Added community contributions to week 5 - separate ingestion and also…

… Obsidian example

week5/community-contributions/day3 - extended for Obsidian files and separate ingestion.ipynb

@@ -0,0 +1,396 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "dfe37963-1af6-44fc-a841-8e462443f5e6",
+   "metadata": {},
+   "source": [
+    "## Expert Knowledge Worker\n",
+    "\n",
+    "### A question answering agent that is an expert knowledge worker\n",
+    "### To be used by employees of Insurellm, an Insurance Tech company\n",
+    "### The agent needs to be accurate and the solution should be low cost.\n",
+    "\n",
+    "This project will use RAG (Retrieval Augmented Generation) to ensure our question/answering assistant has high accuracy."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ba2779af-84ef-4227-9e9e-6eaf0df87e77",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# imports\n",
+    "\n",
+    "import os\n",
+    "import glob\n",
+    "from dotenv import load_dotenv\n",
+    "import gradio as gr"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "802137aa-8a74-45e0-a487-d1974927d7ca",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# imports for langchain and Chroma and plotly\n",
+    "\n",
+    "from langchain.document_loaders import DirectoryLoader, TextLoader\n",
+    "from langchain.text_splitter import CharacterTextSplitter\n",
+    "from langchain.schema import Document\n",
+    "from langchain_openai import OpenAIEmbeddings, ChatOpenAI\n",
+    "from langchain_chroma import Chroma\n",
+    "import numpy as np\n",
+    "from sklearn.manifold import TSNE\n",
+    "import plotly.graph_objects as go"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "58c85082-e417-4708-9efe-81a5d55d1424",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# price is a factor for our company, so we're going to use a low cost model\n",
+    "\n",
+    "MODEL = \"gpt-4o-mini\"\n",
+    "db_name = \"vector_db\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ee78efcb-60fe-449e-a944-40bab26261af",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load environment variables in a file called .env\n",
+    "\n",
+    "load_dotenv()\n",
+    "os.environ['OPENAI_API_KEY'] = os.getenv('OPENAI_API_KEY', 'your-key-if-not-using-env')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "730711a9-6ffe-4eee-8f48-d6cfb7314905",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Read in documents using LangChain's loaders\n",
+    "# Take everything in all the sub-folders of our knowledgebase\n",
+    "\n",
+    "folders = glob.glob(\"knowledge-base/*\")\n",
+    "\n",
+    "# With thanks to Jon R, a student on the course, for this fix needed for some users \n",
+    "text_loader_kwargs={'autodetect_encoding': True}\n",
+    "\n",
+    "documents = []\n",
+    "for folder in folders:\n",
+    "    doc_type = os.path.basename(folder)\n",
+    "    loader = DirectoryLoader(folder, glob=\"**/*.md\", loader_cls=TextLoader, loader_kwargs=text_loader_kwargs)\n",
+    "    folder_docs = loader.load()\n",
+    "    for doc in folder_docs:\n",
+    "        doc.metadata[\"doc_type\"] = doc_type\n",
+    "        documents.append(doc)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6717e706",
+   "metadata": {},
+   "source": [
+    "## A Variation to loading the default project files included in the course \n",
+    "## (a.k.a., how to get your LLM chatbot to talk to your Obsidian files)\n",
+    "I noticed that Ed (our instructor) had used markdown files (*.md) for the RAG sources. That got me thinking about whether \n",
+    "I could try these RAG techniques on my Obsidian data, since Obsidian stores all its files as *.md as well. \n",
+    "\n",
+    "If you are not familiar with Obsidian, it's a great productivity tool that stores notes that are more in line with how we work. It's similar to Evernote and other tools of this nature. But it's all local (although you can pay for synching to the cloud). Just search on google for Obsidian md.\n",
+    "\n",
+    "I did actually try an Obsidian plugin called Smart Second Brain, which is supposed to do something similar directly inside Obsidian. But it was quite buggy. It would take forever on even a small vault (vaults are like new knowledge bases. So you could create vaults on different categories like sports, LLMs, training, etc) I chose instead to try out the techniques taught here, and I now can use that to query my Obsidian vaults.\n",
+    "\n",
