def test_repressilator(self):
print(">> Synchronizer benchmark <repressilator>:")
dataset_filepath = "datasets/repressilator.csv"
features_col_header = ["p_t_1", "q_t_1", "r_t_1"]
targets_col_header = ["p_t", "q_t", "r_t"]
dataset = transitions_dataset_from_csv(
path=dataset_filepath,
feature_names=features_col_header,
target_names=targets_col_header)
# Expected rules
expected_string_rules = """
p_t(1) :- q_t_1(1).
q_t(1) :- p_t_1(1), r_t_1(1).
r_t(1) :- p_t_1(0).
p_t(0) :- q_t_1(0).
q_t(0) :- p_t_1(0).
q_t(0) :- r_t_1(0).
r_t(0) :- p_t_1(1)."""
expected_string_constraints = ""
self._check_rules_and_predictions(dataset, expected_string_rules,
expected_string_constraints)
def test_toy_all_or_nothing_change(self):
print(">> Synchronizer benchmark <toy_all_or_nothing_change>:")
dataset_filepath = "datasets/toy_all_or_nothing_change.csv"
features_col_header = ["x0", "x1"]
targets_col_header = ["y0", "y1"]
dataset = transitions_dataset_from_csv(
path=dataset_filepath,
feature_names=features_col_header,
target_names=targets_col_header)
# Expected rules
expected_string_rules = """
y0(0) :- x0(0).
y0(0) :- x1(1).
y0(1) :- x0(1).
y0(1) :- x1(0).
y1(0) :- x0(1).
y1(0) :- x1(0).
y1(1) :- x0(0).
y1(1) :- x1(1).
"""
expected_string_constraints = """
:- x1(0), y0(0), y1(1).
:- x0(0), y0(1), y1(0).
:- x1(1), y0(1), y1(0).
:- x0(1), y0(0), y1(1).
"""
self._check_rules_and_predictions(dataset, expected_string_rules,
expected_string_constraints)
def test_disjonctive_boolean_network(self):
print(">> Synchronizer benchmark <disjonctive_boolean_network>:")
dataset_filepath = "datasets/disjonctive_boolean_network.csv"
features_col_header = ["a", "b", "c"]
targets_col_header = ["a_t", "b_t", "c_t"]
dataset = transitions_dataset_from_csv(
path=dataset_filepath,
feature_names=features_col_header,
target_names=targets_col_header)
# Expected rules
expected_string_rules = """
a_t(1) :- b(1).
a_t(1) :- a(1), c(1).
b_t(1) :- a(0).
b_t(1) :- b(0), c(1).
c_t(1) :- a(0).
a_t(0) :- b(0).
b_t(0) :- .
c_t(0) :- ."""
expected_string_constraints = """
:- b_t(1), c_t(1).
:- a(0), b_t(0), c_t(0).
:- b(0), a_t(1), b_t(1).
:- a(1), a_t(1), b_t(1).
:- c(1), a_t(0), b_t(0), c_t(0).
:- a(1), c(1), a_t(0), b_t(0).
"""
self._check_rules_and_predictions(dataset, expected_string_rules,
expected_string_constraints)
def test_mammalian(self):
print(">> PRIDE benchmark <mammalian>:")
dataset_filepath = "datasets/mammalian.csv"
features_col_header = [
"CycD_t_1", "CycE_t_1", "Rb_t_1", "E2F_t_1", "CycA_t_1", "p27_t_1",
"Cdc20_t_1", "UbcH10_t_1", "Cdh1_t_1", "CycB_t_1"
]
targets_col_header = [
"CycD_t", "CycE_t", "Rb_t", "E2F_t", "CycA_t", "p27_t", "Cdc20_t",
"UbcH10_t", "Cdh1_t", "CycB_t"
]
dataset = transitions_dataset_from_csv(
path=dataset_filepath,
feature_names=features_col_header,
target_names=targets_col_header)
# Expected rules
expected_string_rules = """
CycD_t(1) :- CycD_t_1(1).
CycE_t(1) :- Rb_t_1(0), E2F_t_1(1).
Rb_t(1) :- CycD_t_1(0), CycE_t_1(0), CycA_t_1(0), CycB_t_1(0).
Rb_t(1) :- CycD_t_1(0), p27_t_1(1), CycB_t_1(0).
E2F_t(1) :- Rb_t_1(0), CycA_t_1(0), CycB_t_1(0).
E2F_t(1) :- Rb_t_1(0), p27_t_1(1), CycB_t_1(0).
CycA_t(1) :- Rb_t_1(0), E2F_t_1(1), Cdc20_t_1(0), UbcH10_t_1(0).
CycA_t(1) :- Rb_t_1(0), E2F_t_1(1), Cdc20_t_1(0), Cdh1_t_1(0).
