{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"name": "graph_example.ipynb",
"provenance": [],
"collapsed_sections": []
},
"kernelspec": {
"display_name": "Python 3",
"name": "python3"
},
"language_info": {
"name": "python"
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"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "6anJNPgZx4zJ"
},
"source": [
"# グラフマイニングの例\n",
"- データセット\n",
" - [social circles: Facebook](http://snap.stanford.edu/data/ego-Facebook.html)から facebook_combined.txt.zip を利用。\n",
" - graph1.txt, graph2.txt, graph_modularity_simple.txt: 小さなグラフ例\n",
"- ツール等\n",
" - [Graphviz](https://www.graphviz.org/): ノードとエッジで構成されるグラフ描画ツール。\n",
" - [pygraphviz](https://pygraphviz.github.io/): GraphvizをPythonから使うためのラッパー。\n",
" - [networkx](https://networkx.github.io/): ネットワーク解析パッケージ。"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "yu-0uyPqyz7w"
},
"source": [
"## 環境構築"
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "_F6U30TpltBr",
"outputId": "a51f1b71-19d7-416d-ace4-0d82893c860b"
},
"source": [
"!apt install libgraphviz-dev\n",
"!pip install pygraphviz"
],
"execution_count": 1,
"outputs": [
{
"output_type": "stream",
"text": [
"Reading package lists... Done\n",
"Building dependency tree \n",
"Reading state information... Done\n",
"The following additional packages will be installed:\n",
" libgail-common libgail18 libgtk2.0-0 libgtk2.0-bin libgtk2.0-common\n",
" libgvc6-plugins-gtk libxdot4\n",
"Suggested packages:\n",
" gvfs\n",
"The following NEW packages will be installed:\n",
" libgail-common libgail18 libgraphviz-dev libgtk2.0-0 libgtk2.0-bin\n",
" libgtk2.0-common libgvc6-plugins-gtk libxdot4\n",
"0 upgraded, 8 newly installed, 0 to remove and 39 not upgraded.\n",
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"Get:1 http://archive.ubuntu.com/ubuntu bionic/main amd64 libgtk2.0-common all 2.24.32-1ubuntu1 [125 kB]\n",
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"Get:5 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libxdot4 amd64 2.40.1-2 [15.7 kB]\n",
"Get:6 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libgvc6-plugins-gtk amd64 2.40.1-2 [18.2 kB]\n",
"Get:7 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libgraphviz-dev amd64 2.40.1-2 [57.3 kB]\n",
"Get:8 http://archive.ubuntu.com/ubuntu bionic/main amd64 libgtk2.0-bin amd64 2.24.32-1ubuntu1 [7,536 B]\n",
"Fetched 2,120 kB in 1s (1,456 kB/s)\n",
"Selecting previously unselected package libgtk2.0-common.\n",
"(Reading database ... 160772 files and directories currently installed.)\n",
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"Preparing to unpack .../7-libgtk2.0-bin_2.24.32-1ubuntu1_amd64.deb ...\n",
"Unpacking libgtk2.0-bin (2.24.32-1ubuntu1) ...\n",
"Setting up libgtk2.0-common (2.24.32-1ubuntu1) ...\n",
"Setting up libxdot4 (2.40.1-2) ...\n",
"Setting up libgtk2.0-0:amd64 (2.24.32-1ubuntu1) ...\n",
"Setting up libgail18:amd64 (2.24.32-1ubuntu1) ...\n",
"Setting up libgail-common:amd64 (2.24.32-1ubuntu1) ...\n",
"Setting up libgvc6-plugins-gtk (2.40.1-2) ...\n",
"Setting up libgraphviz-dev (2.40.1-2) ...\n",
"Setting up libgtk2.0-bin (2.24.32-1ubuntu1) ...\n",
"Processing triggers for man-db (2.8.3-2ubuntu0.1) ...\n",
"Processing triggers for libc-bin (2.27-3ubuntu1.2) ...\n",
"/sbin/ldconfig.real: /usr/local/lib/python3.7/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link\n",
"\n",
"Collecting pygraphviz\n",
"\u001b[?25l Downloading https://files.pythonhosted.org/packages/3a/d6/2c56f09ee83dbebb62c40487e4c972135661b9984fec9b30b77fb497090c/pygraphviz-1.7.zip (118kB)\n",
"\u001b[K |████████████████████████████████| 122kB 7.9MB/s \n",
"\u001b[?25hBuilding wheels for collected packages: pygraphviz\n",
" Building wheel for pygraphviz (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
" Created wheel for pygraphviz: filename=pygraphviz-1.7-cp37-cp37m-linux_x86_64.whl size=166142 sha256=6bbbb96a20c7c22804e6b3f842eb5a71b5a652364c064af09c58727fae084d8b\n",
" Stored in directory: /root/.cache/pip/wheels/32/59/00/14934a4292c4359eeabcdbf90f33d309b55d0f1be8a1262523\n",
"Successfully built pygraphviz\n",
"Installing collected packages: pygraphviz\n",
"Successfully installed pygraphviz-1.7\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "kVEGEdS0ytAk"
},
"source": [
"import pandas as pd\n",
"import networkx as nx\n",
"import pygraphviz\n",
"import matplotlib.pyplot as plt"
],
"execution_count": 2,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "xtsOL96B11iw"
},
"source": [
"## やや大きめの実データを用いたグラフ化例\n",
"- facebook_combined.txt には「どのノード間にエッジがあるか」というリンク情報が保存されている。例えば「0 1」という行なら「ノード0とノード1の間にエッジがある」ことを意味している。\n",
"- このままではグラフではないため、データを一度DataFrameとして読み込み、それを from_edges_to_networks() によりグラフに変換する。"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "H6u1cNaV1LLC"
},
"source": [
"### データ準備（facebook_combined.txt）"
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "QX2Gu9aOxjh4",
"outputId": "acb7772f-461e-4dd3-aa73-fbeea38a5e80"
},
"source": [
"!curl -O http://snap.stanford.edu/data/facebook_combined.txt.gz\n",
"!gzip -d facebook_combined.txt.gz"
],
"execution_count": 3,
"outputs": [
{
"output_type": "stream",
"text": [
" % Total % Received % Xferd Average Speed Time Time Time Current\n",
" Dload Upload Total Spent Left Speed\n",
"100 213k 100 213k 0 0 808k 0 --:--:-- --:--:-- --:--:-- 808k\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "ZJ8TW3jkxs_g",
"outputId": "31c6c2cc-06ee-49e2-e19e-a2b5e78506d3"
},
"source": [
"!head facebook_combined.txt"
],
"execution_count": 4,
"outputs": [
{
"output_type": "stream",
"text": [
"0 1\n",
"0 2\n",
"0 3\n",
"0 4\n",
"0 5\n",
"0 6\n",
"0 7\n",
"0 8\n",
"0 9\n",
"0 10\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 204
},
"id": "U0bnzFpGyJIe",
"outputId": "8097d07c-5009-4012-9c76-36bbe209efcf"
},
"source": [
"filename = \"facebook_combined.txt\"\n",
"df = pd.read_csv(filename, sep=' ')\n",
"df[:5]"
],
"execution_count": 5,
"outputs": [
{
"output_type": "execute_result",
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