Medical_assistant.ipynb

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  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/karamih/QA/blob/master/Medical_assistant.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# QA with custom documents: LangChain and OpenAI"
      ],
      "metadata": {
        "id": "jWKsLpJ47mtN"
      }
    },
    {
      "cell_type": "markdown",
      "source": [
        "### install packages"
      ],
      "metadata": {
        "id": "9CnaRnCT73y0"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "!pip -q install langchain openai tiktoken chromadb pypdf InstructorEmbedding sentence_transformers"
      ],
      "metadata": {
        "id": "gO-ujYxxE_jF"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "### import libraries"
      ],
      "metadata": {
        "id": "RsQ9KlPv8CD0"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "import os\n",
        "\n",
        "from langchain.document_loaders import DirectoryLoader, PyPDFLoader, TextLoader\n",
        "from langchain.text_splitter import RecursiveCharacterTextSplitter\n",
        "from langchain.embeddings import HuggingFaceInstructEmbeddings\n",
        "from langchain.vectorstores import Chroma\n",
        "from langchain.chat_models import ChatOpenAI\n",
        "from langchain.chains import RetrievalQA\n",
        "from langchain.memory import ConversationBufferMemory\n",
        "from langchain import OpenAI\n",
        "\n",
        "import torch\n",
        "\n",
        "from InstructorEmbedding import INSTRUCTOR\n",
        "\n",
        "import textwrap"
      ],
      "metadata": {
        "id": "L_KcWzAF5mmG"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "### Customization\n",
        "\n",
        "modify `DATA_DIRECTORY_PATH` for creating qa on your documents.\n",
        "\n",
        "`VECTOR_DB_PATH` take the path and create your db in there.\n",
        "\n",
        "set `OPENAI_API_KEY` with your key."
      ],
      "metadata": {
        "id": "YnRSuqIi8JXd"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "DATA_DIRECTORY_PATH = '/content/drive/MyDrive/docs/' # Gale encyclopedia of medicine vol 1-5 / nurses drug handbook 2022 / meylers's side effects of endocrine and metabolic\n",
        "VECTOR_DB_PATH = '/content/drive/MyDrive/medical_knowledge/'\n",
        "\n",
        "DEVICE = 'cuda' if torch.cuda.is_available() else 'cpu'\n",
        "\n",
        "os.environ[\"OPENAI_API_KEY\"] = \"\""
      ],
      "metadata": {
        "id": "kU7tPzDz51_d"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "### Prepare data and database"
      ],
      "metadata": {
        "id": "4kxj4bjn-Quh"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "class Data:\n",
        "    docs = None\n",
        "\n",
        "    data_classes = {\"pdf\": PyPDFLoader,\n",
        "                    \"text\": TextLoader}\n",
        "\n",
        "    def __init__(self, *, document_dir, data_type, chunk_size, chunk_overlap):\n",
        "        self.document_dir = document_dir\n",
        "        self.data_type = data_type\n",
        "        self.chunk_size = chunk_size\n",
        "        self.chunk_overlap = chunk_overlap\n",
        "\n",
        "    def __len__(self):\n",
        "        return len(self.docs)\n",
        "\n",
        "    def __getitem__(self, item):\n",
        "        return self.docs[item]\n",
        "\n",
        "    def _split(self):\n",
        "        loader = DirectoryLoader(self.document_dir, glob=f\"*.{self.data_type}\",\n",
        "                                 loader_cls=self.data_classes[self.data_type])\n",
        "\n",
        "        content = loader.load()\n",
        "\n",
        "        splitter = RecursiveCharacterTextSplitter(chunk_size=self.chunk_size,\n",
        "                                                  chunk_overlap=self.chunk_overlap)\n",
        "\n",
        "        self.docs = splitter.split_documents(content)\n",
        "\n",
        "    def document(self):\n",
        "        self._split()\n",
        "        return self.docs\n",
        "\n",
        "\n",
        "class VectorDb:\n",
        "    def __init__(self, *, vectordb_path, embedding, device='cuda'):\n",
        "        self.vectordb_path = vectordb_path\n",
        "        self.device = device\n",
        "        self.embedding = embedding\n",
        "\n",
        "    def create_vectordb(self, *, document):\n",
        "        vectordb = Chroma.from_documents(documents=document,\n",
