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Merge pull request #449 from biosustain/fix_dgf
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Fix dgfs
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@teddygroves
teddygroves authored Oct 19, 2023
2 parents 152b460 + 631a17f commit 52390de
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Showing 18 changed files with 701 additions and 139 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/run_tox.yml
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Expand Up @@ -12,7 +12,7 @@ on:
workflow_dispatch: {}

env:
CMDSTAN_VERSION: "2.32.2"
CMDSTAN_VERSION: "2.33.1"

jobs:
build:
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31 changes: 31 additions & 0 deletions docs/inputting.md
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Expand Up @@ -454,3 +454,34 @@ kcat = [
{enzyme = "PROT1", reaction = "PROT", init = 0.264744},
]
```

## Fixing parameter values

Sometimes it is useful to model a parameter as if its value were known exactly.
For example, the formation energies of metabolites that are only involved in
irreversible reactions are typically not identified by Maud's statistical
model. Fixing these unidentified parameters can improve computational
performance without loss of any information. Another use might be to test
whether a particular parameter value is feasible at all.

Maud currently supports fixing the values of `dgf` parameters. This can be done
for independent parameter inputs by adding a `fixed_value` field to the
relevant items as shown here:

```toml
dgf = [
{location = -1, metabolite = "M1", scale = 0.05, fixed_value = -1},
]
```

If a multivariate input is used for `dgf`, fixed values can be specified using
a separate table, like this:

```toml
[dgf]
ids = ["M1", "M2", "M3"]
mean_vector = [1, 2, 3]
covariance_matrix = [[1, 2, 3], [1, 2, 1], [3, 2, 1]]
[dgf.fixed_values]
M1 = -1
```
8 changes: 8 additions & 0 deletions maud/cli.py
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Expand Up @@ -16,6 +16,7 @@

"""Functions that are exposed to the command line interface live here."""

import json
import os
import shutil
from datetime import datetime
Expand Down Expand Up @@ -102,6 +103,13 @@ def do_sample(data_path, output_dir):
stanfit = sample(mi, samples_path)
print(stanfit.diagnose())
print(stanfit.summary())
if stanfit.metric is not None:
for i, chain_metric in enumerate(stanfit.metric):
chain_metric_dict = {"inv_metric": chain_metric.tolist()}
with open(
os.path.join(samples_path, f"metric-{str(i)}.json"), "w"
) as f:
json.dump(chain_metric_dict, f)
idata = get_idata(stanfit.runset.csv_files, mi, "train")
idata.to_json(os.path.join(output_path, "idata.json"))
return output_path
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119 changes: 1 addition & 118 deletions maud/data/example_inputs/example_ode/inits.json
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@@ -1,118 +1 @@
{
"dgf": [
10.0,
2.0,
5.0,
0.0
],
"km": [
0.5,
1.0,
2.0,
0.5,
1.0,
2.0,
0.5,
2.0,
1.0,
3.0000000000000004
],
"kcat": [
0.5,
2.0,
1.0,
2.0,
1.0
],
"kcat_phos": [],
"ki": [
1.0
],
"psi": [
0.0
],
"dissociation_constant": [
0.3,
0.9
],
"transfer_constant": [
1.0,
1.0
],
"conc_unbalanced_train": [
[
4.999999999999999,
0.5
]
],
"drain_train": [
[]
],
"conc_enzyme_train": [
[
1.0,
2.0,
3.0000000000000004,
