Text_Exploration.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "a283bdb6-9104-425a-af5c-ecdb0dedf343",
   "metadata": {},
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "6ca9073a",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/gpfs/ysm/project/rtaylor/vs428/conda_envs/n2c2_env2/lib/python3.8/site-packages/cupy/_environment.py:437: UserWarning: \n",
      "--------------------------------------------------------------------------------\n",
      "\n",
      "  CuPy may not function correctly because multiple CuPy packages are installed\n",
      "  in your environment:\n",
      "\n",
      "    cupy, cupy-cuda111\n",
      "\n",
      "  Follow these steps to resolve this issue:\n",
      "\n",
      "    1. For all packages listed above, run the following command to remove all\n",
      "       existing CuPy installations:\n",
      "\n",
      "         $ pip uninstall <package_name>\n",
      "\n",
      "      If you previously installed CuPy via conda, also run the following:\n",
      "\n",
      "         $ conda uninstall cupy\n",
      "\n",
      "    2. Install the appropriate CuPy package.\n",
      "       Refer to the Installation Guide for detailed instructions.\n",
      "\n",
      "         https://docs.cupy.dev/en/stable/install.html\n",
      "\n",
      "--------------------------------------------------------------------------------\n",
      "\n",
      "  warnings.warn(f'''\n",
      "/gpfs/ysm/project/rtaylor/vs428/conda_envs/n2c2_env2/lib/python3.8/site-packages/cupy/_environment.py:437: UserWarning: \n",
      "--------------------------------------------------------------------------------\n",
      "\n",
      "  CuPy may not function correctly because multiple CuPy packages are installed\n",
      "  in your environment:\n",
      "\n",
      "    cupy, cupy-cuda111\n",
      "\n",
      "  Follow these steps to resolve this issue:\n",
      "\n",
      "    1. For all packages listed above, run the following command to remove all\n",
      "       existing CuPy installations:\n",
      "\n",
      "         $ pip uninstall <package_name>\n",
      "\n",
      "      If you previously installed CuPy via conda, also run the following:\n",
      "\n",
      "         $ conda uninstall cupy\n",
      "\n",
      "    2. Install the appropriate CuPy package.\n",
      "       Refer to the Installation Guide for detailed instructions.\n",
      "\n",
      "         https://docs.cupy.dev/en/stable/install.html\n",
      "\n",
      "--------------------------------------------------------------------------------\n",
      "\n",
      "  warnings.warn(f'''\n",
      "/gpfs/ysm/project/rtaylor/vs428/conda_envs/n2c2_env2/lib/python3.8/site-packages/cupy/_environment.py:437: UserWarning: \n",
      "--------------------------------------------------------------------------------\n",
      "\n",
      "  CuPy may not function correctly because multiple CuPy packages are installed\n",
      "  in your environment:\n",
      "\n",
      "    cupy, cupy-cuda111\n",
      "\n",
      "  Follow these steps to resolve this issue:\n",
      "\n",
      "    1. For all packages listed above, run the following command to remove all\n",
      "       existing CuPy installations:\n",
      "\n",
      "         $ pip uninstall <package_name>\n",
      "\n",
      "      If you previously installed CuPy via conda, also run the following:\n",
      "\n",
      "         $ conda uninstall cupy\n",
      "\n",
      "    2. Install the appropriate CuPy package.\n",
      "       Refer to the Installation Guide for detailed instructions.\n",
      "\n",
      "         https://docs.cupy.dev/en/stable/install.html\n",
      "\n",
      "--------------------------------------------------------------------------------\n",
      "\n",
      "  warnings.warn(f'''\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd \n",
    "import numpy as np\n",
    "from preprocessing.cleaning_utils import *\n",
    "from functools import partial\n",
    "import torch \n",
    "\n",
    "from datasets import load_dataset\n",
    "from datasets import Value, ClassLabel, Features, DatasetDict\n",
    "import transformers\n",
    "from transformers import AutoTokenizer, AutoModel, AutoModelForMaskedLM, AutoModelForSequenceClassification\n",
    "from transformers import DataCollatorWithPadding\n",
    "from transformers import logging\n",
    "from transformers import TrainingArguments, Trainer\n",
    "\n",
    "logging.set_verbosity_warning()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "11c4f12b-0788-4c85-ba74-4c8e5d06fbf5",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "02011b8f-4e31-403b-9d3b-3bc02c779929",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "# !python -m torch.utils.collect_env"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "7367c7f6-5b97-4b22-964a-bce4eee7e5d8",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "device(type='cpu')"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "device = torch.device(\"cuda\") if torch.cuda.is_available() else torch.device(\"cpu\")\n",
    "device"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e3e4894f-bd82-40cf-8ea5-e6e34750d070",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "82b75e6e",
   "metadata": {},
   "outputs": [],
   "source": [
    "mimic_dir = \"/home/vs428/project/MIMIC/files/mimiciii/1.4/\"\n",
    "n2c2_dir = \"/home/vs428/project/n2c2/2022/N2C2-AP-Reasoning/\"\n",
    "n2c2_data_dir =  \"/home/vs428/project/n2c2/2022/Data/\"\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "dbfd91c0",
   "metadata": {},
   "outputs": [],
   "source": [
    "samples = pd.read_csv(n2c2_dir + \"n2c2_sample.csv\")\n",
    "samples_raw = pd.read_csv(n2c2_dir + \"n2c2_sample_raw.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "29d1f30f-f949-4674-9e7a-b3f72df35aa8",
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "# classes = ['Not Relevant', 'Neither', 'Indirect', 'Direct']\n",
    "# features = Features({\n",
    "#     'ROW ID':Value(\"int64\"),\n",
    "#     'HADM ID':Value(\"int64\"),\n",
    "#     'Assessment':Value(\"string\"),\n",
    "#     'PlanSubsection':Value(\"string\"),\n",
    "#     \"Relation\":Value(\"string\")\n",
    "# }) \n",
    "# dataset = load_dataset(\"csv\", data_files=n2c2_dir + \"n2c2_sample_raw.csv\", \n",
    "#                        features=features)\n",
    "# dataset = dataset.class_encode_column(\"Relation\")\n",
    "# dataset = dataset.rename_column(\"Relation\", \"label\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8eccde34-98c5-405c-a6ca-2e837e08d031",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ce76fc2b-aee6-4084-bfbe-e08b1cf06b48",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "063c05f7-cf1a-4727-b3e8-5d21aa09f32c",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e72d98fd",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "4acd8952-99d2-4215-8ceb-4490325d9bb7",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Using custom data configuration default-b1948d86214b7517\n",