        "                                         embedding=self.embedding,\n",
        "                                         persist_directory=self.vectordb_path)\n",
        "\n",
        "        vectordb.persist()\n",
        "\n",
        "    def crate_retriever(self, *, k_top_document=3):\n",
        "        vectordb = Chroma(persist_directory=self.vectordb_path,\n",
        "                          embedding_function=self.embedding)\n",
        "        retriever = vectordb.as_retriever(search_kwargs={'k': k_top_document})\n",
        "\n",
        "        return retriever\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "9gOVlvBTFpp-",
        "outputId": "06431562-271b-448b-f707-cc89ce594f9f"
      },
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "/usr/local/lib/python3.10/dist-packages/InstructorEmbedding/instructor.py:7: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)\n",
            "  from tqdm.autonotebook import trange\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#### Splitting documents"
      ],
      "metadata": {
        "id": "2WSRXZ9C9OVL"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "data = Data(document_dir=DATA_DIRECTORY_PATH, chunk_size=1000, chunk_overlap=200, data_type='pdf')\n",
        "document = data.document()"
      ],
      "metadata": {
        "id": "wrkT_-Q0GHhR"
      },
      "execution_count": 4,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "len(document), document[10]"
      ],
      "metadata": {
        "id": "wEQcEkJUGq5S"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "#### Hugging Face embedding"
      ],
      "metadata": {
        "id": "0FT9O-nC9V8S"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "embedding = HuggingFaceInstructEmbeddings(model_name='hkunlp/instructor-xl',\n",
        "                                          model_kwargs={'device': DEVICE'})"
      ],
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            }
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          "metadata": {}
        },
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              "Downloading pytorch_model.bin:   0%|          | 0.00/3.15M [00:00<?, ?B/s]"
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          "metadata": {}
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            ],
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            }
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          "metadata": {}
        },
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "load INSTRUCTOR_Transformer\n",
            "max_seq_length  512\n"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "#### Creating vector database and retriever"
      ],
      "metadata": {
        "id": "vigxR1pE9eYi"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "vector_db = VectorDb(vectordb_path=VECTOR_DB_PATH, embedding=embedding)\n",
        "\n",
        "vector_db.create_vectordb(document=document)"
      ],
      "metadata": {
        "id": "xWMMdoqtHARI"
      },
      "execution_count": 8,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "retriever = vector_db.crate_retriever(k_top_document=5)\n",
        "\n",
        "retriever"
      ],
      "metadata": {
        "id": "U0oFsIRbHAOr"
      },
      "execution_count": 20,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "#### Testing retriever\n"
      ],
      "metadata": {
        "id": "Tg0STzqN93Lk"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "query1 = 'what is daiabet?'\n",
        "query2 = 'what does amoksisilyn pill good for?'\n",
        "query3 = \"اگزمای پوستی چیست؟\"\n",
        "query4 = \"چه قرصی برای معده درد مفید است؟\""
      ],
      "metadata": {
        "id": "ZBVWs_24HALM"
      },
      "execution_count": 22,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "doc1 = retriever.get_relevant_documents(query1)\n",
        "doc1"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "TOn2hLUTHAH_",
        "outputId": "39351706-47a4-4b0b-c8bb-e529085bb260"
      },