2.0,
3.0000000000000004
]
],
"conc_phos_train": [
[]
],
"log_km_z": [
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0
],
"log_kcat_z": [
0.0,
0.0,
0.0,
0.0,
0.0
],
"log_kcat_phos_z": [],
"log_ki_z": [
0.0
],
"psi_z": [
0.0
],
"log_dissociation_constant_z": [
0.0,
0.0
],
"log_transfer_constant_z": [
0.0,
0.0
],
"log_conc_unbalanced_train_z": [
[
0.0,
0.0
]
],
"drain_train_z": [
[]
],
"log_conc_enzyme_train_z": [
[
0.0,
0.0,
0.0,
0.0,
0.0
]
],
"log_conc_phos_train_z": [
[]
]
}
{"dgf": [10.0, 2.0, 5.0, 0.0], "dgf_free": [10.0, 2.0, 5.0, 0.0], "km": [0.5, 1.0, 2.0, 0.5, 1.0, 2.0, 0.5, 2.0, 1.0, 3.0000000000000004], "log_km_z": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "ki": [1.0], "log_ki_z": [0.0], "kcat": [0.5, 2.0, 1.0, 2.0, 1.0], "log_kcat_z": [0.0, 0.0, 0.0, 0.0, 0.0], "dissociation_constant": [0.3, 0.9], "log_dissociation_constant_z": [0.0, 0.0], "transfer_constant": [1.0, 1.0], "log_transfer_constant_z": [0.0, 0.0], "kcat_pme": [], "log_kcat_pme_z": [], "drain_train": [[]], "drain_train_z": [[]], "drain_test": [[]], "drain_test_z": [[]], "conc_enzyme_train": [[1.0, 2.0, 3.0000000000000004, 2.0, 3.0000000000000004]], "log_conc_enzyme_train_z": [[0.0, 0.0, 0.0, 0.0, 0.0]], "conc_enzyme_test": [[1.0, 2.0, 3.0000000000000004, 2.0, 3.0000000000000004]], "log_conc_enzyme_test_z": [[0.0, 0.0, 0.0, 0.0, 0.0]], "conc_unbalanced_train": [[4.999999999999999, 0.5]], "log_conc_unbalanced_train_z": [[0.0, 0.0]], "conc_unbalanced_test": [[4.999999999999999, 0.5]], "log_conc_unbalanced_test_z": [[0.0, 0.0]], "conc_pme_train": [[]], "log_conc_pme_train_z": [[]], "conc_pme_test": [[]], "log_conc_pme_test_z": [[]], "psi_train": [0.0], "psi_train_z": [0.0], "psi_test": [0.0], "psi_test_z": [0.0]}
2 changes: 1 addition & 1 deletion maud/data/example_inputs/example_ode/input_data_train.json
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@@ -1 +1 @@
{"N_mic": 4, "N_edge_sub": 5, "N_edge_prod": 5, "N_edge": 5, "N_unbalanced": 2, "N_enzyme": 5, "N_phosphorylation": 0, "N_pme": 0, "N_competitive_inhibition": 1, "N_allostery": 2, "N_allosteric_enzyme": 2, "N_drain": 0, "N_km": 10, "N_sub_km": 5, "N_prod_km": 5, "S": [[-1, -1, -1, 0, 0], [1, 0, 0, -1, 0], [0, 1, 1, 0, -1], [0, 0, 0, 1, 1]], "N_reaction": 4, "N_metabolite": 4, "balanced_mic_ix": [2, 3], "unbalanced_mic_ix": [1, 4], "ci_mic_ix": [4], "edge_type": [1, 1, 1, 1, 1], "edge_to_enzyme": [1, 2, 3, 4, 5], "edge_to_tc": [0, 1, 2, 0, 0], "edge_to_drain": [0, 0, 0, 0, 0], "edge_to_reaction": [1, 2, 2, 3, 4], "water_stoichiometry": [0.0, 0.0, 0.0, 0.0, 0.0], "transported_charge": [0.0, 0.0, 0.0, 0.0, 0.0], "mic_to_met": [1, 2, 3, 4], "subunits": [1, 1, 1, 1, 1], "sub_by_edge_long": [1, 1, 1, 2, 3], "sub_by_edge_bounds": [[1, 1], [2, 2], [3, 3], [4, 4], [5, 5]], "prod_by_edge_long": [2, 3, 3, 4, 4], "prod_by_edge_bounds": [[1, 1], [2, 2], [3, 3], [4, 4], [5, 5]], "sub_km_ix_by_edge_long": [1, 3, 5, 7, 9], "sub_km_ix_by_edge_bounds": [[1, 1], [2, 2], [3, 3], [4, 4], [5, 5]], "prod_km_ix_by_edge_long": [2, 4, 6, 8, 10], "prod_km_ix_by_edge_bounds": [[1, 1], [2, 2], [3, 3], [4, 4], [5, 5]], "ci_ix_long": [1], "ci_ix_bounds": [[1, 1], [2, 1], [2, 1], [2, 1], [2, 1]], "allostery_ix_long": [1, 2], "allostery_ix_bounds": [[1, 0], [1, 1], [2, 2], [3, 2], [3, 2]], "allostery_type": [1, 2], "allostery_mic": [3, 