2674 lines (2673 with data), 168.3 kB

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "36f07a16",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[nltk_data] Error loading punkt: <urlopen error [SSL:\n",
      "[nltk_data]     CERTIFICATE_VERIFY_FAILED] certificate verify failed:\n",
      "[nltk_data]     unable to get local issuer certificate (_ssl.c:1131)>\n",
      "[nltk_data] Error loading stopwords: <urlopen error [SSL:\n",
      "[nltk_data]     CERTIFICATE_VERIFY_FAILED] certificate verify failed:\n",
      "[nltk_data]     unable to get local issuer certificate (_ssl.c:1131)>\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "sys.path.append('../scripts')\n",
    "from predict import NER"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "0343fbb3",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Model provided:  Bidirectional LSTM Model with single LSTM layer\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2023-04-10 10:34:04.285190: W tensorflow/core/platform/profile_utils/cpu_utils.cc:128] Failed to get CPU frequency: 0 Hz\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1/1 [==============================] - 0s 422ms/step\n",
      "Predicted Named Entities:\n",
      "57: Age\n",
      "year: Age\n",
      "old: Age\n",
      "man: Sex\n",
      "presented: Nonbiological_location\n",
      "emergency: Nonbiological_location\n",
      "department: Duration\n",
      "2: Duration\n",
      "day: O\n",
      "history: Sign_symptom\n",
      "worsening: Sign_symptom\n",
      "shortness: Biological_structure\n",
      "breath: Sign_symptom\n",
      "chest: History\n",
      "pain: History\n",
      "reported: History\n",
      "recent: History\n",
      "travel: History\n",
      "sick: History\n",
      "contacts: History\n",
      "medical: History\n",
      "history: History\n",
      "significant: History\n",
      "hypertension: History\n",
      "dyslipidemia: History\n",
      "type: History\n",
      "2: Sign_symptom\n",
      "diabetes: History\n",
      "mellitus: Diagnostic_procedure\n",
      "examination: O\n",
      "tachycardic: Detailed_description\n",
      "tachypneic: Detailed_description\n",
      "oxygen: Biological_structure\n",
      "saturation: Diagnostic_procedure\n",
      "88: Detailed_description\n",
      "room: O\n",
      "air: Distance\n",
      "chest: Distance\n",
      "radiography: O\n",
      "revealed: Distance\n",
      "bilateral: O\n",
      "opacities: O\n",
      "consistent: O\n",
      "pulmonary: Detailed_description\n",
      "edema: Distance\n",
      "patient: Distance\n",
      "admitted: Distance\n",
      "intensive: Medication\n",
      "care: Therapeutic_procedure\n",
      "unit: Medication\n",
      "management: Dosage\n",
      "acute: Dosage\n",
      "decompensated: Dosage\n",
      "heart: Clinical_event\n",
      "failure: Other_entity\n",
      "started: Nonbiological_location\n",
      "intravenous: Date\n",
      "diuretics: Date\n",
      "inotropic: O\n",
      "support: O\n",
      "dobutamine: O\n",
      "next: O\n",
      "several: O\n",
      "days: O\n",
      "symptoms: O\n",
      "improved: O\n",
      "discharged: O\n",
      "home: O\n",
      "instructions: O\n",
      "follow: O\n",
      "primary: O\n",
      "care: O\n",
      "provider: O\n",
      "1: O\n",
      "week: O\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<span class=\"tex2jax_ignore\"><div class=\"entities\" style=\"line-height: 2.5; direction: ltr\">A \n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    57\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    year\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    old\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    man\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sex</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    presented\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    emergency\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    department\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " with a \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       "-day \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    worsening\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    shortness\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    breath\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pain\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". He \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    reported\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " no \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    recent\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    travel\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " or \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    sick\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    contacts\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". His \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    medical\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    significant\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    hypertension\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    dyslipidemia\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", and \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    type\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diabetes\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    mellitus\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       ". On examination, he was \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachycardic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachypneic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       ", with \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    oxygen\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    saturation\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    88\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       "% on room \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    air\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       ". \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    Chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       " radiography \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    revealed\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       " bilateral opacities consistent with \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pulmonary\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    edema\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       ". The \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    patient\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    admitted\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intensive\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e6ccb2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    care\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Therapeutic_procedure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    unit\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    management\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    acute\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    decompensated\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #77c5d5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    heart\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Clinical_event</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #d5f5e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    failure\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Other_entity</span>\n",