      "Reusing dataset csv (/home/vs428/.cache/huggingface/datasets/csv/default-b1948d86214b7517/0.0.0/433e0ccc46f9880962cc2b12065189766fbb2bee57a221866138fb9203c83519)\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "62d56d6aa88542fa8e464fd137c4d868",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "  0%|          | 0/2 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "classes = ['Not Relevant', 'Neither', 'Indirect', 'Direct']\n",
    "features = Features({\n",
    "    'ROW ID':Value(\"int64\"),\n",
    "    'HADM ID':Value(\"int64\"),\n",
    "    'Assessment':Value(\"string\"),\n",
    "    'Plan Subsection':Value(\"string\"),\n",
    "    \"Relation\":Value(\"string\")\n",
    "}) \n",
    "\n",
    "dataset = load_dataset(\"csv\", data_files={\n",
    "                            \"train\":n2c2_data_dir + \"train.csv\",\n",
    "                            \"valid\":n2c2_data_dir + \"dev.csv\",\n",
    "                        },\n",
    "\n",
    "                       features=features)\n",
    "# dataset = dataset.class_encode_column(\"Relation\")\n",
    "dataset = dataset.rename_column(\"Relation\", \"label\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "9cd9f7ed-d488-493f-8163-73e295a286a8",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'ROW ID': 711150,\n",
       " 'HADM ID': 183333,\n",
       " 'Assessment': '75 yo M with h/o cardiomyopahy (EF 15%), atrial fibrillation, pulmonary\\n   embolism (on coumadin), adrenal insufficiency, and s/p several recent\\n   admissions following episode of Klebsilella pneumonia complicated by\\n   respiratory failure and septic shock. Presents to hospital with\\n   syncope, hypoxia, hypotension and altered mental status.',\n",
       " 'Plan Subsection': '# Adrenal insufficiency:\\n   Patient on 10 mg hydrocortisone at home.\\n   - Increase to 50 mg hydrocortisone given stress of acute illness (day 2\\n   today)',\n",
       " 'label': 'Indirect'}"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dataset['train'][23]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6dc7ac4f-b903-4db4-a710-b8f7a0e95bdb",
   "metadata": {},
   "source": [
    "# Check some assumptions about the data"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "470e709a-0765-4a6a-a6e7-8d7de3467f89",
   "metadata": {},
   "source": [
    "## Check if any \"direct\" relations have no overlap"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "b788254e-390a-458d-90cb-9ee2215e3aa9",
   "metadata": {},
   "outputs": [],
   "source": [
    "import scispacy\n",
    "import spacy\n",
    "from scispacy.abbreviation import AbbreviationDetector\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "849aa70f-d07c-46e1-bd75-db12c84ef362",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<scispacy.abbreviation.AbbreviationDetector at 0x2adc5b6defe0>"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nlp = spacy.load(\"en_core_sci_lg\")\n",
    "nlp.add_pipe(\"abbreviation_detector\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "111cf5f8-d817-4f13-a2dd-7d91dbb305a8",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/gpfs/ysm/project/rtaylor/vs428/conda_envs/myenv/lib/python3.10/site-packages/scispacy/abbreviation.py:230: UserWarning: [W036] The component 'matcher' does not have any patterns defined.\n",
      "  global_matches = self.global_matcher(doc)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'ROW ID': 476539, 'HADM ID': 111846, 'Assessment': 'This is a 55M with COPD/CO2 retainer, VTE,  bilateral chronic\\n   lymphedema and multiple ulcers who was admited for LE cellulitis/sepsis\\n   and who underwent BKA three days ago is transferred to MICU for medical\\n   management', 'Plan Subsection': 'Hypotension: resolved', 'label': 'Direct'}\n",
      "{'ROW ID': 358146, 'HADM ID': 106860, 'Assessment': '79F Russian speaking s/p CABG, dCHF s/p dual pacemaker, DMII, AF,\\n   CRI that presents with decreased PO and hypotension likely [**2-19**] to\\n   decresed PO in setting of UTI and potential PNA.', 'Plan Subsection': 'HYPOTENSION (NOT SHOCK)\\n COUGH', 'label': 'Direct'}\n",
      "{'ROW ID': 634432, 'HADM ID': 199781, 'Assessment': '57 y.o. man with DM, HTN, and paranoid schizophrenia, presents from\\n   inpatient Psych facility altered mental status', 'Plan Subsection': 'Respiratory alkalosis: Resolved on intubation', 'label': 'Direct'}\n",
      "{'ROW ID': 685471, 'HADM ID': 106691, 'Assessment': '48yo F intoxicated s/p fall down stairs with\\n   severe facial trauma, elective OSH intubation for airway protection.', 'Plan Subsection': 'Pain: fentanyl', 'label': 'Direct'}\n",
      "{'ROW ID': 429862, 'HADM ID': 110437, 'Assessment': '53 year old female with hx of alcoholism presents with hepatic and\\n   renal failure.  Transfered to ICU with new oxygen requirement.\\n   .', 'Plan Subsection': 'HEPATIC FAILURE, FULMINANT\\n RENAL FAILURE, ACUTE (ACUTE RENAL FAILURE, ARF)\\n RESPIRATORY FAILURE, ACUTE (NOT ARDS/[**Doctor Last Name 11**])', 'label': 'Direct'}\n",
      "{'ROW ID': 657674, 'HADM ID': 108863, 'Assessment': '55yo female with resolving ARDS and H. flu bacteremia presents for\\n   re-admission to the MICU for increased O2 requirement.\\n   .', 'Plan Subsection': 'AROUSAL, ATTENTION, AND COGNITION, IMPAIRED\\n MUSCLE PERFORMACE, IMPAIRED\\n RESPIRATION / GAS EXCHANGE, IMPAIRED\\n KNOWLEDGE, IMPAIRED', 'label': 'Direct'}\n",
      "{'ROW ID': 657674, 'HADM ID': 108863, 'Assessment': '55yo female with resolving ARDS and H. flu bacteremia presents for\\n   re-admission to the MICU for increased O2 requirement.\\n   .', 'Plan Subsection': 'PNEUMONIA, OTHER', 'label': 'Direct'}\n",
      "{'ROW ID': 376139, 'HADM ID': 111063, 'Assessment': '66 yo M with obesity hypoventilation, ? COPD, afib, ESRD on HD, PVD\\n   with recent TMA ulcer, who presents with confusion, shortness of\\n   breath, fever and hypotension.\\n   .', 'Plan Subsection': 'SEPSIS WITHOUT ORGAN DYSFUNCTION', 'label': 'Direct'}\n",
      "{'ROW ID': 376139, 'HADM ID': 111063, 'Assessment': '66 yo M with obesity hypoventilation, ? COPD, afib, ESRD on HD, PVD\\n   with recent TMA ulcer, who presents with confusion, shortness of\\n   breath, fever and hypotension.\\n   .', 'Plan Subsection': 'ALTERED MENTAL STATUS (NOT DELIRIUM)', 'label': 'Direct'}\n",
      "{'ROW ID': 376139, 'HADM ID': 111063, 'Assessment': '66 yo M with obesity hypoventilation, ? COPD, afib, ESRD on HD, PVD\\n   with recent TMA ulcer, who presents with confusion, shortness of\\n   breath, fever and hypotension.\\n   .', 'Plan Subsection': 'HYPOTENSION (NOT SHOCK)', 'label': 'Direct'}\n",