CycA_t(1) :- Rb_t_1(0), CycA_t_1(1), Cdc20_t_1(0), UbcH10_t_1(0).
CycA_t(1) :- Rb_t_1(0), CycA_t_1(1), Cdc20_t_1(0), Cdh1_t_1(0).
p27_t(1) :- CycD_t_1(0), CycE_t_1(0), CycA_t_1(0), CycB_t_1(0).
p27_t(1) :- CycD_t_1(0), CycE_t_1(0), p27_t_1(1), CycB_t_1(0).
p27_t(1) :- CycD_t_1(0), CycA_t_1(0), p27_t_1(1), CycB_t_1(0).
Cdc20_t(1) :- CycB_t_1(1).
UbcH10_t(1) :- Cdh1_t_1(0).
UbcH10_t(1) :- CycA_t_1(1), UbcH10_t_1(1).
UbcH10_t(1) :- Cdc20_t_1(1), UbcH10_t_1(1).
UbcH10_t(1) :- UbcH10_t_1(1), CycB_t_1(1).
Cdh1_t(1) :- CycA_t_1(0), CycB_t_1(0).
Cdh1_t(1) :- Cdc20_t_1(1).
Cdh1_t(1) :- p27_t_1(1), CycB_t_1(0).
CycB_t(1) :- Cdc20_t_1(0), Cdh1_t_1(0).
CycD_t(0) :- CycD_t_1(0).
CycE_t(0) :- Rb_t_1(1).
CycE_t(0) :- E2F_t_1(0).
Rb_t(0) :- CycD_t_1(1).
Rb_t(0) :- CycE_t_1(1), p27_t_1(0).
Rb_t(0) :- CycA_t_1(1), p27_t_1(0).
Rb_t(0) :- CycB_t_1(1).
E2F_t(0) :- Rb_t_1(1).
E2F_t(0) :- CycA_t_1(1), p27_t_1(0).
E2F_t(0) :- CycB_t_1(1).
CycA_t(0) :- Rb_t_1(1).
CycA_t(0) :- E2F_t_1(0), CycA_t_1(0).
CycA_t(0) :- Cdc20_t_1(1).
CycA_t(0) :- UbcH10_t_1(1), Cdh1_t_1(1).
p27_t(0) :- CycD_t_1(1).
p27_t(0) :- CycE_t_1(1), CycA_t_1(1).
p27_t(0) :- CycE_t_1(1), p27_t_1(0).
p27_t(0) :- CycA_t_1(1), p27_t_1(0).
p27_t(0) :- CycB_t_1(1).
Cdc20_t(0) :- CycB_t_1(0).
UbcH10_t(0) :- CycA_t_1(0), Cdc20_t_1(0), Cdh1_t_1(1), CycB_t_1(0).
UbcH10_t(0) :- UbcH10_t_1(0), Cdh1_t_1(1).
Cdh1_t(0) :- CycA_t_1(1), p27_t_1(0), Cdc20_t_1(0).
Cdh1_t(0) :- Cdc20_t_1(0), CycB_t_1(1).
CycB_t(0) :- Cdc20_t_1(1).
CycB_t(0) :- Cdh1_t_1(1)."""
self._check_rules_and_predictions(dataset, expected_string_rules)
def _test_arabidopsis(self):
print(">> PRIDE benchmark <arabidopsis>:")
dataset_filepath = "datasets/arabidopsis.csv"
features_col_header = [
"AP3_t_1", "UFO_t_1", "FUL_t_1", "FT_t_1", "AP1_t_1", "EMF1_t_1",
"LFY_t_1", "AP2_t_1", "WUS_t_1", "AG_t_1", "LUG_t_1", "CLF_t_1",
"TFL1_t_1", "PI_t_1", "SEP_t_1"
]
targets_col_header = [
"AP3_t", "UFO_t", "FUL_t", "FT_t", "AP1_t", "EMF1_t", "LFY_t",
"AP2_t", "WUS_t", "AG_t", "LUG_t", "CLF_t", "TFL1_t", "PI_t",
"SEP_t"
]
dataset = transitions_dataset_from_csv(
path=dataset_filepath,
feature_names=features_col_header,
target_names=targets_col_header)
# Expected rules
expected_string_rules = """
AP3_t(1) :- AP3_t_1(1), AP1_t_1(1), PI_t_1(1), SEP_t_1(1).
AP3_t(1) :- AP3_t_1(1), AG_t_1(1), PI_t_1(1), SEP_t_1(1).
AP3_t(1) :- UFO_t_1(1), LFY_t_1(1).
UFO_t(1) :- UFO_t_1(1).
FUL_t(1) :- AP1_t_1(0), TFL1_t_1(0).
FT_t(1) :- EMF1_t_1(0).
AP1_t(1) :- AG_t_1(0), TFL1_t_1(0).
AP1_t(1) :- FT_t_1(1), AG_t_1(0).
