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  },
  "cells": [
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "VgZwIG1dnatg",
        "outputId": "92b5fcfe-970d-4eb3-9ae1-6f15addf13c5"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Mounted at /content/drive\n"
          ]
        }
      ],
      "source": [
        "from google.colab import drive\n",
        "drive.mount('/content/drive', force_remount=True)\n",
        "import os\n",
        "os.listdir(\"./drive/MyDrive/711/HW3\")\n",
        "os.chdir(\"./drive/MyDrive/711/HW3\")\n"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#!git clone https://kelvinlll: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@github.com/Aaalan-Zhang/11711-proj-3-sota-reimplement.git\n"
      ],
      "metadata": {
        "id": "of-aD-wXnfcR"
      },
      "execution_count": 2,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "os.listdir(\"./11711-proj-3-sota-reimplement\")\n",
        "os.chdir(\"./11711-proj-3-sota-reimplement\")"
      ],
      "metadata": {
        "id": "4sGGdgw6oQ0D"
      },
      "execution_count": 3,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!ls"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "UoSq1rfaoXPT",
        "outputId": "443d1192-a954-496d-b588-7a8f4fe64b0f"
      },
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "MedRAG\tREADME.md\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!git pull --recurse-submodules\n",
        "!git submodule update --init --recursive\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "y5WaE0V6o3ao",
        "outputId": "ef5dc7b3-462c-4527-b5c1-01a998a61e60"
      },
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Fetching submodule MedRAG\n",
            "Already up to date.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!ls"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "yQXaumcCo3Yk",
        "outputId": "e072e7d9-2da8-4924-e025-97ee470633b9"
      },
      "execution_count": 35,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "MedRAG\tREADME.md\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Download Datasets"
      ],
      "metadata": {
        "id": "mPwDOadho38-"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "### Settings"
      ],
      "metadata": {
        "id": "ADHp01unrh9H"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!pip install huggingface_hub\n",
        "!pip install datasets\n",
        "from datasets import load_dataset"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "pVV67BlKoXwI",
        "outputId": "9d88262c-fb53-4cf8-99ea-2c3c359e8ddf"
      },
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Requirement already satisfied: huggingface_hub in /usr/local/lib/python3.10/dist-packages (0.24.7)\n",
            "Requirement already satisfied: filelock in /usr/local/lib/python3.10/dist-packages (from huggingface_hub) (3.16.1)\n",
            "Requirement already satisfied: fsspec>=2023.5.0 in /usr/local/lib/python3.10/dist-packages (from huggingface_hub) (2023.10.0)\n",
            "Requirement already satisfied: packaging>=20.9 in /usr/local/lib/python3.10/dist-packages (from huggingface_hub) (23.2)\n",
            "Requirement already satisfied: pyyaml>=5.1 in /usr/local/lib/python3.10/dist-packages (from huggingface_hub) (6.0.2)\n",
            "Requirement already satisfied: requests in /usr/local/lib/python3.10/dist-packages (from huggingface_hub) (2.32.3)\n",
            "Requirement already satisfied: tqdm>=4.42.1 in /usr/local/lib/python3.10/dist-packages (from huggingface_hub) (4.66.1)\n",
            "Requirement already satisfied: typing-extensions>=3.7.4.3 in /usr/local/lib/python3.10/dist-packages (from huggingface_hub) (4.12.2)\n",
            "Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests->huggingface_hub) (3.4.0)\n",
            "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests->huggingface_hub) (3.10)\n",
            "Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests->huggingface_hub) (2.2.3)\n",
            "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests->huggingface_hub) (2024.8.30)\n",
            "Requirement already satisfied: datasets in /usr/local/lib/python3.10/dist-packages (2.16.1)\n",
            "Requirement already satisfied: filelock in /usr/local/lib/python3.10/dist-packages (from datasets) (3.16.1)\n",
            "Requirement already satisfied: numpy>=1.17 in /usr/local/lib/python3.10/dist-packages (from datasets) (1.26.4)\n",
            "Requirement already satisfied: pyarrow>=8.0.0 in /usr/local/lib/python3.10/dist-packages (from datasets) (17.0.0)\n",
            "Requirement already satisfied: pyarrow-hotfix in /usr/local/lib/python3.10/dist-packages (from datasets) (0.6)\n",
