DotMotif-Search-in-Custom-NetworkX.ipynb

dotmotif-search-in-custom-networkx.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "DotMotif-Search-in-Custom-NetworkX.ipynb",
      "provenance": [],
      "collapsed_sections": [],
      "authorship_tag": "ABX9TyMpnafhK2FKFbVkGc1l97oA",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/gist/j6k4m8/d02259dfedc2321973be4d2e665653f4/dotmotif-search-in-custom-networkx.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "source": [
        "# Using DotMotif to search for motifs in a custom graph\n",
        "\n",
        "[DotMotif](https://github.com/aplbrain/dotmotif) is a performant, powerful query framework to search for network motifs.\n"
      ],
      "metadata": {
        "id": "ZjweaPr1LtEk"
      }
    },
    {
      "cell_type": "code",
      "source": [
        "%%capture\n",
        "# Install dotmotif with one line.\n",
        "# On your own computer, you can run this in the terminal.\n",
        "!pip3 install dotmotif networkx\n",
        "\n",
        "import networkx as nx\n",
        "from dotmotif import Motif, GrandIsoExecutor"
      ],
      "metadata": {
        "id": "qVIoPW6UK3rG"
      },
      "execution_count": 44,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# Create a new graph from scratch:\n",
        "host = nx.fast_gnp_random_graph(100, 0.1, directed=True)"
      ],
      "metadata": {
        "id": "-4U9mEOQK7rG"
      },
      "execution_count": 45,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# Create the search engine.\n",
        "E = GrandIsoExecutor(graph=host)"
      ],
      "metadata": {
        "id": "ooxAE9DuLSyB"
      },
      "execution_count": 46,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# Build your own motif here!\n",
        "motif = Motif(\"\"\"\n",
        "\n",
        "# Example motif:\n",
        "\n",
        "onewayEdge(a, b) {\n",
        "    # An edge that only points in one direction,\n",
        "    # with no reciprocal edge: \n",
        "    a -> b\n",
        "    b !> a\n",
        "}\n",
        "\n",
        "# A triangle that only has edges pointing\n",
        "# in one direction:\n",
        "onewayEdge(A, B)\n",
        "onewayEdge(B, C)\n",
        "onewayEdge(C, A)\n",
        "\n",
        "\"\"\")"
      ],
      "metadata": {
        "id": "B8_jzbUvLUHd"
      },
      "execution_count": 47,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "results = E.find(motif)"
      ],
      "metadata": {
        "id": "kTRYjBSDLWzY"
      },
      "execution_count": 48,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "print(len(results))"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "b7paIFMBLYiZ",
        "outputId": "5599e144-c252-410c-ee36-5f8826ebca6b"
      },
      "execution_count": 49,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "639\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        ""
      ],
      "metadata": {
        "id": "7tqVQfx8O7cJ"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}