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fix more bugs
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@Denis-Titov
Denis-Titov committed Jul 5, 2024
1 parent 6f09062 commit 657393f
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Showing 2 changed files with 46 additions and 15 deletions.
46 changes: 32 additions & 14 deletions src/data_driven_rate_equation_selection.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,7 @@ function data_driven_rate_equation_selection(
param_names,
param_removal_code_names,
metab_names,
practically_unidentifiable_params,
num_alpha_params,
max_zero_alpha,
)
Expand All @@ -108,6 +109,7 @@ function data_driven_rate_equation_selection(
param_names,
param_removal_code_names,
metab_names,
practically_unidentifiable_params,
num_alpha_params,
max_zero_alpha,
)
Expand All @@ -127,13 +129,15 @@ function data_driven_rate_equation_selection(
nt_param_removal_codes = forward_selection_next_param_removal_codes(
nt_previous_param_removal_codes,
metab_names,
practically_unidentifiable_params,
num_alpha_params,
max_zero_alpha,
)
elseif !forward_model_selection
nt_param_removal_codes = reverse_selection_next_param_removal_codes(
nt_previous_param_removal_codes,
metab_names,
practically_unidentifiable_params,
num_alpha_params,
max_zero_alpha,
)
Expand Down Expand Up @@ -356,6 +360,7 @@ function calculate_all_parameter_removal_codes_w_num_params(
param_names::Tuple{Symbol,Vararg{Symbol}},
param_removal_code_names::Tuple{Symbol,Vararg{Symbol}},
metab_names::Tuple{Symbol,Vararg{Symbol}},
practically_unidentifiable_params::Tuple{Vararg{Symbol}},
num_alpha_params::Int,
max_zero_alpha::Int,
)
Expand Down Expand Up @@ -388,16 +393,17 @@ function calculate_all_parameter_removal_codes_w_num_params(
metab_names,
)
end
if isempty(nt_param_removal_codes)
filtered_nt_param_removal_codes = NamedTuple[]
if isempty(filtered_nt_param_removal_codes)
filtered_nt_param_removal_codes_max_alpha = NamedTuple[]
else
filtered_nt_param_removal_codes =
filtered_nt_param_removal_codes_max_alpha =
filter_param_removal_codes_for_max_zero_alpha(
nt_param_removal_codes,
practically_unidentifiable_params,
max_zero_alpha,
)
end
return filtered_nt_param_removal_codes
return filtered_nt_param_removal_codes_max_alpha
end

"""
Expand Down Expand Up @@ -464,6 +470,7 @@ Calculate `nt_param_removal_codes` with `num_params` including non-zero term com
function forward_selection_next_param_removal_codes(
nt_previous_param_removal_codes::Vector{T} where {T<:NamedTuple},
metab_names::Tuple{Symbol,Vararg{Symbol}},
practically_unidentifiable_params::Tuple{Vararg{Symbol}},
num_alpha_params::Int,
max_zero_alpha::Int,
)
Expand Down Expand Up @@ -505,16 +512,17 @@ function forward_selection_next_param_removal_codes(
metab_names,
)
end
if isempty(nt_param_removal_codes)
filtered_nt_param_removal_codes = NamedTuple[]
if isempty(filtered_nt_param_removal_codes)
filtered_nt_param_removal_codes_max_alpha = NamedTuple[]
else
filtered_nt_param_removal_codes =
filtered_nt_param_removal_codes_max_alpha =
filter_param_removal_codes_for_max_zero_alpha(
nt_param_removal_codes,
practically_unidentifiable_params,
max_zero_alpha,
)
end
return filtered_nt_param_removal_codes
return filtered_nt_param_removal_codes_max_alpha
end

"""
Expand All @@ -523,6 +531,7 @@ Use `nt_previous_param_removal_codes` to calculate `nt_next_param_removal_codes`
function reverse_selection_next_param_removal_codes(
nt_previous_param_removal_codes::Vector{T} where {T<:NamedTuple},
metab_names::Tuple{Symbol,Vararg{Symbol}},
practically_unidentifiable_params::Tuple{Vararg{Symbol}},
num_alpha_params::Int,
max_zero_alpha::Int,
)
Expand All @@ -549,16 +558,17 @@ function reverse_selection_next_param_removal_codes(
metab_names,
)
end
if isempty(nt_param_removal_codes)
filtered_nt_param_removal_codes = NamedTuple[]
if isempty(filtered_nt_param_removal_codes)
filtered_nt_param_removal_codes_max_alpha = NamedTuple[]
else
filtered_nt_param_removal_codes =
filtered_nt_param_removal_codes_max_alpha =
filter_param_removal_codes_for_max_zero_alpha(
nt_param_removal_codes,
practically_unidentifiable_params,
max_zero_alpha,
)
end
return filtered_nt_param_removal_codes
return filtered_nt_param_removal_codes_max_alpha
end

