Skip to content

Commit

Permalink
Implemented basic workflow
Browse files Browse the repository at this point in the history
  • Loading branch information
@Alex6022
Alex6022 committed Mar 27, 2024
1 parent 0571abd commit 98f43ee
Showing 1 changed file with 78 additions and 31 deletions.
109 changes: 78 additions & 31 deletions BayBE_basic.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 27,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -21,7 +21,32 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 28,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" Time_h pH Inhib_Concentrat_M Efficiency\n",
"count 611.000000 611.000000 611.000000 611.000000\n",
"mean 135.801964 6.342062 0.006808 26.736841\n",
"std 201.683867 2.529080 0.014059 288.788317\n",
"min 0.500000 0.000000 0.000010 -4834.000000\n",
"25% 24.000000 4.000000 0.000500 30.000000\n",
"50% 24.000000 7.000000 0.001000 58.000000\n",
"75% 144.000000 7.000000 0.003000 87.950000\n",
"max 672.000000 10.000000 0.100000 100.000000\n"
]
}
],
"source": [
"print(df_AA2024.describe())\n"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -52,12 +77,12 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"## Set objectives and parameters in BayBE"
"## Set objectives and parameters in BayBE to define the search space"
]
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 30,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -73,53 +98,75 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 31,
"metadata": {},
"outputs": [
{
"ename": "OptionalImportError",
"evalue": "The requested functionality requires the installation of optional chemistry dependencies. Please run \"pip install 'baybe[chem]'\".",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"File \u001b[0;32m~/.local/lib/python3.10/site-packages/baybe/utils/chemistry.py:17\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 17\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mmordred\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Calculator, descriptors\n\u001b[1;32m 18\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mrdkit\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Chem, RDLogger\n",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'mordred'",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mOptionalImportError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[18], line 18\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mbaybe\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mparameters\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m (\n\u001b[1;32m 2\u001b[0m CategoricalParameter,\n\u001b[1;32m 3\u001b[0m NumericalDiscreteParameter,\n\u001b[1;32m 4\u001b[0m SubstanceParameter,\n\u001b[1;32m 5\u001b[0m )\n\u001b[1;32m 7\u001b[0m parameters \u001b[38;5;241m=\u001b[39m [\n\u001b[1;32m 8\u001b[0m CategoricalParameter(\n\u001b[1;32m 9\u001b[0m name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGranularity\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 10\u001b[0m values\u001b[38;5;241m=\u001b[39m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcoarse\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmedium\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mfine\u001b[39m\u001b[38;5;124m\"\u001b[39m],\n\u001b[1;32m 11\u001b[0m encoding\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mOHE\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;66;03m# one-hot encoding of categories\u001b[39;00m\n\u001b[1;32m 12\u001b[0m ),\n\u001b[1;32m 13\u001b[0m NumericalDiscreteParameter(\n\u001b[1;32m 14\u001b[0m name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mPressure[bar]\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 15\u001b[0m values\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m1\u001b[39m, \u001b[38;5;241m5\u001b[39m, \u001b[38;5;241m10\u001b[39m],\n\u001b[1;32m 16\u001b[0m tolerance\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0.2\u001b[39m, \u001b[38;5;66;03m# allows experimental inaccuracies up to 0.2 when reading values\u001b[39;00m\n\u001b[1;32m 17\u001b[0m ),\n\u001b[0;32m---> 18\u001b[0m \u001b[43mSubstanceParameter\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 19\u001b[0m \u001b[43m \u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mSolvent\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 20\u001b[0m \u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m{\u001b[49m\n\u001b[1;32m 21\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mSolvent A\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mCOC\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 22\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mSolvent B\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mCCC\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;66;43;03m# label-SMILES pairs\u001b[39;49;00m\n\u001b[1;32m 23\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mSolvent C\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mO\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 24\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mSolvent D\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mCS(=O)C\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 25\u001b[0m \u001b[43m \u001b[49m\u001b[43m}\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 26\u001b[0m \u001b[43m \u001b[49m\u001b[43mencoding\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mMORDRED\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;66;43;03m# chemical encoding via mordred package\u001b[39;49;00m\n\u001b[1;32m 27\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m,\n\u001b[1;32m 28\u001b[0m ]\n",
