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adding figures

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Karthik Soman
2024-03-17 23:27:09 -07:00
parent 3995749c42
commit e0d5f6227c
6 changed files with 2194 additions and 22 deletions
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@@ -1,3 +1,4 @@
notebooks/neo4j_rag_using_langchain_3M.ipynb
cachegpt
kg_rag/cachegpt
data/vectorDB

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data/results/figures/retrieval_accuracy_comparison.svg Normal file
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17
notebooks/neo4j_rag_using_langchain.ipynb
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@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 113,
"execution_count": 126,
"id": "f0ed1d29",
"metadata": {},
"outputs": [],
@@ -28,7 +28,7 @@
},
{
"cell_type": "code",
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"execution_count": 127,
"id": "763d7ad7",
"metadata": {},
"outputs": [],
@@ -46,7 +46,7 @@
},
{
"cell_type": "code",
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"execution_count": 130,
"id": "43772231",
"metadata": {},
"outputs": [],
@@ -65,7 +65,7 @@
},
{
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"execution_count": 131,
"id": "611fee8c",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": 117,
"execution_count": 132,
"id": "29b40370",
"metadata": {},
"outputs": [
@@ -128,15 +128,16 @@
"text": [
"WARNING! engine is not default parameter.\n",
" engine was transferred to model_kwargs.\n",
" Please confirm that engine is what you intended.\n"
" Please confirm that engine is what you intended.\n",
"Failed to write data to connection IPv4Address(('spoke.cgl.ucsf.edu', 7687)) (ResolvedIPv4Address(('169.230.27.11', 7687)))\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 70.8 ms, sys: 5.76 ms, total: 76.6 ms\n",
"Wall time: 22.7 s\n"
"CPU times: user 70.5 ms, sys: 11.6 ms, total: 82.1 ms\n",
"Wall time: 1min\n"
]
}
],

305
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29
test_notebooks/neo4j_langchain.ipynb
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"cells": [
{
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"execution_count": 12,
"id": "293b41f7",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
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"execution_count": 13,
"id": "ca51ba69",
"metadata": {},
"outputs": [],
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"load_dotenv(os.path.join(os.path.expanduser('~'), '.spoke_neo4j_config.env'))\n",
"username = os.environ.get('NEO4J_USER')\n",
"password = os.environ.get('NEO4J_PSW')\n",
"url = os.environ.get('NEO4J_URL')\n",
"url = os.environ.get('NEO4J_URI')\n",
"database = os.environ.get('NEO4J_DB')\n"
]
},
{
"cell_type": "code",
"execution_count": 70,
"execution_count": 14,
"id": "5db0b6ca",
"metadata": {},
"outputs": [
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"name": "stdout",
"output_type": "stream",
"text": [
"CPU times: user 67.5 ms, sys: 9.32 ms, total: 76.8 ms\n",
"Wall time: 1min 14s\n"
"CPU times: user 419 ms, sys: 72.2 ms, total: 491 ms\n",
"Wall time: 27.6 s\n"
]
}
],
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},
{
"cell_type": "code",
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"execution_count": 15,
"id": "5a6aa873",
"metadata": {},
"outputs": [
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},
{
"cell_type": "code",
"execution_count": 72,
"execution_count": 16,
"id": "76437285",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": 73,
"execution_count": 17,
"id": "3fd3b9c5",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": 98,
"execution_count": 20,
"id": "ed67a504",
"metadata": {},
"outputs": [
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"\n",
"\u001b[1m> Entering new GraphCypherQAChain chain...\u001b[0m\n",
"Generated Cypher:\n",
"\u001b[32;1m\u001b[1;3mMATCH (c:Compound)-[r:TREATS_CtD]->(d:Disease) WHERE c.name = 'levodopa' AND d.name = 'parkinson disease' RETURN r.phase\u001b[0m\n",
"\u001b[32;1m\u001b[1;3mMATCH (c:Compound {name: 'levodopa'})-[:TREATS_CtD]->(d:Disease {name: 'Parkinson\\'s disease'}) RETURN c,d\u001b[0m\n",
"Full Context:\n",
"\u001b[32;1m\u001b[1;3m[]\u001b[0m\n",
"\n",
"\u001b[1m> Finished chain.\u001b[0m\n",
"I'm sorry, but I don't know the answer.\n"
"I'm sorry, but I don't have the information to answer that question.\n"
]
}
],
"source": [
"question = 'What are the genes associated with multiple sclerosis?'\n",
"question=\"Which gene has stronger association with the disease 'liver benign neoplasm', is it PNPLA3 or HLA-B?\"\n",
"question='What is the clinical phase of levodopa in treating parkinson disease?'\n",
"question = \"Is Parkinson's disease associated with levodopa?\"\n",
"# question=\"Which gene has stronger association with the disease 'liver benign neoplasm', is it PNPLA3 or HLA-B?\"\n",
"# question='What is the clinical phase of levodopa in treating parkinson disease?'\n",
"with get_openai_callback() as cb:\n",
" out = chain.run(query=question, return_final_only=False)\n",
" print(out)\n"