rag

MaastrichtU-IDS · Mar 18, 2024 · c517d4e · c517d4e
1 parent daf518e
commit c517d4e
Showing 1 changed file with 9 additions and 82 deletions.
diff --git a/2024/lab9/Lab9 - RAG over KG.ipynb b/2024/lab9/Lab9 - RAG over KG.ipynb
@@ -154,22 +154,7 @@
     "\n",
     "SELECT ?uri ?predicate ?label ?type\n",
     "WHERE {\n",
-    "    ?uri a ?type ;\n",
-    "        ?predicate ?label .\n",
-    "    FILTER (\n",
-    "        ?type = owl:Class ||\n",
-    "            ?type = owl:DatatypeProperty ||\n",
-    "            ?type = owl:ObjectProperty\n",
-    "    )\n",
-    "    FILTER (\n",
-    "        ?predicate = rdfs:label ||\n",
-    "            ?predicate = skos:prefLabel ||\n",
-    "            ?predicate = skos:altLabel ||\n",
-    "            ?predicate = skos:definition ||\n",
-    "            ?predicate = rdfs:comment ||\n",
-    "            ?predicate = dcterms:description ||\n",
-    "            ?predicate = dc:title\n",
-    "    )\n",
+    "    TODO\n",
     "}\"\"\"\n",
     "\n",
     "class OntologyLoader(BaseLoader):\n",
@@ -215,31 +200,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\u001b[32m2024-03-17 11:02:48.072\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mfastembed.embedding\u001b[0m:\u001b[36m<module>\u001b[0m:\u001b[36m7\u001b[0m - \u001b[33m\u001b[1mDefaultEmbedding, FlagEmbedding, JinaEmbedding are deprecated. Use TextEmbedding instead.\u001b[0m\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "4e0eea67b54c477ea3fd7e5ecd8e7e45",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Fetching 9 files:   0%|          | 0/9 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "flag_embeddings = FastEmbedEmbeddings(model_name=\"BAAI/bge-small-en-v1.5\", max_length=512)\n",
     "loader = OntologyLoader(\"https://semanticscience.org/ontology/sio.owl\", format=\"xml\")\n",
@@ -288,10 +251,7 @@
     ")\n",
     "\n",
     "# Prompt to reformulate the question using the chat history\n",
-    "reform_template = \"\"\"Given the following chat history and a follow up question,\n",
-    "rephrase the follow up question to be a standalone straightforward question, in its original language.\n",
-    "Do not answer the question! Just rephrase reusing informations from the chat history.\n",
-    "Make it short and straight to the point.\n",
+    "reform_template = \"\"\"TODO\n",
     "\n",
     "Chat History:\n",
     "{chat_history}\n",
@@ -300,8 +260,7 @@
     "REFORM_QUESTION_PROMPT = PromptTemplate.from_template(reform_template)\n",
     "\n",
     "# Prompt to ask to answer the reformulated question\n",
-    "answer_template = \"\"\"Briefly answer the question based only on the following context,\n",
-    "do not use any information outside this context:\n",
+    "answer_template = \"\"\"TODO\n",
     "{context}\n",
     "\n",
     "Question: {question}\n",
@@ -392,25 +351,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "💭 Reformulated question:  Can you give me the definition of a protein?\n",
-      "📚 Documents retrieved:\n",
-      "· protein (http://semanticscience.org/resource/SIO_010043)\n",
-      "· A protein is an organic polymer that is composed of one or more linear polymers of amino acids. (http://semanticscience.org/resource/SIO_010043)\n",
-      "· A protein complex is a molecular complex composed of at least two polypeptide chains. (http://semanticscience.org/resource/SIO_010497)\n",
-      "· A polypeptide is an organic polymer composed of amino acid residues, typically of less than 50 amino acids in length. (http://semanticscience.org/resource/SIO_010007)\n",
-      "· amino acid (http://semanticscience.org/resource/SIO_001224)\n",
-      "\n",
-      "Answer: A protein is an organic polymer composed of one or more linear polymers of amino acids."
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# set_debug(True)   # Uncomment to enable detailed LangChain debugging\n",
     "output = stream_chain(final_chain, memory, {\n",
@@ -420,25 +363,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "💭 Reformulated question:  What is the URI for the concept of a protein?\n",
-      "📚 Documents retrieved:\n",
-      "· protein (http://semanticscience.org/resource/SIO_010043)\n",
-      "· A protein complex is a molecular complex composed of at least two polypeptide chains. (http://semanticscience.org/resource/SIO_010497)\n",
-      "· protein complex (http://semanticscience.org/resource/SIO_010497)\n",
-      "· A protein-protein association is an association between two proteins. (http://semanticscience.org/resource/SIO_001438)\n",
-      "· protein-protein association (http://semanticscience.org/resource/SIO_001438)\n",
-      "\n",
-      "http://semanticscience.org/resource/SIO_010043"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "output = stream_chain(final_chain, memory, {\n",
     "    \"question\": \"What is the URI for this concept?\"\n",