"File \u001b[0;32m<attrs generated init baybe.parameters.substance.SubstanceParameter>:10\u001b[0m, in \u001b[0;36m__init__\u001b[0;34m(self, name, data, decorrelate, encoding)\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m _config\u001b[38;5;241m.\u001b[39m_run_validators \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[1;32m 9\u001b[0m __attr_validator_name(\u001b[38;5;28mself\u001b[39m, __attr_name, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mname)\n\u001b[0;32m---> 10\u001b[0m \u001b[43m__attr_validator_data\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m__attr_data\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 11\u001b[0m __attr_validator_decorrelate(\u001b[38;5;28mself\u001b[39m, __attr_decorrelate, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdecorrelate)\n",
"File \u001b[0;32m~/.local/lib/python3.10/site-packages/attr/_make.py:3059\u001b[0m, in \u001b[0;36m_AndValidator.__call__\u001b[0;34m(self, inst, attr, value)\u001b[0m\n\u001b[1;32m 3057\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__call__\u001b[39m(\u001b[38;5;28mself\u001b[39m, inst, attr, value):\n\u001b[1;32m 3058\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m v \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_validators:\n\u001b[0;32m-> 3059\u001b[0m \u001b[43mv\u001b[49m\u001b[43m(\u001b[49m\u001b[43minst\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mattr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mvalue\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/.local/lib/python3.10/site-packages/baybe/parameters/substance.py:77\u001b[0m, in \u001b[0;36mSubstanceParameter._validate_substance_data\u001b[0;34m(self, _, data)\u001b[0m\n\u001b[1;32m 67\u001b[0m \u001b[38;5;129m@data\u001b[39m\u001b[38;5;241m.\u001b[39mvalidator\n\u001b[1;32m 68\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_validate_substance_data\u001b[39m( \u001b[38;5;66;03m# noqa: DOC101, DOC103\u001b[39;00m\n\u001b[1;32m 69\u001b[0m \u001b[38;5;28mself\u001b[39m, _: Any, data: \u001b[38;5;28mdict\u001b[39m[\u001b[38;5;28mstr\u001b[39m, Smiles]\n\u001b[1;32m 70\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 71\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Validate that the substance data, provided as SMILES, is valid.\u001b[39;00m\n\u001b[1;32m 72\u001b[0m \n\u001b[1;32m 73\u001b[0m \u001b[38;5;124;03m Raises:\u001b[39;00m\n\u001b[1;32m 74\u001b[0m \u001b[38;5;124;03m ValueError: If one or more of the SMILES are invalid.\u001b[39;00m\n\u001b[1;32m 75\u001b[0m \u001b[38;5;124;03m ValueError: If the several entries represent the same substance.\u001b[39;00m\n\u001b[1;32m 76\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m---> 77\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mbaybe\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mutils\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m chemistry\n\u001b[1;32m 79\u001b[0m \u001b[38;5;66;03m# Check for invalid SMILES\u001b[39;00m\n\u001b[1;32m 80\u001b[0m canonical_smiles \u001b[38;5;241m=\u001b[39m {}\n",
"File \u001b[0;32m~/.local/lib/python3.10/site-packages/baybe/utils/chemistry.py:21\u001b[0m\n\u001b[1;32m 19\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mrdkit\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mChem\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mrdMolDescriptors\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m GetMorganFingerprintAsBitVect\n\u001b[1;32m 20\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mImportError\u001b[39;00m:\n\u001b[0;32m---> 21\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m OptionalImportError(\n\u001b[1;32m 22\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"The requested functionality requires the installation of optional \"\"\"\u001b[39;00m\n\u001b[1;32m 23\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"chemistry dependencies. Please run \"pip install 'baybe[chem]'\".\"\"\"\u001b[39;00m\n\u001b[1;32m 24\u001b[0m )\n\u001b[1;32m 26\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mbaybe\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mutils\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mnumerical\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m DTypeFloatNumpy\n\u001b[1;32m 28\u001b[0m _mordred_calculator \u001b[38;5;241m=\u001b[39m Calculator(descriptors)\n",
"\u001b[0;31mOptionalImportError\u001b[0m: The requested functionality requires the installation of optional chemistry dependencies. Please run \"pip install 'baybe[chem]'\"."
]
}
],
"outputs": [],
"source": [
"from baybe.parameters import (\n",
" CategoricalParameter,\n",
" NumericalDiscreteParameter,\n",
" SubstanceParameter,\n",
" NumericalContinuousParameter,\n",
")\n",
"\n",
"parameters = [\n",
" NumericalDiscreteParameter(\n",
" NumericalContinuousParameter(\n",
" name=\"Time[h]\",\n",
" bounds=(0.500000, 672),\n",
" ),\n",
" NumericalContinuousParameter(\n",
" name=\"pH\",\n",
" bounds=(1, 14),\n",
" ),\n",
"]"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 32,
"metadata": {},
"outputs": [],
"source": [
"from baybe.searchspace import SearchSpace\n",
"\n",
"searchspace = SearchSpace.from_product(parameters)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Run the campaign"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [],
"source": [
"from baybe import Campaign\n",
"\n",
"campaign = Campaign(searchspace, objective)"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" Time[h] pH\n",
"0 638.310058 2.638211\n",
"1 475.753030 2.599470\n",
"2 452.512074 4.018597\n"
]
}
],
"source": [
"df = campaign.recommend(batch_size=3)\n",
"print(df)"
]
}
],
"metadata": {
Expand Down

0 comments on commit 98f43ee

Please sign in to comment.