+    "If you want to give this a go, here is the code change for loading your obsidian files. You will need to locate the directories of your vault (they can exist on multiple folders/drives, etc.)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f634ccb1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# If you wish to try your Obsidian vaults, replace the full block for loading documents \n",
+    "# starting with the comment above # Read in documents using LangChain's loaders. \n",
+    "# NOTE: If you do not wish to try out connecting the chatbot to your Obsidian, \n",
+    "# please skip over this entire block up to and include the # End of block for Obsidian\n",
+    "\n",
+    "folders = glob.glob(\"{ADD IN YOUR PATH TO THE OBSIDIAN .MD FILES HERE}\") # IMPORTANT: change this to your Obsidian vault folder\n",
+    "\n",
+    "# Filter out folders that start with a period (you don't want these to be embedded and indexed)\n",
+    "folders = [folder for folder in folders if not os.path.basename(folder).startswith('.')]\n",
+    "\n",
+    "documents = []\n",
+    "for folder in folders:\n",
+    "  doc_type = os.path.basename(folder)\n",
+    "  loader = DirectoryLoader(folder, glob=\"**/*.md\", loader_cls=TextLoader)\n",
+    "  folder_docs = loader.load()\n",
+    "  for doc in folder_docs:\n",
+    "      doc.metadata[\"doc_type\"] = doc_type\n",
+    "      documents.append(doc)\n",
+    "\n",
+    "# End of block for Obsidian"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7310c9c8-03c1-4efc-a104-5e89aec6db1a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "text_splitter = CharacterTextSplitter(chunk_size=1000, chunk_overlap=200)\n",
+    "chunks = text_splitter.split_documents(documents)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cd06e02f-6d9b-44cc-a43d-e1faa8acc7bb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "len(chunks)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2c54b4b6-06da-463d-bee7-4dd456c2b887",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "doc_types = set(chunk.metadata['doc_type'] for chunk in chunks)\n",
+    "print(f\"Document types found: {', '.join(doc_types)}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "77f7d2a6-ccfa-425b-a1c3-5e55b23bd013",
+   "metadata": {},
+   "source": [
+    "## A sidenote on Embeddings, and \"Auto-Encoding LLMs\"\n",
+    "\n",
+    "We will be mapping each chunk of text into a Vector that represents the meaning of the text, known as an embedding.\n",
+    "\n",
+    "OpenAI offers a model to do this, which we will use by calling their API with some LangChain code.\n",
+    "\n",
+    "This model is an example of an \"Auto-Encoding LLM\" which generates an output given a complete input.\n",
+    "It's different to all the other LLMs we've discussed today, which are known as \"Auto-Regressive LLMs\", and generate future tokens based only on past context.\n",
+    "\n",
+    "Another example of an Auto-Encoding LLMs is BERT from Google. In addition to embedding, Auto-encoding LLMs are often used for classification."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "78998399-ac17-4e28-b15f-0b5f51e6ee23",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Put the chunks of data into a Vector Store that associates a Vector Embedding with each chunk\n",
+    "\n",
+    "embeddings = OpenAIEmbeddings()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "763e51ff-5787-4a56-8176-36b7c5796fe3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Check if a Chroma Datastore already exists - if so, delete the collection to start from scratch\n",
+    "\n",
+    "if os.path.exists(db_name):\n",
+    "    Chroma(persist_directory=db_name, embedding_function=embeddings).delete_collection()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "99fe3a37-480f-4d55-be48-120588d5846b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create our Chroma vectorstore!\n",
+    "\n",
+    "vectorstore = Chroma.from_documents(documents=chunks, embedding=embeddings, persist_directory=db_name)\n",
+    "print(f\"Vectorstore created with {vectorstore._collection.count()} documents\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "00a9c406",
+   "metadata": {},
+   "source": [
+    "## When implementing this outside of Jupyter Notebooks\n",
+    "Jupyter notebooks are great for learning but when you're ready to put the techniques to use on a project, you'll need to separate out the loading, chunking, embedding and storing in the vector database. Otherwise, if you couple this functionality with your main functionality (like the Gradio chatbot), this processing of vectors will happen for each call. \n",
