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Merge pull request #324 from gyorilab/eval-sc1-initials
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Eval sc1 initials
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@bgyori
bgyori authored Apr 9, 2024
2 parents ab2f58f + 20f714c commit 4bf4b32
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151 changes: 135 additions & 16 deletions notebooks/evaluation_2024.03/epi_scenario1/epi_eval_sc1_strains.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
{
"cell_type": "code",
"execution_count": 1,
"id": "fe970922-3aa4-40b5-9caf-4afc08cef04d",
"id": "b1d20fb5-6925-4bda-b652-f9281d8c5ba4",
"metadata": {},
"outputs": [
{
Expand All @@ -30,14 +30,37 @@
"source": [
"# Get an ready-made example SIR model that has parameters and initial values already set\n",
"# (note that the model is missing units)\n",
"from mira.examples.sir import sir_parameterized_init\n",
"from mira.examples.sir import sir_parameterized_init, sir_init_val_norm\n",
"from mira.metamodel import *\n",
"\n",
"susceptible = sir_parameterized_init.get_concepts_name_map()['susceptible_population']\n",
"infected = sir_parameterized_init.get_concepts_name_map()['infected_population']\n",
"recovered = sir_parameterized_init.get_concepts_name_map()['immune_population']\n",
"\n",
"sir_parameterized_init.draw_jupyter()\n"
"sir_parameterized_init.draw_jupyter()"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "def6891b-4dac-4216-842f-705b8efdf36f",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'susceptible_population': Initial(concept=Concept(name='susceptible_population', display_name=None, description=None, identifiers={'ido': '0000514'}, context={}, units=Unit(expression=person)), expression=99999.0),\n",
" 'infected_population': Initial(concept=Concept(name='infected_population', display_name=None, description=None, identifiers={'ido': '0000511'}, context={}, units=Unit(expression=person)), expression=1),\n",
" 'immune_population': Initial(concept=Concept(name='immune_population', display_name=None, description=None, identifiers={'ido': '0000592'}, context={}, units=Unit(expression=person)), expression=0)}"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sir_parameterized_init.initials"
]
},
{
Expand All @@ -51,7 +74,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 3,
"id": "745c1649-8e91-42f8-a931-766c51ed1f5e",
"metadata": {},
"outputs": [
Expand All @@ -62,7 +85,7 @@
"<IPython.core.display.Image object>"
]
},
"execution_count": 2,
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -77,11 +100,36 @@
" key='strain', \n",
" strata=strains, \n",
" concepts_to_preserve=['susceptible_population'], \n",
" structure=[]\n",
" structure=[],\n",
")\n",
"strain_model.draw_jupyter(\"sir.png\")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "32077ecc-7cf4-4c49-a449-44b80844beaa",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"susceptible_population 99999.0\n",
"infected_population_alpha 1/3\n",
"infected_population_delta 1/3\n",
"infected_population_omicron 1/3\n",
"immune_population_alpha 0\n",
"immune_population_delta 0\n",
"immune_population_omicron 0\n"
]
}
],
"source": [
"for name, init in strain_model.initials.items():\n",
" print(name, init.expression)"
]
},
{
"cell_type": "markdown",
"id": "e1a19ab7-6ba5-4d2f-9dd8-bc50532deb8c",
Expand All @@ -93,61 +141,93 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 5,
"id": "237f6485-1960-4127-bdb1-9e160bac74b6",
"metadata": {},
"outputs": [],
"source": [
"initials = {}\n",
"\n",
"# Reset the infected populations to 1 (they're set to 1/3 when stratified)\n",
"initials['susceptible_population'] = Initial(concept=Concept(name='susceptible_population'), expression=sir_init_val_norm - 3.0)\n",
"\n",