      "execution_count": 23,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "[Document(page_content='severity of the diabetes. Mild forms can be treated withdiet (decreasing the intake of sugars and fats, in particu-lar). Many women are put on strict, detailed diets , and are\\nasked to stay within a certain range of calorie intake.Exercise is sometimes used to keep blood sugar levels\\nlower. Patients are often asked to regularly measure theirblood sugar. This is done by poking a finger with a needlecalled a lancet, putting a drop of blood on a special type ofpaper, and feeding the paper into a meter which analyzesand reports the blood sugar level. When diet and exercisedo not keep blood glucose levels within an acceptablerange, a patient may need to take regular shots of insulin.KEY TERMS\\nGlucose —A form of sugar. The final product of the\\nbreakdown of carbohydrates (starches).\\nInsulin —A hormone produced by the pancreas\\nthat is central to the processing of sugars and car-bohydrates in the diet.\\nPlacenta —An organ that is attached to the inside', metadata={'page': 86, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 3 (G-M).pdf'}),\n",
              " Document(page_content='glycemia (a condition where there is abnormally low lev-\\nels of glucose or sugar in the blood). These patients mayrequire several injections of different types of insulinduring the day to keep the blood sugar level within a fair-ly normal range.\\nThe more common form of diabetes, Type II, occurs\\nin approximately 3–5% of Americans under 50 years ofage, and increases to 10–15% in those over 50. Morethan 90% of the diabetics in the United States are Type IIdiabetics. Sometimes called age-onset or adult-onset dia-betes, this form of diabetes occurs most often in peoplewho are overweight and who do not exercise . It is also\\nmore common in people of Native American, Hispanic,and African-American descent. People who have migrat-ed to Western cultures from East India, Japan, and Aus-tralian Aboriginal cultures are also more likely to devel-op Type II diabetes than those who remain in their origi-nal countries.\\nType II is considered a milder form of diabetes', metadata={'page': 435, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 2 (C-F).pdf'}),\n",
              " Document(page_content='glucose in the blood cannot be absorbed into the cells of\\nthe body. Symptoms include frequent urination, lethargy,excessive thirst, and hunger. The treatment includeschanges in diet, oral medications, and in some cases,daily injections of insulin.\\nDescription\\nDiabetes mellitus is a chronic disease that causes\\nserious health complications including renal (kidney)failure, heart disease, stroke , and blindness. Approxi-\\nmately 14 million Americans (about 5% of the popula-tion) have diabetes. Unfortunately, as many as one-halfare unaware that they have it.\\nBackground\\nEvery cell in the human body needs energy in order', metadata={'page': 435, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 2 (C-F).pdf'}),\n",
              " Document(page_content='begin to fall. A person with diabetes mellitus either does\\nnot make enough insulin, or makes insulin that does notwork properly. The result is blood sugar that remainshigh, a condition called hyperglycemia.\\nDiabetes must be diagnosed as early as possible. If\\nleft untreated, it can damage or cause failure of the eyes,kidneys, nerves, heart, blood vessels, and other bodyorgans. Hypoglycemia , or low blood sugar, may also be\\ndiscovered through blood sugar testing. Hypoglycemia iscaused by various hormone disorders and liver disease,as well as by too much insulin.\\nDescription\\nThere are a variety of ways to measure a person’s\\nblood sugar.\\nWhole blood glucose test\\nWhole blood glucose testing can be performed by a', metadata={'page': 542, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 1 (A-B).pdf'}),\n",
              " Document(page_content='Treatment\\nThere is currently no cure for diabetes; the condi-\\ntion, however, can be managed so that patients can live arelatively normal life. Treatment of diabetes focuses ontwo goals: keeping blood glucose within normal rangeand preventing the development of long-term complica-tions. Careful monitoring of diet, exercise, and bloodglucose levels are as important as the use of insulin ororal medications in preventing complications of diabetes.\\nDietary changes\\nDiet and moderate exercise are the first treatments', metadata={'page': 438, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 2 (C-F).pdf'})]"
            ]
          },
          "metadata": {},
          "execution_count": 23
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "doc2 = retriever.get_relevant_documents(query2)\n",
        "doc2"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "wwTPVJLOIsVU",
        "outputId": "2330ede3-2cc6-4191-82fe-de092cca0eff"
      },
