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Fixes for qssa search parameter snooping #36

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merged 3 commits into from
Jul 6, 2024
Merged

Fixes for qssa search parameter snooping #36

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4eda5d7
correct bug that prevents filter_param_removal_codes_for_max_zero_alp…
Denis-Titov Jul 6, 2024
b42eb12
update test for snooping
Denis-Titov Jul 6, 2024
51c1ead
comment TestEnv
Denis-Titov Jul 6, 2024
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6 changes: 3 additions & 3 deletions src/data_driven_rate_equation_selection.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -410,7 +410,7 @@ function calculate_all_parameter_removal_codes_w_num_params(
else
filtered_nt_param_removal_codes_max_alpha =
filter_param_removal_codes_for_max_zero_alpha(
nt_param_removal_codes,
filtered_nt_param_removal_codes,
practically_unidentifiable_params,
max_zero_alpha,
)
Expand Down Expand Up @@ -533,7 +533,7 @@ function forward_selection_next_param_removal_codes(
else
filtered_nt_param_removal_codes_max_alpha =
filter_param_removal_codes_for_max_zero_alpha(
nt_param_removal_codes,
filtered_nt_param_removal_codes,
practically_unidentifiable_params,
max_zero_alpha,
)
Expand Down Expand Up @@ -581,7 +581,7 @@ function reverse_selection_next_param_removal_codes(
else
filtered_nt_param_removal_codes_max_alpha =
filter_param_removal_codes_for_max_zero_alpha(
nt_param_removal_codes,
filtered_nt_param_removal_codes,
practically_unidentifiable_params,
max_zero_alpha,
)
Expand Down
53 changes: 25 additions & 28 deletions test/tests_for_optimal_rate_eq_selection.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -242,36 +242,29 @@ unidentifiable_params =

#test filter_param_removal_codes_to_prevent_wrong_param_combos
nt_param_removal_codes = [
NamedTuple{(:Vmax, :K_S1, :K_S2, :K_S1_S2)}(combo) for
combo in Iterators.product([[0, 1], [0, 1], [0, 1], [0, 1, 2]]...)
NamedTuple{(:Vmax, :K_S1, :K_S2, :K_S3, :K_S1_S2, :K_S1_S3, :K_S2_S3, :K_S1_S2_S3)}(
combo,
) for combo in Iterators.product(
[[0, 1], [0, 1], [0, 1], [0, 1], [0, 1, 2], [0, 1, 2], [0, 1, 2], [0, 1, 2]]...,
)
]
metab_names = (:S1, :S2)
metab_names = (:S1, :S2, :S3)
filtered_nt =
DataDrivenEnzymeRateEqs.filter_param_removal_codes_to_prevent_wrong_param_combos(
nt_param_removal_codes,
metab_names,
)
correct_answer = [
(Vmax = 0, K_S1 = 0, K_S2 = 0, K_S1_S2 = 0)
(Vmax = 1, K_S1 = 0, K_S2 = 0, K_S1_S2 = 0)
(Vmax = 0, K_S1 = 1, K_S2 = 0, K_S1_S2 = 0)
(Vmax = 1, K_S1 = 1, K_S2 = 0, K_S1_S2 = 0)
(Vmax = 0, K_S1 = 0, K_S2 = 1, K_S1_S2 = 0)
(Vmax = 1, K_S1 = 0, K_S2 = 1, K_S1_S2 = 0)
(Vmax = 0, K_S1 = 1, K_S2 = 1, K_S1_S2 = 0)
(Vmax = 1, K_S1 = 1, K_S2 = 1, K_S1_S2 = 0)
(Vmax = 0, K_S1 = 0, K_S2 = 0, K_S1_S2 = 1)
(Vmax = 1, K_S1 = 0, K_S2 = 0, K_S1_S2 = 1)
(Vmax = 0, K_S1 = 1, K_S2 = 0, K_S1_S2 = 1)
(Vmax = 1, K_S1 = 1, K_S2 = 0, K_S1_S2 = 1)
(Vmax = 0, K_S1 = 0, K_S2 = 1, K_S1_S2 = 1)
(Vmax = 1, K_S1 = 0, K_S2 = 1, K_S1_S2 = 1)
(Vmax = 0, K_S1 = 1, K_S2 = 1, K_S1_S2 = 1)
(Vmax = 1, K_S1 = 1, K_S2 = 1, K_S1_S2 = 1)
(Vmax = 0, K_S1 = 0, K_S2 = 0, K_S1_S2 = 2)
(Vmax = 1, K_S1 = 0, K_S2 = 0, K_S1_S2 = 2)
]
@test filtered_nt == correct_answer
for filtered_code in filtered_nt
for param in [:K_S1, :K_S2, :K_S3]
if filtered_code[param] == 1
for param_combo in [:K_S1_S2, :K_S1_S3, :K_S2_S3, :K_S1_S2_S3]
if occursin(string(param), string(param_combo))
@test filtered_code[param_combo] != 2
end
end
end
end
end

#test filter_param_removal_codes_for_max_zero_alpha
#TODO: add a test with practically_unidentifiable_alphas
Expand Down Expand Up @@ -405,8 +398,10 @@ reverse_selection_result = @time data_driven_rate_equation_selection(
#TODO: remove the filtering for 4 parameters after we add the automatic determination of the best number of parameters
nt_param_removal_code =
filter(x -> x.num_params .== 4, selection_result.test_results).nt_param_removal_codes[1]
nt_reverse_param_removal_code =
filter(x -> x.num_params .== 4, reverse_selection_result.test_results).nt_param_removal_codes[1]
nt_reverse_param_removal_code = filter(
x -> x.num_params .== 4,
reverse_selection_result.test_results,
).nt_param_removal_codes[1]

using Symbolics
selected_sym_rate_equation = display_rate_equation(
Expand Down Expand Up @@ -524,8 +519,10 @@ reverse_selection_result = @time data_driven_rate_equation_selection(
#TODO: remove the filtering for 3 parameters after we add the automatic determination of the best number of parameters
nt_param_removal_code =
filter(x -> x.num_params .== 3, selection_result.test_results).nt_param_removal_codes[1]
nt_reverse_param_removal_code =
filter(x -> x.num_params .== 3, reverse_selection_result.test_results).nt_param_removal_codes[1]
nt_reverse_param_removal_code = filter(
x -> x.num_params .== 3,
reverse_selection_result.test_results,
).nt_param_removal_codes[1]

using Symbolics
selected_sym_rate_equation = display_rate_equation(
Expand Down