docs/tutorials/linkpred/nn.ipynb

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   "cell_type": "markdown",
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    }
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   "source": [
    "# Link prediction"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "This notebook illustrates the prediction of links of a graph by nearest neighbors in the embedding space. Most links are supposed to be actual edges of the graph."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
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    "ExecuteTime": {
     "end_time": "2019-07-15T12:29:50.554431Z",
     "start_time": "2019-07-15T12:29:50.414075Z"
    },
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "from IPython.display import SVG"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "from sknetwork.data import karate_club, painters, movie_actor\n",
    "from sknetwork.linkpred import NNLinker\n",
    "from sknetwork.embedding import Spectral\n",
    "from sknetwork.visualization import visualize_graph, visualize_bigraph"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Graphs"
   ]
  },
  {
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   "execution_count": 14,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "graph = karate_club(metadata=True)\n",
    "adjacency = graph.adjacency\n",
    "position = graph.position\n",
    "labels_true = graph.labels"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
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    "image = visualize_graph(adjacency, position)\n",
    "SVG(image)"
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   "source": [
    "linker = NNLinker(n_neighbors=3)\n",
    "links = linker.fit_predict(adjacency)"
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      "text/plain": [
       "<IPython.core.display.SVG object>"
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     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "image = visualize_graph(links, position, directed=False, display_edge_weight=False)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "linker = NNLinker(threshold=0.5)\n",
    "links = linker.fit_predict(adjacency)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
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      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "image = visualize_graph(links, position, directed=False, display_edge_weight=False)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "# Nearest neighbors in embedding space\n",
    "linker = NNLinker(n_neighbors=5, threshold=0.5, embedding_method=Spectral(2))\n",
    "links = linker.fit_predict(adjacency)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
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       "<circle cx=\"246\" cy=\"82\" r=\"7.0\" style=\"fill:gray;stroke:black;stroke-width:1.0\"/>\n",
       "</svg>"
      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "image = visualize_graph(links, position, directed=False, display_edge_weight=False)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Directed graphs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "graph = painters(metadata=True)\n",
    "adjacency = graph.adjacency\n",
    "position = graph.position\n",
    "names = graph.names"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
     "data": {
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       "<circle cx=\"164\" cy=\"55\" r=\"7.0\" style=\"fill:gray;stroke:black;stroke-width:1.0\"/>\n",
       "<circle cx=\"132\" cy=\"92\" r=\"7.0\" style=\"fill:gray;stroke:black;stroke-width:1.0\"/>\n",
       "<circle cx=\"93\" cy=\"131\" r=\"7.0\" style=\"fill:gray;stroke:black;stroke-width:1.0\"/>\n",
       "<circle cx=\"404\" cy=\"94\" r=\"7.0\" style=\"fill:gray;stroke:black;stroke-width:1.0\"/>\n",
       "<text text-anchor=\"start\" x=\"257\" y=\"48\" font-size=\"12\">Pablo Picasso</text><text text-anchor=\"start\" x=\"30\" y=\"108\" font-size=\"12\">Claude Monet</text><text text-anchor=\"start\" x=\"84\" y=\"268\" font-size=\"12\">Michel Angelo</text><text text-anchor=\"start\" x=\"81\" y=\"64\" font-size=\"12\">Edouard Manet</text><text text-anchor=\"start\" x=\"154\" y=\"227\" font-size=\"12\">Peter Paul Rubens</text><text text-anchor=\"start\" x=\"218\" y=\"257\" font-size=\"12\">Rembrandt</text><text text-anchor=\"start\" x=\"430\" y=\"20\" font-size=\"12\">Gustav Klimt</text><text text-anchor=\"start\" x=\"65\" y=\"162\" font-size=\"12\">Edgar Degas</text><text text-anchor=\"start\" x=\"215\" y=\"140\" font-size=\"12\">Vincent van Gogh</text><text text-anchor=\"start\" x=\"161\" y=\"320\" font-size=\"12\">Leonardo da Vinci</text><text text-anchor=\"start\" x=\"174\" y=\"55\" font-size=\"12\">Henri Matisse</text><text text-anchor=\"start\" x=\"142\" y=\"92\" font-size=\"12\">Paul Cezanne</text><text text-anchor=\"start\" x=\"103\" y=\"131\" font-size=\"12\">Pierre-Auguste Renoir</text><text text-anchor=\"start\" x=\"414\" y=\"94\" font-size=\"12\">Egon Schiele</text></svg>"
      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "image = visualize_graph(adjacency, position, names)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "linker = NNLinker(embedding_method=Spectral(3))\n",
    "links = linker.fit_predict(adjacency)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