      "execution_count": 24,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "[Document(page_content='To treat endocervical, rectal, and urethral infections caused by\\nChlamydia trachomatis\\nCapsules, Delayed-Release T ablets, Oral Suspension, Syrup,\\nTablets\\nAdults.  100 mg (120 mg Doryx MPC) twice daily for 7 days.\\nTo treat unco mplicated gonococcal infections except anorectal\\ninfections in men\\nCapsules, Delayed-Release T ablets, Oral Suspension, Syrup,\\nTablets\\nAdults.  100 mg (120 mg Doryx MPC) twice a day for 7 days.\\nAlternatively , 300 mg (360 mg Doryx MPC) followed in 1 hr by a\\nsecond 300 mg (360 mg Doryx MPC) dose.\\nTo treat epididymoorchitis caused by C. trachomatis or Neisseria\\ngonorrhoeae\\nCapsules, Delayed-Release T ablets, Oral Suspension, Syrup,\\nTablets\\nAdults.  100 mg (120 mg Doryx MPC) twice daily for at least 10\\ndays.\\nTo prevent malaria\\nCapsules, Delayed-Release T ablets, Oral Suspension, Syrup,\\nTablets\\nAdults.  100 mg (120 mg Doryx MPC) daily starting 1 to 2 days\\nbefore travel, continued daily during travel, and then daily for 4 wk\\nafter travel ends.', metadata={'page': 1161, 'source': '/content/drive/MyDrive/docs/nurses-drug-handbook-2022-edition-pdf-k7i.pdf'}),\n",
              " Document(page_content='erectile dysfunction, impotence, infertility , or lack of\\nmenstruation. Encourage patient to report any such symptoms.\\nhydroxychloroquine sulfate\\nPlaquenil\\nClass and Category\\nPharmacologic class:  Aminoquinoline\\nTherapeutic class:  Antimalarial, antirheumatic, lupus erythematosus\\nsuppressant\\nIndications and Dosages\\nTo prevent malaria\\nTablets\\nAdults.  400 mg the same day of each week starting 2 wk before\\nentering endemic area and continued for 4 wk after departure from\\nendemic area.\\nChildren.  6.5 mg/kg weekly on the same day of each week, startin g\\n2 wk before entering endemic area and continued for 4 wk after\\ndeparture from endemic area. Maximum:  400 mg once weekly .\\nTo treat uncomplicated malaria caused by  Plasmodium falciparum, P .\\nmalariae, P . ovale, or P . vivax\\nTablets\\nAdults.  Initial:  800 mg, follow ed by 400 mg in 6 hr, 24 hr, and 48 hr\\nafter initial dose.\\nChildren.  Initial : 13 mg/kg (up to 800 mg), then 6.5 mg/kg (up to 400', metadata={'page': 1813, 'source': '/content/drive/MyDrive/docs/nurses-drug-handbook-2022-edition-pdf-k7i.pdf'}),\n",
              " Document(page_content='omadacycline\\nNuzyra\\nClass and Category\\nPharmacologic class:  Aminomethylcycline of the tetracycline class\\nTherapeutic class:  Antibacterial\\nIndications and Dosages\\nTo treat community-acquired bacterial pneumonia caused by\\nChlamydophila pneumoniae , Haemophilus influenzae , H.\\nparainfluenzae , Klebsiella pneumoniae , Legionella pneumophilia ,\\nMycoplasma pneumoniae , Staphylococcus aureus  (methicillin-\\nsusceptible isolates), or  Streptococcus pneumoniae\\nI.v. Infusion, T ablets\\nAdults.  Loading:  200 mg I.V. on day 1. Alternatively , 100 mg I.V.\\ntwice on day 1. Maintenance:  100 mg I.V . once daily for 7 to 14 days.\\nAlternatively , 300 mg P .O. once daily for 7 to 14 days.\\nTo treat acute bacterial skin structure and skin infections caused by\\nEnterobacter cloacae , Enterococcus faecalis , K. pneumoniae, S.\\naureus  (methicillin- susceptible and-resistant isolates),  S.\\nlugdunensis , S. anginosus group , or S. pyogenes\\nI.V. Infusion, T ablets', metadata={'page': 2683, 'source': '/content/drive/MyDrive/docs/nurses-drug-handbook-2022-edition-pdf-k7i.pdf'}),\n",
              " Document(page_content='IV:2957, 2958\\nMoose elm. SeeSlippery elm\\nMOPP chemotherapy, III:1646, 1647\\nMoraxella catarrhalis\\nlaryngitis from, III:1957otitis media from, IV:2433\\nMorbid obesity, surgery for,\\nIV:2378–2380\\nMorbilli. SeeMeasles\\nMorbus herculeus. SeeElephantiasis\\nMorgan, Christiana, V:3279\\nMormon tea. SeeEphedra\\nMorning after pill. SeeEmergency con-\\ntraception\\nMorning glory\\ndelirium from, II:1021poisoning from, IV:2644\\nMorning sickness, IV:2325\\nSee also Hyperemesis gravidarum\\nMorphine\\nabuse of, IV:3207\\ndelirium from, II:1021\\nfor diabetic neuropathies, II:1058galactorrhea from, III:1375\\nheartburn from, III:1553\\nfor kidney stones, III:1918with lipase test, III:2002\\noverdose, II:1105\\nfor pain, I:174, 175, IV:2460for mood disorders, III:2217\\nwith opioid analgesics, I:178for personality disorders, IV:2566\\nfor phobias, IV:2583\\nprolactin test and, IV:2723for seasonal affective disorder,\\nIV:2980\\nwith smoking cessation drugs,\\nIV:3111\\nwith SSRIs, IV:2991, 2993\\nwith tricyclic antidepressants,\\nI:260–261', metadata={'page': 604, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 5 (T-Z).pdf'}),\n",