AP1_t(1) :- LFY_t_1(1), AG_t_1(0).
EMF1_t(1) :- LFY_t_1(0).
LFY_t(1) :- TFL1_t_1(0).
LFY_t(1) :- EMF1_t_1(0).
AP2_t(1) :- TFL1_t_1(0).
WUS_t(1) :- WUS_t_1(1), SEP_t_1(0).
WUS_t(1) :- WUS_t_1(1), AG_t_1(0).
AG_t(1) :- AP2_t_1(0), TFL1_t_1(0).
AG_t(1) :- LFY_t_1(1), AG_t_1(1), SEP_t_1(1).
AG_t(1) :- LFY_t_1(1), CLF_t_1(0).
AG_t(1) :- LFY_t_1(1), LUG_t_1(0).
AG_t(1) :- AP1_t_1(0), LFY_t_1(1).
AG_t(1) :- LFY_t_1(1), WUS_t_1(1).
AG_t(1) :- LFY_t_1(1), AP2_t_1(0).
LUG_t(1) :- .
CLF_t(1) :- .
TFL1_t(1) :- AP1_t_1(0), EMF1_t_1(1), LFY_t_1(0).
PI_t(1) :- AP3_t_1(1), AP1_t_1(1), PI_t_1(1), SEP_t_1(1).
PI_t(1) :- AP3_t_1(1), AG_t_1(1), PI_t_1(1), SEP_t_1(1).
PI_t(1) :- LFY_t_1(1), AG_t_1(1).
PI_t(1) :- AP3_t_1(1), LFY_t_1(1).
SEP_t(1) :- LFY_t_1(1).
AP3_t(0) :- AP3_t_1(0), UFO_t_1(0).
AP3_t(0) :- AP3_t_1(0), LFY_t_1(0).
AP3_t(0) :- UFO_t_1(0), AP1_t_1(0), AG_t_1(0).
AP3_t(0) :- AP1_t_1(0), LFY_t_1(0), AG_t_1(0).
AP3_t(0) :- UFO_t_1(0), PI_t_1(0).
AP3_t(0) :- LFY_t_1(0), PI_t_1(0).
AP3_t(0) :- UFO_t_1(0), SEP_t_1(0).
AP3_t(0) :- LFY_t_1(0), SEP_t_1(0).
UFO_t(0) :- UFO_t_1(0).
FUL_t(0) :- AP1_t_1(1).
FUL_t(0) :- TFL1_t_1(1).
FT_t(0) :- EMF1_t_1(1).
AP1_t(0) :- AG_t_1(1).
AP1_t(0) :- FT_t_1(0), LFY_t_1(0), TFL1_t_1(1).
EMF1_t(0) :- LFY_t_1(1).
LFY_t(0) :- EMF1_t_1(1), TFL1_t_1(1).
AP2_t(0) :- TFL1_t_1(1).
WUS_t(0) :- WUS_t_1(0).
WUS_t(0) :- AG_t_1(1), SEP_t_1(1).
AG_t(0) :- LFY_t_1(0), AP2_t_1(1).
AG_t(0) :- AP1_t_1(1), AP2_t_1(1), WUS_t_1(0), AG_t_1(0), LUG_t_1(1), CLF_t_1(1).
AG_t(0) :- AP1_t_1(1), AP2_t_1(1), WUS_t_1(0), LUG_t_1(1), CLF_t_1(1), SEP_t_1(0).
AG_t(0) :- LFY_t_1(0), TFL1_t_1(1).
TFL1_t(0) :- AP1_t_1(1).
TFL1_t(0) :- EMF1_t_1(0).
TFL1_t(0) :- LFY_t_1(1).
PI_t(0) :- AP3_t_1(0), LFY_t_1(0).
PI_t(0) :- AP3_t_1(0), AG_t_1(0).
PI_t(0) :- AP1_t_1(0), LFY_t_1(0), AG_t_1(0).
PI_t(0) :- LFY_t_1(0), PI_t_1(0).
PI_t(0) :- LFY_t_1(0), SEP_t_1(0).
SEP_t(0) :- LFY_t_1(0).
"""
self._check_rules_and_predictions(dataset, expected_string_rules)
def test_budding_yeast(self):
print(">> PRIDE benchmark <budding_yeast>:")
dataset_filepath = "datasets/budding_yeast.csv"
features_col_header = [
"size_t_1", "Cln3_t_1", "SBF_t_1", "MBF_t_1", "Cln1_2_t_1",
"Sic1_t_1", "Cln5_6_t_1", "Cdh1_t_1", "Clb1_2_t_1", "Mcm1/SFF_t_1",
"Cdc20&Cdc14_t_1", "Swi5_t_1"
]
targets_col_header = [
"size_t", "Cln3_t", "SBF_t", "MBF_t", "Cln1_2_t", "Sic1_t",
"Cln5_6_t", "Cdh1_t", "Clb1_2_t", "Mcm1/SFF_t", "Cdc20&Cdc14_t",
"Swi5_t"
]
dataset = transitions_dataset_from_csv(
path=dataset_filepath,
feature_names=features_col_header,
target_names=targets_col_header)
#Sic1_t(1) :- Cln1_2_t_1(0), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1), Swi5_t_1(1).
