multi-task.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Using TensorFlow backend.\n"
     ]
    }
   ],
   "source": [
    "import numpy as np\n",
    "from tensorflow.keras.layers import Conv1D, Dense, MaxPooling1D, Flatten\n",
    "from tensorflow.keras.models import Sequential\n",
    "from sklearn.preprocessing import MinMaxScaler\n",
    "from keras import backend as K\n",
    "import matplotlib.pyplot as plt\n",
    "import scipy\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "gene_region_size = 200 # x 250bp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from tensorflow.keras.layers import Conv1D, Conv2D, Conv3D, Dense, MaxPooling1D, MaxPooling2D, MaxPooling3D, Flatten, Dropout, Input\n",
    "from tensorflow.keras.models import Sequential\n",
    "#from tensorflow.python.keras import Sequential\n",
    "from keras.models import Model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "input_reads = Input(shape=(gene_region_size, 2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "shared_model = (Conv1D(filters=int(gene_region_size / 2), kernel_size=3, activation='relu',\n",
    "                 input_shape=(gene_region_size,2),\n",
    "                 padding='same'))(input_reads)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# model.add(MaxPooling1D(pool_size=2))\n",
    "shared_model = (Dropout(0.25))(shared_model)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "shared_model = (Conv1D(filters=int(gene_region_size / 2), kernel_size=3, activation='relu', padding='same'))(shared_model)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# model.add(MaxPooling1D(pool_size=2))\n",
    "shared_model = (Dropout(0.25))(shared_model)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "shared_model = (Conv1D(filters=int(gene_region_size / 4), kernel_size=3, activation='relu', dilation_rate=2, padding='same'))(shared_model)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "shared_model = (Conv1D(filters=int(gene_region_size / 4), kernel_size=3, activation='relu', dilation_rate=4, padding='same'))(shared_model)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "shared_model = (Conv1D(filters=int(gene_region_size / 4), kernel_size=3, activation='relu', dilation_rate=8, padding='same'))(shared_model)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "H3K4me3_output = Dense(2, activation='relu', name='H3K4me3')(shared_model)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "H3K27ac_output = Dense(2, activation='relu', name='H3K27ac')(shared_model)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'Tensor' object has no attribute '_keras_shape'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-14-88fd4fd22dc6>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mfinal_model\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mModel\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minputs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0minput_reads\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutputs\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mH3K4me3_output\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mH3K27ac_output\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/opt/miniconda3/lib/python3.6/site-packages/keras/legacy/interfaces.py\u001b[0m in \u001b[0;36mwrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     89\u001b[0m                 warnings.warn('Update your `' + object_name + '` call to the ' +\n\u001b[1;32m     90\u001b[0m                               'Keras 2 API: ' + signature, stacklevel=2)\n\u001b[0;32m---> 91\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     92\u001b[0m         \u001b[0mwrapper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_original_function\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     93\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mwrapper\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/miniconda3/lib/python3.6/site-packages/keras/engine/network.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m     91\u001b[0m                 'inputs' in kwargs and 'outputs' in kwargs):\n\u001b[1;32m     92\u001b[0m             \u001b[0;31m# Graph network\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 93\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_init_graph_network\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     94\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     95\u001b[0m             \u001b[0;31m# Subclassed network\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/miniconda3/lib/python3.6/site-packages/keras/engine/network.py\u001b[0m in \u001b[0;36m_init_graph_network\u001b[0;34m(self, inputs, outputs, name)\u001b[0m\n\u001b[1;32m    245\u001b[0m              \u001b[0minput_masks\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;32mNone\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0m_\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    246\u001b[0m              \u001b[0moutput_masks\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;32mNone\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0m_\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moutputs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 247\u001b[0;31m              \u001b[0minput_shapes\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_keras_shape\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    248\u001b[0m              output_shapes=[x._keras_shape for x in self.outputs])\n\u001b[1;32m    249\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/opt/miniconda3/lib/python3.6/site-packages/keras/engine/network.py\u001b[0m in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m    245\u001b[0m              \u001b[0minput_masks\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;32mNone\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0m_\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    246\u001b[0m              \u001b[0moutput_masks\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;32mNone\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0m_\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moutputs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 247\u001b[0;31m              \u001b[0minput_shapes\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_keras_shape\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    248\u001b[0m              output_shapes=[x._keras_shape for x in self.outputs])\n\u001b[1;32m    249\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mAttributeError\u001b[0m: 'Tensor' object has no attribute '_keras_shape'"
     ]
    }
   ],
   "source": [
    "final_model = Model(inputs=input_reads, outputs=[H3K4me3_output, H3K27ac_output])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [],
   "source": [
    "final_model.compile(loss=['mean_squared_error'], optimizer='adam', \n",
    "              metrics=['mean_squared_error', earth_mover_distance_loss])"
   ]
  }
 ],
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