              " Document(page_content='Etibi (CAN), Myambutol\\nClass and Category\\nPharmacologic class:  Synthetic antituberculotic\\nTherapeutic class:  Antituberculotic\\nIndications and Dosages\\nAs adjunct to treat pulmonary tuberculosis caused by  Mycobacterium\\ntuberculosis\\nTablets\\nAdults and adolescents who haven’t received previous\\nantituberculotic therapy . 15 mg/kg daily .\\nAdults and adolescents who have received antitu berculotic\\ntherapy . 25 mg/kg daily; after 60 days, decreased to 15 mg/kg daily .\\nDrug Administration\\nP.O.\\nAdminister with food if GI distress occurs.\\nRoute Onset Peak Duration\\nP.O. Unknown 2–4 hr Unknown\\nHalf-life:  2.5–3.5 hr\\nMechanism of Action\\nMay suppress bacterial multiplication by interfering with RNA\\nsynthesis in susceptible bacteria that are actively dividing.', metadata={'page': 1416, 'source': '/content/drive/MyDrive/docs/nurses-drug-handbook-2022-edition-pdf-k7i.pdf'})]"
            ]
          },
          "metadata": {},
          "execution_count": 24
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "doc3 = retriever.get_relevant_documents(query3)\n",
        "doc3"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "x-lpKlViItNN",
        "outputId": "a0a0ac03-ac16-4f6a-b3ee-3570c70da013"
      },
      "execution_count": 25,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "[Document(page_content='Lesion —A pathologic change in tissues.\\nMalignancy —A locally invasive and destructive\\ngrowth.White, C.S., C.A. Meyer, and P. A. Templeton. “CT Fluo-\\nroscopy for Throacic Interventional Procedures.” Radio-\\nlogic Clinics of North America 38 (March 2000).\\nWhite, C.S., et. al. “Transbronchial Needle Aspiration: Guid-\\nance with CT Fluoroscopy.” Chest 118 (December 2000).\\nKim A. Sharp\\nCT-myelogram seeMyelography\\nCT scan seeComputed tomography scans\\nCulture-fair test\\nDefinition\\nA culture-fair test is a test designed to be free of cul-\\ntural bias, as far as possible, so that no one culture has anadvantage over another. The test is designed to not beinfluenced by verbal ability, cultural climate, or educa-tional level.\\nPurpose\\nThe purpose of a culture-fair test is to eliminate any', metadata={'page': 357, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 2 (C-F).pdf'}),\n",
              " Document(page_content='years old. The patient only needs the ability to recognize\\nshapes and figures and perceive their respective relation-ships. Some examples of tasks in the test may include:\\n• completing series• classifying\\n• solving matrices\\n• evaluating conditions\\nThe culture-fair test is also often referred to as a cul-\\nture-free test or unbiased test. There are many variationsof the test including class, economic, and intelligencetests. The threading theme among the various tests istheir design to be culturally unbiased.\\nPreparation\\nThe only preparation necessary to administer the test\\nis pre-ordered materials and a quiet and secluded loca-tion for the duration of the test.\\nAftercare\\nPost-test treatment depends on the results of the test\\nand the specifics of the individual patient. Any furthertreatment is best prescribed by the doctor.\\nRisks\\nThere are no risks associated with the culture-fair\\ntest.\\nNormal results\\nThe results can be compared to the key that comes', metadata={'page': 358, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 2 (C-F).pdf'}),\n",
              " Document(page_content='Avenue, 5th Floor, Suite 300, Silver Spring, MD 20910.(888) 650-9127.\\nMaureen Haggerty\\nKevin O. Hwang, M.D.KEY TERMS\\nComputed tomography —A radiology test by\\nwhich images of cross-sectional planes of thebody are obtained.\\nEndoscopic ultrasound —A radiology test utilizing\\nhigh frequency sound waves, conducted via anendoscope.\\nLaparoscopy —Examination of the contents of the\\nabdomen through a thin, lighted tube passedthrough a small incision.\\nPositron emission tomography —A radiology test\\nby which images of cross-sectional planes of thebody are obtained, utilizing the properties of thepositron. The positron is a subatomic particle ofequal mass to the electron, but of opposite charge.\\nSynergistic —The combined action of two or more\\nprocesses is greater than the sum of each actingseparately.\\nThoracoscopy —Examination of the contents of the\\nchest through a thin, lighted tube passed through asmall incision.Esophageal diverticula seeEsophageal\\npouches\\nEsophageal function tests\\nDefinition', metadata={'page': 628, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 2 (C-F).pdf'}),\n",