       "</mark>\n",
       ". He was \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    started\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " on \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intravenous\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diuretics\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       " and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.</div></span>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "NER(\"model_1\",\n",
    "        \"A 57-year-old man presented to the emergency department with a 2-day history of worsening shortness of breath and chest pain. He reported no recent travel or sick contacts. His medical history was significant for hypertension, dyslipidemia, and type 2 diabetes mellitus. On examination, he was tachycardic and tachypneic, with oxygen saturation of 88% on room air. Chest radiography revealed bilateral opacities consistent with pulmonary edema. The patient was admitted to the intensive care unit for management of acute decompensated heart failure. He was started on intravenous diuretics and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d8b3b880",
   "metadata": {},
   "source": [
    "## MODEL 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "27ca7748",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Model provided:  Bidirectional LSTM Model with two LSTM layers and one Hidden Dense Layer\n",
      "1/1 [==============================] - 1s 651ms/step\n",
      "Predicted Named Entities:\n",
      "57: Age\n",
      "year: Age\n",
      "old: Age\n",
      "man: Sex\n",
      "presented: Nonbiological_location\n",
      "emergency: Nonbiological_location\n",
      "department: History\n",
      "2: Date\n",
      "day: O\n",
      "history: Sign_symptom\n",
      "worsening: Sign_symptom\n",
      "shortness: Biological_structure\n",
      "breath: Sign_symptom\n",
      "chest: O\n",
      "pain: Nonbiological_location\n",
      "reported: History\n",
      "recent: History\n",
      "travel: History\n",
      "sick: History\n",
      "contacts: History\n",
      "medical: Nonbiological_location\n",
      "history: Nonbiological_location\n",
      "significant: History\n",
      "hypertension: Nonbiological_location\n",
      "dyslipidemia: Nonbiological_location\n",
      "type: Nonbiological_location\n",
      "2: Biological_structure\n",
      "diabetes: Diagnostic_procedure\n",
      "mellitus: Diagnostic_procedure\n",
      "examination: Lab_value\n",
      "tachycardic: Detailed_description\n",
      "tachypneic: Detailed_description\n",
      "oxygen: Biological_structure\n",
      "saturation: Diagnostic_procedure\n",
      "88: Detailed_description\n",
      "room: O\n",
      "air: Biological_structure\n",
      "chest: Sign_symptom\n",
      "radiography: O\n",
      "revealed: Biological_structure\n",
      "bilateral: Biological_structure\n",
      "opacities: Biological_structure\n",
      "consistent: O\n",
      "pulmonary: Detailed_description\n",
      "edema: Distance\n",
      "patient: Therapeutic_procedure\n",
      "admitted: Medication\n",
      "intensive: Medication\n",
      "care: Medication\n",
      "unit: Medication\n",
      "management: Dosage\n",
      "acute: Dosage\n",
      "decompensated: History\n",
      "heart: Date\n",
      "failure: Nonbiological_location\n",
      "started: History\n",
      "intravenous: History\n",
      "diuretics: Duration\n",
      "inotropic: O\n",
      "support: O\n",
      "dobutamine: O\n",
      "next: O\n",
      "several: O\n",
      "days: O\n",
      "symptoms: O\n",
      "improved: O\n",
      "discharged: O\n",
      "home: O\n",
      "instructions: O\n",
      "follow: O\n",
      "primary: O\n",
      "care: O\n",
      "provider: O\n",
      "1: O\n",
      "week: O\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<span class=\"tex2jax_ignore\"><div class=\"entities\" style=\"line-height: 2.5; direction: ltr\">A \n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    57\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    year\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    old\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    man\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sex</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    presented\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    emergency\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    department\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " with a \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       "-day \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    worsening\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    shortness\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    breath\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " and chest \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pain\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       ". He \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    reported\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " no \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    recent\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    travel\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " or \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    sick\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    contacts\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". His \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    medical\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    significant\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    hypertension\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       ", \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    dyslipidemia\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       ", and \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    type\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diabetes\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    mellitus\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       ". On \n",
       "<mark class=\"entity\" style=\"background: #f4b3c2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    examination\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Lab_value</span>\n",
       "</mark>\n",
       ", he was \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachycardic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachypneic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       ", with \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    oxygen\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    saturation\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    88\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       "% on room \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    air\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       ". \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    Chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " radiography \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    revealed\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    bilateral\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    opacities\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " consistent with \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pulmonary\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    edema\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       ". The \n",