#Sic1_t(1) :- Cln1_2_t_1(0), Sic1_t_1(1), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
#Sic1_t(1) :- Cln1_2_t_1(0), Sic1_t_1(1), Cdc20&Cdc14_t_1(1), Swi5_t_1(1).
#Sic1_t(1) :- Sic1_t_1(1), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1), Swi5_t_1(1).
# Expected rules
expected_string_rules = """
Cln3_t(1) :- size_t_1(1).
SBF_t(1) :- SBF_t_1(1), Clb1_2_t_1(0).
SBF_t(1) :- Cln3_t_1(1), Clb1_2_t_1(0).
SBF_t(1) :- Cln3_t_1(1), SBF_t_1(1).
MBF_t(1) :- MBF_t_1(1), Clb1_2_t_1(0).
MBF_t(1) :- Cln3_t_1(1), Clb1_2_t_1(0).
MBF_t(1) :- Cln3_t_1(1), MBF_t_1(1).
Cln1_2_t(1) :- SBF_t_1(1).
Sic1_t(1) :- Cln1_2_t_1(0), Sic1_t_1(1), Cln5_6_t_1(0), Clb1_2_t_1(0).
Sic1_t(1) :- Cln1_2_t_1(0), Cln5_6_t_1(0), Clb1_2_t_1(0), Swi5_t_1(1).
Sic1_t(1) :- Cln1_2_t_1(0), Cln5_6_t_1(0), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Sic1_t(1) :- Cln1_2_t_1(0), Sic1_t_1(1), Cln5_6_t_1(0), Swi5_t_1(1).
Sic1_t(1) :- Cln1_2_t_1(0), Cln5_6_t_1(0), Cdc20&Cdc14_t_1(1), Swi5_t_1(1).
Sic1_t(1) :- Cln1_2_t_1(0), Sic1_t_1(1), Clb1_2_t_1(0), Swi5_t_1(1).
Sic1_t(1) :- Cln1_2_t_1(0), Sic1_t_1(1), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Sic1_t(1) :- Cln1_2_t_1(0), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1), Swi5_t_1(1).
Sic1_t(1) :- Sic1_t_1(1), Cln5_6_t_1(0), Clb1_2_t_1(0), Swi5_t_1(1).
Sic1_t(1) :- Sic1_t_1(1), Cln5_6_t_1(0), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Sic1_t(1) :- Sic1_t_1(1), Cln5_6_t_1(0), Cdc20&Cdc14_t_1(1), Swi5_t_1(1).
Sic1_t(1) :- Sic1_t_1(1), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1), Swi5_t_1(1).
Sic1_t(1) :- Cln5_6_t_1(0), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1), Swi5_t_1(1).
Sic1_t(1) :- Cln1_2_t_1(0), Sic1_t_1(1), Cln5_6_t_1(0), Cdc20&Cdc14_t_1(1).
Sic1_t(1) :- Cln1_2_t_1(0), Sic1_t_1(1), Cdc20&Cdc14_t_1(1), Swi5_t_1(1).
Cln5_6_t(1) :- Sic1_t_1(0), Cln5_6_t_1(1), Cdc20&Cdc14_t_1(0).
Cln5_6_t(1) :- MBF_t_1(1), Sic1_t_1(0), Cdc20&Cdc14_t_1(0).
Cln5_6_t(1) :- MBF_t_1(1), Sic1_t_1(0), Cln5_6_t_1(1).
Cln5_6_t(1) :- MBF_t_1(1), Cln5_6_t_1(1), Cdc20&Cdc14_t_1(0).
Cdh1_t(1) :- Cln1_2_t_1(0), Cln5_6_t_1(0), Cdh1_t_1(1), Clb1_2_t_1(0).
Cdh1_t(1) :- Cln1_2_t_1(0), Cln5_6_t_1(0), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Cdh1_t(1) :- Cln1_2_t_1(0), Cln5_6_t_1(0), Cdh1_t_1(1), Cdc20&Cdc14_t_1(1).
Cdh1_t(1) :- Cln1_2_t_1(0), Cdh1_t_1(1), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Cdh1_t(1) :- Cln5_6_t_1(0), Cdh1_t_1(1), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Clb1_2_t(1) :- Sic1_t_1(0), Cdh1_t_1(0), Clb1_2_t_1(1), Cdc20&Cdc14_t_1(0).