      "{'ROW ID': 586068, 'HADM ID': 188769, 'Assessment': 'BACTEREMIA\\n ATRIAL FIBRILLATION (AFIB)\\n FEVER, UNKNOWN ORIGIN (FUO, HYPERTHERMIA, PYREXIA)', 'Plan Subsection': '# afib: cont coumadin', 'label': 'Direct'}\n",
      "{'ROW ID': 527062, 'HADM ID': 103550, 'Assessment': '89 year old right handed man with type 2 diabetes\\n   mellitus, peripheral vascular disease, atrial\\n   fibrillation on coumadin with a sub therapeutic INR, CAD, HLD\\n   presenting with a C2 fracture and acute/subacute right cerebellar\\n   infarct', 'Plan Subsection': 'Pain:  Fentanyl', 'label': 'Direct'}\n"
     ]
    }
   ],
   "source": [
    "non_overlap_direct_rels = []\n",
    "for data in dataset['train']:\n",
    "    if data['label'] == \"Direct\":\n",
    "        assessment_tokens = set(w.orth for w in nlp(data['Assessment']))\n",
    "        plan_tokens = set(w.orth for w in nlp(data['Plan Subsection']))\n",
    "        if len(assessment_tokens.intersection(plan_tokens)) < 1:\n",
    "            print(data)\n",
    "            non_overlap_direct_rels.append(data)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "7f5268aa-f043-42f4-871e-d462c00a25f7",
   "metadata": {},
   "outputs": [],
   "source": [
    "non_overlap_direct_df = pd.DataFrame(non_overlap_direct_rels)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "65d9151f-01ba-4d04-92af-7ebf06d92dea",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Assessment: This is a 55M with COPD/CO2 retainer, VTE,  bilateral chronic\n",
      "   lymphedema and multiple ulcers who was admited for LE cellulitis/sepsis\n",
      "   and who underwent BKA three days ago is transferred to MICU for medical\n",
      "   management\n",
      "Plan: Hypotension: resolved\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 79F Russian speaking s/p CABG, dCHF s/p dual pacemaker, DMII, AF,\n",
      "   CRI that presents with decreased PO and hypotension likely [**2-19**] to\n",
      "   decresed PO in setting of UTI and potential PNA.\n",
      "Plan: HYPOTENSION (NOT SHOCK)\n",
      " COUGH\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 57 y.o. man with DM, HTN, and paranoid schizophrenia, presents from\n",
      "   inpatient Psych facility altered mental status\n",
      "Plan: Respiratory alkalosis: Resolved on intubation\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 48yo F intoxicated s/p fall down stairs with\n",
      "   severe facial trauma, elective OSH intubation for airway protection.\n",
      "Plan: Pain: fentanyl\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 53 year old female with hx of alcoholism presents with hepatic and\n",
      "   renal failure.  Transfered to ICU with new oxygen requirement.\n",
      "   .\n",
      "Plan: HEPATIC FAILURE, FULMINANT\n",
      " RENAL FAILURE, ACUTE (ACUTE RENAL FAILURE, ARF)\n",
      " RESPIRATORY FAILURE, ACUTE (NOT ARDS/[**Doctor Last Name 11**])\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 55yo female with resolving ARDS and H. flu bacteremia presents for\n",
      "   re-admission to the MICU for increased O2 requirement.\n",
      "   .\n",
      "Plan: AROUSAL, ATTENTION, AND COGNITION, IMPAIRED\n",
      " MUSCLE PERFORMACE, IMPAIRED\n",
      " RESPIRATION / GAS EXCHANGE, IMPAIRED\n",
      " KNOWLEDGE, IMPAIRED\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 55yo female with resolving ARDS and H. flu bacteremia presents for\n",
      "   re-admission to the MICU for increased O2 requirement.\n",
      "   .\n",
      "Plan: PNEUMONIA, OTHER\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 66 yo M with obesity hypoventilation, ? COPD, afib, ESRD on HD, PVD\n",
      "   with recent TMA ulcer, who presents with confusion, shortness of\n",
      "   breath, fever and hypotension.\n",
      "   .\n",
      "Plan: SEPSIS WITHOUT ORGAN DYSFUNCTION\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 66 yo M with obesity hypoventilation, ? COPD, afib, ESRD on HD, PVD\n",
      "   with recent TMA ulcer, who presents with confusion, shortness of\n",
      "   breath, fever and hypotension.\n",
      "   .\n",
      "Plan: ALTERED MENTAL STATUS (NOT DELIRIUM)\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 66 yo M with obesity hypoventilation, ? COPD, afib, ESRD on HD, PVD\n",
      "   with recent TMA ulcer, who presents with confusion, shortness of\n",
      "   breath, fever and hypotension.\n",
      "   .\n",
      "Plan: HYPOTENSION (NOT SHOCK)\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: BACTEREMIA\n",
      " ATRIAL FIBRILLATION (AFIB)\n",
      " FEVER, UNKNOWN ORIGIN (FUO, HYPERTHERMIA, PYREXIA)\n",
      "Plan: # afib: cont coumadin\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 89 year old right handed man with type 2 diabetes\n",
      "   mellitus, peripheral vascular disease, atrial\n",
      "   fibrillation on coumadin with a sub therapeutic INR, CAD, HLD\n",
      "   presenting with a C2 fracture and acute/subacute right cerebellar\n",
      "   infarct\n",
      "Plan: Pain:  Fentanyl\n",
      "Label: Direct\n",
      "\n",
      "---------------------------------------------\n",
      "\n"
     ]
    }
   ],
   "source": [
    "\n",
    "for idx, data in non_overlap_direct_df.iterrows():\n",
    "    prompt_str = 'Assessment: ' + data['Assessment'] + '\\nPlan: ' + data['Plan Subsection'] + '\\nLabel: ' \\\n",
    "        + str(data['label'])\n",
    "    print(prompt_str)\n",
    "    print(\"\\n---------------------------------------------\\n\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9236840a-7297-4371-81c8-2e0b57266cf5",
   "metadata": {},
   "source": [
    "## \"Indirect\" Relations that don't have much overlap"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "id": "e387b831-a6c4-4277-bff6-de122fddcfef",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/gpfs/ysm/project/rtaylor/vs428/conda_envs/myenv/lib/python3.10/site-packages/scispacy/abbreviation.py:230: UserWarning: [W036] The component 'matcher' does not have any patterns defined.\n",
      "  global_matches = self.global_matcher(doc)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'ROW ID': 553008, 'HADM ID': 195768, 'Assessment': 'MYOCARDIAL INFARCTION, ACUTE (AMI, STEMI, NSTEMI)\\n GASTROINTESTINAL BLEED, LOWER (HEMATOCHEZIA, BRBPR, GI BLEED, GIB)\\n TACHYCARDIA, OTHER\\n RESPIRATORY FAILURE, ACUTE (NOT ARDS/[**Doctor Last Name 2**])\\n   69F w/ h/o afib on coumadin, PUD, COPD, CKD, h/o CVA, HTN,\\n   hyperlipidemia transferred from [**Hospital1 709**] by family request after presenting\\n   with black stools, developed hypoxemia and tachyarrhythmia with RVR,\\n   now with continued respiratory distress complicated by demand ischemia.', 'Plan Subsection': '# Hypercholesterolemia: Continue statin', 'label': 'Indirect'}\n",
