{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "85377d78",
   "metadata": {},
   "source": [
    "# Alarm data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "cb30bfe1-f462-4aad-9660-c120d5904da5",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/usr/local/Caskroom/miniconda/base/envs/cstrees/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
      "  from .autonotebook import tqdm as notebook_tqdm\n"
     ]
    }
   ],
   "source": [
    "import random\n",
    "import time\n",
    "\n",
    "from causallearn.search.ConstraintBased.PC import pc\n",
    "from causallearn.utils.cit import chisq\n",
    "\n",
    "import pandas as pd\n",
    "import cslearn.scoring as sc\n",
    "import cslearn.learning as ctl\n",
    "import cslearn.ldag as ldag\n",
    "import numpy as np\n",
    "\n",
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "830d1445",
   "metadata": {},
   "source": [
    "## Read data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "450c930d-4cbd-4958-b4c9-b6a11d130a27",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CVP</th>\n",
       "      <th>PCWP</th>\n",
       "      <th>HIST</th>\n",
       "      <th>TPR</th>\n",
       "      <th>BP</th>\n",
       "      <th>CO</th>\n",
       "      <th>HRBP</th>\n",
       "      <th>HREK</th>\n",
       "      <th>HRSA</th>\n",
       "      <th>PAP</th>\n",
       "      <th>...</th>\n",
       "      <th>ERLO</th>\n",
       "      <th>HR</th>\n",
       "      <th>ERCA</th>\n",
       "      <th>SHNT</th>\n",
       "      <th>PVS</th>\n",
       "      <th>ACO2</th>\n",
       "      <th>VALV</th>\n",
       "      <th>VLNG</th>\n",
       "      <th>VTUB</th>\n",
       "      <th>VMCH</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NORMAL</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>False</td>\n",
       "      <td>LOW</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>HIGH</td>\n",
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       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>NORMAL</td>\n",
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       "      <td>False</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>False</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>LOW</td>\n",
       "      <td>ZERO</td>\n",
       "      <td>NORMAL</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NORMAL</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>False</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>LOW</td>\n",
       "      <td>LOW</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>False</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>LOW</td>\n",
       "      <td>LOW</td>\n",
       "      <td>ZERO</td>\n",
       "      <td>ZERO</td>\n",
       "      <td>LOW</td>\n",
       "      <td>NORMAL</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NORMAL</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>False</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>False</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>LOW</td>\n",
       "      <td>LOW</td>\n",
       "      <td>ZERO</td>\n",
       "      <td>ZERO</td>\n",
       "      <td>LOW</td>\n",
       "      <td>NORMAL</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NORMAL</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>False</td>\n",
       "      <td>LOW</td>\n",
       "      <td>LOW</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>False</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>LOW</td>\n",
       "      <td>ZERO</td>\n",
       "      <td>ZERO</td>\n",
       "      <td>LOW</td>\n",
       "      <td>NORMAL</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NORMAL</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>False</td>\n",
       "      <td>LOW</td>\n",
       "      <td>LOW</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>HIGH</td>\n",
       "      <td>NORMAL</td>\n",
       "      <td>...</td>\n",
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       "      <td>HIGH</td>\n",
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       "      <td>ZERO</td>\n",
       "      <td>LOW</td>\n",
       "      <td>NORMAL</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 37 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      CVP    PCWP   HIST     TPR      BP      CO  HRBP  HREK  HRSA     PAP  \\\n",
       "0  NORMAL  NORMAL  False     LOW  NORMAL    HIGH  HIGH  HIGH  HIGH  NORMAL   \n",
       "1  NORMAL  NORMAL  False  NORMAL     LOW     LOW  HIGH  HIGH  HIGH  NORMAL   \n",
       "2  NORMAL    HIGH  False  NORMAL  NORMAL    HIGH  HIGH  HIGH  HIGH  NORMAL   \n",
       "3  NORMAL  NORMAL  False     LOW     LOW    HIGH  HIGH  HIGH  HIGH  NORMAL   \n",
       "4  NORMAL  NORMAL  False     LOW     LOW  NORMAL  HIGH  HIGH  HIGH  NORMAL   \n",
       "\n",
       "   ...   ERLO    HR   ERCA    SHNT     PVS    ACO2  VALV  VLNG  VTUB    VMCH  \n",
       "0  ...  False  HIGH  False  NORMAL  NORMAL  NORMAL  HIGH   LOW  ZERO  NORMAL  \n",