"name_map = strain_model.get_concepts_name_map()\n",
"\n",
"infected_alpha = strain_model.get_concepts_name_map()['infected_population_alpha']\n",
"initials[infected_alpha.name] = Initial(concept=Concept(name=infected_alpha.name), expression=1.0)\n",
"\n",
"infected_delta = strain_model.get_concepts_name_map()['infected_population_delta']\n",
"initials[infected_delta.name] = Initial(concept=Concept(name=infected_delta.name), expression=1.0)\n",
"\n",
"infected_omicron = strain_model.get_concepts_name_map()['infected_population_omicron']\n",
"initials[infected_omicron.name] = Initial(concept=Concept(name=infected_omicron.name), expression=1.0)\n",
"\n",
"recovered_alpha = strain_model.get_concepts_name_map()['immune_population_alpha']\n",
"recovered_delta = strain_model.get_concepts_name_map()['immune_population_delta']\n",
"recovered_omicron = strain_model.get_concepts_name_map()['immune_population_omicron']\n",
"\n",
"# Get reinfected states and reinfected recovered states\n",
"# Get reinfected states and reinfected recovered states, set all initials to zero\n",
"# alpha delta/delta alpha\n",
"infected_alpha_delta = infected.with_context(history='alpha', strain='delta')\n",
"infected_alpha_delta.name = 'infected_population_alpha_delta'\n",
"initials[infected_alpha_delta.name] = Initial(concept=Concept(name=infected_alpha_delta.name), expression=0.0)\n",
"\n",
"infected_delta_alpha = infected.with_context(history='delta', strain='alpha')\n",
"infected_delta_alpha.name = 'infected_population_delta_alpha'\n",
"initials[infected_delta_alpha.name] = Initial(concept=Concept(name=infected_delta_alpha.name), expression=0.0)\n",
"\n",
"recovered_alpha_delta = recovered.with_context(history='alpha_delta')\n",
"recovered_alpha_delta.name = 'immune_population_alpha_delta'\n",
"initials[recovered_alpha_delta.name] = Initial(concept=Concept(name=recovered_alpha_delta.name), expression=0.0)\n",
"\n",
"# alpha omicron/omicron alpha\n",
"infected_alpha_omicron = infected.with_context(history='alpha', strain='omicron')\n",
"infected_alpha_omicron.name = 'infected_population_alpha_omicron'\n",
"initials[infected_alpha_omicron.name] = Initial(concept=Concept(name=infected_alpha_omicron.name), expression=0.0)\n",
"\n",
"infected_omicron_alpha = infected.with_context(history='omicron', strain='alpha')\n",
"infected_omicron_alpha.name = 'infected_population_omicron_alpha'\n",
"initials[infected_omicron_alpha.name] = Initial(concept=Concept(name=infected_omicron_alpha.name), expression=0.0)\n",
"\n",
"recovered_alpha_omicron = recovered.with_context(history='alpha_omicron')\n",
"recovered_alpha_omicron.name = 'immune_population_alpha_omicron'\n",
"initials[recovered_alpha_omicron.name] = Initial(concept=Concept(name=recovered_alpha_omicron.name), expression=0.0)\n",
"\n",
"# delta omicron/omicron delta\n",
"infected_delta_omicron = infected.with_context(history='delta', strain='omicron')\n",
"infected_delta_omicron.name = 'infected_population_delta_omicron'\n",
"initials[infected_delta_omicron.name] = Initial(concept=Concept(name=infected_delta_omicron.name), expression=0.0)\n",
"\n",
"infected_omicron_delta = infected.with_context(history='omicron', strain='delta')\n",
"infected_omicron_delta.name = 'infected_population_omicron_delta'\n",
"initials[infected_omicron_delta.name] = Initial(concept=Concept(name=infected_omicron_delta.name), expression=0.0)\n",
"\n",
"recovered_delta_omicron = recovered.with_context(strain='delta_omicron')\n",
"recovered_delta_omicron.name = 'immune_population_delta_omicron'\n",
"initials[recovered_delta_omicron.name] = Initial(concept=Concept(name=recovered_delta_omicron.name), expression=0.0)\n",
"\n",
"# alpha delta omicron (third and final infection for any branch)\n",