       "<mark class=\"entity\" style=\"background: #e6ccb2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    patient\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Therapeutic_procedure</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    admitted\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intensive\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    care\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    unit\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    management\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    acute\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    decompensated\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    heart\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    failure\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       ". He was \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    started\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " on \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intravenous\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diuretics\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.</div></span>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "NER(\"model_2\",\n",
    "        \"A 57-year-old man presented to the emergency department with a 2-day history of worsening shortness of breath and chest pain. He reported no recent travel or sick contacts. His medical history was significant for hypertension, dyslipidemia, and type 2 diabetes mellitus. On examination, he was tachycardic and tachypneic, with oxygen saturation of 88% on room air. Chest radiography revealed bilateral opacities consistent with pulmonary edema. The patient was admitted to the intensive care unit for management of acute decompensated heart failure. He was started on intravenous diuretics and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d0f9b03d",
   "metadata": {},
   "source": [
    "## MODEL 3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "e3fb5de6",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Model provided:  Bidirectional LSTM model with BioWordVecEmbedding Layers followed two LSTM layers and one Hidden Dense Layer\n",
      "1/1 [==============================] - 1s 616ms/step\n",
      "Predicted Named Entities:\n",
      "57: Age\n",
      "year: Age\n",
      "old: Age\n",
      "man: Sex\n",
      "presented: Nonbiological_location\n",
      "emergency: Nonbiological_location\n",
      "department: Date\n",
      "2: Duration\n",
      "day: O\n",
      "history: Sign_symptom\n",
      "worsening: Sign_symptom\n",
      "shortness: Biological_structure\n",
      "breath: Sign_symptom\n",
      "chest: O\n",
      "pain: History\n",
      "reported: History\n",
      "recent: History\n",
      "travel: O\n",
      "sick: History\n",
      "contacts: History\n",
      "medical: History\n",
      "history: History\n",
      "significant: History\n",
      "hypertension: History\n",
      "dyslipidemia: History\n",
      "type: O\n",
      "2: Sign_symptom\n",
      "diabetes: Diagnostic_procedure\n",
      "mellitus: Diagnostic_procedure\n",
      "examination: Date\n",
      "tachycardic: History\n",
      "tachypneic: Detailed_description\n",
      "oxygen: Biological_structure\n",
      "saturation: Diagnostic_procedure\n",
      "88: Detailed_description\n",
      "room: O\n",
      "air: Distance\n",
      "chest: Sign_symptom\n",
      "radiography: O\n",
      "revealed: Nonbiological_location\n",
      "bilateral: Nonbiological_location\n",
      "opacities: Nonbiological_location\n",
      "consistent: O\n",
      "pulmonary: Detailed_description\n",
      "edema: Distance\n",
      "patient: Distance\n",
      "admitted: Administration\n",
      "intensive: Medication\n",
      "care: Medication\n",
      "unit: Medication\n",
      "management: O\n",
      "acute: Clinical_event\n",
      "decompensated: Nonbiological_location\n",
      "heart: Clinical_event\n",
      "failure: Nonbiological_location\n",
      "started: Nonbiological_location\n",
      "intravenous: Date\n",
      "diuretics: Duration\n",
      "inotropic: O\n",
      "support: O\n",
      "dobutamine: O\n",
      "next: O\n",
      "several: O\n",
      "days: O\n",
      "symptoms: O\n",
      "improved: O\n",
      "discharged: O\n",
      "home: O\n",
      "instructions: O\n",
      "follow: O\n",
      "primary: O\n",
      "care: O\n",
      "provider: O\n",
      "1: O\n",
      "week: O\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<span class=\"tex2jax_ignore\"><div class=\"entities\" style=\"line-height: 2.5; direction: ltr\">A \n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    57\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    year\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    old\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    man\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sex</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    presented\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    emergency\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    department\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       " with a \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       "-day \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    worsening\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    shortness\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    breath\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " and chest \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pain\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". He \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    reported\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " no \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    recent\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " travel or \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    sick\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    contacts\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". His \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    medical\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    significant\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    hypertension\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    dyslipidemia\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", and type \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diabetes\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    mellitus\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       ". On \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    examination\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       ", he was \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachycardic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachypneic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       ", with \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    oxygen\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    saturation\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    88\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       "% on room \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    air\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       ". \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    Chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " radiography \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    revealed\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    bilateral\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    opacities\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " consistent with \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pulmonary\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    edema\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       ". The \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    patient\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    admitted\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Administration</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intensive\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    care\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    unit\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " for management of \n",
