DataAnalysis.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "24b672b1",
   "metadata": {},
   "source": [
    "Load in the Julia Machine learning packages, plotting package, and file loader, as well as custom utility functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "71bcd057",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "evalmpe (generic function with 1 method)"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "using Flux,Statistics,Plots,MLDataUtils,DelimitedFiles,StatsPlots\n",
    "using Flux.Data: DataLoader\n",
    "include(\"utilityfunc.jl\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6389dfdc",
   "metadata": {},
   "source": [
    "Set bounds and scaler on baseline full integration model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "15ab8e51",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "inv_iscalerbatchb (generic function with 1 method)"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#set lower and upper bounds on Lpt,Kt and Rs (Lpt is first element and Kt is second element and Rs is third element)\n",
    "lb=Float32[5e-7,5e-7,5]\n",
    "ub=Float32[5e-6,5e-6,30]\n",
    "\n",
    "iscalerb(x)=(x-lb)./(ub-lb) #Define Min-Max Noramization function\n",
    "inv_iscalerb(x)=x.*(ub.-lb).+lb\n",
    "\n",
    "function iscalerbatchb(x)\n",
    "    nfeat,sl = size(x)\n",
    "    out=Array{Float32,2}(undef,nfeat,sl)\n",
    "    for i=1:sl\n",
    "        out[:,i]=iscalerb(x[:,i])\n",
    "    end\n",
    "    return out\n",
    "end\n",
    "\n",
    "function inv_iscalerbatchb(x)\n",
    "    nfeat,sl = size(x)\n",
    "    out=Array{Float32,2}(undef,nfeat,sl)\n",
    "    for i=1:sl\n",
    "        out[:,i]=inv_iscalerb(x[:,i])\n",
    "    end\n",
    "    return out\n",
    "end"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5483db33",
   "metadata": {},
   "source": [
    "Set bounds and scaler on Dynamic models"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "02513c33",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "inv_oscaler (generic function with 1 method)"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "conc_ub=Float32(.6)\n",
    "\n",
    "i_lb=Float32[5e-7,7e-7,5.0,0.0,0.0]\n",
    "i_ub=Float32[3.5e-6,4e-6,30,(300/3600),conc_ub]\n",
    "iscaler(x)=(x-i_lb)./(i_ub-i_lb)\n",
    "inv_iscaler(x)=x.*(i_ub.-i_lb).+i_lb\n",
    "oscaler(x)= x ./ conc_ub\n",
    "inv_oscaler(x)=x.*conc_ub"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7f19eae9",
   "metadata": {},
   "source": [
    "Load in the latest machine learning models"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "00605742",
   "metadata": {},
   "outputs": [],
   "source": [
    "using BSON: @load\n",
    "@load \"m_baseline.bson\" m_baseline\n",
    "@load \"m_MLP_f.bson\" m_MLP\n",
    "@load \"m_RNN_f.bson\" m_RNN\n",
    "@load \"m_LSTM_f.bson\" m_LSTM"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6471c292",
   "metadata": {},
   "source": [
    "Set up models without scalers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "4b10d074",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "NN_l (generic function with 1 method)"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "NN_b(x)=inv_oscaler(m_baseline(iscalerb(x)))\n",
    "NN_m(x)=inv_oscaler(m_MLP(iscaler(x)))\n",
    "NN_r(x)=inv_oscaler(m_RNN(iscaler(x)))\n",