            "Requirement already satisfied: dill<0.3.8,>=0.3.0 in /usr/local/lib/python3.10/dist-packages (from datasets) (0.3.7)\n",
            "Requirement already satisfied: pandas in /usr/local/lib/python3.10/dist-packages (from datasets) (2.2.2)\n",
            "Requirement already satisfied: requests>=2.19.0 in /usr/local/lib/python3.10/dist-packages (from datasets) (2.32.3)\n",
            "Requirement already satisfied: tqdm>=4.62.1 in /usr/local/lib/python3.10/dist-packages (from datasets) (4.66.1)\n",
            "Requirement already satisfied: xxhash in /usr/local/lib/python3.10/dist-packages (from datasets) (3.5.0)\n",
            "Requirement already satisfied: multiprocess in /usr/local/lib/python3.10/dist-packages (from datasets) (0.70.15)\n",
            "Requirement already satisfied: fsspec<=2023.10.0,>=2023.1.0 in /usr/local/lib/python3.10/dist-packages (from fsspec[http]<=2023.10.0,>=2023.1.0->datasets) (2023.10.0)\n",
            "Requirement already satisfied: aiohttp in /usr/local/lib/python3.10/dist-packages (from datasets) (3.10.10)\n",
            "Requirement already satisfied: huggingface-hub>=0.19.4 in /usr/local/lib/python3.10/dist-packages (from datasets) (0.24.7)\n",
            "Requirement already satisfied: packaging in /usr/local/lib/python3.10/dist-packages (from datasets) (23.2)\n",
            "Requirement already satisfied: pyyaml>=5.1 in /usr/local/lib/python3.10/dist-packages (from datasets) (6.0.2)\n",
            "Requirement already satisfied: aiohappyeyeballs>=2.3.0 in /usr/local/lib/python3.10/dist-packages (from aiohttp->datasets) (2.4.3)\n",
            "Requirement already satisfied: aiosignal>=1.1.2 in /usr/local/lib/python3.10/dist-packages (from aiohttp->datasets) (1.3.1)\n",
            "Requirement already satisfied: attrs>=17.3.0 in /usr/local/lib/python3.10/dist-packages (from aiohttp->datasets) (24.2.0)\n",
            "Requirement already satisfied: frozenlist>=1.1.1 in /usr/local/lib/python3.10/dist-packages (from aiohttp->datasets) (1.5.0)\n",
            "Requirement already satisfied: multidict<7.0,>=4.5 in /usr/local/lib/python3.10/dist-packages (from aiohttp->datasets) (6.1.0)\n",
            "Requirement already satisfied: yarl<2.0,>=1.12.0 in /usr/local/lib/python3.10/dist-packages (from aiohttp->datasets) (1.17.0)\n",
            "Requirement already satisfied: async-timeout<5.0,>=4.0 in /usr/local/lib/python3.10/dist-packages (from aiohttp->datasets) (4.0.3)\n",
            "Requirement already satisfied: typing-extensions>=3.7.4.3 in /usr/local/lib/python3.10/dist-packages (from huggingface-hub>=0.19.4->datasets) (4.12.2)\n",
            "Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests>=2.19.0->datasets) (3.4.0)\n",
            "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests>=2.19.0->datasets) (3.10)\n",
            "Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests>=2.19.0->datasets) (2.2.3)\n",
            "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests>=2.19.0->datasets) (2024.8.30)\n",
            "Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.10/dist-packages (from pandas->datasets) (2.8.2)\n",
            "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas->datasets) (2024.2)\n",
            "Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.10/dist-packages (from pandas->datasets) (2024.2)\n",
            "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.8.2->pandas->datasets) (1.16.0)\n",
            "Requirement already satisfied: propcache>=0.2.0 in /usr/local/lib/python3.10/dist-packages (from yarl<2.0,>=1.12.0->aiohttp->datasets) (0.2.0)\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "### MedRAG/wikipedia"
      ],
      "metadata": {
        "id": "WlhU9N-Hp9oe"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "# Load the dataset and specify where to save it locally\n",
        "ds = load_dataset(\"MedRAG/wikipedia\", cache_dir=\"data/wikipedia\")"
      ],
      "metadata": {
        "collapsed": true,
        "id": "w6bCIeOMqcrh"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "### MedRAG/pubmed"
      ],
      "metadata": {
        "id": "UIFgRlKJrqR5"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from datasets import load_dataset\n",
        "\n",
        "ds = load_dataset(\"MedRAG/pubmed\", cache_dir=\"data/pubmed\")"
      ],
      "metadata": {
        "id": "nhKtZzqzq4CP"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "### MedRAG/textbooks"
      ],
      "metadata": {
        "id": "4j0O3iHXrvBR"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from datasets import load_dataset\n",
        "\n",
        "ds = load_dataset(\"MedRAG/textbooks\", cache_dir=\"data/textbooks\")"
      ],