       "<mark class=\"entity\" style=\"background: #77c5d5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    acute\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Clinical_event</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    decompensated\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #77c5d5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    heart\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Clinical_event</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    failure\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       ". He was \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    started\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " on \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intravenous\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diuretics\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.</div></span>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "NER(\"model_3\",\n",
    "        \"A 57-year-old man presented to the emergency department with a 2-day history of worsening shortness of breath and chest pain. He reported no recent travel or sick contacts. His medical history was significant for hypertension, dyslipidemia, and type 2 diabetes mellitus. On examination, he was tachycardic and tachypneic, with oxygen saturation of 88% on room air. Chest radiography revealed bilateral opacities consistent with pulmonary edema. The patient was admitted to the intensive care unit for management of acute decompensated heart failure. He was started on intravenous diuretics and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "839cf967",
   "metadata": {},
   "source": [
    "## MODEL 4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "16e0a82c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Model provided:  Bidirectional LSTM Model with Time Distributed Dense Layers - Single LSTM layer and Two time distributed dense layers\n",
      "1/1 [==============================] - 0s 319ms/step\n",
      "Predicted Named Entities:\n",
      "57: Age\n",
      "year: Age\n",
      "old: Age\n",
      "man: Sex\n",
      "presented: Nonbiological_location\n",
      "emergency: Nonbiological_location\n",
      "department: Date\n",
      "2: Duration\n",
      "day: History\n",
      "history: Sign_symptom\n",
      "worsening: Sign_symptom\n",
      "shortness: Sign_symptom\n",
      "breath: Sign_symptom\n",
      "chest: History\n",
      "pain: History\n",
      "reported: History\n",
      "recent: History\n",
      "travel: History\n",
      "sick: History\n",
      "contacts: History\n",
      "medical: History\n",
      "history: History\n",
      "significant: History\n",
      "hypertension: History\n",
      "dyslipidemia: History\n",
      "type: Diagnostic_procedure\n",
      "2: Biological_structure\n",
      "diabetes: Diagnostic_procedure\n",
      "mellitus: Diagnostic_procedure\n",
      "examination: Lab_value\n",
      "tachycardic: Detailed_description\n",
      "tachypneic: Detailed_description\n",
      "oxygen: Biological_structure\n",
      "saturation: Diagnostic_procedure\n",
      "88: Detailed_description\n",
      "room: O\n",
      "air: Biological_structure\n",
      "chest: O\n",
      "radiography: O\n",
      "revealed: Distance\n",
      "bilateral: Nonbiological_location\n",
      "opacities: Nonbiological_location\n",
      "consistent: O\n",
      "pulmonary: O\n",
      "edema: Medication\n",
      "patient: Medication\n",
      "admitted: Administration\n",
      "intensive: Medication\n",
      "care: Medication\n",
      "unit: Medication\n",
      "management: Dosage\n",
      "acute: Dosage\n",
      "decompensated: Nonbiological_location\n",
      "heart: Clinical_event\n",
      "failure: Medication\n",
      "started: Nonbiological_location\n",
      "intravenous: Date\n",
      "diuretics: Duration\n",
      "inotropic: O\n",
      "support: O\n",
      "dobutamine: O\n",
      "next: O\n",
      "several: O\n",
      "days: O\n",
      "symptoms: O\n",
      "improved: O\n",
      "discharged: O\n",
      "home: O\n",
      "instructions: O\n",
      "follow: O\n",
      "primary: O\n",
      "care: O\n",
      "provider: O\n",
      "1: O\n",
      "week: O\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<span class=\"tex2jax_ignore\"><div class=\"entities\" style=\"line-height: 2.5; direction: ltr\">A \n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    57\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    year\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    old\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    man\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sex</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    presented\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    emergency\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    department\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       " with a \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    day\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    worsening\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    shortness\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    breath\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pain\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". He \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    reported\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " no \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    recent\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    travel\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " or \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    sick\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    contacts\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". His \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    medical\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    significant\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    hypertension\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    dyslipidemia\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", and \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    type\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diabetes\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    mellitus\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       ". On \n",
       "<mark class=\"entity\" style=\"background: #f4b3c2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    examination\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Lab_value</span>\n",
       "</mark>\n",
