NER_biomedical_with_stanza_and_summarization.ipynb

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      "cell_type": "markdown",
      "source": [
        "# Biomedical NER Summarization\n",
        "Medical entity detection (NER) is performed using Stanza, a language analysis tool. However, current NLP models lack fine-tuning for clinical entities like diseases and treatments."
      ],
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        "id": "3R_y77yV-cXI"
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        "\n",
        "\n",
        "| Code Credits | Link |\n",
        "| ----------- | ---- |\n",
        "| 🎉 Repository | [![GitHub Repository](https://img.shields.io/github/stars/machinelearnear/asr-restore-punctuation-summarization-biomedical-ehr?style=social)](https://github.com/machinelearnear/asr-restore-punctuation-summarization-biomedical-ehr) |\n",
        "| Original Colab | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/machinelearnear/asr-restore-punctuation-summarization-biomedical-ehr/blob/main/2_biomedical_ner_summarization.ipynb) |\n",
        "| 🔥 Discover More Colab Notebooks | [![GitHub Repository](https://img.shields.io/badge/GitHub-Repository-black?style=flat-square&logo=github)](https://github.com/R3gm/InsightSolver-Colab/) |"
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      "id": "dBJQkTkENQzF"
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    {
      "cell_type": "code",
      "source": [
        "!pip -q install stanza transformers"
      ],
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    {
      "cell_type": "markdown",
      "source": [
        "* data"
      ],
      "metadata": {
        "id": "QjvodBDzOLi8"
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      "id": "QjvodBDzOLi8"
    },
    {
      "cell_type": "code",
      "source": [
        "!mkdir /content/transcripts"
      ],
      "metadata": {
        "id": "T2wr4xudNSSB"
      },
      "id": "T2wr4xudNSSB",
      "execution_count": null,
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    {
      "cell_type": "code",
      "source": [
        "%%writefile transcripts/transcribed_speech_w_corrected_punctuation.txt\n",
        "Estamos con Marcelo Ferre. es gastro enterólogo. Cómo le va a doctor? buenas noches. Unasa ver, hoy charlaba con nuestros compañeros de trabajo y decía: no, pero murió de un cáncer y había otra enfermedad previa. y cómo es estocuéntenos La enfermedad de Croncque? esla enfermedad de Cron, correcto, Fernando? La enfermedad de Cron es una enfermedad inflamatoria del intestino sque entra dentro del grupo de las enfermedades inflamatorias intestinales, que son enfermedades crónicas, son autoinmunes, tienen una base genética, Son raras en el sentido del diagnóstico, Son poco frecuentes. hay pacientes en todo el país empacientes con esta enfermedad, nada más, nada más en todo el país, o al menos diagnosticados, Se diagnosticado y conocido, sicon algún seguimiento por parte de sus médicos. Uno cada chabitantes puede tener esta enfermedad, aunque no la diagnostiquemos tan frecuentemente y en realidadcuesta diagnosticarla en el sentido al no verla y al no estar en contacto con ellos. el diagnóstico es de difícil acceso. Eldoctor, cuéntenos, por ejemplo, esa imagen que estamos observando nosotrosaimagen completa. por favor dire: vamos a agradecer porqe Eldoctor, vamos a utilizar una cuestión didáctica- Esto es un video que nosotros bajamos de las redes, como para entender cuálesporahí Estamos viendo el aparato digestio correcto. En ese aparato digestivo, La lupa se está posando en dónde, en el intestino delgado, yahí va hacía el grueso. ahí va ahacía el gruesoeesta enfermedad se manifiesta en el grueso, en el delgado o en ambos enambos, desde la boca alano aopor eso las complicaciones tremendas porlas complicaciones que tiene la enfermedad cuando no se le diagnosticuae y no se la atrata. Esta enfermedad es mortal. en realidad es una enfermedad crónica y, como todas las enfermedades crónicas, Yo se la comparo con una diabetes, por ejemploes una enfermedad que puede terminar siendo mortal, pero si no se la controla primero, si no se la diagnostica, no se la controla y no tiene un seguimiento. Yo puedo intuir que tengo la enfermedad, debien digo de cron. por qué síntomas? lossíntomas más comunes, generalmente gente entre taños, esla edad del debut y tienen dolor abdominal. Pueden tener diarrea, Pueden tener