3], "phosphorylation_ix_long": [], "phosphorylation_ix_bounds": [[1, 0], [1, 0], [1, 0], [1, 0], [1, 0]], "phosphorylation_type": [], "phosphorylation_pme": [], "priors_km": [[-0.6931471805599453, 0.0, 0.6931471805599453, -0.6931471805599453, 0.0, 0.6931471805599453, -0.6931471805599453, 0.6931471805599453, 0.0, 1.0986122886681098], [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2]], "priors_ki": [[0.0], [0.2]], "priors_kcat": [[-0.6931471805599453, 0.6931471805599453, 0.0, 0.6931471805599453, 0.0], [0.2, 0.2, 0.2, 0.2, 0.2]], "priors_dissociation_constant": [[-1.2039728043259361, -0.10536051565782628], [0.2, 0.2]], "priors_transfer_constant": [[0.0, 0.0], [0.2, 0.2]], "priors_kcat_pme": [[], []], "priors_drain_train": [[[]], [[]]], "priors_conc_enzyme_train": [[[0.0, 0.6931471805599453, 1.0986122886681098, 0.6931471805599453, 1.0986122886681098]], [[0.2, 0.2, 0.2, 0.2, 0.2]]], "priors_conc_unbalanced_train": [[[1.6094379124341003, -0.6931471805599453]], [[0.2, 0.2]]], "priors_conc_pme_train": [[[]], [[]]], "priors_psi_train": [[0.0], [2.0]], "prior_loc_dgf": [10.0, 2.0, 5.0, 0.0], "prior_cov_dgf": [[0.2, 0.0, 0.0, 0.0], [0.0, 0.2, 0.0, 0.0], [0.0, 0.0, 0.2, 0.0], [0.0, 0.0, 0.0, 0.2]], "N_experiment_train": 1, "N_flux_measurement_train": 2, "N_enzyme_measurement_train": 0, "N_conc_measurement_train": 2, "N_enzyme_knockout_train": 0, "N_pme_knockout_train": 0, "temperature_train": [298.15], "enzyme_knockout_train_long": [], "enzyme_knockout_train_bounds": [[1, 0]], "pme_knockout_train_long": [], "pme_knockout_train_bounds": [[1, 0]], "yconc_train": [0.323117, 3.02187], "sigma_yconc_train": [0.1, 0.1], "experiment_yconc_train": [1, 1], "mic_ix_yconc_train": [2, 3], "yflux_train": [0.421816, 2.11674], "sigma_yflux_train": [0.01, 0.01], "experiment_yflux_train": [1, 1], "reaction_yflux_train": [3, 4], "yenz_train": [], "sigma_yenz_train": [], "experiment_yenz_train": [], "enzyme_yenz_train": [], "likelihood": 1, "drain_small_conc_corrector": 1e-06, "reject_non_steady": 1, "penalize_non_steady": 0, "steady_state_threshold_abs": 1e-08, "steady_state_threshold_rel": 0.001, "steady_state_penalty_rel": 1e-08, "rel_tol_ode": 1e-09, "abs_tol_ode": 1e-09, "max_num_steps_ode": 1000000000, "rel_tol_alg": 1e-07, "abs_tol_alg": 1e-07, "max_num_steps_alg": 1000000, "conc_init": [[0.323117, 3.02187]]}
{"N_mic": 4, "N_edge_sub": 5, "N_edge_prod": 5, "N_edge": 5, "N_unbalanced": 2, "N_enzyme": 5, "N_phosphorylation": 0, "N_pme": 0, "N_competitive_inhibition": 1, "N_allostery": 2, "N_allosteric_enzyme": 2, "N_drain": 0, "N_km": 10, "N_sub_km": 5, "N_prod_km": 5, "S": [[-1, -1, -1, 0, 0], [1, 0, 0, -1, 0], [0, 1, 1, 0, -1], [0, 0, 0, 1, 1]], "N_reaction": 4, "N_metabolite": 4, "balanced_mic_ix": [2, 3], "unbalanced_mic_ix": [1, 4], "ci_mic_ix": [4], "edge_type": [1, 1, 1, 1, 1], "edge_to_enzyme": [1, 2, 3, 4, 5], "edge_to_tc": [0, 1, 2, 0, 0], "edge_to_drain": [0, 0, 0, 0, 0], "edge_to_reaction": [1, 2, 2, 3, 4], "water_stoichiometry": [0.0, 0.0, 0.0, 0.0, 0.0], "transported_charge": [0.0, 0.0, 0.0, 0.0, 0.0], "mic_to_met": [1, 2, 3, 4], "subunits": [1, 1, 1, 1, 1], "sub_by_edge_long": [1, 1, 1, 2, 3], "sub_by_edge_bounds": [[1, 1], [2, 2], [3, 3], [4, 4], [5, 5]], "prod_by_edge_long": [2, 3, 3, 4, 4], "prod_by_edge_bounds": [[1, 1], [2, 2], [3, 3], [4, 4], [5, 5]], "sub_km_ix_by_edge_long": [1, 3, 5, 