87 lines (86 with data), 2.6 kB

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "VAE_FCTAE_EM:\t0.0490555\tAE_FAETC_EM:\t0.04782872\tAE_FCTAE_EM:\t0.1351901\tDAE_FAETC_EM:\t0.05422764\tDAE_FCTAE_EM:\t0.06826419\tSVAE_FCTAE_EM:\t0.08426949\tMMDVAE_EM:\t0.07765315\t"
     ]
    }
   ],
   "source": [
    "library(\"clusterCrit\")\n",
    "data_names<-c('VAE_FCTAE_EM','AE_FAETC_EM', 'AE_FCTAE_EM', 'DAE_FAETC_EM', 'DAE_FCTAE_EM','SVAE_FCTAE_EM','MMDVAE_EM')\n",
    "for(data_name in data_names){\n",
    "    cat(data_name)\n",
    "    cat(':\\t')\n",
    "    \n",
    "    number_cl=3\n",
    "    ind <- 0\n",
    "    JI_final <- matrix(data=NA, nrow=number_cl, ncol=1)\n",
    "    #cat(JI_final,\"\\n\")\n",
    "    # Read clusters imposed on simulated data \n",
    "    \n",
    "    cl  <- as.matrix(read.table(\"../data/single-cell/celltype2.txt\", \n",
    "                                sep=\"\\t\",  header=FALSE))\n",
    "    cl2 <- as.matrix(as.numeric(cl[,2]))\n",
    "    rownames(cl2) <- cl[,1]\n",
    "    #cat(cl2)\n",
    "\n",
    "    factor_path=paste(\"../data/single-cell/\",data_name,'.txt',sep='')\n",
    "    factorization=read.table(factor_path, sep=\" \",row.names=cl[,1],  header=FALSE)\n",
    "\n",
    "\n",
    "    factors <- factorization\n",
    "\n",
    "    # Clustering by Kmeans\n",
    "    JI_good <- numeric(0)\n",
    "    all_c_index <- numeric(0)\n",
    "    for (run in 1:100) {\n",
    "        kmeans.out <- kmeans(factors, centers=number_cl) \n",
    "        clust_iCluster <- kmeans.out$cluster\n",
    "#         cat(\"clust_iCluster:\",clust_iCluster,\"\\n\")\n",
    "        c_index <- numeric(0)\n",
    "        c_index <- c(c_index, intCriteria(as.matrix(factors),clust_iCluster, crit=c(\"C_index\"))$c_index)\n",
    "        all_c_index<-rbind(all_c_index,c_index)\n",
    "    \n",
    "    }\n",
    "    avg_c_index=apply(all_c_index,2,mean)\n",
    "    cat(avg_c_index)\n",
    "    cat('\\t')\n",
    "    \n",
    "    \n",
    "    }"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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