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       "<text text-anchor=\"start\" x=\"257\" y=\"48\" font-size=\"12\">Pablo Picasso</text><text text-anchor=\"start\" x=\"30\" y=\"108\" font-size=\"12\">Claude Monet</text><text text-anchor=\"start\" x=\"84\" y=\"268\" font-size=\"12\">Michel Angelo</text><text text-anchor=\"start\" x=\"81\" y=\"64\" font-size=\"12\">Edouard Manet</text><text text-anchor=\"start\" x=\"154\" y=\"227\" font-size=\"12\">Peter Paul Rubens</text><text text-anchor=\"start\" x=\"218\" y=\"257\" font-size=\"12\">Rembrandt</text><text text-anchor=\"start\" x=\"430\" y=\"20\" font-size=\"12\">Gustav Klimt</text><text text-anchor=\"start\" x=\"65\" y=\"162\" font-size=\"12\">Edgar Degas</text><text text-anchor=\"start\" x=\"215\" y=\"140\" font-size=\"12\">Vincent van Gogh</text><text text-anchor=\"start\" x=\"161\" y=\"320\" font-size=\"12\">Leonardo da Vinci</text><text text-anchor=\"start\" x=\"174\" y=\"55\" font-size=\"12\">Henri Matisse</text><text text-anchor=\"start\" x=\"142\" y=\"92\" font-size=\"12\">Paul Cezanne</text><text text-anchor=\"start\" x=\"103\" y=\"131\" font-size=\"12\">Pierre-Auguste Renoir</text><text text-anchor=\"start\" x=\"414\" y=\"94\" font-size=\"12\">Egon Schiele</text></svg>"
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       "<IPython.core.display.SVG object>"
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     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "image = visualize_graph(links, position, names, directed=True, display_edge_weight=False)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "pycharm": {
     "name": "#%% md\n"
    }
   },
   "source": [
    "## Bipartite graphs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "graph = movie_actor(metadata=True)\n",
    "biadjacency = graph.biadjacency\n",
    "names_row = graph.names_row\n",
    "names_col = graph.names_col"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
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       "<text text-anchor=\"end\" x=\"178\" y=\"89\" font-size=\"12\">Inception</text><text text-anchor=\"end\" x=\"178\" y=\"69\" font-size=\"12\">The Dark Knight Rises</text><text text-anchor=\"end\" x=\"178\" y=\"230\" font-size=\"12\">The Big Short</text><text text-anchor=\"end\" x=\"178\" y=\"49\" font-size=\"12\">Drive</text><text text-anchor=\"end\" x=\"178\" y=\"30\" font-size=\"12\">The Great Gatsby</text><text text-anchor=\"end\" x=\"178\" y=\"210\" font-size=\"12\">La La Land</text><text text-anchor=\"end\" x=\"178\" y=\"190\" font-size=\"12\">Crazy Stupid Love</text><text text-anchor=\"end\" x=\"178\" y=\"170\" font-size=\"12\">Vice</text><text text-anchor=\"end\" x=\"178\" y=\"310\" font-size=\"12\">The Grand Budapest Hotel</text><text text-anchor=\"end\" x=\"178\" y=\"150\" font-size=\"12\">Aviator</text><text text-anchor=\"end\" x=\"178\" y=\"290\" font-size=\"12\">007 Spectre</text><text text-anchor=\"end\" x=\"178\" y=\"270\" font-size=\"12\">Inglourious Basterds</text><text text-anchor=\"end\" x=\"178\" y=\"249\" font-size=\"12\">Midnight In Paris</text><text text-anchor=\"end\" x=\"178\" y=\"130\" font-size=\"12\">Murder on the Orient Express</text><text text-anchor=\"end\" x=\"178\" y=\"110\" font-size=\"12\">Fantastic Beasts 2</text><text text-anchor=\"start\" x=\"598\" y=\"140\" font-size=\"12\">Leonardo DiCaprio</text><text text-anchor=\"start\" x=\"598\" y=\"59\" font-size=\"12\">Marion Cotillard</text><text text-anchor=\"start\" x=\"598\" y=\"40\" font-size=\"12\">Joseph Gordon Lewitt</text><text text-anchor=\"start\" x=\"598\" y=\"220\" font-size=\"12\">Christian Bale</text><text text-anchor=\"start\" x=\"598\" y=\"200\" font-size=\"12\">Ryan Gosling</text><text text-anchor=\"start\" x=\"598\" y=\"320\" font-size=\"12\">Brad Pitt</text><text text-anchor=\"start\" x=\"598\" y=\"20\" font-size=\"12\">Carey Mulligan</text><text text-anchor=\"start\" x=\"598\" y=\"180\" font-size=\"12\">Emma Stone</text><text text-anchor=\"start\" x=\"598\" y=\"160\" font-size=\"12\">Steve Carell</text><text text-anchor=\"start\" x=\"598\" y=\"300\" font-size=\"12\">Lea Seydoux</text><text text-anchor=\"start\" x=\"598\" y=\"280\" font-size=\"12\">Ralph Fiennes</text><text text-anchor=\"start\" x=\"598\" y=\"120\" font-size=\"12\">Jude Law</text><text text-anchor=\"start\" x=\"598\" y=\"100\" font-size=\"12\">Willem Dafoe</text><text text-anchor=\"start\" x=\"598\" y=\"260\" font-size=\"12\">Christophe Waltz</text><text text-anchor=\"start\" x=\"598\" y=\"79\" font-size=\"12\">Johnny Depp</text><text text-anchor=\"start\" x=\"598\" y=\"240\" font-size=\"12\">Owen Wilson</text></svg>"
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     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "image = visualize_bigraph(biadjacency, names_row, names_col)\n",
    "SVG(image)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [],
   "source": [
    "linker = NNLinker(n_neighbors=5, threshold=0.5, embedding_method=Spectral(3))\n",
    "links = linker.fit_predict(biadjacency)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {
    "pycharm": {
     "name": "#%%\n"
    }
   },
   "outputs": [
    {
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     },
     "execution_count": 52,
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   "source": [
    "image = visualize_bigraph(links, names_row, names_col, display_edge_weight=False)\n",
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