Clb1_2_t(1) :- Sic1_t_1(0), Cdh1_t_1(0), Mcm1/SFF_t_1(1), Cdc20&Cdc14_t_1(0).
Clb1_2_t(1) :- Sic1_t_1(0), Cdh1_t_1(0), Clb1_2_t_1(1), Mcm1/SFF_t_1(1).
Clb1_2_t(1) :- Sic1_t_1(0), Clb1_2_t_1(1), Mcm1/SFF_t_1(1), Cdc20&Cdc14_t_1(0).
Clb1_2_t(1) :- Sic1_t_1(0), Cln5_6_t_1(1), Cdh1_t_1(0), Cdc20&Cdc14_t_1(0).
Clb1_2_t(1) :- Sic1_t_1(0), Cln5_6_t_1(1), Cdh1_t_1(0), Clb1_2_t_1(1).
Clb1_2_t(1) :- Sic1_t_1(0), Cln5_6_t_1(1), Cdh1_t_1(0), Mcm1/SFF_t_1(1).
Clb1_2_t(1) :- Sic1_t_1(0), Cln5_6_t_1(1), Clb1_2_t_1(1), Cdc20&Cdc14_t_1(0).
Clb1_2_t(1) :- Sic1_t_1(0), Cln5_6_t_1(1), Mcm1/SFF_t_1(1), Cdc20&Cdc14_t_1(0).
Clb1_2_t(1) :- Sic1_t_1(0), Cln5_6_t_1(1), Clb1_2_t_1(1), Mcm1/SFF_t_1(1).
Clb1_2_t(1) :- Cdh1_t_1(0), Clb1_2_t_1(1), Mcm1/SFF_t_1(1), Cdc20&Cdc14_t_1(0).
Clb1_2_t(1) :- Cln5_6_t_1(1), Cdh1_t_1(0), Clb1_2_t_1(1), Cdc20&Cdc14_t_1(0).
Clb1_2_t(1) :- Cln5_6_t_1(1), Cdh1_t_1(0), Mcm1/SFF_t_1(1), Cdc20&Cdc14_t_1(0).
Clb1_2_t(1) :- Cln5_6_t_1(1), Cdh1_t_1(0), Clb1_2_t_1(1), Mcm1/SFF_t_1(1).
Clb1_2_t(1) :- Cln5_6_t_1(1), Clb1_2_t_1(1), Mcm1/SFF_t_1(1), Cdc20&Cdc14_t_1(0).
Mcm1/SFF_t(1) :- Cln5_6_t_1(1).
Mcm1/SFF_t(1) :- Clb1_2_t_1(1).
Cdc20&Cdc14_t(1) :- Clb1_2_t_1(1).
Cdc20&Cdc14_t(1) :- Mcm1/SFF_t_1(1).
Swi5_t(1) :- Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Swi5_t(1) :- Clb1_2_t_1(0), Mcm1/SFF_t_1(1).
Swi5_t(1) :- Mcm1/SFF_t_1(1), Cdc20&Cdc14_t_1(1).
size_t(0) :- .
Cln3_t(0) :- size_t_1(0).
SBF_t(0) :- Cln3_t_1(0), SBF_t_1(0).
SBF_t(0) :- Cln3_t_1(0), Clb1_2_t_1(1).
SBF_t(0) :- SBF_t_1(0), Clb1_2_t_1(1).
MBF_t(0) :- Cln3_t_1(0), MBF_t_1(0).
MBF_t(0) :- Cln3_t_1(0), Clb1_2_t_1(1).
MBF_t(0) :- MBF_t_1(0), Clb1_2_t_1(1).
Cln1_2_t(0) :- SBF_t_1(0).
Sic1_t(0) :- Sic1_t_1(0), Cdc20&Cdc14_t_1(0), Swi5_t_1(0).
Sic1_t(0) :- Sic1_t_1(0), Clb1_2_t_1(1), Cdc20&Cdc14_t_1(0).
Sic1_t(0) :- Sic1_t_1(0), Clb1_2_t_1(1), Swi5_t_1(0).
Sic1_t(0) :- Clb1_2_t_1(1), Cdc20&Cdc14_t_1(0), Swi5_t_1(0).
Sic1_t(0) :- Sic1_t_1(0), Cln5_6_t_1(1), Cdc20&Cdc14_t_1(0).
Sic1_t(0) :- Sic1_t_1(0), Cln5_6_t_1(1), Swi5_t_1(0).
Sic1_t(0) :- Cln5_6_t_1(1), Cdc20&Cdc14_t_1(0), Swi5_t_1(0).
Sic1_t(0) :- Sic1_t_1(0), Cln5_6_t_1(1), Clb1_2_t_1(1).
Sic1_t(0) :- Cln5_6_t_1(1), Clb1_2_t_1(1), Cdc20&Cdc14_t_1(0).