       ", he was \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachycardic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachypneic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       ", with \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    oxygen\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    saturation\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    88\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       "% on room \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    air\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       ". Chest radiography \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    revealed\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    bilateral\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    opacities\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " consistent with pulmonary \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    edema\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       ". The \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    patient\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    admitted\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Administration</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intensive\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    care\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    unit\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    management\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    acute\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    decompensated\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #77c5d5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    heart\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Clinical_event</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    failure\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       ". He was \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    started\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " on \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intravenous\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diuretics\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.</div></span>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "NER(\"model_4\",\n",
    "        \"A 57-year-old man presented to the emergency department with a 2-day history of worsening shortness of breath and chest pain. He reported no recent travel or sick contacts. His medical history was significant for hypertension, dyslipidemia, and type 2 diabetes mellitus. On examination, he was tachycardic and tachypneic, with oxygen saturation of 88% on room air. Chest radiography revealed bilateral opacities consistent with pulmonary edema. The patient was admitted to the intensive care unit for management of acute decompensated heart failure. He was started on intravenous diuretics and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d4bf4681",
   "metadata": {},
   "source": [
    "## MODEL 5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "b5c6fa06",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Model provided:  Bidirectional LSTM Model with two LSTM layers and one Hidden Dense Layer\n",
      "WARNING:tensorflow:5 out of the last 5 calls to <function Model.make_predict_function.<locals>.predict_function at 0x2eb898310> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.\n",
      "1/1 [==============================] - 0s 337ms/step\n",
      "Predicted Named Entities:\n",
      "57: Age\n",
      "year: Age\n",
      "old: Age\n",
      "man: Sex\n",
      "presented: Nonbiological_location\n",
      "emergency: Nonbiological_location\n",
      "department: Duration\n",
      "2: Duration\n",
      "day: O\n",
      "history: Sign_symptom\n",
      "worsening: Sign_symptom\n",
      "shortness: Biological_structure\n",
      "breath: Sign_symptom\n",
      "chest: History\n",
      "pain: History\n",
      "reported: History\n",
      "recent: O\n",
      "travel: O\n",
      "sick: O\n",
      "contacts: History\n",
      "medical: History\n",
      "history: History\n",
      "significant: History\n",
      "hypertension: History\n",
      "dyslipidemia: History\n",
      "type: O\n",
      "2: O\n",
      "diabetes: Diagnostic_procedure\n",
      "mellitus: Diagnostic_procedure\n",
      "examination: Lab_value\n",
      "tachycardic: Detailed_description\n",
      "tachypneic: Detailed_description\n",
      "oxygen: Biological_structure\n",
      "saturation: Diagnostic_procedure\n",
      "88: Detailed_description\n",
      "room: O\n",
      "air: Biological_structure\n",
      "chest: Sign_symptom\n",
      "radiography: O\n",
      "revealed: Nonbiological_location\n",
      "bilateral: Nonbiological_location\n",
      "opacities: Nonbiological_location\n",
      "consistent: O\n",
      "pulmonary: Detailed_description\n",
      "edema: Therapeutic_procedure\n",
      "patient: Distance\n",
      "admitted: Administration\n",
      "intensive: Medication\n",
      "care: Medication\n",
      "unit: Medication\n",
      "management: O\n",
      "acute: O\n",
      "decompensated: Nonbiological_location\n",
      "heart: Clinical_event\n",
      "failure: O\n",
      "started: Nonbiological_location\n",
      "intravenous: Duration\n",
      "diuretics: Duration\n",
      "inotropic: O\n",
      "support: O\n",
      "dobutamine: O\n",
      "next: O\n",
      "several: O\n",
      "days: O\n",
      "symptoms: O\n",
      "improved: O\n",
      "discharged: O\n",
      "home: O\n",
      "instructions: O\n",
      "follow: O\n",
      "primary: O\n",
      "care: O\n",
      "provider: O\n",
      "1: O\n",
      "week: O\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<span class=\"tex2jax_ignore\"><div class=\"entities\" style=\"line-height: 2.5; direction: ltr\">A \n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    57\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    year\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    old\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    man\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sex</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    presented\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    emergency\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    department\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " with a \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       "-day \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    worsening\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    shortness\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    breath\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pain\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". He \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    reported\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " no recent travel or sick \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    contacts\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". His \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    medical\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    significant\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    hypertension\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    dyslipidemia\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", and type 2 \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diabetes\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    mellitus\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       ". On \n",