fiebre, Pueden tener algún sangrado intestinal, pero a su vez tienen manifestaciones extraintestinales, como pueden ser dolores articulares. Es decir, es una enfermedad sistémica. Es una enfermedad que no solamente puede afectar el intestino delgado, Quees MsU, parte más frecuente, lugar que lo afecta. puede afectar el colón, pero también hay enfermedad de crón, de estómago, de sófago. Son más raras. dentro de la rareza de la propia enfermedad, Estas también son más raras Las localizacione. nosotrosentendemos que en estos espacios, lo que vemos hacer es no llenar de miedo, sino que instruir a través de la palabra de UtDsye Los profesionales, de cómo no puede estar advertido esto? porque, por ejemplo, si tengo diarrea esta noche, no significa que estoy enfermo para itimatología. puede responder un montón de cosas. Me comió un lechón y me cayó mal. pero lo que te quiero decir des estos elementos qsonaquellos que se conjugan para establecer un primer diagnóstico, Una aproximación yenel caso de Hendler Aél le demandó como trebarracuatro años para diagnosticarla, porque son difíciles de diagnosticar. al verse poco, son difíciles de diagnosticar. todo depende por donde uno vaya a consultar. Si vos me dices, yo voy con estos síntomas que acabamos de hablar a un médico clínico Por ahí es más gamodifícil para el clínico que para un gastro enterólogo, que las vemos más. Pero no significa que el clínico no las pueda diagnosticar. También las puede diagnosticalguna preguntaesta enfermedad podemos decir que decanta en el cáncer, que luego termina con la vida de genre o no necesariamente una cosa vaatada a la otra? no necesariamente. La enfermedad de crón es una enfermedad, repito, crónica, autinmune, que, si tiene un seguimiento y tiene un tratamiento, no debería terminar en un cancertres patas del tratamiento que usted, por ejemplo, me diagnosticaría a mí. si usted dice, mireidalgo, usted tiene o padece esta patología, tres patas del tratamiento enel tratamiento básicamente tiene que haber un tratamiento psicológicoporque Ese paciente tiene que tener una contención, Tiene que tener un seguimiento y tiene que entender de que esta enfermedad la puede llevar hasta el final de sus días y morir de cualquier otra cosa, menos de a enfermedad de Crom. es muy importante el enfoque y el apoyo psicológico. después el tratamiento médico. hoy endía Hay tratamiento farmacológico, Un tratamiento farmacológico con anticuerpos monoclonales. Es un tratamiento realmente que hoy lo curre en todas las obras sociales. Es decir: tiene tratamiento, no tiene cura, tiene trataiteneso cambia los hábitos de alimentación, También los hábitos de alimentación. También estos pacientes tienen una dieta a seguir, una dieta más conveniente, Una dieta saludablerica en fibras, con un cuidado especial del intestino. No es una dieta que no la pueda hacer, o sea no es algo extraordinario. si vienes una enfermedad rara, cuando se detecta, se la puede tratar. Dctor, le ha tocado diagnosticar sísss. claro, No son muchos los pacientes que hahy el mendoza menos site imagina que a nivel país hay ade, los que están documentados, estadificados y demás. es poco frecuente. usted ha podido llevar adelante buenos tratamientos sitenés buenos resultados. por qué me habloó el tratamiento psicológico? Porque es una parte muy importante del paciéntte. Todas las enfermedades inflamatorias del intestino tienen que tener un acompañamiento psicológico, porque están influenciando. Se considera quel intestino Es el segundo cerebro y tiene comunicación con nuestro primer cerebro, que es el que la geneque todos conocemoshabitualmente exactamente, y de la armonía de los dos cerebros, El resultado también del seguimiento deestresfastidios, ira, cibilidad, alibrmentaciónmacedentaría, mostavaquismo, alcolismo. bueno, todo lo que te puedas imaginar agrede y tiene sus consecuencias. Doctorcomo mensaje final, No hay que temerles estas cosas, sino que hay que enfrentarlas y tratarlas totalmente. Estos pacientes tienen un seguimiento, tienen un tratamiento, y no es sinónimo ypara tranquilidad de todos estos pacientes que pueden tener o nos pueden estar escuchando. No es sinónimo que van a padecer un cáncer deintestino, ni mucho menos tienen exactamente estos pacientes Las mismas posibilidades de hacer un cáncer de colón que cualquier otro Paciente, siempre y cuando estén en tratamiento y en seguimiento. rhasido Umuy Amabl, gracias por su tiempo. buenas noches."