      "{'ROW ID': 580343, 'HADM ID': 183659, 'Assessment': '53M with HIV/hepC, admitted with nausea, weakness, hypotension', 'Plan Subsection': '# hypoglycemia - likely [**12-30**] septic picture and possibly complicated by\\n   ESLD.\\n   - D50 as needed.\\n   - check FSBS QID.', 'label': 'Indirect'}\n",
      "{'ROW ID': 657100, 'HADM ID': 100571, 'Assessment': 'his is a 66 y/o M hx seizures from EEE encephalitis p/w status c/b\\n   aspiration PNA, intubated in NICU, and NSTEMI and extubated on [**2-21**].\\n   Transferred to floor on [**2-24**] and continues to have some mild\\n   respiratory distress, tachypnea.\\n   .', 'Plan Subsection': 'H/O ENCEPHALITIS', 'label': 'Indirect'}\n",
      "{'ROW ID': 566675, 'HADM ID': 109844, 'Assessment': '79 yof with hx of HTN, Hyperlipidemia, Hypothyroidism, who presented to\\n   [**Hospital 839**] Hosp with SOB and chest pressure, found to be in acute CHF,\\n   transferred here s/p traumatic intubation c/b tracheal tear and\\n   subcutaneous emphysema.  Now transferred to CCU for management of afib\\n   with RVR. Febrile overnight with episode of afib/rvr, converted to\\n   sinus with amiodarone.', 'Plan Subsection': 'Hyperthyroidism: restart Levothyroxine when POs OK', 'label': 'Indirect'}\n",
      "{'ROW ID': 638868, 'HADM ID': 198207, 'Assessment': 'FEVER (HYPERTHERMIA, PYREXIA, NOT FEVER OF UNKNOWN ORIGIN)\\n TACHYCARDIA, OTHER\\n CANCER (MALIGNANT NEOPLASM), PANCREAS\\n SUPRAVENTRICULAR TACHYCARDIA (SVT)\\n RENAL FAILURE, ACUTE (ACUTE RENAL FAILURE, ARF)\\n LIVER FUNCTION ABNORMALITIES\\n ANEMIA, CHRONIC\\n HYPERTENSION, BENIGN\\n   58 year-old male with history of pancreatic cancer presented [**2117-10-6**]\\n   with fever and tachycardia.', 'Plan Subsection': 'HTN: hold lopressor for now', 'label': 'Indirect'}\n",
      "{'ROW ID': 398915, 'HADM ID': 149546, 'Assessment': '79 yo female with CAD s/p CABG with only patent LIMA-LAD, COPD, HTN,\\n   afib who presents with hematochezia, anemia, and angina', 'Plan Subsection': 'DYSPNEA (SHORTNESS OF BREATH)', 'label': 'Indirect'}\n",
      "{'ROW ID': 705139, 'HADM ID': 190704, 'Assessment': '49 yo female with history of hypercholesterolemia admitted for chest\\n   pain and EKG changes consistent with inferior STEMI, found to have no\\n   obstructing lesions on cath, most consistent with Takotsubos\\n   cardiomyopathy', 'Plan Subsection': '# Hypercholesterolemia:  Continue statin', 'label': 'Indirect'}\n",
      "{'ROW ID': 657674, 'HADM ID': 108863, 'Assessment': '55yo female with resolving ARDS and H. flu bacteremia presents for\\n   re-admission to the MICU for increased O2 requirement.\\n   .', 'Plan Subsection': 'ELECTROLYTE & FLUID DISORDER, OTHER', 'label': 'Indirect'}\n",
      "{'ROW ID': 534086, 'HADM ID': 111116, 'Assessment': '82 year old man with hx of T3N0 colon ca s/p transverse colectomy in\\n   [**2122**] c/b incisional hernia, dementia, DM2, HTN presents with high\\n   fever, lethargy, emesis, positive u/a.', 'Plan Subsection': 'DM\\n ISS', 'label': 'Indirect'}\n",
      "{'ROW ID': 325354, 'HADM ID': 112343, 'Assessment': '87 year old Russian-speaking female with h/o breast cancer, esophageal\\n   cancer (requiring esophogeal stent), afib, DMII, s/p EGD with\\n   additional stent placement adm with hematemesis/UGIB initially HD\\n   stable with decompensation\\n   .', 'Plan Subsection': 'DM: sliding scale', 'label': 'Indirect'}\n",
      "{'ROW ID': 721481, 'HADM ID': 101199, 'Assessment': '52y F with 2wk HA found to have L SDH with midline\\n   shift.', 'Plan Subsection': 'h/o GERD, PUD - cont PPI', 'label': 'Indirect'}\n",
      "{'ROW ID': 437644, 'HADM ID': 199705, 'Assessment': 'This 51F with alcoholic cirrhosis presents with hematemesis.', 'Plan Subsection': '# EtoH abuse\\n   - monitor per CIWA, ativan prn\\n   - MVT/thiamine/folate (banana bag daily\\n   - social work/[**First Name8 (NamePattern2) 780**] [**Last Name (NamePattern1) 820**] consult in AM', 'label': 'Indirect'}\n",
      "{'ROW ID': 559423, 'HADM ID': 149752, 'Assessment': '79M w/ pmh significant for SIADH, COPD, BPH s/p TURP, ulcerative\\n   colitis,  presenting with abdominal pain, diahrrea, leukocytosis, and\\n   severe hyponatremia.', 'Plan Subsection': 'Peripheral Neuropathy: Continue neurontin', 'label': 'Indirect'}\n",
      "{'ROW ID': 439899, 'HADM ID': 192999, 'Assessment': '89 F w/ PMHx of hypothyroid, prior syncopal episodes of unknown\\n   etiology presents w/ syncope and high degree AV block, now s/p\\n   temporary pacer placement.', 'Plan Subsection': '#) Hypothyroidism: Continue levothyroxine', 'label': 'Indirect'}\n",
      "{'ROW ID': 709485, 'HADM ID': 149619, 'Assessment': '52 year old male with diabetes, hypertension, active smoker presenting\\n   with inferior STEMI s/p placement of 3 stents to proximal, mid, and\\n   distal RCA admitted to CCU for observation\\n   .', 'Plan Subsection': 'Dyslipidemia\\n holding statin (see above)', 'label': 'Indirect'}\n",
      "{'ROW ID': 639467, 'HADM ID': 110316, 'Assessment': '89 year old woman with hypertension, paroxysmal atrial fibrillation,\\n   aortic stenosis, recent pseudomonas bacteremia, presenting with nausea,\\n   vomiting, bradycardia, hypotension and respiratory failure, in critical\\n   condition. [**2121-10-24**] patient experienced R anterior MCA infarct.\\n   .', 'Plan Subsection': 'Hypothyroidism: continue levothyroxine', 'label': 'Indirect'}\n",
      "{'ROW ID': 625154, 'HADM ID': 105444, 'Assessment': '73F PMHx of IDDM, seizure disorder and breast cancer presenting with R\\n   hip fx s/p fall and admitted to the ICU initially with ARF and troponin\\n   leak; now s/p ORIF of R hip with post-op hypoxia.', 'Plan Subsection': 'Seizure Disorder: continue home medications', 'label': 'Indirect'}\n",
      "{'ROW ID': 585163, 'HADM ID': 106334, 'Assessment': 'ALTERED MENTAL STATUS (NOT DELIRIUM)\\n HYPOXEMIA\\n CARDIAC DYSRHYTHMIA OTHER\\n FEVER (HYPERTHERMIA, PYREXIA, NOT FEVER OF UNKNOWN ORIGIN)\\n IMPAIRED SKIN INTEGRITY\\n   This is a 55 year-old man with metastatic melanoma who presents with\\n   altered mental status and hemorrhagic brain mets.\\n   .', 'Plan Subsection': 'Tachycardia/bradycardia: Pt', 'label': 'Indirect'}\n",
      "{'ROW ID': 527062, 'HADM ID': 103550, 'Assessment': '89 year old right handed man with type 2 diabetes\\n   mellitus, peripheral vascular disease, atrial\\n   fibrillation on coumadin with a sub therapeutic INR, CAD, HLD\\n   presenting with a C2 fracture and acute/subacute right cerebellar\\n   infarct', 'Plan Subsection': 'Cont. beta blockade for heart rate control due to h/o afib.', 'label': 'Indirect'}\n",
      "{'ROW ID': 438035, 'HADM ID': 199238, 'Assessment': 'H/O CVA (STROKE, CEREBRAL INFARCTION), OTHER\\n PNEUMONIA, [**Hospital 50**] HOSPITAL ACQUIRED (NON-VAP)\\n HYPOTENSION (NOT SHOCK)\\n   78F with h/o stroke with R hemiparesis and aphasia presents with\\n   hypoxia, volume overload/CHF, and hypotension', 'Plan Subsection': '# ? RIJ/RSC DVT: f/u RUE UE', 'label': 'Indirect'}\n",
