checked out scenario1 from main so that it doesn't clobber Vignesh's …

…changes
ciemss · Jul 10, 2023 · 8c4512f · 8c4512f
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diff --git a/notebook/hackathon_prep/scenario1.ipynb b/notebook/hackathon_prep/scenario1.ipynb
@@ -2,7 +2,7 @@
  "cells": [
  {
  "cell_type": "code",
- "execution_count": 14,
+ "execution_count": 1,
  "id": "1c8e7493",
  "metadata": {},
  "outputs": [],
@@ -39,7 +39,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 15,
+ "execution_count": 2,
  "id": "1e3199e5",
  "metadata": {},
  "outputs": [],
@@ -139,26 +139,10 @@
  },
  {
  "cell_type": "code",
- "execution_count": 16,
+ "execution_count": 4,
  "id": "595a9cdf",
  "metadata": {},
- "outputs": [
- {
- "ename": "ValueError",
- "evalue": "Model file not found: scenario1_a.json",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
- "Cell \u001b[0;32mIn[16], line 8\u001b[0m\n\u001b[1;32m 5\u001b[0m timepoints \u001b[38;5;241m=\u001b[39m get_tspan(start_time, end_time, num_timepoints)\n\u001b[1;32m 6\u001b[0m \u001b[38;5;66;03m# TODO: Add intervention to set beta value as 1.\u001b[39;00m\n\u001b[1;32m 7\u001b[0m \u001b[38;5;66;03m# Run sampling w/o an intervention\u001b[39;00m\n\u001b[0;32m----> 8\u001b[0m control_samples \u001b[38;5;241m=\u001b[39m \u001b[43mload_and_sample_petri_model\u001b[49m\u001b[43m(\u001b[49m\u001b[43mSEIRD_model_path\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mnum_samples\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimepoints\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimepoints\u001b[49m\u001b[43m)\u001b[49m\n",
- "File \u001b[0;32m~/Projects/Proposals/ASKEM/build/clean-build/src/pyciemss/PetriNetODE/interfaces.py:91\u001b[0m, in \u001b[0;36mload_and_sample_petri_model\u001b[0;34m(petri_model_or_path, num_samples, timepoints, interventions, start_state, pseudocount, start_time, method, compile_rate_law_p)\u001b[0m\n\u001b[1;32m 49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mload_and_sample_petri_model\u001b[39m(\n\u001b[1;32m 50\u001b[0m petri_model_or_path: Union[\u001b[38;5;28mstr\u001b[39m, mira\u001b[38;5;241m.\u001b[39mmetamodel\u001b[38;5;241m.\u001b[39mTemplateModel, mira\u001b[38;5;241m.\u001b[39mmodeling\u001b[38;5;241m.\u001b[39mModel],\n\u001b[1;32m 51\u001b[0m num_samples: \u001b[38;5;28mint\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 59\u001b[0m compile_rate_law_p: \u001b[38;5;28mbool\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[1;32m 60\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m pd\u001b[38;5;241m.\u001b[39mDataFrame:\n\u001b[1;32m 61\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 62\u001b[0m \u001b[38;5;124;03m Load a petri net from a file, compile it into a probabilistic program, and sample from it.\u001b[39;00m\n\u001b[1;32m 63\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 89\u001b[0m \u001b[38;5;124;03m - The samples from the model as a pandas DataFrame.\u001b[39;00m\n\u001b[1;32m 90\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m---> 91\u001b[0m model \u001b[38;5;241m=\u001b[39m \u001b[43mload_petri_model\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 92\u001b[0m \u001b[43m \u001b[49m\u001b[43mpetri_model_or_path\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpetri_model_or_path\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 93\u001b[0m \u001b[43m \u001b[49m\u001b[43madd_uncertainty\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 94\u001b[0m \u001b[43m \u001b[49m\u001b[43mpseudocount\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpseudocount\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 95\u001b[0m \u001b[43m \u001b[49m\u001b[43mcompile_rate_law_p\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcompile_rate_law_p\u001b[49m\n\u001b[1;32m 96\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 98\u001b[0m \u001b[38;5;66;03m# If the user doesn't override the start state, use the initial values from the model.\u001b[39;00m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m start_state \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