      ],
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    {
      "cell_type": "markdown",
      "id": "47d4231e-aefd-439a-83df-3dbbab9f30ec",
      "metadata": {
        "id": "47d4231e-aefd-439a-83df-3dbbab9f30ec"
      },
      "source": [
        "# Detect medical entities from transcribed speech"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "efbc0a00-7696-4cf7-a167-270d112dd532",
      "metadata": {
        "id": "efbc0a00-7696-4cf7-a167-270d112dd532"
      },
      "outputs": [],
      "source": [
        "input_text = open('transcripts/transcribed_speech_w_corrected_punctuation.txt','r').readlines()[0]"
      ]
    },
    {
      "cell_type": "markdown",
      "id": "0c3cd15a-e205-402a-939d-7018d757dbe9",
      "metadata": {
        "tags": [],
        "id": "0c3cd15a-e205-402a-939d-7018d757dbe9"
      },
      "source": [
        "## Use `stanza-nlp`\n",
        "- https://stanfordnlp.github.io/stanza/\n",
        "- https://stanfordnlp.github.io/stanza/available_biomed_models.html\n",
        "- https://stanfordnlp.github.io/stanza/biomed_model_usage.html"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "dda4e5f8-59d5-4508-ae38-27bcc1f99671",
      "metadata": {
        "id": "dda4e5f8-59d5-4508-ae38-27bcc1f99671"
      },
      "outputs": [],
      "source": [
        "import stanza"
      ]
    },
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            "INFO:stanza:Downloading these customized packages for language: en (English)...\n",
            "=============================\n",
            "| Processor       | Package |\n",
            "-----------------------------\n",
            "| tokenize        | mimic   |\n",
            "| pos             | mimic   |\n",
            "| lemma           | mimic   |\n",
            "| depparse        | mimic   |\n",
            "| ner             | i2b2    |\n",
            "| backward_charlm | mimic   |\n",
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            "| forward_charlm  | mimic   |\n",
            "=============================\n",
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              "Downloading https://huggingface.co/stanfordnlp/stanza-en/resolve/v1.5.0/models/depparse/mimic.pt:   0%|       …"
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          "output_type": "display_data",
          "data": {
            "text/plain": [
              "Downloading https://huggingface.co/stanfordnlp/stanza-en/resolve/v1.5.0/models/ner/i2b2.pt:   0%|          | 0…"
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        {
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          "data": {
            "text/plain": [
              "Downloading https://huggingface.co/stanfordnlp/stanza-en/resolve/v1.5.0/models/backward_charlm/mimic.pt:   0%|…"
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            "text/plain": [
              "Downloading https://huggingface.co/stanfordnlp/stanza-en/resolve/v1.5.0/models/pretrain/mimic.pt:   0%|       …"
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              "Downloading https://huggingface.co/stanfordnlp/stanza-en/resolve/v1.5.0/models/forward_charlm/mimic.pt:   0%| …"
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        {
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          "text": [
            "INFO:stanza:Finished downloading models and saved to /root/stanza_resources.\n",
            "INFO:stanza:Checking for updates to resources.json in case models have been updated.  Note: this behavior can be turned off with download_method=None or download_method=DownloadMethod.REUSE_RESOURCES\n"
          ]
        },
        {
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          "data": {
            "text/plain": [
              "Downloading https://raw.githubusercontent.com/stanfordnlp/stanza-resources/main/resources_1.5.0.json:   0%|   …"
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          },
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        },
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "INFO:stanza:Loading these models for language: en (English):\n",
            "=======================\n",
            "| Processor | Package |\n",
            "-----------------------\n",
            "| tokenize  | mimic   |\n",
            "| pos       | mimic   |\n",
            "| lemma     | mimic   |\n",
            "| depparse  | mimic   |\n",
            "| ner       | i2b2    |\n",
            "=======================\n",
            "\n",
            "INFO:stanza:Using device: cpu\n",
            "INFO:stanza:Loading: tokenize\n",
            "INFO:stanza:Loading: pos\n",