              " Document(page_content='blood ( SeeBlood culture)\\nfor enteroviruses, II:1213\\nfungal ( SeeFungal culture)\\nfor herpesviridae, V:3424\\nfor inclusion conjunctivitis, III:1811\\nfor lacrimal duct obstruction,\\nIII:1938\\nfor Reiter’s syndrome, IV:2851\\nfor rubella, IV:2927for skin lesions, IV:3076\\nfor somatitis, IV:3170\\nfor travelers diarrhea, V:3379for vulvovaginitis, V:3540\\nfor wounds, V:3578–3580\\nCultures (Civilization)\\nvs.learning disorders, III:1969\\npica and, IV:2595–2596\\npiercing and tatoos in,\\nIV:2598–2599\\nin somatoform disorders, IV:3115\\nCumin, for anemia, I:184Cumulative trauma disorders. SeeRep-\\netition strain injury\\nCunningham clamp, for neurogenic\\nbladder, IV:2348\\nCupping, acupuncture and, I:17, 41Cuprimine. SeePenicillamine\\nCurative cancer therapy. SeeDefinitive\\ncancer therapy\\nCurcuma domestica. See Turmeric\\nCurcuma longa. See\\nTurmeric\\nCurettage\\nfor cerumen impaction, II:710\\ndilatation and ( SeeDilatation and\\ncurettage)\\nfor non-melanoma skin cancer,\\nIV:3067\\nfor skin lesion removal, IV:3073', metadata={'page': 484, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 5 (T-Z).pdf'}),\n",
              " Document(page_content='mus (AAPOS). <http://med-aapos.bu.edu>.\\nAmerican Optometric Association. 243 North Lindbergh Blvd.,\\nSt. Louis, MO 63141. (314) 991-4100. <http://www.aoanet.org>.\\nOTHER\\n“Strabismus.” The American Academy of Opthamology Page. 7\\nMay 1998 <http://www.aao.org>.\\n“Strabismus (Crossed Eyes).” The Eye Station Page. 8 May\\n1998 <http://www.theeyestation.com>.\\nMaureen Haggerty\\nStrawberry marks seeBirthmarks\\nStrengthening exercises seeExercise\\nStrep culture seeThroat culture\\nStrep test seeStreptococcal antibody tests\\nStrep throat\\nDefinition\\nStreptococcal sore throat , or strep throat as it is\\nmore commonly called, is an infection of the mucousmembranes lining the pharynx. Sometimes the tonsils arealso infected ( tonsillitis ). The disease is caused by groupA Streptococcus bacteria. Untreated strep throat may\\ndevelop into rheumatic fever or other serious conditions.\\nDescription\\nStrep throat accounts for between 5–10% of all sore', metadata={'page': 881, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 4 (N-S).pdf'})]"
            ]
          },
          "metadata": {},
          "execution_count": 25
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "doc4 = retriever.get_relevant_documents(query4)\n",
        "doc4"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "XShHyQXrIs9G",
        "outputId": "76533ed4-16c9-4597-91a9-b4442388e3c7"
      },
      "execution_count": 26,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "[Document(page_content='Salmonella paratyphi :S. paratyphi A ; S. schottmuelleri\\n(also called S. paratyphi B ); or S. hirschfeldii (also called\\nS. paratyphi C ). It can be transmitted from animals or\\nanimal products to humans or from person to person. Theincubation period is one to two weeks but is often shorterin children. Symptom onset may be gradual in adults butis often sudden in children.\\nParatyphoid fever is marked by high fever,\\nheadache , loss of appetite, vomiting, and constipation\\nor diarrhea . The patient typically develops an enlarged\\nspleen. About 30% of patients have rose spots on thefront of the chest during the first week of illness. Therose spots develop into small hemorrhages that may behard to see in African or Native Americans.\\nPatients with intestinal complications have symp-\\ntoms resembling those of appendicitis : intense cramping\\npain with soreness in the right lower quadrant of theabdomen.\\nDiagnosis\\nThe diagnosis is usually made on the basis of a his-', metadata={'page': 205, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 4 (N-S).pdf'}),\n",
              " Document(page_content='Chart, H., M. Sussman, and D. E. S. Stewart-Tull, eds. “ E. coli -\\nFriend or Foe?” Journal of Applied Microbiology The Soci-\\nety for Applied Microbiology Symposium Series No. 29.\\nLong K., E. Vasquez-Garibay, J. Mathewson, J. de la Cabada, and\\nH. DuPont. “The Impact of Infant Feeding Patterns on Infec-tion and Diarrheal Disease Due to EnterotoxigenicEscherichia coli .”Salud Publica Mex (July/Aug. 1999): 263-\\n70.\\nRondeau, Eric, and Marie-Noëlle Peraldi. “ Escherichia coli\\nand the Hemolytic-Uremic Syndrome.” New England\\nJournal of Medicine 335 (1996): 660.\\n“Traveler’s Diarrhea: Don’t Let It Ruin Your Trip.” Mayo Clin-\\nic Health Letter (Jan. 1997).\\nORGANIZATION\\nDivision of Bacterial and Mycotic Diseases. National Center\\nfor Infectious Diseases Centers for Disease Control andPrevention. 1600 Clifton Road, Mailstop C09 Atlanta,Georgia 30333. 21 May, 2001 <http://www.cdc.gov>.\\nOTHER\\n“Preventing Foodborne Illness: Escherichia coli 0157:H7.” (9', metadata={'page': 624, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 2 (C-F).pdf'}),\n",
