TCS-Benchmark-PBN.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "16ad3419",
   "metadata": {},
   "source": [
    "# Initialization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "443667e8",
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   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "INFO Note: NumExpr detected 16 cores but \"NUMEXPR_MAX_THREADS\" not set, so enforcing safe limit of 8.\n",
      "INFO NumExpr defaulting to 8 threads.\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<Handlers.SIG_DFL: 0>"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from logging import ERROR\n",
    "import os\n",
    "from pathlib import Path\n",
    "import signal\n",
    "from subprocess import CalledProcessError\n",
    "import time\n",
    "\n",
    "# PyBoolNet initialization\n",
    "from pyboolnet.repository import get_all_names, get_bnet\n",
    "from pyboolnet.file_exchange import bnet2primes\n",
    "from pyboolnet.trap_spaces import compute_trap_spaces\n",
    "from pyboolnet import log\n",
    "log.setLevel(ERROR)\n",
    "\n",
    "# mpbn init\n",
    "import mpbn\n",
    "\n",
    "# trappist init\n",
    "import trappist\n",
    "\n",
    "# timeout with signals\n",
    "class TimeOutException(Exception):\n",
    "   pass\n",
    "\n",
    "def handler(_signnum, _frame):\n",
    "    print(\"Timeout\")\n",
    "    raise TimeOutException()\n",
    "    \n",
    "signal.signal(signal.SIGALRM, handler)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "77261084",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2022-07-17T15:34:48.314141Z"
    }
   },
   "outputs": [],
   "source": [
    "# compute trapspaces using PyBoolNet\n",
    "def bench_pyboolnet(models, timeout=180, number=1, max_output=1000):\n",
    "    for model in models:\n",
    "        print(model)        \n",
    "        successes = 0\n",
    "        total_time = 0\n",
    "        nb_tspaces = 0\n",
    "        for i in range(number):\n",
    "            signal.alarm(timeout)\n",
    "            try:\n",
    "                start = time.perf_counter()\n",
    "                primes = bnet2primes(model + \".bnet\")\n",
    "                tspaces = compute_trap_spaces(primes, \"min\", max_output=max_output)\n",
    "                nb_tspaces = len(tspaces)\n",
    "                end = time.perf_counter()\n",
    "                total_time += end - start\n",
    "                successes += 1\n",
    "            except (TimeOutException, CalledProcessError, Exception):\n",
    "                total_time += timeout\n",
    "            except MemoryError:\n",
    "                print (\"MemoryError\")\n",
    "                total_time += timeout\n",
    "            signal.alarm(0)\n",
    "        \n",
    "        os.system(\"killall -9 BNetToPrime_linux64\")\n",
    "        if successes > 0:\n",
    "            if successes < number:\n",
    "                print(f\"{number - successes} failures…\")\n",
    "            print(f\"{nb_tspaces} trap spaces {total_time/number:.2f}\\n===\")\n",
    "        else:\n",
    "            print(\"DNF\\n===\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "bc1b4dcb",
   "metadata": {
    "execution": {
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     "iopub.status.busy": "2022-07-17T15:34:48.317089Z",
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     "shell.execute_reply": "2022-07-17T15:34:48.323017Z"
    }
   },
   "outputs": [],
   "source": [
    "# compute trapspaces using mpbn\n",
    "def bench_mpbn(models, timeout=180, number=1, max_output=1000):\n",
    "    for model in models:\n",
    "        print(model)\n",
    "        successes = 0\n",
    "        total_time = 0\n",
    "        nb_tspaces = 0\n",
    "        for i in range(number):\n",
    "            signal.alarm(timeout)\n",
    "            try:\n",
    "                start = time.perf_counter()\n",
    "                mbn = mpbn.load(model + \".bnet\")\n",
    "                tspaces = list(mbn.attractors(limit=max_output))\n",
    "                nb_tspaces = len(tspaces)\n",
    "                end = time.perf_counter()\n",
    "                total_time += end - start\n",
    "                successes += 1\n",
    "            except AssertionError:\n",
    "                if i == 0:\n",
    "                    print(\"Non-monotonic\")\n",
    "            except TimeOutException:\n",
    "                total_time += timeout\n",
    "            signal.alarm(0)\n",
    "        if successes > 0:\n",
    "            if successes < number:\n",
    "                print(f\"{number - successes} failures…\")\n",
    "            print(f\"{nb_tspaces} trap spaces {total_time/number:.2f}\\n===\")\n",
    "        else:\n",
    "            print(\"DNF\\n===\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "aad67e2d",
   "metadata": {
    "execution": {
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     "iopub.status.busy": "2022-07-17T15:34:48.325841Z",
     "iopub.status.idle": "2022-07-17T15:34:48.332910Z",
     "shell.execute_reply": "2022-07-17T15:34:48.332289Z"
    }
   },
   "outputs": [],
   "source": [
    "# compute trapspaces using trappist\n",
    "def bench_trappist(models, timeout=180, number=1, max_output=1000, **kwargs):\n",
    "    for model in models:\n",
    "        print(model)\n",
    "        successes = 0\n",
    "        total_time = 0\n",
    "        nb_tspaces = 0\n",
    "        for i in range(number):\n",
    "            signal.alarm(timeout)\n",
    "            try:\n",
    "                start = time.perf_counter()\n",
    "                tspaces = trappist.compute_trap_spaces(model + \".bnet\", max_output=max_output, time_limit=timeout, **kwargs)\n",
    "                nb_tspaces = len(list(tspaces))\n",
    "                end = time.perf_counter()\n",
    "                total_time += end - start\n",
    "                successes += 1\n",