    "NN_l(x)=inv_oscaler(m_LSTM(iscaler(x)))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "121fc96e",
   "metadata": {},
   "source": [
    "Read in just the test data and define characteristics"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "22e257e7",
   "metadata": {},
   "outputs": [],
   "source": [
    "testdat=readdlm(\"TestData.csv\",',',Float32);"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "3c0297aa",
   "metadata": {},
   "outputs": [],
   "source": [
    "ntestbatch=1000;\n",
    "ntestsamp=ntestbatch*20;\n",
    "nfeat=5; #5 features\n",
    "ntarg=1; #1 target values\n",
    "sl=20; #sequence length of 20"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "08a1174e",
   "metadata": {},
   "outputs": [],
   "source": [
    "x_test = testdat[1:5,:];\n",
    "y_test=testdat[6,:];"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ffacfb53",
   "metadata": {},
   "source": [
    "Set up baseline data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "f5563af8",
   "metadata": {},
   "outputs": [],
   "source": [
    "S=Array{Float32,2}(undef,3,ntestbatch)\n",
    "Xn=inv_iscalerbatch(x_test)\n",
    "for i=1:ntestbatch\n",
    "    S[:,i]=Xn[1:3,20*i]\n",
    "end\n",
    "XS=iscalerbatchb(S);\n",
    "YS=reshape(y_test,(20,ntestbatch));\n",
    "YS_sc=inv_oscaler(YS);"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2d35856c",
   "metadata": {},
   "source": [
    "Load in the points of interest that correspond to different cancer treatments from prior optimization study"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "03d9b4a3",
   "metadata": {},
   "outputs": [],
   "source": [
    "data_oi=readdlm(\"data_oi.csv\",',',Float32)\n",
    "s_oi = data_oi[1:3,:];\n",
    "y_oi=data_oi[4:end,:];\n",
    "t=(300/3600)*(1/20)*[t for t=1:20];"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "21eb4279",
   "metadata": {},
   "source": [
    "Evaluate the MSE, the RMSE, and the MPE on the test set for the full integration MLP model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "71e63a4c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cust_mse(XS, YS, m_baseline) = 2.6885914f-6\n",
      "RMSE(XS, YS, m_baseline) = 0.0016396925f0\n",
      "mean_error_func(XS, YS, m_baseline) = 0.7113812f0\n"
     ]
    }
   ],
   "source": [
    "@show cust_mse(XS,YS,m_baseline);\n",
    "@show RMSE(XS,YS,m_baseline);\n",
    "@show mean_error_func(XS,YS,m_baseline);"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "61626d51",
   "metadata": {},
   "source": [
    "Evaluate the MSE, the RMSE, and the MPE on the test set and the MPE on just biological parameters for the dynamic MLP models"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "95bffaef",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cust_mse(x_test, y_test, m_MLP) = 5.316399f-7\n",
      "mean_error_func(x_test, y_test, m_MLP) = 0.551797f0\n",
      "RMSE(x_test, y_test, m_MLP) = 0.0007291364f0\n",
      "evalmpe(S, YS, m_MLP) = 39.406616f0\n"
     ]
    }
   ],
   "source": [
    "@show cust_mse(x_test,y_test,m_MLP);\n",
    "@show mean_error_func(x_test,y_test,m_MLP);\n",
    "@show RMSE(x_test,y_test,m_MLP);\n",
    "@show evalmpe(S,YS,m_MLP);"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "59aa945b",
   "metadata": {},
   "source": [