      "metadata": {
        "colab": {
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        "id": "fx5Sp79jrwUN",
        "outputId": "67051275-75e8-4be0-b841-86faa60627c3"
      },
      "execution_count": 20,
      "outputs": [
        {
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        {
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            "text/plain": [
              "Generating train split:   0%|          | 0/125847 [00:00<?, ? examples/s]"
            ],
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    {
      "cell_type": "markdown",
      "source": [
        "### statpearls\n"
      ],
      "metadata": {
        "id": "FMfmDMSMryrf"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "os.listdir(\"./MedRAG\")\n",
        "os.chdir(\"./MedRAG\")"
      ],
      "metadata": {
        "id": "Sw2lDqqdsSVB"
      },
      "execution_count": 21,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!wget https://ftp.ncbi.nlm.nih.gov/pub/litarch/3d/12/statpearls_NBK430685.tar.gz -P ./corpus/statpearls\n",
        "!tar -xzvf ./corpus/statpearls/statpearls_NBK430685.tar.gz -C ./corpus/statpearls\n",
        "!python src/data/statpearls.py"
      ],
      "metadata": {
        "collapsed": true,
        "id": "-to6mJZQr4YY"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "os.chdir(\"..\")"
      ],
      "metadata": {
        "id": "W8ah1MdcscHX"
      },
      "execution_count": 23,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Running"
      ],
      "metadata": {
        "id": "FV8jAK9QweHI"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "### Requirements"
      ],
      "metadata": {
        "id": "2zNd7RFbwfcp"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "Requirements\n",
        "First, install PyTorch suitable for your system's CUDA version by following the official instructions (2.1.1+cu121 in our case).\n",
        "\n",
        "New LLMs such as Llama 3.1 and Llama 3.2 were tested with '2.4.1+cu124' on our machine.\n",
        "Then, install the remaining requirements using: pip install -r requirements.txt,\n",
        "\n",
        "For GPT-3.5/GPT-4, an OpenAI API key is needed. Replace the placeholder with your key in src/config.py.\n",
        "\n",
        "Git-lfs is required to download and load corpora for the first time.\n",
        "\n",
        "Java is requried for using BM25."
      ],
      "metadata": {
        "id": "b_wHGnTNwhfM"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!ls"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "_vdCMz78wxnP",
        "outputId": "ce0d706d-c308-467b-eb9a-e1ddd1461298"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "figs  LICENSE  README.md  requirements.txt  src  templates\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "os.listdir(\"./MedRAG\")\n",
        "os.chdir(\"./MedRAG\")"
      ],
      "metadata": {
        "id": "9NhZ64x7wvXg"
      },
      "execution_count": 6,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!pip install -r requirements.txt\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "collapsed": true,
        "id": "1nYiZg3iwfF7",
        "outputId": "3c0587c4-b711-4219-e3ec-ab485363caed"
      },
      "execution_count": 16,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
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            "Requirement already satisfied: confection<1.0.0,>=0.0.1 in /usr/local/lib/python3.10/dist-packages (from thinc<8.3.0,>=8.2.2->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (0.1.5)\n",
            "Requirement already satisfied: shellingham>=1.3.0 in /usr/local/lib/python3.10/dist-packages (from typer<1.0.0,>=0.3.0->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (1.5.4)\n",
            "Requirement already satisfied: rich>=10.11.0 in /usr/local/lib/python3.10/dist-packages (from typer<1.0.0,>=0.3.0->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (13.9.3)\n",
            "Requirement already satisfied: mypy-extensions>=0.3.0 in /usr/local/lib/python3.10/dist-packages (from typing-inspect<1,>=0.4.0->dataclasses-json<0.7,>=0.5.7->langchain==0.0.345->-r requirements.txt (line 4)) (1.0.0)\n",
            "Requirement already satisfied: cloudpathlib<1.0.0,>=0.7.0 in /usr/local/lib/python3.10/dist-packages (from weasel<0.5.0,>=0.1.0->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (0.20.0)\n",
            "Requirement already satisfied: smart-open<8.0.0,>=5.2.1 in /usr/local/lib/python3.10/dist-packages (from weasel<0.5.0,>=0.1.0->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (7.0.5)\n",
            "Requirement already satisfied: propcache>=0.2.0 in /usr/local/lib/python3.10/dist-packages (from yarl<2.0,>=1.12.0->aiohttp->openai==0.28.0->-r requirements.txt (line 3)) (0.2.0)\n",