              " Document(page_content='three days without decreasing in amount,\\n• patients with disorders of the immune system.\\nThe patient history is useful for public health reasons\\nas well as helping the doctor determine what type ofenterobacterium may be causing the infection. The doctorwill ask about the frequency and appearance of the diar-rhea as well as other digestive symptoms. If the patient isnauseated and vomiting, the infection is more likely to belocated in the small intestine. If the patient is running afever , a diagnosis of dysentery is more likely. The doctor\\nwill also ask if anyone else in the patient’s family orworkplace is sick. Some types of enterobacteriaceae aremore likely to cause group outbreaks than others. Otherquestions include the patient’s food intake over the lastfew days and whether he or she has recently traveled tocountries with typhoid fever or cholera outbreaks.\\nPhysical examination\\nThe most important parts of the physical examina-', metadata={'page': 591, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 2 (C-F).pdf'}),\n",
              " Document(page_content='ba histolytica ),Cryptosporidium , and Cyclospora are\\nbeing found with increasing frequency.\\nYounger age groups, particularly students, are at great-\\nest risk, probably because of where and what they eat. Indi-viduals over 55 years of age, persons staying with relatives,or business travelers are at lower risk. Foods with the high-est chance of transmitting disease are uncooked vegetables,unpeeled fruits, meat, and seafood. Tap water and even icecan be dangerous unless one is sure of the source.\\nSymptoms usually start within a few days after arrival,\\nbut can be delayed for as long as two weeks. Illness lasts anaverage of three to five days, but is sometimes longer.Cramping abdominal pain , lack of appetite, and diarrhea\\nare the main complaints. In approximately 10% of patients,diarrhea turns bloody and fever develops in about half of', metadata={'page': 155, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 5 (T-Z).pdf'}),\n",
              " Document(page_content='Resources\\nBOOKS\\nD’Alonzo, T. L., O.D. Your Eyes! A Comprehensive Look at the\\nUnderstanding and Treatment of Vision Problems. Clifton\\nHeights, PA: Avanti, 1992.\\nNewell, Frank W. Ophthalmology: Principles and Concepts.\\n8th ed. St. Louis: Mosby, 1996.\\nORGANIZATIONS\\nAmerican Academy of Ophthalmology. 655 Beach Street, P.O.\\nBox 7424, San Francisco, CA 94120-7424. <http://www.eyenet.org>.\\nAmerican Optometric Association. 243 North Lindbergh Blvd.,\\nSt. Louis, MO 63141. (314) 991-4100. <http://www.aoanet.org>.\\nLorraine Steefel, RN\\nAmebiasis\\nDefinition\\nAmebiasis is an infectious disease caused by a para-\\nsitic one-celled microorganism (protozoan) called Enta-\\nmoeba histolytica . Persons with amebiasis may experi-\\nence a wide range of symptoms, including diarrhea ,\\nfever , and cramps. The disease may also affect the\\nintestines, liver, or other parts of the body.\\nDescription\\nAmebiasis, also known as amebic dysentery, is one', metadata={'page': 156, 'source': '/content/drive/MyDrive/docs/Gale Encyclopedia of Medicine Vol. 1 (A-B).pdf'})]"
            ]
          },
          "metadata": {},
          "execution_count": 26
        }
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "### Chain"
      ],
      "metadata": {
        "id": "dDybbpao-B1_"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "memory = ConversationBufferMemory()\n",
        "\n",
        "\n",
        "class QARetrievalChain:\n",
        "    def __init__(self, *, retriever, temperature=0, chain_type='stuff', memory=None):\n",
        "        self.retriever = retriever\n",
        "        self.temperature = temperature\n",
        "        self.chain_type = chain_type\n",
        "        self.memory = memory\n",
        "\n",
        "        self.llm = ChatOpenAI(model_name=\"gpt-3.5-turbo\", temperature=self.temperature)\n",
        "\n",
        "        self.chain = RetrievalQA.from_chain_type(llm=self.llm,\n",
        "                                                 retriever=self.retriever,\n",