            "INFO:stanza:Loading: lemma\n",
            "INFO:stanza:Loading: depparse\n",
            "INFO:stanza:Loading: ner\n",
            "INFO:stanza:Done loading processors!\n"
          ]
        }
      ],
      "source": [
        "# download and initialize a mimic pipeline with an i2b2 NER model\n",
        "stanza.download('en', package='mimic', processors={'ner': 'i2b2'})\n",
        "nlp = stanza.Pipeline('en', package='mimic', processors={'ner': 'i2b2'})"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "be3ec37f-869c-4fd1-bdd6-a47b4adf457a",
      "metadata": {
        "id": "be3ec37f-869c-4fd1-bdd6-a47b4adf457a",
        "outputId": "fb415b03-19e6-405a-9c6d-9aadb0d51a11",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "previa\tPROBLEM\n",
            "intestinales\tPROBLEM\n",
            "Eldoctor\tTEST\n",
            "esa\tTREATMENT\n",
            "una diabetes\tPROBLEM\n",
            "qué síntomas\tPROBLEM\n",
            "lossíntomas\tTEST\n",
            "a su vez tienen manifestaciones extraintestinales\tTREATMENT\n",
            "También\tTREATMENT\n",
            "necesariamente\tPROBLEM\n",
            "cibilidad\tTREATMENT\n",
            "alibrmentaciónmacedentaría\tTREATMENT\n",
            "mostavaquismo\tTREATMENT\n",
            "alcolismo\tTREATMENT\n"
          ]
        }
      ],
      "source": [
        "# annotate clinical text\n",
        "doc = nlp(input_text)\n",
        "# print out all entities\n",
        "for ent in doc.entities:\n",
        "    print(f'{ent.text}\\t{ent.type}')"
      ]
    },
    {
      "cell_type": "markdown",
      "id": "a826affe-307a-4fcf-bab0-f2c24252c6e9",
      "metadata": {
        "id": "a826affe-307a-4fcf-bab0-f2c24252c6e9"
      },
      "source": [
        "## Summarization with Hugging Face Transformers"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "56178d30-10e7-4530-9971-ebd616fc73a4",
      "metadata": {
        "id": "56178d30-10e7-4530-9971-ebd616fc73a4"
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      "outputs": [],
      "source": [
        "# model_name = \"google/pegasus-large\"\n",
        "model_name = \"google/pegasus-xsum\"\n",
        "# model_name = \"csebuetnlp/mT5_multilingual_XLSum\"\n",
        "# model_name = \"sshleifer/distilbart-cnn-12-6\"\n",
        "# model_name = 'ELiRF/NASES'"
      ]
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      "outputs": [
        {
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          "data": {
            "text/plain": [
              "Downloading (…)lve/main/config.json:   0%|          | 0.00/1.39k [00:00<?, ?B/s]"
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          "data": {
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              "Downloading pytorch_model.bin:   0%|          | 0.00/2.28G [00:00<?, ?B/s]"
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        {
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          "data": {
            "text/plain": [
              "Downloading (…)neration_config.json:   0%|          | 0.00/259 [00:00<?, ?B/s]"
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              "Downloading (…)okenizer_config.json:   0%|          | 0.00/87.0 [00:00<?, ?B/s]"
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              "Downloading (…)ve/main/spiece.model:   0%|          | 0.00/1.91M [00:00<?, ?B/s]"
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        {
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          "data": {
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              "Downloading (…)/main/tokenizer.json:   0%|          | 0.00/3.52M [00:00<?, ?B/s]"
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        "from transformers import pipeline\n",
        "pipe = pipeline(model=model_name)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "c124c601-512e-4e01-8746-520bc960eac4",
      "metadata": {
        "id": "c124c601-512e-4e01-8746-520bc960eac4"
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      "source": [
        "summary = pipe(input_text,truncation=True)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "id": "2ba0705e-e432-434b-a681-52be9b46eb8c",
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        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "'La enfermedad de Cron es una enfermedad inflamatoria del intestino sque entra dentro del grupo de las enfermedades inflamatorias intestinales.'"
            ],
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          "execution_count": 17
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