr, Tr_shift, samples = P.slow_mmcs(
ess, psrf, parallel_mmcs, num_threads
)
A, b, Tr, Tr_shift, samples = P.mmcs(
ess, psrf, parallel_mmcs, num_threads, solver
)

steady_states = map_samples_to_steady_states(samples, N, N_shift)

Expand Down Expand Up @@ -381,20 +335,8 @@ def metabolic_network(self):
def facet_redundancy_removal(self, value):
self._parameters["remove_redundant_facets"] = value

if (not self._parameters["fast_computations"]) and value:
warnings.warn(
"Since you are in slow mode the redundancy removal step is skipped (dingo does not currently support this functionality in slow mode)"
)

def set_fast_mode(self):

self._parameters["fast_computations"] = True
self._parameters["tol"] = 1e-06

def set_slow_mode(self):

self._parameters["fast_computations"] = False
self._parameters["tol"] = 1e-03
def set_solver(self, solver):
self._parameters["solver"] = solver

def set_distribution(self, value):

Expand Down
Loading
Loading