       "<mark class=\"entity\" style=\"background: #f4b3c2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    examination\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Lab_value</span>\n",
       "</mark>\n",
       ", he was \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachycardic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachypneic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       ", with \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    oxygen\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    saturation\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    88\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       "% on room \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    air\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       ". \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    Chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " radiography \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    revealed\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    bilateral\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    opacities\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " consistent with \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pulmonary\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e6ccb2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    edema\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Therapeutic_procedure</span>\n",
       "</mark>\n",
       ". The \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    patient\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    admitted\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Administration</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intensive\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    care\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    unit\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " for management of acute \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    decompensated\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #77c5d5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    heart\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Clinical_event</span>\n",
       "</mark>\n",
       " failure. He was \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    started\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " on \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intravenous\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diuretics\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.</div></span>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
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   ],
   "source": [
    "NER(\"model_5\",\n",
    "        \"A 57-year-old man presented to the emergency department with a 2-day history of worsening shortness of breath and chest pain. He reported no recent travel or sick contacts. His medical history was significant for hypertension, dyslipidemia, and type 2 diabetes mellitus. On examination, he was tachycardic and tachypneic, with oxygen saturation of 88% on room air. Chest radiography revealed bilateral opacities consistent with pulmonary edema. The patient was admitted to the intensive care unit for management of acute decompensated heart failure. He was started on intravenous diuretics and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fbd84584",
   "metadata": {},
   "source": [
    "## MODEL 6"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "73fb52a0",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Model provided:  Bidirectional LSTM Time Distirbuted Dense Layers and Convolutional 1D layer\n",
      "WARNING:tensorflow:6 out of the last 6 calls to <function Model.make_predict_function.<locals>.predict_function at 0x2d766ce50> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.\n",
      "1/1 [==============================] - 0s 318ms/step\n",
      "Predicted Named Entities:\n",
      "57: Age\n",
      "year: Age\n",
      "old: Age\n",
      "man: Sex\n",
      "presented: Personal_background\n",
      "emergency: Nonbiological_location\n",
      "department: Nonbiological_location\n",
      "2: Nonbiological_location\n",
      "day: History\n",
      "history: Sign_symptom\n",
      "worsening: Sign_symptom\n",
      "shortness: Biological_structure\n",
      "breath: Sign_symptom\n",
      "chest: History\n",
      "pain: History\n",
      "reported: History\n",
      "recent: History\n",
      "travel: History\n",
      "sick: History\n",
      "contacts: History\n",
      "medical: History\n",
      "history: History\n",
      "significant: History\n",
      "hypertension: History\n",
      "dyslipidemia: History\n",
      "type: Sign_symptom\n",
      "2: Sign_symptom\n",
      "diabetes: Biological_structure\n",
      "mellitus: Diagnostic_procedure\n",
      "examination: Detailed_description\n",
      "tachycardic: Detailed_description\n",
      "tachypneic: Detailed_description\n",
      "oxygen: Biological_structure\n",
      "saturation: Diagnostic_procedure\n",
      "88: Lab_value\n",
      "room: O\n",
      "air: Biological_structure\n",
      "chest: Detailed_description\n",
      "radiography: O\n",
      "revealed: Nonbiological_location\n",
      "bilateral: Nonbiological_location\n",
      "opacities: Nonbiological_location\n",
      "consistent: O\n",
      "pulmonary: Detailed_description\n",
      "edema: Detailed_description\n",
      "patient: Detailed_description\n",
      "admitted: Therapeutic_procedure\n",
      "intensive: Medication\n",
      "care: Therapeutic_procedure\n",
      "unit: Therapeutic_procedure\n",
      "management: Dosage\n",
      "acute: Dosage\n",
      "decompensated: Dosage\n",
      "heart: O\n",
      "failure: Medication\n",
      "started: Medication\n",
      "intravenous: Duration\n",
      "diuretics: Duration\n",
      "inotropic: O\n",
      "support: O\n",
      "dobutamine: O\n",
      "next: O\n",
      "several: O\n",
      "days: O\n",
      "symptoms: O\n",
      "improved: O\n",
      "discharged: O\n",
      "home: O\n",
      "instructions: O\n",
      "follow: O\n",
      "primary: O\n",
      "care: O\n",
      "provider: O\n",
      "1: O\n",
      "week: O\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<span class=\"tex2jax_ignore\"><div class=\"entities\" style=\"line-height: 2.5; direction: ltr\">A \n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    57\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    year\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    old\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    man\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sex</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #a0ced9; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    presented\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Personal_background</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    emergency\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    department\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " with a \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    day\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    worsening\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    shortness\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    breath\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pain\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". He \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    