    "            except (TimeOutException, CalledProcessError):\n",
    "                total_time += timeout\n",
    "            signal.alarm(0)\n",
    "        if successes > 0:\n",
    "            if successes < number:\n",
    "                print(f\"{number - successes} failures…\")\n",
    "            print(f\"{nb_tspaces} trap spaces {total_time/number:.2f}\\n===\")\n",
    "        else:\n",
    "            print(\"DNF\\n===\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "15ce8425",
   "metadata": {},
   "source": [
    "## PyBoolNet repository\n",
    "\n",
    "Unfortunately all models are very easy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "1a12f3c6",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2022-07-17T15:34:48.342829Z"
    }
   },
   "outputs": [],
   "source": [
    "models = [str(Path().absolute() / \"TCS-data-set/PyBoolNet\" / name[:-5]) for name in os.listdir(\"TCS-data-set/PyBoolNet\") if name.endswith(\".bnet\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "22f5879a",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2022-07-17T15:34:48.347730Z"
    },
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/saadatpour_guardcell\n",
      "1 trap spaces 0.06\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1a\n",
      "2 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_stomatal\n",
      "1 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/raf\n",
      "2 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n7k3\n",
      "10 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/klamt_tcr\n",
      "8 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl\n",
      "156 trap spaces 0.09\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n15k3\n",
      "3 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/xiao_wnt5a\n",
      "4 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl_v2\n",
      "258 trap spaces 0.04\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/selvaggio_emt\n",
      "1000 trap spaces 0.48\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n7s3\n",
      "3 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/davidich_yeast\n",
      "12 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/faure_cellcycle\n",
      "2 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/krumsiek_myeloid\n",
      "6 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_life\n",
      "7 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/arellano_rootstem\n",
      "4 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/calzone_cellfate\n",
      "27 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/irons_yeast\n",
      "1 trap spaces 0.03\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dahlhaus_neuroplastoma\n",
      "32 trap spaces 0.03\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/multivalued\n",
      "4 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/tournier_apoptosis\n",
      "3 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/grieco_mapk\n",
      "18 trap spaces 0.03\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/jaoude_thdiff\n",
      "1000 trap spaces 0.85\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1b\n",
      "2 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n12c5\n",
      "5 trap spaces 17.83\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n5s3\n",
      "3 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n6s1c2\n",
      "3 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/remy_tumorigenesis\n",
      "25 trap spaces 0.94\n",
      "===\n"
     ]
    }
   ],
   "source": [
    "bench_pyboolnet(models)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "0f710ad3",
   "metadata": {
    "execution": {
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     "iopub.status.busy": "2022-07-17T15:34:48.350490Z",
     "iopub.status.idle": "2022-07-17T15:34:48.353010Z",
     "shell.execute_reply": "2022-07-17T15:34:48.352460Z"
    },
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/saadatpour_guardcell\n",
      "1 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1a\n",
      "2 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_stomatal\n",
      "1 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/raf\n",
      "2 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n7k3\n",
      "Non-monotonic\n",
      "DNF\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/klamt_tcr\n",
      "8 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl\n",
      "156 trap spaces 0.09\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n15k3\n",
      "Non-monotonic\n",
      "DNF\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/xiao_wnt5a\n",
      "4 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl_v2\n",
      "258 trap spaces 0.08\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/selvaggio_emt\n",
      "1000 trap spaces 0.28\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n7s3\n",
      "3 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/davidich_yeast\n",
      "12 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/faure_cellcycle\n",
      "2 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/krumsiek_myeloid\n",
      "6 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_life\n",
      "7 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/arellano_rootstem\n",
      "4 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/calzone_cellfate\n",
      "27 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/irons_yeast\n",
      "1 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dahlhaus_neuroplastoma\n",
      "32 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/multivalued\n",
      "4 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/tournier_apoptosis\n",
      "3 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/grieco_mapk\n",
      "18 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/jaoude_thdiff\n",
      "1000 trap spaces 0.45\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1b\n",