      "{'ROW ID': 656572, 'HADM ID': 190187, 'Assessment': '87 year old female with a h/o CAD s/p PCI, htn, hyperlipidemia, breast\\n   cancer s/p lumpectomy and XRT who presents with altered mental status\\n   found to be hyponatremic', 'Plan Subsection': '# Hypercholesterolemia: cont statin', 'label': 'Indirect'}\n",
      "{'ROW ID': 361936, 'HADM ID': 191117, 'Assessment': '59M with CAD, CHF, DM, ESRD on HD, who presents with hypotension and\\n   sepsis now much improved, off pressors, extubated, mental status\\n   appears normal.', 'Plan Subsection': '# HyperKalemia - resolved', 'label': 'Indirect'}\n"
     ]
    }
   ],
   "source": [
    "non_overlap_indirect_rels = []\n",
    "for data in dataset['train']:\n",
    "    if data['label'] == \"Indirect\":\n",
    "        assessment_tokens = set(w.orth for w in nlp(data['Assessment']))\n",
    "        plan_tokens = set(w.orth for w in nlp(data['Plan Subsection']))\n",
    "        if len(assessment_tokens.intersection(plan_tokens)) < 1:\n",
    "            print(data)\n",
    "            non_overlap_indirect_rels.append(data)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "af81ff6e-8182-4c5b-b09f-4c1856d27908",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b32b423c-e173-4d1c-822b-af6c051185b6",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "id": "99463524-5504-479b-9925-57cbbeb8fd58",
   "metadata": {},
   "outputs": [],
   "source": [
    "non_overlap_indirect_df = pd.DataFrame(non_overlap_indirect_rels)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "id": "5c5d00f7-d8db-4e70-ba58-ec7bcfa07e19",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Assessment: MYOCARDIAL INFARCTION, ACUTE (AMI, STEMI, NSTEMI)\n",
      " GASTROINTESTINAL BLEED, LOWER (HEMATOCHEZIA, BRBPR, GI BLEED, GIB)\n",
      " TACHYCARDIA, OTHER\n",
      " RESPIRATORY FAILURE, ACUTE (NOT ARDS/[**Doctor Last Name 2**])\n",
      "   69F w/ h/o afib on coumadin, PUD, COPD, CKD, h/o CVA, HTN,\n",
      "   hyperlipidemia transferred from [**Hospital1 709**] by family request after presenting\n",
      "   with black stools, developed hypoxemia and tachyarrhythmia with RVR,\n",
      "   now with continued respiratory distress complicated by demand ischemia.\n",
      "Plan: # Hypercholesterolemia: Continue statin\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 53M with HIV/hepC, admitted with nausea, weakness, hypotension\n",
      "Plan: # hypoglycemia - likely [**12-30**] septic picture and possibly complicated by\n",
      "   ESLD.\n",
      "   - D50 as needed.\n",
      "   - check FSBS QID.\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: his is a 66 y/o M hx seizures from EEE encephalitis p/w status c/b\n",
      "   aspiration PNA, intubated in NICU, and NSTEMI and extubated on [**2-21**].\n",
      "   Transferred to floor on [**2-24**] and continues to have some mild\n",
      "   respiratory distress, tachypnea.\n",
      "   .\n",
      "Plan: H/O ENCEPHALITIS\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 79 yof with hx of HTN, Hyperlipidemia, Hypothyroidism, who presented to\n",
      "   [**Hospital 839**] Hosp with SOB and chest pressure, found to be in acute CHF,\n",
      "   transferred here s/p traumatic intubation c/b tracheal tear and\n",
      "   subcutaneous emphysema.  Now transferred to CCU for management of afib\n",
      "   with RVR. Febrile overnight with episode of afib/rvr, converted to\n",
      "   sinus with amiodarone.\n",
      "Plan: Hyperthyroidism: restart Levothyroxine when POs OK\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: FEVER (HYPERTHERMIA, PYREXIA, NOT FEVER OF UNKNOWN ORIGIN)\n",
      " TACHYCARDIA, OTHER\n",
      " CANCER (MALIGNANT NEOPLASM), PANCREAS\n",
      " SUPRAVENTRICULAR TACHYCARDIA (SVT)\n",
      " RENAL FAILURE, ACUTE (ACUTE RENAL FAILURE, ARF)\n",
      " LIVER FUNCTION ABNORMALITIES\n",
      " ANEMIA, CHRONIC\n",
      " HYPERTENSION, BENIGN\n",
      "   58 year-old male with history of pancreatic cancer presented [**2117-10-6**]\n",
      "   with fever and tachycardia.\n",
      "Plan: HTN: hold lopressor for now\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 79 yo female with CAD s/p CABG with only patent LIMA-LAD, COPD, HTN,\n",
      "   afib who presents with hematochezia, anemia, and angina\n",
      "Plan: DYSPNEA (SHORTNESS OF BREATH)\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 49 yo female with history of hypercholesterolemia admitted for chest\n",
      "   pain and EKG changes consistent with inferior STEMI, found to have no\n",
      "   obstructing lesions on cath, most consistent with Takotsubos\n",
      "   cardiomyopathy\n",
      "Plan: # Hypercholesterolemia:  Continue statin\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 55yo female with resolving ARDS and H. flu bacteremia presents for\n",
      "   re-admission to the MICU for increased O2 requirement.\n",
      "   .\n",
      "Plan: ELECTROLYTE & FLUID DISORDER, OTHER\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 82 year old man with hx of T3N0 colon ca s/p transverse colectomy in\n",
      "   [**2122**] c/b incisional hernia, dementia, DM2, HTN presents with high\n",
      "   fever, lethargy, emesis, positive u/a.\n",
      "Plan: DM\n",
      " ISS\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 87 year old Russian-speaking female with h/o breast cancer, esophageal\n",
      "   cancer (requiring esophogeal stent), afib, DMII, s/p EGD with\n",
      "   additional stent placement adm with hematemesis/UGIB initially HD\n",
      "   stable with decompensation\n",
      "   .\n",
      "Plan: DM: sliding scale\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 52y F with 2wk HA found to have L SDH with midline\n",
      "   shift.\n",
      "Plan: h/o GERD, PUD - cont PPI\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: This 51F with alcoholic cirrhosis presents with hematemesis.\n",
      "Plan: # EtoH abuse\n",
      "   - monitor per CIWA, ativan prn\n",
      "   - MVT/thiamine/folate (banana bag daily\n",
      "   - social work/[**First Name8 (NamePattern2) 780**] [**Last Name (NamePattern1) 820**] consult in AM\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 79M w/ pmh significant for SIADH, COPD, BPH s/p TURP, ulcerative\n",
      "   colitis,  presenting with abdominal pain, diahrrea, leukocytosis, and\n",
      "   severe hyponatremia.\n",
      "Plan: Peripheral Neuropathy: Continue neurontin\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 89 F w/ PMHx of hypothyroid, prior syncopal episodes of unknown\n",
      "   etiology presents w/ syncope and high degree AV block, now s/p\n",
      "   temporary pacer placement.\n",
      "Plan: #) Hypothyroidism: Continue levothyroxine\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 52 year old male with diabetes, hypertension, active smoker presenting\n",
