data/molecules/prepare_molecules_ZINC_full.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Notebook for preparing and saving MOLECULAR (ZINC full) graphs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import torch\n",
    "import pickle\n",
    "import time\n",
    "import os\n",
    "%matplotlib inline\n",
    "import matplotlib.pyplot as plt\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Download ZINC full dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "File already downloaded\n"
     ]
    }
   ],
   "source": [
    "if not os.path.isfile('molecules_zinc_full.zip'):\n",
    "    print('downloading..')\n",
    "    !curl https://www.dropbox.com/s/grhitgnuuixoxwl/molecules_zinc_full.zip?dl=1 -o molecules_zinc_full.zip -J -L -k\n",
    "    !unzip molecules_zinc_full.zip -d ../\n",
    "    # !tar -xvf molecules_zinc_full.zip -C ../\n",
    "else:\n",
    "    print('File already downloaded')\n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Convert to DGL format and save with pickle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/vijay/graphdeeplearning/benchmarking-gnns\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "os.chdir('../../') # go to root folder of the project\n",
    "print(os.getcwd())\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The autoreload extension is already loaded. To reload it, use:\n",
      "  %reload_ext autoreload\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Using backend: pytorch\n"
     ]
    }
   ],
   "source": [
    "import pickle\n",
    "\n",
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "\n",
    "from data.molecules import MoleculeDatasetDGL \n",
    "\n",
    "from data.data import LoadData\n",
    "from torch.utils.data import DataLoader\n",
    "from data.molecules import MoleculeDataset\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "preparing 220011 graphs for the TRAIN set...\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/vijay/graphdeeplearning/benchmarking-gnns/data/molecules.py:61: UserWarning: This overload of nonzero is deprecated:\n",
      "\tnonzero()\n",
      "Consider using one of the following signatures instead:\n",
      "\tnonzero(*, bool as_tuple) (Triggered internally at  /opt/conda/conda-bld/pytorch_1595629427478/work/torch/csrc/utils/python_arg_parser.cpp:766.)\n",
      "  edge_list = (adj != 0).nonzero()  # converting adj matrix to edge_list\n",
      "/home/vijay/miniconda3/envs/benchmark_gnn_dgl_05/lib/python3.7/site-packages/dgl/base.py:45: DGLWarning: Recommend creating graphs by `dgl.graph(data)` instead of `dgl.DGLGraph(data)`.\n",
      "  return warnings.warn(message, category=category, stacklevel=1)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "preparing 24445 graphs for the VAL set...\n",
      "preparing 5000 graphs for the TEST set...\n",
      "Time taken: 4012.6295s\n"
     ]
    }
   ],
   "source": [
    "DATASET_NAME = 'ZINC-full'\n",
    "dataset = MoleculeDatasetDGL(DATASET_NAME) \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "min/max : 6 38\n"
     ]
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "min/max : 6 38\n"
     ]
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "min/max : 8 37\n"
     ]
    }
   ],
   "source": [
    "def plot_histo_graphs(dataset, title):\n",
    "    # histogram of graph sizes\n",
    "    graph_sizes = []\n",
    "    for graph in dataset:\n",
    "        graph_sizes.append(graph[0].number_of_nodes())\n",
    "    plt.figure(1)\n",
    "    plt.hist(graph_sizes, bins=20)\n",
    "    plt.title(title)\n",
    "    plt.show()\n",
    "    graph_sizes = torch.Tensor(graph_sizes)\n",
    "    print('min/max :',graph_sizes.min().long().item(),graph_sizes.max().long().item())\n",
    "    \n",
    "plot_histo_graphs(dataset.train,'trainset')\n",
    "plot_histo_graphs(dataset.val,'valset')\n",
    "plot_histo_graphs(dataset.test,'testset')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "220011\n",
      "24445\n",
      "5000\n",
      "(Graph(num_nodes=33, num_edges=72,\n",
      "      ndata_schemes={'feat': Scheme(shape=(), dtype=torch.int64)}\n",
      "      edata_schemes={'feat': Scheme(shape=(), dtype=torch.int64)}), tensor([3.0464]))\n",
      "(Graph(num_nodes=21, num_edges=44,\n",
      "      ndata_schemes={'feat': Scheme(shape=(), dtype=torch.int64)}\n",
      "      edata_schemes={'feat': Scheme(shape=(), dtype=torch.int64)}), tensor([2.0992]))\n",
      "(Graph(num_nodes=24, num_edges=52,\n",
      "      ndata_schemes={'feat': Scheme(shape=(), dtype=torch.int64)}\n",
      "      edata_schemes={'feat': Scheme(shape=(), dtype=torch.int64)}), tensor([3.1382]))\n"
     ]
    }
   ],
   "source": [
    "print(len(dataset.train))\n",
    "print(len(dataset.val))\n",
    "print(len(dataset.test))\n",
    "\n",
    "print(dataset.train[0])\n",
    "print(dataset.val[0])\n",
    "print(dataset.test[0])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [],
   "source": [
    "num_atom_type = 28\n",
    "num_bond_type = 4\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Time (sec): 133.74254989624023\n"
     ]
    }
   ],
   "source": [
    "start = time.time()\n",
    "with open('data/molecules/ZINC-full.pkl','wb') as f:\n",
    "        pickle.dump([dataset.train,dataset.val,dataset.test,num_atom_type,num_bond_type],f)\n",
    "print('Time (sec):',time.time() - start)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Test load function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[I] Loading dataset ZINC-full...\n",
      "train, test, val sizes : 220011 5000 24445\n",
      "[I] Finished loading.\n",
      "[I] Data load time: 151.4532s\n"
     ]
    }
   ],
   "source": [
    "DATASET_NAME = 'ZINC-full'\n",
    "dataset = LoadData(DATASET_NAME)\n",
    "trainset, valset, testset = dataset.train, dataset.val, dataset.test\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'data.molecules.MoleculeDataset'>\n"
     ]
    }
   ],
   "source": [
    "batch_size = 10\n",
    "collate = MoleculeDataset.collate\n",
    "print(MoleculeDataset)\n",
    "train_loader = DataLoader(trainset, batch_size=batch_size, shuffle=True, collate_fn=collate)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.4"
  }
 },
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}