            "Requirement already satisfied: humanfriendly>=9.1 in /usr/local/lib/python3.10/dist-packages (from coloredlogs->onnxruntime>=1.8.1->pyserini==0.22.1->-r requirements.txt (line 8)) (10.0)\n",
            "Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from jinja2->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (3.0.2)\n",
            "Requirement already satisfied: marisa-trie>=0.7.7 in /usr/local/lib/python3.10/dist-packages (from language-data>=1.2->langcodes<4.0.0,>=3.2.0->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (1.2.1)\n",
            "Requirement already satisfied: markdown-it-py>=2.2.0 in /usr/local/lib/python3.10/dist-packages (from rich>=10.11.0->typer<1.0.0,>=0.3.0->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (3.0.0)\n",
            "Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /usr/local/lib/python3.10/dist-packages (from rich>=10.11.0->typer<1.0.0,>=0.3.0->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (2.18.0)\n",
            "Requirement already satisfied: wrapt in /usr/local/lib/python3.10/dist-packages (from smart-open<8.0.0,>=5.2.1->weasel<0.5.0,>=0.1.0->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (1.16.0)\n",
            "Requirement already satisfied: mdurl~=0.1 in /usr/local/lib/python3.10/dist-packages (from markdown-it-py>=2.2.0->rich>=10.11.0->typer<1.0.0,>=0.3.0->spacy>=3.2.1->pyserini==0.22.1->-r requirements.txt (line 8)) (0.1.2)\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Check the latest CUDA version supported by Colab\n",
        "!nvidia-smi\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "J7iu_5-hxkEB",
        "outputId": "683a5836-1dcd-4ed9-cbc3-947efc746de2"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Wed Nov  6 18:59:38 2024       \n",
            "+---------------------------------------------------------------------------------------+\n",
            "| NVIDIA-SMI 535.104.05             Driver Version: 535.104.05   CUDA Version: 12.2     |\n",
            "|-----------------------------------------+----------------------+----------------------+\n",
            "| GPU  Name                 Persistence-M | Bus-Id        Disp.A | Volatile Uncorr. ECC |\n",
            "| Fan  Temp   Perf          Pwr:Usage/Cap |         Memory-Usage | GPU-Util  Compute M. |\n",
            "|                                         |                      |               MIG M. |\n",
            "|=========================================+======================+======================|\n",
            "|   0  Tesla T4                       Off | 00000000:00:04.0 Off |                    0 |\n",
            "| N/A   38C    P8               9W /  70W |      0MiB / 15360MiB |      0%      Default |\n",
            "|                                         |                      |                  N/A |\n",
            "+-----------------------------------------+----------------------+----------------------+\n",
            "                                                                                         \n",
            "+---------------------------------------------------------------------------------------+\n",
            "| Processes:                                                                            |\n",
            "|  GPU   GI   CI        PID   Type   Process name                            GPU Memory |\n",
            "|        ID   ID                                                             Usage      |\n",
            "|=======================================================================================|\n",
            "|  No running processes found                                                           |\n",
            "+---------------------------------------------------------------------------------------+\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!pip install torch torchvision torchaudio"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "4rTVvQS-xnc1",
        "outputId": "ea060709-f426-44b6-9935-249de7418b89"
      },
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Requirement already satisfied: torch in /usr/local/lib/python3.10/dist-packages (2.5.0+cu121)\n",
            "Requirement already satisfied: torchvision in /usr/local/lib/python3.10/dist-packages (0.20.0+cu121)\n",
            "Requirement already satisfied: torchaudio in /usr/local/lib/python3.10/dist-packages (2.5.0+cu121)\n",
            "Requirement already satisfied: filelock in /usr/local/lib/python3.10/dist-packages (from torch) (3.16.1)\n",
            "Requirement already satisfied: typing-extensions>=4.8.0 in /usr/local/lib/python3.10/dist-packages (from torch) (4.12.2)\n",