      "   with inferior STEMI s/p placement of 3 stents to proximal, mid, and\n",
      "   distal RCA admitted to CCU for observation\n",
      "   .\n",
      "Plan: Dyslipidemia\n",
      " holding statin (see above)\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 89 year old woman with hypertension, paroxysmal atrial fibrillation,\n",
      "   aortic stenosis, recent pseudomonas bacteremia, presenting with nausea,\n",
      "   vomiting, bradycardia, hypotension and respiratory failure, in critical\n",
      "   condition. [**2121-10-24**] patient experienced R anterior MCA infarct.\n",
      "   .\n",
      "Plan: Hypothyroidism: continue levothyroxine\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 73F PMHx of IDDM, seizure disorder and breast cancer presenting with R\n",
      "   hip fx s/p fall and admitted to the ICU initially with ARF and troponin\n",
      "   leak; now s/p ORIF of R hip with post-op hypoxia.\n",
      "Plan: Seizure Disorder: continue home medications\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: ALTERED MENTAL STATUS (NOT DELIRIUM)\n",
      " HYPOXEMIA\n",
      " CARDIAC DYSRHYTHMIA OTHER\n",
      " FEVER (HYPERTHERMIA, PYREXIA, NOT FEVER OF UNKNOWN ORIGIN)\n",
      " IMPAIRED SKIN INTEGRITY\n",
      "   This is a 55 year-old man with metastatic melanoma who presents with\n",
      "   altered mental status and hemorrhagic brain mets.\n",
      "   .\n",
      "Plan: Tachycardia/bradycardia: Pt\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 89 year old right handed man with type 2 diabetes\n",
      "   mellitus, peripheral vascular disease, atrial\n",
      "   fibrillation on coumadin with a sub therapeutic INR, CAD, HLD\n",
      "   presenting with a C2 fracture and acute/subacute right cerebellar\n",
      "   infarct\n",
      "Plan: Cont. beta blockade for heart rate control due to h/o afib.\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: H/O CVA (STROKE, CEREBRAL INFARCTION), OTHER\n",
      " PNEUMONIA, [**Hospital 50**] HOSPITAL ACQUIRED (NON-VAP)\n",
      " HYPOTENSION (NOT SHOCK)\n",
      "   78F with h/o stroke with R hemiparesis and aphasia presents with\n",
      "   hypoxia, volume overload/CHF, and hypotension\n",
      "Plan: # ? RIJ/RSC DVT: f/u RUE UE\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 87 year old female with a h/o CAD s/p PCI, htn, hyperlipidemia, breast\n",
      "   cancer s/p lumpectomy and XRT who presents with altered mental status\n",
      "   found to be hyponatremic\n",
      "Plan: # Hypercholesterolemia: cont statin\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n",
      "Assessment: 59M with CAD, CHF, DM, ESRD on HD, who presents with hypotension and\n",
      "   sepsis now much improved, off pressors, extubated, mental status\n",
      "   appears normal.\n",
      "Plan: # HyperKalemia - resolved\n",
      "Label: Indirect\n",
      "\n",
      "---------------------------------------------\n",
      "\n"
     ]
    }
   ],
   "source": [
    "\n",
    "for idx, data in non_overlap_indirect_df.iterrows():\n",
    "    prompt_str = 'Assessment: ' + data['Assessment'] + '\\nPlan: ' + data['Plan Subsection'] + '\\nLabel: ' \\\n",
    "        + str(data['label'])\n",
    "    print(prompt_str)\n",
    "    print(\"\\n---------------------------------------------\\n\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "id": "8144d86e-cd89-4899-b50e-914ac1e8c09b",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/tmp/ipykernel_4338/2468265868.py:2: DtypeWarning: Columns (4,5) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  notes = pd.read_csv(mimic_dir + \"NOTEEVENTS.csv\")\n"
     ]
    }
   ],
   "source": [
    "mimic_dir = \"/home/vs428/project/MIMIC/files/mimiciii/1.4/\"\n",
    "notes = pd.read_csv(mimic_dir + \"NOTEEVENTS.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "id": "1d2d2399-6cf1-40cf-8b8f-c94e0ed45485",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Chief Complaint:  weakness, shortness of breath.\n",
      "   HPI:\n",
      "   53M with h/o ESLD [**12-30**] hepC, HIV (CD4 322), pHTN, presenting to ED this\n",
      "   morning with weakness, nausea, and cough.  Per his caregiver [**Name (NI) 1708**], he\n",
      "   was in his USOH until 4AM, and had been doing relatively well since his\n",
      "   last discharge [**3-29**] at which time dobhoff was replaced [**12-30**] weight loss,\n",
      "   tolerating tube feeds poorly, but recently switching to oral feeds only\n",
      "   for the past 1.5 weeks.\n",
      "   .\n",
      "   He had no complaints prior to going to bed, other than his baseline\n",
      "   abdominal discomfort, and nausea.  His caregiver found him at 4AM\n",
      "   slumped towards the left on the couch, incontient of urine and stool\n",
      "   (wears depends at baseline), and disoriented.  EMS was activated, and\n",
      "   he was brought to ED.\n",
      "   .\n",
      "   The patient denies confusion, hemetemesis, melena, or change in his\n",
      "   chronic abdominal pain, and has been having daily soft bowel movements\n",
      "   on lactulose.\n",
      "   .\n",
      "   In ED VS=98.1  98/70  103  24  92%RA.  Labs notable for LACTATE 8.0,\n",
      "   WBC 25.2, 9%bands, CRE 1.2 (bl 0.9), CE flat, TBIL 5.5 (bl [**3-3**]).  CXR\n",
      "   with RLL effusion, and ?infiltrate.  RUQ with moderate abdominal fluid,\n",
      "   single large gallstone with gallbladder wall thickening.  His BP\n",
      "   dropped to the 85/63, for which he received 500cc with improved BP.  In\n",
      "   total he received 5L IV with repeat lactate was 8.4, and 800cc UOP\n",
      "   after foley placement.  He had a single FSBS 30s for which he received\n",
      "   1AMP D50.  He received CTX/azithro/vanc, and then zosyn.  Plan was for\n",
      "   CVL, however pt declined this.  His access is 2 PIVs.  Guaic negative\n",
      "   rectal exam.\n",
      "   .\n",
      "   Of note, he was recently admitted to [**Hospital1 1**] [**Date range (1) 6701**] with clogged\n",
      "   dobhoff, ascites, and dyspnea.  PEG was placed for enteric feeding.\n",
      "   Paracentesis removed 4L of fluid, with WBC 1100 with 2%PMN.  CTA and\n",
      "   RHC found no PE, and worsening pHTN.  1.6L left side thoracentesis was\n",
      "   reported as transudative though by LDH, appears exudative given\n",
      "   pLDH/sLDH 0.7 (LDH 145, TP 2.7, WBC 100, RBC 20,500, serum LDH 200 (ULN\n",
      "   250), serum TP not measured).\n",
      "   .\n",
      "   Upon arrival to the ICU, pt and caregiver note improved mental status,\n",
      "   but worsening tachypnea after having recieved IVF in ED.\n",
      "   Patient admitted from: [**Hospital1 1**] ER\n",
      "   History obtained from Patient, Family / Friend\n",