reported\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " no \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    recent\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    travel\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " or \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    sick\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    contacts\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". His \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    medical\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    significant\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    hypertension\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    dyslipidemia\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", and \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    type\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diabetes\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    mellitus\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       ". On \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    examination\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       ", he was \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachycardic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachypneic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       ", with \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    oxygen\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    saturation\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #f4b3c2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    88\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Lab_value</span>\n",
       "</mark>\n",
       "% on room \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    air\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       ". \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    Chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " radiography \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    revealed\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    bilateral\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    opacities\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " consistent with \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pulmonary\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    edema\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       ". The \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    patient\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #e6ccb2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    admitted\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Therapeutic_procedure</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intensive\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e6ccb2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    care\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Therapeutic_procedure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e6ccb2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    unit\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Therapeutic_procedure</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    management\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    acute\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #b9e8d8; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    decompensated\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Dosage</span>\n",
       "</mark>\n",
       " heart \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    failure\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       ". He was \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    started\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " on \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intravenous\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diuretics\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.</div></span>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
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    }
   ],
   "source": [
    "NER(\"model_6\",\n",
    "        \"A 57-year-old man presented to the emergency department with a 2-day history of worsening shortness of breath and chest pain. He reported no recent travel or sick contacts. His medical history was significant for hypertension, dyslipidemia, and type 2 diabetes mellitus. On examination, he was tachycardic and tachypneic, with oxygen saturation of 88% on room air. Chest radiography revealed bilateral opacities consistent with pulmonary edema. The patient was admitted to the intensive care unit for management of acute decompensated heart failure. He was started on intravenous diuretics and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e92dfa6e",
   "metadata": {},
   "source": [
    "## MODEL 7"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "21b2b199",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Model provided:  Bidirectional LSTM CRF model with BioWordVecEmbedding Layers followed two LSTM layers, Time Distirbuted Dense Layers and Convolutional 1D layer\n",
      "1/1 [==============================] - 0s 365ms/step\n",
      "Predicted Named Entities:\n",
      "57: Age\n",
      "year: Age\n",
      "old: Age\n",
      "man: Sex\n",
      "presented: Nonbiological_location\n",
      "emergency: Nonbiological_location\n",
      "department: Date\n",
      "2: Duration\n",
      "day: O\n",
      "history: Sign_symptom\n",
      "worsening: Detailed_description\n",
      "shortness: Biological_structure\n",
      "breath: Sign_symptom\n",
      "chest: History\n",
      "pain: History\n",
      "reported: History\n",
      "recent: History\n",
      "travel: History\n",
      "sick: History\n",
      "contacts: History\n",
      "medical: History\n",
      "history: History\n",
      "significant: History\n",
      "hypertension: History\n",
      "dyslipidemia: History\n",
      "type: O\n",
      "2: Sign_symptom\n",
      "diabetes: Diagnostic_procedure\n",
      "mellitus: Diagnostic_procedure\n",
      "examination: Lab_value\n",
      "tachycardic: Detailed_description\n",
      "tachypneic: Detailed_description\n",
      "oxygen: Biological_structure\n",
      "saturation: Diagnostic_procedure\n",
      "88: Detailed_description\n",
      "room: O\n",
      "air: Biological_structure\n",
      "chest: Sign_symptom\n",
      "radiography: O\n",
      "revealed: Nonbiological_location\n",
      "bilateral: Nonbiological_location\n",
      "opacities: Nonbiological_location\n",
      "consistent: O\n",
      "pulmonary: Detailed_description\n",
      "edema: Distance\n",
      "patient: History\n",
      "admitted: Detailed_description\n",
      "intensive: Medication\n",
      "care: Medication\n",
      "unit: Medication\n",
      "management: O\n",
      "acute: O\n",
      "decompensated: Nonbiological_location\n",
      "heart: Clinical_event\n",
      "failure: Nonbiological_location\n",
      "started: Nonbiological_location\n",
      "intravenous: Date\n",
      "diuretics: Duration\n",
      "inotropic: O\n",
      "support: O\n",
      "dobutamine: O\n",
      "next: O\n",
      "several: O\n",
      "days: O\n",
      "symptoms: O\n",
      "improved: O\n",
      "discharged: O\n",
      "home: O\n",
      "instructions: O\n",
      "follow: O\n",
      "primary: O\n",
      "care: O\n",
      "provider: O\n",
      "1: O\n",