    "Evaluate the MSE, the RMSE, and the MPE on the test set and the MPE on just biological parameters for the dynamic RNN models"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "e596a509",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cust_mse(x_test, y_test, m_RNN) = 1.4627354f-6\n",
      "mean_error_func(x_test, y_test, m_RNN) = 1.6145294f0\n",
      "RMSE(x_test, y_test, m_RNN) = 0.001209436f0\n",
      "evalmpe(S, YS, m_RNN) = 33.268154f0\n"
     ]
    }
   ],
   "source": [
    "@show cust_mse(x_test,y_test,m_RNN);\n",
    "@show mean_error_func(x_test,y_test,m_RNN);\n",
    "@show RMSE(x_test,y_test,m_RNN);\n",
    "Flux.reset!(m_RNN);\n",
    "@show evalmpe(S,YS,m_RNN);"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4670458a",
   "metadata": {},
   "source": [
    "Evaluate the MSE, the RMSE, and the MPE on the test set and the MPE on just biological parameters for the dynamic LSTM models"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "ef8972f2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cust_mse(x_test, y_test, m_LSTM) = 4.1018444f-7\n",
      "mean_error_func(x_test, y_test, m_LSTM) = 0.8519007f0\n",
      "RMSE(x_test, y_test, m_LSTM) = 0.00064045645f0\n",
      "evalmpe(S, YS, m_LSTM) = 38.787144f0\n"
     ]
    }
   ],
   "source": [
    "@show cust_mse(x_test,y_test,m_LSTM);\n",
    "@show mean_error_func(x_test,y_test,m_LSTM);\n",
    "@show RMSE(x_test,y_test,m_LSTM);\n",
    "Flux.reset!(m_LSTM);\n",
    "@show evalmpe(S,YS,m_LSTM);"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "52722504",
   "metadata": {},
   "source": [
    "Read in epoch vs validation error from spreadsheet and plot it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "2b9c9758",
   "metadata": {},
   "outputs": [
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     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "epochE=readdlm(\"EpochLog.csv\",',',Float32);\n",
    "plot(1:100,[epochE[:,1],epochE[:,2],epochE[:,3],epochE[:,4]],\n",
    "title=\"Validation Error vs Epochs\",\n",
    "    ylabel=\"Validation MSE\",\n",
    "    xlabel=\"Epochs\",\n",
    "    label=[\"Baseline MLP Model\" \"Dynamic MLP\" \"Dynamic RNN\" \"Dynamic LSTM\"],\n",
    "    legend=:topright,\n",
    "    grid=:off,\n",
    "    #color_palette=[:blue,:gold,:darkorange,:red]\n",
    "    color_palette=[:blue,:red,:darkorange,:gold]\n",
    ")\n",
    "#savefig(\"valepocherror.png\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2cf9d3d7",
   "metadata": {},
   "source": [
    "Plot the accumulation profile of the mechanistic and all ML surrogate models at each of the samples of interest from past optimization study on the effect of different cancer treatments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "5da24422",
   "metadata": {},
   "outputs": [
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     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "#Plot 1 - control DEX - 70kDa\n",
    "Flux.reset!(m_LSTM)\n",
    "Flux.reset!(m_RNN)\n",
    "case=1\n",
    "plot(t,\n",
    "    [y_oi[:,case], NN_b(s_oi[:,case]),evalprofile(s_oi[:,case],m_MLP),evalprofile(s_oi[:,case],m_RNN),evalprofile(s_oi[:,case],m_LSTM)],\n",
    "    title=\"Control DEX - 70kDa\",\n",
    "    ylabel=\"Accmulation\",\n",
    "    xlabel=\"Time (seconds)\",\n",
    "    label=[\"Mechanistic Model\" \"Baseline Model\" \"Dynamic MLP\" \"Dynamic RNN\" \"Dynamic LSTM\"],\n",