      "   Allergies:\n",
      "   Sulfa (Sulfonamides)\n",
      "   Fever/Chills;\n",
      "   Last dose of Antibiotics:\n",
      "   Infusions:\n",
      "   Other ICU medications:\n",
      "   Other medications:\n",
      "   1. Peptamen 60) ml/hr PO continuousto be administered by post-pyloric\n",
      "   Dobhoff tube.\n",
      "   2. Abacavir 300 mg PO BID (2 times a day).\n",
      "   3. Clotrimazole 10 mg Troche 5 TIMES PER DAY -> NOT TAKING\n",
      "   4. Lactulose 30 ML PO DAILY.\n",
      "   5. Lamivudine 300 mg PO once a day.\n",
      "   6. Lopinavir-Ritonavir 200-50 mg 2 Tablet PO BID (2 times a day).\n",
      "   7. Metoclopramide 5 mg PO three times a day -> NOT TAKING\n",
      "   8. Omeprazole 20 mg PO DAILY (Daily).\n",
      "   9. Oxycodone 5 mg PO Q6H\n",
      "   10. Propranolol 20 mg PO BID\n",
      "   11. Rifaximin 200 mg PO BID\n",
      "   12. Tenofovir Disoproxil Fumarate 300 mg PO DAILY (Daily).\n",
      "   13. Cholecalciferol (Vitamin D3) 800 unit PO DAILY (Daily).\n",
      "   14. Ferrous Sulfate 325 mg PO DAILY (Daily).\n",
      "   15. Latanoprost 0.005 % Drops 1Ophthalmic HS\n",
      "   16. compazine prn.\n",
      "   17. megace prn.\n",
      "   Past medical history:\n",
      "   Family history:\n",
      "   Social History:\n",
      "   - HIV x26yr (CD4 322, VL undetectable [**3-6**])\n",
      "   - hepC x10yr cirrhosis, c/b grade [**11-29**] esophageal varices [**2-3**], hepatic\n",
      "   hydrothorax s/p thoracentesis [**3-6**], ascites, portal htn, de-listed on\n",
      "   [**3-6**] [**12-30**] PAH.\n",
      "   - pulmonary htn - RHC in [**3-6**] showed:\n",
      "     PA {s/d/m} baseline: 65/26/40  100%O2 67/25/38 inhald NO 65/28/39)\n",
      "     WEDGE {a/v/m}        22/23/16         25/25/19           23/24/19\n",
      "   - ?LLL lung nodule - incidental finding on CTA [**3-6**], PET-CT without\n",
      "   uptake in lung c/w rounded atelectasis, but low-level uptake in benign\n",
      "   appearing neck nodules, plan for sildenafil once prior auth complete.\n",
      "   - s/p hip replacement in [**2146**] for avascular necrosis\n",
      "   - osteopenia\n",
      "   NC\n",
      "   Occupation: disabled\n",
      "   Drugs: former (quit 19y ago)\n",
      "   Tobacco: former\n",
      "   Alcohol: former\n",
      "   Other:\n",
      "   Review of systems:\n",
      "   Constitutional: Fatigue\n",
      "   Ear, Nose, Throat: Dry mouth\n",
      "   Nutritional Support: Tube feeds\n",
      "   Respiratory: Cough, Dyspnea\n",
      "   Gastrointestinal: Abdominal pain\n",
      "   Pain: [**11-29**] Minimal\n",
      "   Flowsheet Data as of [**2155-5-13**] 02:00 PM\n",
      "   Vital Signs\n",
      "   Hemodynamic monitoring\n",
      "   Fluid Balance\n",
      "                                                                  24 hours\n",
      "                                                               Since 12 AM\n",
      "   Tmax: 36.2\n",
      "C (97.2\n",
      "   Tcurrent: 36.2\n",
      "C (97.2\n",
      "   HR: 85 (85 - 93) bpm\n",
      "   BP: 96/63(72) {96/63(72) - 118/78(82)} mmHg\n",
      "   RR: 27 (20 - 28) insp/min\n",
      "   SpO2: 97%\n",
      "   Heart rhythm: SR (Sinus Rhythm)\n",
      "   Height: 72 Inch\n",
      "             Total In:\n",
      "             5,838 mL\n",
      "   PO:\n",
      "             TF:\n",
      "   IVF:\n",
      "   38 mL\n",
      "   Blood products:\n",
      "   Total out:\n",
      "                                                                      0 mL\n",
      "                                                                    330 mL\n",
      "   Urine:\n",
      "   240 mL\n",
      "   NG:\n",
      "   Stool:\n",
      "   Drains:\n",
      "   Balance:\n",
      "                                                                      0 mL\n",
      "                                                                  5,508 mL\n",
      "   Respiratory\n",
      "   O2 Delivery Device: Nasal cannula, Venti mask\n",
      "   SpO2: 97%\n",
      "   Physical Examination\n",
      "   General Appearance: Thin, cachectic\n",
      "   Eyes / Conjunctiva: PERRL, Pupils dilated, Conjunctiva pale\n",
      "   Head, Ears, Nose, Throat: Normocephalic, Poor dentition, NG tube\n",
      "   Lymphatic: Cervical WNL\n",
      "   Cardiovascular: (Murmur: Systolic)\n",
      "   Peripheral Vascular: (Right radial pulse: Present), (Left radial pulse:\n",
      "   Present), (Right DP pulse: Present), (Left DP pulse: Present)\n",
      "   Respiratory / Chest: (Expansion: Symmetric), (Breath Sounds: No(t)\n",
      "   Clear : , Crackles : , Diminished: RLL)\n",
      "   Abdominal: Soft, Bowel sounds present, distended, tense.\n",
      "   Extremities: Right: Absent, Left: Trace\n",
      "   Musculoskeletal: Muscle wasting\n",
      "   Skin:  Not assessed\n",
      "   Neurologic: Attentive, Follows simple commands, Responds to: Verbal\n",
      "   stimuli, Oriented (to): person, place, time, president., Movement:\n",
      "   Purposeful, Tone: Not assessed, [**4-1**] deltoid, bicep, tricep, wrist\n",
      "   extension, hip flexion, [**Last Name (un) 6702**]/plantarflexion. denies neck pain, full\n",
      "   ROM of neck.  negative kernig/burdzinksi.\n",
      "   Labs / Radiology\n",
      "   65\n",
      "        [image002.jpg]\n",
      "                                  [**2151-11-29**]\n",
      "                          2:33 A6/16/[**2154**]  01:00 PM\n",
      "                                  [**2151-12-3**]\n",
      "                                   10:20 P\n",
      "                                  [**2151-12-4**]\n",
      "                                   1:20 P\n",
      "                                  [**2151-12-5**]\n",
      "                                   11:50 P\n",
      "                                  [**2151-12-6**]\n",
      "                                   1:20 A\n",
      "                                  [**2151-12-7**]\n",
      "                                   7:20 P\n",
      "                                  1//11/006\n",
      "                                   1:23 P\n",
      "                                  [**2151-12-30**]\n",
      "                                   1:20 P\n",
      "                                  [**2151-12-30**]\n",
      "                                   11:20 P\n",
      "                                  [**2151-12-30**]\n",
      "                                   4:20 P\n",
      "   Glucose\n",
      "                                     65\n",
      "   Other labs: PT / PTT / INR:22.6/43.3/2.1\n",
      "   Assessment and Plan\n",
      "   53M with HIV/hepC, admitted with nausea, weakness, hypotension.\n",
      "   .\n",
      "   # weakness/atered mental status - no focal neurologic deficits, and no\n",