      "week: O\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<span class=\"tex2jax_ignore\"><div class=\"entities\" style=\"line-height: 2.5; direction: ltr\">A \n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    57\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    year\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       "-\n",
       "<mark class=\"entity\" style=\"background: #f6c3d0; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    old\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Age</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    man\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sex</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    presented\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    emergency\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    department\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       " with a \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       "-day \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    worsening\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    shortness\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    breath\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pain\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". He \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    reported\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " no \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    recent\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    travel\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " or \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    sick\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    contacts\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ". His \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    medical\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    history\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    significant\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " for \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    hypertension\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    dyslipidemia\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       ", and type \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    2\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diabetes\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    mellitus\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       ". On \n",
       "<mark class=\"entity\" style=\"background: #f4b3c2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    examination\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Lab_value</span>\n",
       "</mark>\n",
       ", he was \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachycardic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " and \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    tachypneic\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       ", with \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    oxygen\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #c5b4e3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    saturation\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Diagnostic_procedure</span>\n",
       "</mark>\n",
       " of \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    88\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       "% on room \n",
       "<mark class=\"entity\" style=\"background: #9ddfd3; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    air\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Biological_structure</span>\n",
       "</mark>\n",
       ". \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    Chest\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Sign_symptom</span>\n",
       "</mark>\n",
       " radiography \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    revealed\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    bilateral\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    opacities\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " consistent with \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    pulmonary\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #bde0fe; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    edema\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Distance</span>\n",
       "</mark>\n",
       ". The \n",
       "<mark class=\"entity\" style=\"background: #e2f0cb; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    patient\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">History</span>\n",
       "</mark>\n",
       " was \n",
       "<mark class=\"entity\" style=\"background: #ffb347; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    admitted\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Detailed_description</span>\n",
       "</mark>\n",
       " to the \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intensive\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    care\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f9d5e5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    unit\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Medication</span>\n",
       "</mark>\n",
       " for management of acute \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    decompensated\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #77c5d5; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    heart\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Clinical_event</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    failure\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       ". He was \n",
       "<mark class=\"entity\" style=\"background: #f7a399; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    started\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Nonbiological_location</span>\n",
       "</mark>\n",
       " on \n",
       "<mark class=\"entity\" style=\"background: #f1f0d2; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    intravenous\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Date</span>\n",
       "</mark>\n",
       " \n",
       "<mark class=\"entity\" style=\"background: #ffdfba; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 1; border-radius: 0.35em;\">\n",
       "    diuretics\n",
       "    <span style=\"font-size: 0.8em; font-weight: bold; line-height: 1; border-radius: 0.35em; vertical-align: middle; margin-left: 0.5rem\">Duration</span>\n",
       "</mark>\n",
       " and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.</div></span>"
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    "NER(\"model_7\",\n",
    "        \"A 57-year-old man presented to the emergency department with a 2-day history of worsening shortness of breath and chest pain. He reported no recent travel or sick contacts. His medical history was significant for hypertension, dyslipidemia, and type 2 diabetes mellitus. On examination, he was tachycardic and tachypneic, with oxygen saturation of 88% on room air. Chest radiography revealed bilateral opacities consistent with pulmonary edema. The patient was admitted to the intensive care unit for management of acute decompensated heart failure. He was started on intravenous diuretics and inotropic support with dobutamine. Over the next several days, his symptoms improved and he was discharged to home with instructions to follow up with his primary care provider in 1 week.\")"
   ]
  },
  {
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   "id": "753f82ed",
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   "outputs": [],
   "source": []
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