       "1  ...  False  HIGH  False  NORMAL     LOW     LOW  ZERO  ZERO   LOW  NORMAL  \n",
       "2  ...  False  HIGH  False  NORMAL     LOW     LOW  ZERO  ZERO   LOW  NORMAL  \n",
       "3  ...  False  HIGH  False  NORMAL  NORMAL     LOW  ZERO  ZERO   LOW  NORMAL  \n",
       "4  ...  False  HIGH  False  NORMAL     LOW     LOW  ZERO  ZERO   LOW  NORMAL  \n",
       "\n",
       "[5 rows x 37 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alarmdf = pd.read_csv('../data/alarm_data.csv')\n",
    "alarmdf = alarmdf.drop(columns = ['Unnamed: 0'],axis=1)\n",
    "alarmdf.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9b0566ca",
   "metadata": {},
   "source": [
    "Convert all the outcomes into numeric values."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "28703f41-03bd-4c40-8419-2d8332e2be10",
   "metadata": {},
   "outputs": [],
   "source": [
    "alarmnp = alarmdf.to_numpy()\n",
    "alarmnp[:,0] = [0 for i in range(20000)]\n",
    "\n",
    "def convertToNumeric(df):\n",
    "    npdf = df.to_numpy()\n",
    "    vars = list(df.columns)\n",
    "    n = len(df)\n",
    "    for v in vars:\n",
    "        j = vars.index(v)\n",
    "        states = list(alarmdf[v].drop_duplicates().to_numpy())\n",
    "        for i in range(n):\n",
    "            npdf[i,j] = states.index(alarmdf[v].iloc[i])\n",
    "    numdf = pd.DataFrame(npdf)\n",
    "    return numdf\n",
    "\n",
    "numalarmdf = convertToNumeric(alarmdf)\n",
    "\n",
    "cards_row = {0 : 3, 1 : 3, 2 : 2, 3 : 3, 4 : 3, 5 : 3, 6 : 3, 7 : 3, 8 : 3, 9 : 3, 10 : 3, 11 : 2, 12 : 4, 13 : 4, 14 : 4, 15 : 3, 16 : 2, 17 : 2, 18 : 2, 19 : 2, 20 : 2, 21 : 3, 22 : 2, 23 : 2, 24 : 3, 25 : 3, 26 : 2, 27 : 2, 28 : 3, 29 : 2, 30 : 2, 31 : 3, 32 : 3, 33 : 4, 34 : 4, 35 : 4, 36 : 4}\n",
    "numalarmdf.loc[len(numalarmdf)] = cards_row\n",
    "target_row = 20000\n",
    "# Move target row to first element of list.\n",
    "idx = [target_row] + [i for i in range(len(numalarmdf)) if i != target_row]\n",
    "numalarmdf.iloc[idx]\n",
    "numalarmdf_cards = numalarmdf.iloc[idx].reset_index(drop=True)\n",
    "numalarmdf_cards.columns = alarmdf.columns"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d072505d",
   "metadata": {},
   "source": [
    "## MCMC sampling"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "46d9fa1d",
   "metadata": {},
   "source": [
    "We run the PC algorithm to estimate a CPDAG that is used to restrict the possible context variables."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "ccecf833-6113-47a4-89eb-e6b68104f028",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Depth=4, working on node 36: 100%|██████████| 37/37 [00:00<00:00, 1192.31it/s]\n",
      "Context score tables: 100%|██████████| 37/37 [00:00<00:00, 49.17it/s]\n",
      "Creating #stagings tables: 100%|██████████| 37/37 [00:00<00:00, 98.00it/s] \n",
      "Order score tables: 100%|██████████| 37/37 [00:02<00:00, 16.84it/s]\n",
      "Gibbs order sampler: 100%|██████████| 5000/5000 [00:02<00:00, 2248.31it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Computation time in seconds: 8.266073226928711\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n"
     ]
    }
   ],
   "source": [
    "np.random.seed(1)\n",
    "random.seed(1)\n",
    "start = time.time()\n",
    "pcgraph = pc(numalarmdf_cards[1:].values, 0.05, \"chisq\", node_names=numalarmdf_cards.columns)\n",
    "poss_cvars = ctl.causallearn_graph_to_posscvars(pcgraph, labels=numalarmdf_cards.columns)\n",
    "#print(\"Possible context variables per node:\", poss_cvars)\n",
    "\n",
    "score_table, context_scores, context_counts = sc.order_score_tables(numalarmdf_cards,\n",
    "                                                                    max_cvars=2,\n",
    "                                                                    alpha_tot=1.0,\n",
    "                                                                    method=\"BDeu\",\n",
    "                                                                    poss_cvars=poss_cvars)\n",
    "\n",
    "orders, scores = ctl.gibbs_order_sampler(5000, score_table)\n",
    "end = time.time()\n",
    "print('Computation time in seconds:', end - start)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "513123d3-02a1-4ebf-a960-dfb5da5639b8",
   "metadata": {},
   "outputs": [],
   "source": [
    "# optimal variable ordering\n",
    "alarmmaporder = orders[scores.index(max(scores))]\n",
    "#print(alarmmaporder)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "f990832b-2fc2-4efc-8985-cc7f601dc5e8",
   "metadata": {},
   "outputs": [],
   "source": [
    "# get optimal tree for ordering\n",
    "alarmopttree = ctl._optimal_cstree_given_order(alarmmaporder, context_scores)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1fd106fe",
   "metadata": {},
   "source": [
    "## LDAG representation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "f7f87352",
   "metadata": {},
   "outputs": [],
   "source": [
    "LDAG = alarmopttree.to_LDAG()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "ac232beb-90d3-4fc8-aea6-de3816f7d467",