      "2 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n12c5\n",
      "5 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n5s3\n",
      "Non-monotonic\n",
      "DNF\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n6s1c2\n",
      "3 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/remy_tumorigenesis\n",
      "25 trap spaces 0.02\n",
      "===\n"
     ]
    }
   ],
   "source": [
    "bench_mpbn(models)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "b1088dcd",
   "metadata": {
    "execution": {
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     "iopub.status.idle": "2022-07-17T15:34:48.357660Z",
     "shell.execute_reply": "2022-07-17T15:34:48.357100Z"
    },
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   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/saadatpour_guardcell\n",
      "1 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1a\n",
      "2 trap spaces 0.03\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_stomatal\n",
      "1 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/raf\n",
      "2 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n7k3\n",
      "10 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/klamt_tcr\n",
      "8 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl\n",
      "156 trap spaces 0.03\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n15k3\n",
      "3 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/xiao_wnt5a\n",
      "4 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl_v2\n",
      "258 trap spaces 0.03\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/selvaggio_emt\n",
      "1000 trap spaces 0.08\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n7s3\n",
      "3 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/davidich_yeast\n",
      "12 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/faure_cellcycle\n",
      "2 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/krumsiek_myeloid\n",
      "6 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_life\n",
      "7 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/arellano_rootstem\n",
      "4 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/calzone_cellfate\n",
      "27 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/irons_yeast\n",
      "1 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dahlhaus_neuroplastoma\n",
      "32 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/multivalued\n",
      "4 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/tournier_apoptosis\n",
      "3 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/grieco_mapk\n",
      "18 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/jaoude_thdiff\n",
      "1000 trap spaces 0.09\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1b\n",
      "2 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n12c5\n",
      "5 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n5s3\n",
      "3 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n6s1c2\n",
      "3 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/remy_tumorigenesis\n",
      "25 trap spaces 0.02\n",
      "===\n"
     ]
    }
   ],
   "source": [
    "bench_trappist(models)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "a1c747e6",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2022-07-17T15:34:48.364784Z",
     "iopub.status.busy": "2022-07-17T15:34:48.364598Z",
     "iopub.status.idle": "2022-07-17T15:34:48.367239Z",
     "shell.execute_reply": "2022-07-17T15:34:48.366618Z"
    },
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/saadatpour_guardcell\n",
      "1 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1a\n",
      "2 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_stomatal\n",
      "1 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/raf\n",
      "2 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n7k3\n",
      "10 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/klamt_tcr\n",
      "8 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl\n",
      "156 trap spaces 0.05\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n15k3\n",
      "3 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/xiao_wnt5a\n",
      "4 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl_v2\n",
      "258 trap spaces 0.07\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/selvaggio_emt\n",
      "1000 trap spaces 0.18\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n7s3\n",
      "3 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/davidich_yeast\n",
      "12 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/faure_cellcycle\n",
      "2 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/krumsiek_myeloid\n",
      "6 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_life\n",
      "7 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/arellano_rootstem\n",
      "4 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/calzone_cellfate\n",
      "27 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/irons_yeast\n",
      "1 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dahlhaus_neuroplastoma\n",
      "32 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/multivalued\n",
      "4 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/tournier_apoptosis\n",
      "3 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/grieco_mapk\n",
      "18 trap spaces 0.02\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/jaoude_thdiff\n",
      "1000 trap spaces 0.36\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1b\n",
      "2 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n12c5\n",
      "5 trap spaces 0.01\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n5s3\n",
      "3 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n6s1c2\n",
      "3 trap spaces 0.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/remy_tumorigenesis\n",
      "25 trap spaces 0.01\n",
      "===\n"
     ]
    }
   ],
   "source": [