            "Requirement already satisfied: networkx in /usr/local/lib/python3.10/dist-packages (from torch) (3.4.2)\n",
            "Requirement already satisfied: jinja2 in /usr/local/lib/python3.10/dist-packages (from torch) (3.1.4)\n",
            "Requirement already satisfied: fsspec in /usr/local/lib/python3.10/dist-packages (from torch) (2023.10.0)\n",
            "Requirement already satisfied: sympy==1.13.1 in /usr/local/lib/python3.10/dist-packages (from torch) (1.13.1)\n",
            "Requirement already satisfied: mpmath<1.4,>=1.1.0 in /usr/local/lib/python3.10/dist-packages (from sympy==1.13.1->torch) (1.3.0)\n",
            "Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from torchvision) (1.26.4)\n",
            "Requirement already satisfied: pillow!=8.3.*,>=5.3.0 in /usr/local/lib/python3.10/dist-packages (from torchvision) (10.4.0)\n",
            "Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from jinja2->torch) (3.0.2)\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!apt-get install git-lfs\n",
        "!git lfs install\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "8t8nBzJnw2f7",
        "outputId": "5ca5a73e-a70b-4a26-8549-8dcbba574f7c"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Reading package lists... Done\n",
            "Building dependency tree... Done\n",
            "Reading state information... Done\n",
            "git-lfs is already the newest version (3.0.2-1ubuntu0.2).\n",
            "0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.\n",
            "Updated git hooks.\n",
            "Git LFS initialized.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "DLv8nHRv2Sxr"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "## Usage"
      ],
      "metadata": {
        "id": "XOXhLiT23bxw"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "from src.medrag import MedRAG\n",
        "\n",
        "question = \"A lesion causing compression of the facial nerve at the stylomastoid foramen will cause ipsilateral\"\n",
        "options = {\n",
        "    \"A\": \"paralysis of the facial muscles.\",\n",
        "    \"B\": \"paralysis of the facial muscles and loss of taste.\",\n",
        "    \"C\": \"paralysis of the facial muscles, loss of taste and lacrimation.\",\n",
        "    \"D\": \"paralysis of the facial muscles, loss of taste, lacrimation and decreased salivation.\"\n",
        "}"
      ],
      "metadata": {
        "id": "w34ZSMle3cdy"
      },
      "execution_count": 7,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!export OPENAI_API_KEY=\"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\"\n"
      ],
      "metadata": {
        "id": "pxlfU-BI4qga"
      },
      "execution_count": 18,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "cot = MedRAG(llm_name=\"OpenAI/gpt-3.5-turbo-16k\", rag=False)\n",
        "answer, _, _ = cot.answer(question=question, options=options)\n",
        "print(f\"Final answer in json with rationale: {answer}\")\n",
        "# {\n",
        "#   \"step_by_step_thinking\": \"Compression of the facial nerve at the stylomastoid foramen will affect the function of the facial nerve. The facial nerve is responsible for innervating the muscles of facial expression, including those involved in smiling, frowning, and closing the eyes. It also carries taste sensation from the anterior two-thirds of the tongue. Additionally, the facial nerve controls tear production (lacrimation) and salivation. Therefore, compression of the facial nerve at the stylomastoid foramen will cause paralysis of the facial muscles (A), loss of taste (B), lacrimation (C), and decreased salivation (D).\",\n",
        "#   \"answer_choice\": \"D\"\n",
        "# }"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "vOsrL3-M3cOA",
        "outputId": "3a1c1cd1-652c-41bc-d0e8-06bdcb4ad8a8"
      },
      "execution_count": 8,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Final answer in json with rationale: {\"step_by_step_thinking\": \"Compression of the facial nerve at the stylomastoid foramen will affect the function of the facial nerve. The facial nerve is responsible for innervating the muscles of facial expression, including those involved in smiling, frowning, and closing the eyes. It also carries taste sensation from the anterior two-thirds of the tongue. Additionally, the facial nerve controls tear production (lacrimation) and salivation. Therefore, compression of the facial nerve at the stylomastoid foramen will cause paralysis of the facial muscles (A), loss of taste (B), lacrimation (C), and decreased salivation (D).\", \"answer_choice\": \"D\"}\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "DPpqUd1Y3jR1"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}