   "metadata": {},
   "outputs": [
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       "<title>INT&#45;&gt;VLNG</title>\n",
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       "<!-- INT&#45;&gt;PRSS -->\n",
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       "<title>INT&#45;&gt;PRSS</title>\n",
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       "<title>VALV</title>\n",
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       "<title>SHNT</title>\n",
       "<ellipse fill=\"none\" stroke=\"black\" cx=\"308.5\" cy=\"-585\" rx=\"34\" ry=\"18\"/>\n",
       "<text text-anchor=\"middle\" x=\"308.5\" y=\"-581.3\" font-family=\"Times,serif\" font-size=\"14.00\">SHNT</text>\n",
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       "<!-- INT&#45;&gt;SHNT -->\n",
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       "<title>INT&#45;&gt;MINV</title>\n",
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       "<!-- VLNG&#45;&gt;ECO2 -->\n",
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       "<title>VLNG&#45;&gt;ECO2</title>\n",
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       "<!-- PRSS&#45;&gt;KINK -->\n",
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       "<title>PRSS&#45;&gt;KINK</title>\n",
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       "<title>VALV&#45;&gt;ACO2</title>\n",
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       "<title>PVS</title>\n",
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       "<text text-anchor=\"middle\" x=\"315.5\" y=\"-421.3\" font-family=\"Times,serif\" font-size=\"14.00\">PVS</text>\n",
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       "<!-- VALV&#45;&gt;PVS -->\n",
       "<g id=\"edge21\" class=\"edge\">\n",
       "<title>VALV&#45;&gt;PVS</title>\n",
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       "<title>SAO2</title>\n",
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       "<!-- SHNT&#45;&gt;SAO2 -->\n",
       "<g id=\"edge22\" class=\"edge\">\n",
       "<title>SHNT&#45;&gt;SAO2</title>\n",
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       "<!-- PVS&#45;&gt;SAO2 -->\n",
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       "<title>PVS&#45;&gt;SAO2</title>\n",
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       "<!-- SAO2&#45;&gt;CCHL -->\n",
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       "<title>SAO2&#45;&gt;CCHL</title>\n",
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       "<title>ANES</title>\n",
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       "<title>DISC</title>\n",
       "<ellipse fill=\"none\" stroke=\"black\" cx=\"110.5\" cy=\"-759\" rx=\"30.59\" ry=\"18\"/>\n",
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       "<!-- VTUB -->\n",
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       "<!-- DISC&#45;&gt;VTUB -->\n",
       "<g id=\"edge25\" class=\"edge\">\n",
       "<title>DISC&#45;&gt;VTUB</title>\n",
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       "<!-- VTUB&#45;&gt;VLNG -->\n",
       "<g id=\"edge26\" class=\"edge\">\n",
       "<title>VTUB&#45;&gt;VLNG</title>\n",
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       "<!-- VTUB&#45;&gt;PRSS -->\n",
       "<g id=\"edge27\" class=\"edge\">\n",
       "<title>VTUB&#45;&gt;PRSS</title>\n",
       "<path fill=\"none\" stroke=\"black\" d=\"M96.38,-655.41C84.58,-642.39 67.6,-623.64 54.26,-608.91\"/>\n",
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       "<title>PMB</title>\n",
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       "<!-- PMB&#45;&gt;SHNT -->\n",
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       "<title>PMB&#45;&gt;SHNT</title>\n",
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       "<title>PAP</title>\n",
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       "<!-- PMB&#45;&gt;PAP -->\n",
       "<g id=\"edge29\" class=\"edge\">\n",
       "<title>PMB&#45;&gt;PAP</title>\n",
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       "<title>VMCH</title>\n",
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       "<title>VMCH&#45;&gt;VTUB</title>\n",
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       "<title>MVS</title>\n",
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       "<title>VMCH&#45;&gt;MVS</title>\n",
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       "<title>ERCA</title>\n",
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       "<title>ERCA&#45;&gt;HREK</title>\n",
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       "<title>ERCA&#45;&gt;HRSA</title>\n",
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      "text/plain": [
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     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "agraph = LDAG.plot_graphviz()\n",
    "agraph\n",
    "#agraph.draw('alarm_CStree_LDAG.png')"
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