    "    legend=:topleft,\n",
    "    grid=:off,\n",
    "    #color_palette=[:green,:blue,:gold,:darkorange,:red]\n",
    "    color_palette=[:green,:darkorange,:gold,:red,:blue]\n",
    ")\n",
    "annotate!(.065,0.005,(\"L_p=$(s_oi[1,case]),K=$(s_oi[2,case]),Rs=$(s_oi[3,case])\",9))\n",
    "#savefig(\"dexc_70.png\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "dc3b7853",
   "metadata": {},
   "outputs": [
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     "execution_count": 17,
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     "output_type": "execute_result"
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   "source": [
    "#Plot 2 - 3mg/kg DEX - 70kDa\n",
    "Flux.reset!(m_LSTM)\n",
    "Flux.reset!(m_RNN)\n",
    "case=2\n",
    "plot(t,\n",
    "    [y_oi[:,case], NN_b(s_oi[:,case]),evalprofile(s_oi[:,case],m_MLP),evalprofile(s_oi[:,case],m_RNN),evalprofile(s_oi[:,case],m_LSTM)],\n",
    "    title=\"3mg/kg DEX - 70kDa\",\n",
    "    ylabel=\"Accmulation\",\n",
    "    xlabel=\"Time (seconds)\",\n",
    "    label=[\"Mechanistic Model\" \"Baseline Model\" \"Dynamic MLP\" \"Dynamic RNN\" \"Dynamic LSTM\"],\n",
    "    legend=:topleft,\n",
    "    grid=:off,\n",
    "    #color_palette=[:green,:blue,:gold,:darkorange,:red]\n",
    "    color_palette=[:green,:darkorange,:gold,:red,:blue]\n",
    ")\n",
    "annotate!(.065,0.02,(\"L_p=$(s_oi[1,case]),K=$(s_oi[2,case]),Rs=$(s_oi[3,case])\",9))\n",
    "#savefig(\"dex3_70.png\")"
   ]
  },
  {
   "cell_type": "code",
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   "id": "c51512eb",
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   ],
   "source": [
    "#Plot 3 - 30mg/kg DEX - 70kDa\n",
    "Flux.reset!(m_LSTM)\n",
    "Flux.reset!(m_RNN)\n",
    "case=3\n",
    "plot(t,\n",
    "    [y_oi[:,case], NN_b(s_oi[:,case]),evalprofile(s_oi[:,case],m_MLP),evalprofile(s_oi[:,case],m_RNN),evalprofile(s_oi[:,case],m_LSTM)],\n",
    "    title=\"30mg/kg DEX - 70kDa\",\n",
    "    ylabel=\"Accmulation\",\n",
    "    xlabel=\"Time (seconds)\",\n",
    "    label=[\"Mechanistic Model\" \"Baseline Model\" \"Dynamic MLP\" \"Dynamic RNN\" \"Dynamic LSTM\"],\n",
    "    legend=:topleft,\n",
    "    grid=:off,\n",
    "    #color_palette=[:green,:blue,:gold,:darkorange,:red]\n",
    "    color_palette=[:green,:darkorange,:gold,:red,:blue]\n",
    ")\n",
    "annotate!(.065,0.015,(\"L_p=$(s_oi[1,case]),K=$(s_oi[2,case]),Rs=$(s_oi[3,case])\",9))\n",
    "#savefig(\"dex30_70.png\")"
   ]
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  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "dfb17081",
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      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Plot 4 - control DEX - 500kDa\n",
    "Flux.reset!(m_LSTM)\n",
    "Flux.reset!(m_RNN)\n",
    "case=4\n",
    "plot(t,\n",
    "    [y_oi[:,case], NN_b(s_oi[:,case]),evalprofile(s_oi[:,case],m_MLP),evalprofile(s_oi[:,case],m_RNN),evalprofile(s_oi[:,case],m_LSTM)],\n",
    "    title=\"Control DEX - 500kDa\",\n",
    "    ylabel=\"Accmulation\",\n",
    "    xlabel=\"Time (seconds)\",\n",
    "    label=[\"Mechanistic Model\" \"Baseline Model\" \"Dynamic MLP\" \"Dynamic RNN\" \"Dynamic LSTM\"],\n",
    "    legend=:topleft,\n",
    "    grid=:off,\n",
    "    #color_palette=[:green,:blue,:gold,:darkorange,:red]\n",