"""Filter removal codes to ensure that if K_S1 = Inf then all K_S1_S2 and all other K containing S1 in qssa cannot be 2, which stands for (K_S1_S2)^2 = K_S1 * K_S2"""
Expand Down Expand Up @@ -598,10 +608,18 @@ end
"""Filter removal codes to ensure that number of alpha that are 0 is max_zero_alpha"""
function filter_param_removal_codes_for_max_zero_alpha(
nt_param_removal_codes,
practically_unidentifiable_params::Tuple{Vararg{Symbol}},
max_zero_alpha::Int,
)
alpha_keys =
[key for key in keys(nt_param_removal_codes[1]) if occursin("alpha", string(key))]
practically_unidentifiable_alphas = [
param for
param in practically_unidentifiable_params if occursin("alpha", string(param))
]
alpha_keys = [
key for key in keys(nt_param_removal_codes[1]) if
occursin("alpha", string(key)) && key ∉ practically_unidentifiable_alphas
]

if isempty(alpha_keys)
filtered_nt_param_removal_codes = nt_param_removal_codes
else
Expand Down
15 changes: 14 additions & 1 deletion test/tests_for_optimal_rate_eq_selection.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ param_removal_code_names = (
!contains(string(param_name), "_i") && param_name != :Vmax && param_name != :L
]...,
)
practically_unidentifiable_params = ()
all_param_removal_codes =
DataDrivenEnzymeRateEqs.calculate_all_parameter_removal_codes(param_names, ())
param_subset_codes_with_num_params = [
Expand All @@ -47,6 +48,7 @@ nt_funct_output_param_subset_codes =
DataDrivenEnzymeRateEqs.forward_selection_next_param_removal_codes(
nt_previous_param_removal_codes,
metab_names,
practically_unidentifiable_params,
n_alphas,
max_zero_alpha,
)
Expand Down Expand Up @@ -113,6 +115,7 @@ param_removal_code_names = (
!contains(string(param_name), "_i") && param_name != :Vmax && param_name != :L
]...,
)
practically_unidentifiable_params = ()
all_param_removal_codes =
DataDrivenEnzymeRateEqs.calculate_all_parameter_removal_codes(param_names, ())
param_subset_codes_with_num_params = [
Expand All @@ -128,6 +131,7 @@ nt_funct_output_param_subset_codes =
DataDrivenEnzymeRateEqs.reverse_selection_next_param_removal_codes(
nt_previous_param_removal_codes,
metab_names,
practically_unidentifiable_params,
n_alphas,
max_zero_alpha,
)
Expand Down Expand Up @@ -180,6 +184,7 @@ param_names = (
[Symbol(:K_i, "_Metabolite$(i)") for i = 1:num_metabolites]...,
[Symbol(:alpha, "_$(i)") for i = 1:n_alphas]...,
)
practically_unidentifiable_params = ()
param_removal_code_names = (
[
Symbol(replace(string(param_name), "_a_" => "_allo_")) for
Expand All @@ -200,6 +205,7 @@ nt_param_subset_codes_w_num_params =
param_names,
param_removal_code_names,
metab_names,
practically_unidentifiable_params,
n_alphas,
max_zero_alpha,
)
Expand Down Expand Up @@ -270,21 +276,28 @@ correct_answer = [
@test filtered_nt == correct_answer

#test filter_param_removal_codes_for_max_zero_alpha
#TODO: add a test with practically_unidentifiable_alphas
num_alpha_params = rand(5:10)
num_non_alpha_params = rand(5:10)
max_zero_alpha = rand(1:3)
param_names = ([Symbol("param$(i)") for i = 1:num_non_alpha_params]..., [Symbol("alpha$(i)") for i = 1:num_alpha_params]...)
param_names[end-num_alpha_params+1]
nt_param_removal_codes = [
NamedTuple{(param_names)}(combo) for
combo in Iterators.product([[0, 1] for _ in param_names]...)
]
filtered_nt =
DataDrivenEnzymeRateEqs.filter_param_removal_codes_for_max_zero_alpha(
nt_param_removal_codes,
practically_unidentifiable_params,
max_zero_alpha,
)
sum_alpha = [sum(values(nt)[end-num_alpha_params:end]) for nt in filtered_nt]
sum_alpha = [sum(values(nt)[end-num_alpha_params+1:end]) for nt in filtered_nt]
@test all(num_alpha_params .- sum_alpha .<= max_zero_alpha)
@test any(sum_alpha .== num_alpha_params-max_zero_alpha)
@test all(sum_alpha .!= num_alpha_params-max_zero_alpha-1)
@test any(sum_alpha .== num_alpha_params)
@test all(sum_alpha .!= num_alpha_params+1)

#Load and process data
LDH_data_for_fit = CSV.read(joinpath(@__DIR__, "Data_for_tests/LDH_data.csv"), DataFrame)
Expand Down

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