    "bench_trappist(models, method='sat')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "c4055088",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/saadatpour_guardcell\n",
      "1 trap spaces 0.53\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1a\n",
      "2 trap spaces 0.63\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_stomatal\n",
      "1 trap spaces 0.39\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/raf\n",
      "2 trap spaces 0.55\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n7k3\n",
      "10 trap spaces 2.07\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/klamt_tcr\n",
      "8 trap spaces 1.98\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl\n",
      "156 trap spaces 37.26\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n15k3\n",
      "3 trap spaces 0.77\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/xiao_wnt5a\n",
      "4 trap spaces 1.00\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl_v2\n",
      "258 trap spaces 66.95\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/selvaggio_emt\n",
      "Timeout\n",
      "DNF\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n7s3\n",
      "3 trap spaces 0.79\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/davidich_yeast\n",
      "12 trap spaces 2.56\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/faure_cellcycle\n",
      "2 trap spaces 0.58\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/krumsiek_myeloid\n",
      "6 trap spaces 1.48\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_life\n",
      "7 trap spaces 1.68\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/arellano_rootstem\n",
      "4 trap spaces 0.97\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/calzone_cellfate\n",
      "27 trap spaces 5.59\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/irons_yeast\n",
      "1 trap spaces 0.37\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dahlhaus_neuroplastoma\n",
      "32 trap spaces 6.56\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/multivalued\n",
      "4 trap spaces 0.93\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/tournier_apoptosis\n",
      "3 trap spaces 0.74\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/grieco_mapk\n",
      "18 trap spaces 3.93\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/jaoude_thdiff\n",
      "Timeout\n",
      "DNF\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1b\n",
      "2 trap spaces 0.56\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n12c5\n",
      "5 trap spaces 1.21\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n5s3\n",
      "3 trap spaces 0.74\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n6s1c2\n",
      "3 trap spaces 0.91\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/remy_tumorigenesis\n",
      "25 trap spaces 5.98\n",
      "===\n"
     ]
    }
   ],
   "source": [
    "bench_trappist(models, method='cp')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "328fe9c2",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/saadatpour_guardcell\n",
      "1 trap spaces 0.45\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1a\n",
      "2 trap spaces 0.49\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_stomatal\n",
      "1 trap spaces 0.29\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/raf\n",
      "2 trap spaces 0.39\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n7k3\n",
      "10 trap spaces 1.46\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/klamt_tcr\n",
      "8 trap spaces 1.22\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl\n",
      "Timeout\n",
      "DNF\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/randomnet_n15k3\n",
      "3 trap spaces 0.67\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/xiao_wnt5a\n",
      "4 trap spaces 0.89\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/zhang_tlgl_v2\n",
      "Timeout\n",
      "DNF\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/selvaggio_emt\n",
      "Timeout\n",
      "DNF\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n7s3\n",
      "3 trap spaces 0.68\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/davidich_yeast\n",
      "12 trap spaces 2.21\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/faure_cellcycle\n",
      "2 trap spaces 0.46\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/krumsiek_myeloid\n",
      "6 trap spaces 1.26\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dinwoodie_life\n",
      "7 trap spaces 1.39\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/arellano_rootstem\n",
      "4 trap spaces 0.96\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/calzone_cellfate\n",
      "27 trap spaces 6.03\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/irons_yeast\n",
      "1 trap spaces 0.39\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/dahlhaus_neuroplastoma\n",
      "32 trap spaces 6.99\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/multivalued\n",
      "4 trap spaces 0.86\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/tournier_apoptosis\n",
      "3 trap spaces 0.75\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/grieco_mapk\n",
      "18 trap spaces 10.46\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/jaoude_thdiff\n",
      "Timeout\n",
      "DNF\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n3s1c1b\n",
      "2 trap spaces 0.49\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n12c5\n",
      "5 trap spaces 1.10\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n5s3\n",
      "3 trap spaces 0.69\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/n6s1c2\n",
      "3 trap spaces 0.59\n",
      "===\n",
      "/home/giang-trinh/git_repo/trap-spaces-as-siphons/TCS-data-set/PyBoolNet/remy_tumorigenesis\n",
      "25 trap spaces 7.98\n",
      "===\n"
     ]
    }
   ],
   "source": [
    "bench_trappist(models, method='ilp')"
   ]
  }
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