Sic1_t(0) :- Cln5_6_t_1(1), Clb1_2_t_1(1), Swi5_t_1(0).
Sic1_t(0) :- Cln1_2_t_1(1), Sic1_t_1(0), Cdc20&Cdc14_t_1(0).
Sic1_t(0) :- Cln1_2_t_1(1), Sic1_t_1(0), Swi5_t_1(0).
Sic1_t(0) :- Cln1_2_t_1(1), Cdc20&Cdc14_t_1(0), Swi5_t_1(0).
Sic1_t(0) :- Cln1_2_t_1(1), Sic1_t_1(0), Clb1_2_t_1(1).
Sic1_t(0) :- Cln1_2_t_1(1), Clb1_2_t_1(1), Cdc20&Cdc14_t_1(0).
Sic1_t(0) :- Cln1_2_t_1(1), Clb1_2_t_1(1), Swi5_t_1(0).
Sic1_t(0) :- Cln1_2_t_1(1), Sic1_t_1(0), Cln5_6_t_1(1).
Sic1_t(0) :- Cln1_2_t_1(1), Cln5_6_t_1(1), Clb1_2_t_1(1).
Sic1_t(0) :- Cln1_2_t_1(1), Cln5_6_t_1(1), Cdc20&Cdc14_t_1(0).
Sic1_t(0) :- Cln1_2_t_1(1), Cln5_6_t_1(1), Swi5_t_1(0).
Cln5_6_t(0) :- MBF_t_1(0), Cln5_6_t_1(0).
Cln5_6_t(0) :- MBF_t_1(0), Cdc20&Cdc14_t_1(1).
Cln5_6_t(0) :- Cln5_6_t_1(0), Cdc20&Cdc14_t_1(1).
Cln5_6_t(0) :- MBF_t_1(0), Sic1_t_1(1).
Cln5_6_t(0) :- Sic1_t_1(1), Cln5_6_t_1(0).
Cln5_6_t(0) :- Sic1_t_1(1), Cdc20&Cdc14_t_1(1).
Cdh1_t(0) :- Cdh1_t_1(0), Cdc20&Cdc14_t_1(0).
Cdh1_t(0) :- Cdh1_t_1(0), Clb1_2_t_1(1).
Cdh1_t(0) :- Clb1_2_t_1(1), Cdc20&Cdc14_t_1(0).
Cdh1_t(0) :- Cln5_6_t_1(1), Cdh1_t_1(0).
Cdh1_t(0) :- Cln5_6_t_1(1), Clb1_2_t_1(1).
Cdh1_t(0) :- Cln5_6_t_1(1), Cdc20&Cdc14_t_1(0).
Cdh1_t(0) :- Cln1_2_t_1(1), Cln5_6_t_1(1).
Cdh1_t(0) :- Cln1_2_t_1(1), Cdh1_t_1(0).
Cdh1_t(0) :- Cln1_2_t_1(1), Clb1_2_t_1(1).
Cdh1_t(0) :- Cln1_2_t_1(1), Cdc20&Cdc14_t_1(0).
Clb1_2_t(0) :- Cln5_6_t_1(0), Clb1_2_t_1(0), Mcm1/SFF_t_1(0).
Clb1_2_t(0) :- Cln5_6_t_1(0), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Clb1_2_t(0) :- Cln5_6_t_1(0), Mcm1/SFF_t_1(0), Cdc20&Cdc14_t_1(1).
Clb1_2_t(0) :- Clb1_2_t_1(0), Mcm1/SFF_t_1(0), Cdc20&Cdc14_t_1(1).
Clb1_2_t(0) :- Cln5_6_t_1(0), Cdh1_t_1(1), Clb1_2_t_1(0).
Clb1_2_t(0) :- Cln5_6_t_1(0), Cdh1_t_1(1), Mcm1/SFF_t_1(0).
Clb1_2_t(0) :- Cdh1_t_1(1), Clb1_2_t_1(0), Mcm1/SFF_t_1(0).
Clb1_2_t(0) :- Cln5_6_t_1(0), Cdh1_t_1(1), Cdc20&Cdc14_t_1(1).
Clb1_2_t(0) :- Cdh1_t_1(1), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Clb1_2_t(0) :- Cdh1_t_1(1), Mcm1/SFF_t_1(0), Cdc20&Cdc14_t_1(1).
Clb1_2_t(0) :- Sic1_t_1(1), Cln5_6_t_1(0), Clb1_2_t_1(0).
Clb1_2_t(0) :- Sic1_t_1(1), Cln5_6_t_1(0), Mcm1/SFF_t_1(0).
Clb1_2_t(0) :- Sic1_t_1(1), Clb1_2_t_1(0), Mcm1/SFF_t_1(0).
Clb1_2_t(0) :- Sic1_t_1(1), Cln5_6_t_1(0), Cdc20&Cdc14_t_1(1).