        "                                                 chain_type=self.chain_type,\n",
        "                                                 memory=self.memory)\n",
        "\n",
        "    def __call__(self, query, *args, **kwargs):\n",
        "        response = self.chain.run(query)\n",
        "        return response\n"
      ],
      "metadata": {
        "id": "4x-s-iDlxWuo"
      },
      "execution_count": 42,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "chain = QARetrievalChain(retriever=retriever, memory=memory)"
      ],
      "metadata": {
        "id": "ZGOCYlWu0rnE"
      },
      "execution_count": 43,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "source": [
        "#### Testing QA chain"
      ],
      "metadata": {
        "id": "BzOd46RE-HYi"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "for q in [query1, query2, query3, query4]:\n",
        "  response = chain(q)\n",
        "  print(textwrap.fill(response, width=100))\n",
        "  print(\"-\"*20)"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "D0wAmjTIxxAA",
        "outputId": "d57c3adf-7be6-4ee4-a73e-4f03fe07376c"
      },
      "execution_count": 29,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Diabetes is a chronic disease that affects the body's ability to regulate blood sugar levels. There\n",
            "are two main types of diabetes: Type 1 and Type 2. Type 1 diabetes is usually diagnosed in childhood\n",
            "and occurs when the body does not produce enough insulin. Type 2 diabetes is more common and\n",
            "typically develops in adulthood, often in individuals who are overweight and do not exercise\n",
            "regularly. In Type 2 diabetes, the body either does not produce enough insulin or does not use it\n",
            "effectively. Treatment for diabetes involves managing blood sugar levels through diet, exercise,\n",
            "medication, and sometimes insulin injections.\n",
            "--------------------\n",
            "I'm sorry, but I don't have any information about a medication called \"amoksisilyn.\" It's possible\n",
            "that you may have misspelled the name or it could be a brand name specific to a certain country. If\n",
            "you can provide more accurate information or clarify the name, I may be able to assist you further.\n",
            "--------------------\n",
            "من نمی‌دانم.\n",
            "--------------------\n",
            "من نیستم پزشک، اما برخی از قرص‌های معده درد معمولاً شامل ضد اسیدها مانند آنتاگونیست‌های گیرنده H2 و\n",
            "مهارکننده‌های پمپ پروتون می‌شوند. این داروها می‌توانند به کاهش ترشح اسید معده کمک کنند و درمان درد\n",
            "معده را تسهیل کنند. با این حال، بهتر است با پزشک خود مشورت کنید تا بهترین قرص برای شما را تعیین کند.\n",
            "--------------------\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "response = chain(\"دیابت چیست؟\")\n",
        "print(textwrap.fill(response, width=100))"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "7B4-eB6gyMPm",
        "outputId": "a72ffde7-3148-41ff-bc14-df872e8882fd"
      },
      "execution_count": 41,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            " Diabetes is a chronic condition characterized by high levels of sugar in the blood. It is caused by\n",
            "the body's inability to produce or use insulin properly.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "q = \"داروی cyclosporine برای چه چیزی خوبه و عوارض مصرفش چی هست؟\""
      ],
      "metadata": {
        "id": "KZTfaaC11B_9"
      },
      "execution_count": 46,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "response = chain(q)\n",
        "print(textwrap.fill(response, width=100))"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ZKnM7aNj0EJi",
        "outputId": "203815c5-c7f3-478f-c3a2-beca0e201153"
      },
      "execution_count": 47,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "داروی سیکلوسپورین برای پیشگیری از رد شدن اعضای پیوندی در تراشهای اعضای داخلی استفاده می شود. همچنین\n",
            "برای درمان برخی از بیماری های التهابی مانند آرتریت روماتوئید و پسوریازیس نیز استفاده می شود.   عوارض\n",
            "جانبی ممکن از مصرف سیکلوسپورین شامل افزایش خطر عفونت، افزایش فشار خون، افزایش سطح قند خون، اختلالات\n",
            "کلیوی، تغییرات در پوست و مو، تغییرات در شکل بدن و افزایش خطر سرطان می باشد. همچنین ممکن است عوارض\n",
            "دیگری نیز وجود داشته باشد. برای اطلاعات دقیقتر و جزئیات بیشتر، بهتر است با پزشک خود مشورت کنید.\n"
          ]
        }
      ]
    }
  ]
}