+    "\n",
+    "Ed (creator and instructor of this course) had suggested to me that his company usually breaks out these processes into a pipeline and the main script, which makes total sense. I will call the pipeline the intestion module, but pipeline is perfectly fine. The name is not that important. These scripts are regular python files and would be part of a project in Anaconda or Visual Studio Code, etc.\n",
+    "\n",
+    "At this point, the code up to this point will serve as the ingestion script. So, if you were to create a standard python file called ingestion.py, just copy all the code above and then install all the necessary pip packages. (You could use the same requirements.txt)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "057868f6-51a6-4087-94d1-380145821550",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Get one vector and find how many dimensions it has\n",
+    "\n",
+    "collection = vectorstore._collection\n",
+    "sample_embedding = collection.get(limit=1, include=[\"embeddings\"])[\"embeddings\"][0]\n",
+    "dimensions = len(sample_embedding)\n",
+    "print(f\"The vectors have {dimensions:,} dimensions\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "61e393a0-dd4c-419f-842f-60c1cb3b716b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b0d45462-a818-441c-b010-b85b32bcf618",
+   "metadata": {},
+   "source": [
+    "## Visualizing the Vector Store\n",
+    "\n",
+    "Let's take a minute to look at the documents and their embedding vectors to see what's going on."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b98adf5e-d464-4bd2-9bdf-bc5b6770263b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Prework\n",
+    "\n",
+    "result = collection.get(include=['embeddings', 'documents', 'metadatas'])\n",
+    "vectors = np.array(result['embeddings'])\n",
+    "documents = result['documents']\n",
+    "doc_types = [metadata['doc_type'] for metadata in result['metadatas']]\n",
+    "colors = [['blue', 'green', 'red', 'orange'][['products', 'employees', 'contracts', 'company'].index(t)] for t in doc_types]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "427149d5-e5d8-4abd-bb6f-7ef0333cca21",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# We humans find it easier to visalize things in 2D!\n",
+    "# Reduce the dimensionality of the vectors to 2D using t-SNE\n",
+    "# (t-distributed stochastic neighbor embedding)\n",
+    "\n",
+    "tsne = TSNE(n_components=2, random_state=42)\n",
+    "reduced_vectors = tsne.fit_transform(vectors)\n",
+    "\n",
+    "# Create the 2D scatter plot\n",
+    "fig = go.Figure(data=[go.Scatter(\n",
+    "    x=reduced_vectors[:, 0],\n",
+    "    y=reduced_vectors[:, 1],\n",
+    "    mode='markers',\n",
+    "    marker=dict(size=5, color=colors, opacity=0.8),\n",
+    "    text=[f\"Type: {t}<br>Text: {d[:100]}...\" for t, d in zip(doc_types, documents)],\n",
+    "    hoverinfo='text'\n",
+    ")])\n",
+    "\n",
+    "fig.update_layout(\n",
+    "    title='2D Chroma Vector Store Visualization',\n",
+    "    scene=dict(xaxis_title='x',yaxis_title='y'),\n",
+    "    width=800,\n",
+    "    height=600,\n",
+    "    margin=dict(r=20, b=10, l=10, t=40)\n",
+    ")\n",
+    "\n",
+    "fig.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e1418e88-acd5-460a-bf2b-4e6efc88e3dd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Let's try 3D!\n",
+    "\n",
+    "tsne = TSNE(n_components=3, random_state=42)\n",
+    "reduced_vectors = tsne.fit_transform(vectors)\n",
+    "\n",
+    "# Create the 3D scatter plot\n",
+    "fig = go.Figure(data=[go.Scatter3d(\n",
+    "    x=reduced_vectors[:, 0],\n",
+    "    y=reduced_vectors[:, 1],\n",
+    "    z=reduced_vectors[:, 2],\n",
+    "    mode='markers',\n",
+    "    marker=dict(size=5, color=colors, opacity=0.8),\n",
+    "    text=[f\"Type: {t}<br>Text: {d[:100]}...\" for t, d in zip(doc_types, documents)],\n",
+    "    hoverinfo='text'\n",
+    ")])\n",
+    "\n",
+    "fig.update_layout(\n",
+    "    title='3D Chroma Vector Store Visualization',\n",
+    "    scene=dict(xaxis_title='x', yaxis_title='y', zaxis_title='z'),\n",
+    "    width=900,\n",
+    "    height=700,\n",
+    "    margin=dict(r=20, b=10, l=10, t=40)\n",
+    ")\n",
+    "\n",
+    "fig.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9b3ada26-b4b7-42fc-b943-933c14adf89b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}