Clb1_2_t(0) :- Sic1_t_1(1), Clb1_2_t_1(0), Cdc20&Cdc14_t_1(1).
Clb1_2_t(0) :- Sic1_t_1(1), Mcm1/SFF_t_1(0), Cdc20&Cdc14_t_1(1).
Clb1_2_t(0) :- Sic1_t_1(1), Cln5_6_t_1(0), Cdh1_t_1(1).
Clb1_2_t(0) :- Sic1_t_1(1), Cdh1_t_1(1), Clb1_2_t_1(0).
Clb1_2_t(0) :- Sic1_t_1(1), Cdh1_t_1(1), Mcm1/SFF_t_1(0).
Clb1_2_t(0) :- Sic1_t_1(1), Cdh1_t_1(1), Cdc20&Cdc14_t_1(1).
Mcm1/SFF_t(0) :- Cln5_6_t_1(0), Clb1_2_t_1(0).
Cdc20&Cdc14_t(0) :- Clb1_2_t_1(0), Mcm1/SFF_t_1(0).
Swi5_t(0) :- Mcm1/SFF_t_1(0), Cdc20&Cdc14_t_1(0).
Swi5_t(0) :- Clb1_2_t_1(1), Mcm1/SFF_t_1(0).
Swi5_t(0) :- Clb1_2_t_1(1), Cdc20&Cdc14_t_1(0).
"""
self._check_rules_and_predictions(dataset, expected_string_rules)
def test_fission_yeast(self):
print(">> PRIDE benchmark <fission_yeast>:")
dataset_filepath = "datasets/fission_yeast.csv"
features_col_header = [
"Start_t_1", "SK_t_1", "Ste9_t_1", "Cdc2/Cdc13_t_1", "Rum1_t_1",
"PP_t_1", "Cdc25_t_1", "Slp1_t_1", "Wee1/Mik1_t_1",
"Cdc2/Cdc13*_t_1"
]
targets_col_header = [
"Start_t", "SK_t", "Ste9_t", "Cdc2/Cdc13_t", "Rum1_t", "PP_t",
"Cdc25_t", "Slp1_t", "Wee1/Mik1_t", "Cdc2/Cdc13*_t"
]
dataset = transitions_dataset_from_csv(
path=dataset_filepath,
feature_names=features_col_header,
target_names=targets_col_header)
# Expected rules
expected_string_rules = """
SK_t(1) :- Start_t_1(1).
Ste9_t(1) :- SK_t_1(0), Ste9_t_1(1), Cdc2/Cdc13_t_1(0), Cdc2/Cdc13*_t_1(0).
Ste9_t(1) :- SK_t_1(0), Cdc2/Cdc13_t_1(0), PP_t_1(1), Cdc2/Cdc13*_t_1(0).
Ste9_t(1) :- SK_t_1(0), Ste9_t_1(1), Cdc2/Cdc13_t_1(0), PP_t_1(1).
Ste9_t(1) :- SK_t_1(0), Ste9_t_1(1), PP_t_1(1), Cdc2/Cdc13*_t_1(0).
Ste9_t(1) :- Ste9_t_1(1), Cdc2/Cdc13_t_1(0), PP_t_1(1), Cdc2/Cdc13*_t_1(0).
Cdc2/Cdc13_t(1) :- Ste9_t_1(0), Rum1_t_1(0), Slp1_t_1(0).
Cdc2/Cdc13_t(1) :- Ste9_t_1(0), Cdc2/Cdc13_t_1(1), Rum1_t_1(0).
Cdc2/Cdc13_t(1) :- Ste9_t_1(0), Cdc2/Cdc13_t_1(1), Slp1_t_1(0).
Cdc2/Cdc13_t(1) :- Cdc2/Cdc13_t_1(1), Rum1_t_1(0), Slp1_t_1(0).
Rum1_t(1) :- SK_t_1(0), Cdc2/Cdc13_t_1(0), Rum1_t_1(1), Cdc2/Cdc13*_t_1(0).
Rum1_t(1) :- SK_t_1(0), Cdc2/Cdc13_t_1(0), PP_t_1(1), Cdc2/Cdc13*_t_1(0).
Rum1_t(1) :- SK_t_1(0), Cdc2/Cdc13_t_1(0), Rum1_t_1(1), PP_t_1(1).
Rum1_t(1) :- SK_t_1(0), Rum1_t_1(1), PP_t_1(1), Cdc2/Cdc13*_t_1(0).
Rum1_t(1) :- Cdc2/Cdc13_t_1(0), Rum1_t_1(1), PP_t_1(1), Cdc2/Cdc13*_t_1(1).
PP_t(1) :- Slp1_t_1(1).
Cdc25_t(1) :- PP_t_1(0), Cdc25_t_1(1).
Cdc25_t(1) :- Cdc2/Cdc13_t_1(1), PP_t_1(0).