    "    color_palette=[:green,:darkorange,:gold,:red,:blue]\n",
    ")\n",
    "annotate!(.065,0.005,(\"L_p=$(s_oi[1,case]),K=$(s_oi[2,case]),Rs=$(s_oi[3,case])\",9))\n",
    "#savefig(\"dexc_500.png\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "be8a123d",
   "metadata": {},
   "outputs": [
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   "source": [
    "#Plot 5 - 3mg/kg DEX - 500kDa\n",
    "Flux.reset!(m_LSTM)\n",
    "Flux.reset!(m_RNN)\n",
    "case=5\n",
    "plot(t,\n",
    "    [y_oi[:,case], NN_b(s_oi[:,case]),evalprofile(s_oi[:,case],m_MLP),evalprofile(s_oi[:,case],m_RNN),evalprofile(s_oi[:,case],m_LSTM)],\n",
    "    title=\"3mg/kg DEX - 500kDa\",\n",
    "    ylabel=\"Accmulation\",\n",
    "    xlabel=\"Time (seconds)\",\n",
    "    label=[\"Mechanistic Model\" \"Baseline Model\" \"Dynamic MLP\" \"Dynamic RNN\" \"Dynamic LSTM\"],\n",
    "    legend=:topleft,\n",
    "    grid=:off,\n",
    "    #color_palette=[:green,:blue,:gold,:darkorange,:red]\n",
    "    color_palette=[:green,:darkorange,:gold,:red,:blue]\n",
    ")\n",
    "annotate!(.065,0.02,(\"L_p=$(s_oi[1,case]),K=$(s_oi[2,case]),Rs=$(s_oi[3,case])\",9))\n",
    "#savefig(\"dex3_500.png\")"
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  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "b04e9cc8",
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     "execution_count": 21,
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   "source": [
    "#Plot 6 - 30mg/kg DEX - 500kDa\n",
    "Flux.reset!(m_LSTM)\n",
    "Flux.reset!(m_RNN)\n",
    "case=6\n",
    "plot(t,\n",
    "    [y_oi[:,case], NN_b(s_oi[:,case]),evalprofile(s_oi[:,case],m_MLP),evalprofile(s_oi[:,case],m_RNN),evalprofile(s_oi[:,case],m_LSTM)],\n",
    "    title=\"30mg/kg DEX - 500kDa\",\n",
    "    ylabel=\"Accmulation\",\n",
    "    xlabel=\"Time (seconds)\",\n",
    "    label=[\"Mechanistic Model\" \"Baseline Model\" \"Dynamic MLP\" \"Dynamic RNN\" \"Dynamic LSTM\"],\n",
    "    legend=:topleft,\n",
    "    grid=:off,\n",
    "    #color_palette=[:green,:blue,:gold,:darkorange,:red]\n",
    "    color_palette=[:green,:darkorange,:gold,:red,:blue]\n",
    ")\n",
    "annotate!(.065,0.01,(\"L_p=$(s_oi[1,case]),K=$(s_oi[2,case]),Rs=$(s_oi[3,case])\",9))\n",
    "#savefig(\"dex30_500.png\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "a6f54989",
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     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#Plot a bar chart of the accuracy of each model\n",
    "vals = [ mean_error_func(XS,YS,m_baseline),evalmpe(S,YS,m_MLP),evalmpe(S,YS,m_RNN),evalmpe(S,YS,m_LSTM)]\n",
    "cats = [\"Full Integration\\nMLP\", \"Dynamic\\nMLP\", \"Dynamic\\nRNN\", \"Dynamic\\nLSTM\"]\n",
    "colorMap = Dict(\"Full Integration\\nMLP\"=>\"blue\",\"Dynamic\\nMLP\"=>\"gold\",\"Dynamic\\nRNN\"=>\"darkorange\",\"Dynamic\\nLSTM\"=>\"red\")\n",
    "colours = [colorMap[i] for i in cats]\n",
    "accplot=bar(cats,vals,colour=colours,grid=false,legend=false,\n",
    "ylabel = \"Mean Percent Error\",\n",
    "title = \"Surrogate Model Accuracy\",\n",
    "guidefontsize=12,\n",
    "tickfontsize=12,\n",
    "titlefontsize=18\n",
    "#titlefont=font(22,\"Calibri\")\n",
    ")\n",
    "#savefig(accplot,\"accplot.png\")"
   ]
  }
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