- "File \u001b[0;32m~/Projects/Proposals/ASKEM/build/clean-build/src/pyciemss/PetriNetODE/interfaces.py:248\u001b[0m, in \u001b[0;36mload_petri_model\u001b[0;34m(petri_model_or_path, add_uncertainty, pseudocount, compile_rate_law_p)\u001b[0m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 244\u001b[0m \u001b[38;5;124;03mLoad a petri net from a file and compile it into a probabilistic program.\u001b[39;00m\n\u001b[1;32m 245\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 247\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m add_uncertainty:\n\u001b[0;32m--> 248\u001b[0m model \u001b[38;5;241m=\u001b[39m \u001b[43mScaledBetaNoisePetriNetODESystem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfrom_askenet\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpetri_model_or_path\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcompile_rate_law_p\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcompile_rate_law_p\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 249\u001b[0m model\u001b[38;5;241m.\u001b[39mpseudocount \u001b[38;5;241m=\u001b[39m torch\u001b[38;5;241m.\u001b[39mtensor(pseudocount)\n\u001b[1;32m 250\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m model\n",
- "File \u001b[0;32m~/.pyenv/versions/3.10.9/lib/python3.10/functools.py:926\u001b[0m, in \u001b[0;36msingledispatchmethod.__get__.<locals>._method\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 924\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_method\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 925\u001b[0m method \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdispatcher\u001b[38;5;241m.\u001b[39mdispatch(args[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__class__\u001b[39m)\n\u001b[0;32m--> 926\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mmethod\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__get__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[43mobj\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
- "File \u001b[0;32m~/Projects/Proposals/ASKEM/build/clean-build/src/pyciemss/PetriNetODE/base.py:441\u001b[0m, in \u001b[0;36mMiraPetriNetODESystem._from_path\u001b[0;34m(cls, model_json_path, **kwargs)\u001b[0m\n\u001b[1;32m 439\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 440\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m os\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39mexists(model_json_path):\n\u001b[0;32m--> 441\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mModel file not found: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mmodel_json_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 442\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mopen\u001b[39m(model_json_path) \u001b[38;5;28;01mas\u001b[39;00m fh:\n\u001b[1;32m 443\u001b[0m model_json \u001b[38;5;241m=\u001b[39m json\u001b[38;5;241m.\u001b[39mload(fh)\n",
- "\u001b[0;31mValueError\u001b[0m: Model file not found: scenario1_a.json"
- ]
- }
- ],
+ "outputs": [],
  "source": [
  "num_samples = 1\n",
  "start_time = 0\n",
@@ -911,9 +895,9 @@
  ],
  "metadata": {
  "kernelspec": {
- "display_name": "clean-build",
+ "display_name": "pyciemss-main",
  "language": "python",
- "name": "clean-build"
+ "name": "pyciemss-main"
  },
  "language_info": {
  "codemirror_mode": {

diff --git a/notebook/integration_demo/demo_ensemble.ipynb b/notebook/integration_demo/demo_ensemble.ipynb
@@ -121,20 +121,20 @@
  "name": "stdout",
  "output_type": "stream",
  "text": [
- "iteration 0: loss = 66.16035544872284\n",
- "iteration 25: loss = 42.31934851408005\n",
- "iteration 50: loss = 33.17540234327316\n",
- "iteration 75: loss = 27.15283751487732\n",
- "iteration 100: loss = 21.151540756225586\n",
- "iteration 125: loss = 17.88287889957428\n",
- "iteration 150: loss = 19.490506768226624\n",
- "iteration 175: loss = 16.146777868270874\n",
- "iteration 200: loss = 16.498568773269653\n",
- "iteration 225: loss = 15.53571480512619\n",
- "iteration 250: loss = 15.07484495639801\n",
- "iteration 275: loss = 14.595208406448364\n",
- "iteration 300: loss = 14.831865012645721\n",
- "iteration 325: loss = 15.439243197441101\n"
+ "iteration 0: loss = 63.51079273223877\n",
+ "iteration 25: loss = 40.8916078209877\n",
+ "iteration 50: loss = 37.46487545967102\n",
+ "iteration 75: loss = 25.852425813674927\n",
+ "iteration 100: loss = 21.470157742500305\n",
+ "iteration 125: loss = 17.58678960800171\n",
+ "iteration 150: loss = 15.267673671245575\n",
+ "iteration 175: loss = 16.10206639766693\n",
+ "iteration 200: loss = 15.993813276290894\n",
+ "iteration 225: loss = 15.860064268112183\n",
+ "iteration 250: loss = 13.152705788612366\n",
+ "iteration 275: loss = 16.014341235160828\n",
+ "iteration 300: loss = 15.707162857055664\n",
+ "iteration 325: loss = 12.456510186195374\n"
  ]
  }
  ],