Cdc25_t(1) :- Cdc2/Cdc13_t_1(1), Cdc25_t_1(1).
Slp1_t(1) :- Cdc2/Cdc13*_t_1(1).
Wee1/Mik1_t(1) :- Cdc2/Cdc13_t_1(0), Wee1/Mik1_t_1(1).
Wee1/Mik1_t(1) :- Cdc2/Cdc13_t_1(0), PP_t_1(1).
Wee1/Mik1_t(1) :- PP_t_1(1), Wee1/Mik1_t_1(1).
Cdc2/Cdc13*_t(1) :- Ste9_t_1(0), Rum1_t_1(0), Cdc25_t_1(1), Slp1_t_1(0), Wee1/Mik1_t_1(0), Cdc2/Cdc13*_t_1(1).
Start_t(0) :- .
SK_t(0) :- Start_t_1(0).
Ste9_t(0) :- SK_t_1(1), Ste9_t_1(0).
Ste9_t(0) :- SK_t_1(1), Cdc2/Cdc13_t_1(1).
Ste9_t(0) :- SK_t_1(1), PP_t_1(0).
Ste9_t(0) :- SK_t_1(1), Cdc2/Cdc13*_t_1(1).
Ste9_t(0) :- Ste9_t_1(0), Cdc2/Cdc13_t_1(1).
Ste9_t(0) :- Ste9_t_1(0), PP_t_1(0).
Ste9_t(0) :- Ste9_t_1(0), Cdc2/Cdc13*_t_1(1).
Ste9_t(0) :- Cdc2/Cdc13_t_1(1), PP_t_1(0).
Ste9_t(0) :- Cdc2/Cdc13_t_1(1), Cdc2/Cdc13*_t_1(1).
Ste9_t(0) :- PP_t_1(0), Cdc2/Cdc13*_t_1(1).
Cdc2/Cdc13_t(0) :- Ste9_t_1(1), Cdc2/Cdc13_t_1(0).
Cdc2/Cdc13_t(0) :- Ste9_t_1(1), Rum1_t_1(1).
Cdc2/Cdc13_t(0) :- Ste9_t_1(1), Slp1_t_1(1).
Cdc2/Cdc13_t(0) :- Cdc2/Cdc13_t_1(0), Rum1_t_1(1).
Cdc2/Cdc13_t(0) :- Rum1_t_1(1), Slp1_t_1(1).
Cdc2/Cdc13_t(0) :- Cdc2/Cdc13_t_1(0), Slp1_t_1(1).
Rum1_t(0) :- SK_t_1(1), Cdc2/Cdc13_t_1(1).
Rum1_t(0) :- SK_t_1(1), Rum1_t_1(0).
Rum1_t(0) :- SK_t_1(1), PP_t_1(0).
Rum1_t(0) :- SK_t_1(1), Cdc2/Cdc13*_t_1(0).
Rum1_t(0) :- Cdc2/Cdc13_t_1(1), Rum1_t_1(0).
Rum1_t(0) :- Cdc2/Cdc13_t_1(1), PP_t_1(0).
Rum1_t(0) :- Cdc2/Cdc13_t_1(1), Cdc2/Cdc13*_t_1(1).
Rum1_t(0) :- Rum1_t_1(0), PP_t_1(0).
Rum1_t(0) :- Rum1_t_1(0), Cdc2/Cdc13*_t_1(1).
Rum1_t(0) :- PP_t_1(0), Cdc2/Cdc13*_t_1(1).
PP_t(0) :- Slp1_t_1(0).
Cdc25_t(0) :- Cdc2/Cdc13_t_1(0), PP_t_1(1).
Cdc25_t(0) :- PP_t_1(1), Cdc25_t_1(0).
Cdc25_t(0) :- Cdc2/Cdc13_t_1(0), Cdc25_t_1(0).
Slp1_t(0) :- Cdc2/Cdc13*_t_1(0).
Wee1/Mik1_t(0) :- Cdc2/Cdc13_t_1(1), PP_t_1(0).
Wee1/Mik1_t(0) :- Cdc2/Cdc13_t_1(1), Wee1/Mik1_t_1(0).
Wee1/Mik1_t(0) :- PP_t_1(0), Wee1/Mik1_t_1(0).
Cdc2/Cdc13*_t(0) :- Ste9_t_1(1).
Cdc2/Cdc13*_t(0) :- Rum1_t_1(1).
Cdc2/Cdc13*_t(0) :- Cdc25_t_1(0).
Cdc2/Cdc13*_t(0) :- Slp1_t_1(1).
Cdc2/Cdc13*_t(0) :- Wee1/Mik1_t_1(1).
Cdc2/Cdc13*_t(0) :- Cdc2/Cdc13*_t_1(0).
"""
self._check_rules_and_predictions(dataset, expected_string_rules)