"infected_alpha_delta_omicron = infected.with_context(history='alpha_delta', strain='omicron')\n",
"infected_alpha_delta_omicron.name = 'infected_population_alpha_delta_omicron'\n",
"initials[infected_alpha_delta_omicron.name] = Initial(concept=Concept(name=infected_alpha_delta_omicron.name), expression=0.0)\n",
"\n",
"infected_alpha_omicron_delta = infected.with_context(history='alpha_omicron', strain='delta')\n",
"infected_alpha_omicron_delta.name = 'infected_population_alpha_omicron_delta'\n",
"initials[infected_alpha_omicron_delta.name] = Initial(concept=Concept(name=infected_alpha_omicron_delta.name), expression=0.0)\n",
"\n",
"infected_delta_omicron_alpha = infected.with_context(history='delta_omicron', strain='alpha')\n",
"infected_delta_omicron_alpha.name = 'infected_population_delta_omicron_alpha'\n",
"initials[infected_delta_omicron_alpha.name] = Initial(concept=Concept(name=infected_delta_omicron_alpha.name), expression=0.0)\n",
"\n",
"recovered_alpha_delta_omicron = recovered.with_context(history='alpha_delta_omicron')\n",
"recovered_alpha_delta_omicron.name = 'immune_population_alpha_delta_omicron'"
"recovered_alpha_delta_omicron.name = 'immune_population_alpha_delta_omicron'\n",
"initials[recovered_alpha_delta_omicron.name] = Initial(concept=Concept(name=recovered_alpha_delta_omicron.name), expression=0.0)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "29221f5e-3b2b-425e-8186-1bb63f8aa54d",
"execution_count": 6,
"id": "2944a12c-f3ad-48a7-a5df-af4030fee31e",
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -252,14 +332,53 @@
" new_parameters[param_name_rec] = Parameter(name=param_name, value=1)\n",
" new_templates.append(nc)\n",
"\n",
"extenstion_tm = TemplateModel(templates=new_templates, parameters=new_parameters)\n",
"extenstion_tm = TemplateModel(templates=new_templates, parameters=new_parameters, initials=initials)\n",
"\n",
"total_tm = strain_model.extend(extenstion_tm, parameter_mapping=new_parameters)"
"total_tm = strain_model.extend(extenstion_tm, parameter_mapping=new_parameters, initial_mapping=initials)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 7,
"id": "98642a20-9e02-4272-990b-5c3424713d75",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"susceptible_population 99997.0\n",
"infected_population_alpha 1.0\n",
"infected_population_delta 1.0\n",
"infected_population_omicron 1.0\n",
"immune_population_alpha 0\n",
"immune_population_delta 0\n",
"immune_population_omicron 0\n",
"infected_population_alpha_delta 0.0\n",
"immune_population_alpha_delta 0.0\n",
"infected_population_omicron_delta 0.0\n",
"infected_population_alpha_omicron_delta 0.0\n",
"immune_population_delta_omicron 0.0\n",
"immune_population_alpha_omicron 0.0\n",
"immune_population_alpha_delta_omicron 0.0\n",
"infected_population_delta_alpha 0.0\n",
"infected_population_omicron_alpha 0.0\n",
"infected_population_delta_omicron_alpha 0.0\n",
"infected_population_alpha_omicron 0.0\n",
"infected_population_delta_omicron 0.0\n",
"infected_population_alpha_delta_omicron 0.0\n"
]
}
],
"source": [
"for name in total_tm.get_concepts_name_map():\n",
" assert name in total_tm.initials\n",
" print(name, total_tm.initials[name].expression)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "8e82cfe8-a12c-43fa-b62c-93e0c1b4afc1",
"metadata": {},
"outputs": [
Expand All @@ -270,7 +389,7 @@
"<IPython.core.display.Image object>"
]
},
"execution_count": 5,
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -284,7 +403,7 @@
" ('petrinet', template_model_to_petrinet_json)\n",
"]:\n",
" with open(f\"sir_3strain_{out_type}.json\", 'w') as f:\n",
" json.dump(out_fun(total_tm), f, indent=2)\n",
" json.dump(out_fun(total_tm), f, indent=1)\n",
"total_tm.draw_jupyter(\"sir_3strain.png\")"
]
}
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