      "   witnessed seizure activity at home.  has some tremor, but no frank\n",
      "   asterixis.  most concerning for infection given his distended abdomen,\n",
      "   and leukocytosis, with pulmonary and abdominal sources most\n",
      "   concerning.  no evidence of meningitis now.\n",
      "   - continue lactulose, rifaximin.\n",
      "   - seizure precautions.\n",
      "   - check ucx, bcx, stool cx with cdiff.\n",
      "   - d/w liver service how/when to pursue diagnostic paracentesis -> usn\n",
      "   guided paracentesis.\n",
      "   - check serum/urine tox screen.\n",
      "   - continue vanc/zosyn empirically for presumed abdominal/pulmonary\n",
      "   source, and add flagyl.\n",
      "   - consider CT A/P to evaluate for abdominal source given lactate of 8,\n",
      "   though may be [**12-30**] HIV meds.\n",
      "   .\n",
      "   # hypoxia - pt presents with cough, though not frankly hypoxic upon\n",
      "   arrival to ED, with worsening hypoxia in setting of aggressive fluid\n",
      "   repletion.  CXR prior to fluids, at 6am showed chronic bilateral\n",
      "   pleural effusions, though R>>L, with ?RLL infiltrate.  his story is\n",
      "   concerning for RLL pneumonia, and possibly aspiration given his recent\n",
      "   vomitting, but must also consider opportunitistic infections given his\n",
      "   HIV (though typically occur with CD4<200) and empyema given his fluid\n",
      "   collection.\n",
      "   - repeat CXR now.\n",
      "   - DFA to r/o flu.\n",
      "   - continue vanc/zosyn.\n",
      "   - ID consult as above.\n",
      "   - discuss utility of tapping RLL effusion, though seems moderate sized,\n",
      "   and could try diuretics first (though h/o bumping creatinine in this\n",
      "   setting, and recent hypotension), but could r/o empyema also given\n",
      "   leukocytosis. (will need FFP prior to [**Female First Name (un) 231**]).\n",
      "   - consider CTA of CHEST with CT A/P above to r/o PE and evaluate RLL\n",
      "   effusion.\n",
      "   .\n",
      "   # lactate - no prior lactate's in OMR, and although HIV meds can raise\n",
      "   lactate (abacavir, lamivudine -> neutral [**First Name8 (NamePattern2) 24**] [**Doctor Last Name **], tenofovir -> not [**First Name8 (NamePattern2) 24**]\n",
      "   [**Doctor Last Name **]), current overall picture is concerning for sepsis based on\n",
      "   leukocytosis, and hypotension, with failure to improve lactate after 6L\n",
      "   IVF.\n",
      "   - trend lactate Q6H.\n",
      "   - follow UOP closely.\n",
      "   - d/w ID value of holding HIV meds in setting of acute illness with\n",
      "   rising lactate.\n",
      "   - ID consult re how to manage HIV meds (will hold for now), sepsis.\n",
      "   - consider ct abd/pelvis given lack of clear source, to look for\n",
      "   evidence of ischemic colitis, abcess.\n",
      "   .\n",
      "   # ?seizure - unclear history of bowel/bladder incontinence which is new\n",
      "   for patient, though he wears depends at baseline.  no focal neurologic\n",
      "   deficits presently, but hypoglycemia may have contributed.\n",
      "   - seizure precautions.\n",
      "   - follow finger sticks closley.\n",
      "   - consider CT HEAD.\n",
      "   - treat with D5W + 3amps bicarb @ 100cc/hr.\n",
      "   .\n",
      "   # hypoglycemia - likely [**12-30**] septic picture.\n",
      "   - bolus with D5W + 3amps bicarb prior to CT scan.\n",
      "   - continue D5W as above.\n",
      "   - check FSBS QID.\n",
      "   .\n",
      "   # leukocytosis - new leukocytosis, with bandemia.  would look for\n",
      "   infection as above.  he did have an episode of hypoglycemia in ED,\n",
      "   which presumably is [**12-30**] septic physiology, and is without h/o DM to\n",
      "   suggest DKA.\n",
      "   - check cultures as above.\n",
      "   - CT TORSO to evaluate for PNA, and abdominal source.\n",
      "   .\n",
      "   # ESLD - [**12-30**] hepC, h/o encephalopathy, +varices, no h/o SBP, HRS.  off\n",
      "   of transplant list [**12-30**] pHTN. albumin 2.6.  MELD 23.\n",
      "   - liver consult.\n",
      "   - continue lactulose/rifaximin.\n",
      "   - hold propanalol given hypotension.\n",
      "   - discuss diuretics with liver team as apparently poor response in the\n",
      "   past, will hold off for now given hypotension.\n",
      "   .\n",
      "   # metabolic acidosis - gap 16, lactate 8.0, with trace ketones in\n",
      "   urine, and hypoglycemia in ED.  DKA therefore unlikely.  his picture is\n",
      "   more concerning for septic picture, with some possible contribution\n",
      "   from starvation ketosis.\n",
      "   - trend CHEM7 in PM.\n",
      "   - trend lactate.\n",
      "   - check ABG/VBG now.\n",
      "   - give bicarb as above, for CT torso.\n",
      "   .\n",
      "   # ARF - baseline cre 0.9, now 1.2, so he is above his baseline.  at\n",
      "   elevated risk for volume depletion, AIN (abx at last admission), ATN,\n",
      "   and HRS.\n",
      "   - check urine lytes now as he has received 5L IVF in ED.\n",
      "   - consider albumin.\n",
      "   - give bicarb, and mucomyst for CTA.\n",
      "   - trend creatinine.\n",
      "   .\n",
      "   # HIV - CD4 300s, VL undetectable.  concern for elevated lactate [**12-30**]\n",
      "   HIV meds.  should also consider opportunistic pathogens.\n",
      "   - hold home regimen for now.\n",
      "   - ID consult as above.\n",
      "   .\n",
      "   # pulmonary HTN - not yet on sildenafil as outpatient.\n",
      "   .\n",
      "   # FEN: continue tube feeds, megace. compazine/zofran prn.\n",
      "   # Prophylaxis: pneumoboots, outpatient ppi (switch to lansoprazole).\n",
      "   # Access: PIVx2, consider TLC CVL, and a-line if hypotensive.\n",
      "   # Code: FULL\n",
      "   # Communication: Patient, partner [**First Name8 (NamePattern2) **] [**Last Name (NamePattern1) 6703**] (hcp) [**Telephone/Fax (1) 6704**]\n",
      "   # Disposition: pending above\n",
      "   .\n",
      "   ICU Care\n",
      "   Nutrition:\n",
      "   Glycemic Control:\n",
      "   Lines:\n",
      "   18 Gauge - [**2155-5-13**] 11:01 AM\n",
      "   20 Gauge - [**2155-5-13**] 11:01 AM\n",
      "   Prophylaxis:\n",
      "   DVT: SQ UF Heparin\n",
      "   Stress ulcer:\n",
      "   VAP:\n",
      "   Comments:\n",
      "   Communication: Patient discussed on interdisciplinary rounds , Family\n",
      "   meeting held , ICU consent signed Comments:\n",
      "   Code status: Full code\n",
      "   Disposition: ICU\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# notes[notes['HADM_ID'] == 183659]\n",
    "print(notes[notes['ROW_ID'] == 580343]['TEXT'].tolist()[0])"
   ]
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