7, 9], "sub_km_ix_by_edge_bounds": [[1, 1], [2, 2], [3, 3], [4, 4], [5, 5]], "prod_km_ix_by_edge_long": [2, 4, 6, 8, 10], "prod_km_ix_by_edge_bounds": [[1, 1], [2, 2], [3, 3], [4, 4], [5, 5]], "ci_ix_long": [1], "ci_ix_bounds": [[1, 1], [2, 1], [2, 1], [2, 1], [2, 1]], "allostery_ix_long": [1, 2], "allostery_ix_bounds": [[1, 0], [1, 1], [2, 2], [3, 2], [3, 2]], "allostery_type": [1, 2], "allostery_mic": [3, 3], "phosphorylation_ix_long": [], "phosphorylation_ix_bounds": [[1, 0], [1, 0], [1, 0], [1, 0], [1, 0]], "phosphorylation_type": [], "phosphorylation_pme": [], "N_dgf_fixed": 0, "dgf_fixed": [], "ix_dgf_free": [1, 2, 3, 4], "ix_dgf_fixed": [], "priors_km": [[-0.6931471805599453, 0.0, 0.6931471805599453, -0.6931471805599453, 0.0, 0.6931471805599453, -0.6931471805599453, 0.6931471805599453, 0.0, 1.0986122886681098], [0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2]], "priors_ki": [[0.0], [0.2]], "priors_kcat": [[-0.6931471805599453, 0.6931471805599453, 0.0, 0.6931471805599453, 0.0], [0.2, 0.2, 0.2, 0.2, 0.2]], "priors_dissociation_constant": [[-1.2039728043259361, -0.10536051565782628], [0.2, 0.2]], "priors_transfer_constant": [[0.0, 0.0], [0.2, 0.2]], "priors_kcat_pme": [[], []], "priors_drain_train": [[[]], [[]]], "priors_conc_enzyme_train": [[[0.0, 0.6931471805599453, 1.0986122886681098, 0.6931471805599453, 1.0986122886681098]], [[0.2, 0.2, 0.2, 0.2, 0.2]]], "priors_conc_unbalanced_train": [[[1.6094379124341003, -0.6931471805599453]], [[0.2, 0.2]]], "priors_conc_pme_train": [[[]], [[]]], "priors_psi_train": [[0.0], [2.0]], "prior_loc_dgf": [10.0, 2.0, 5.0, 0.0], "prior_cov_dgf": [[0.2, 0.0, 0.0, 0.0], [0.0, 0.2, 0.0, 0.0], [0.0, 0.0, 0.2, 0.0], [0.0, 0.0, 0.0, 0.2]], "N_experiment_train": 1, "N_flux_measurement_train": 2, "N_enzyme_measurement_train": 0, "N_conc_measurement_train": 2, "N_enzyme_knockout_train": 0, "N_pme_knockout_train": 0, "temperature_train": [298.15], "enzyme_knockout_train_long": [], "enzyme_knockout_train_bounds": [[1, 0]], "pme_knockout_train_long": [], "pme_knockout_train_bounds": [[1, 0]], "yconc_train": [0.323117, 3.02187], "sigma_yconc_train": [0.1, 0.1], "experiment_yconc_train": [1, 1], "mic_ix_yconc_train": [2, 3], "yflux_train": [0.421816, 2.11674], "sigma_yflux_train": [0.01, 0.01], "experiment_yflux_train": [1, 1], "reaction_yflux_train": [3, 4], "yenz_train": [], "sigma_yenz_train": [], "experiment_yenz_train": [], "enzyme_yenz_train": [], "likelihood": 1, "drain_small_conc_corrector": 1e-06, "reject_non_steady": 1, "penalize_non_steady": 0, "steady_state_threshold_abs": 1e-08, "steady_state_threshold_rel": 0.001, "steady_state_penalty_rel": 1e-08, "rel_tol_ode": 1e-09, "abs_tol_ode": 1e-09, "max_num_steps_ode": 1000000000, "rel_tol_alg": 1e-07, "abs_tol_alg": 1e-07, "max_num_steps_alg": 1000000, "conc_init": [[0.323117, 3.02187]]}
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8 changes: 4 additions & 4 deletions maud/data/example_inputs/linear/config.toml
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Expand Up @@ -14,11 +14,11 @@ save_warmup = true
seed = 1234

[ode_solver_config]
abs_tol = 1e-7
rel_tol = 1e-7
abs_tol = 1e-4
rel_tol = 1e-6
max_num_steps = 1e6

[algebra_solver_config]
abs_tol = 1e-5
rel_tol = 1e-5
abs_tol = 1e-4
rel_tol = 1e-6
max_num_steps = 1e6
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