day 21 - k-means.ipynb

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   "source": [
    "import numpy as np\n",
    "from bokeh.plotting import figure, gridplot, show, output_notebook"
   ]
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   "cell_type": "markdown",
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   "source": [
    "## algorithm"
   ]
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   "source": [
    "def kmeans(points, n_clusters):\n",
    "    # sample initial centroids\n",
    "    sample = np.random.choice(len(points), n_clusters, replace=False)\n",
    "    centroid = points[sample]\n",
    "    \n",
    "    loss = [-1, -2]\n",
    "    while not np.allclose(*loss):\n",
    "        # compute distance for each pair: point/centroid\n",
    "        distance = [np.sqrt(((points - c) ** 2).sum(1)) for c in centroid]\n",
    "        # new loss\n",
    "        loss = loss[1:] + [np.sum(distance)]\n",
    "        # assign new clusters\n",
    "        cluster = np.argmin(distance, axis=0)\n",
    "        # update centroids by new cluster means\n",
    "        for i in range(n_clusters):\n",
    "            centroid[i] = np.mean(points[cluster == i], axis=0)\n",
    "        \n",
    "    return cluster"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## run"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "generate clusters"
   ]
  },
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   "source": [
    "n = 100\n",
    "A = np.random.multivariate_normal([2, 0], [[1, .1], [-4, 1]], n)\n",
    "B = np.random.multivariate_normal([-2, 0], [[1, -4], [.1, 1]], n)\n",
    "C = np.random.multivariate_normal([2, -2], [[1, 4], [-.1, 1]], n)\n",
    "D = ['red', 'green', 'blue']\n",
    "\n",
    "points = np.r_[A, B, C]\n",
    "original_color = np.repeat(D[:3], n)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "detect k-means clusters"
   ]
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   "execution_count": 4,
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   "source": [
    "cluster = kmeans(points, 3)\n",
    "new_color = [D[i] for i in cluster]"
   ]
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "plot original and new clusters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
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       "  \n",
       "    }\n",
       "  \n",
       "    if (window._bokeh_is_loading === 0) {\n",
       "      console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "      run_inline_js();\n",
       "    } else {\n",
       "      load_libs(js_urls, function() {\n",
       "        console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "        run_inline_js();\n",
       "      });\n",
       "    }\n",
       "  }(this));\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "output_notebook()\n",
    "\n",
    "plot1 = figure(title='original clusters', plot_height=300)\n",
    "plot1.scatter(x=points[:, 0], y=points[:, 1], color=original_color)\n",
    "\n",
    "plot2 = figure(title='k-means clusters', plot_height=300)\n",
    "plot2.scatter(x=points[:, 0], y=points[:, 1], color=new_color)\n",
    "\n",
    "show(gridplot([[plot1], [plot2]]))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
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    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
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