changed mild model, added maxpooling

DeepDrug.ipynb

     "# DeepDrug3D"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Importing library"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Using TensorFlow backend.\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "import numpy as np\n",
-    "\n",
+    "import tensorflow as tf\n",
     "from sklearn.preprocessing import LabelEncoder\n",
     "from keras.models import Sequential\n",
-    "from keras import optimizers\n",
-    "from keras.layers import Dense, Flatten, TimeDistributedn, Dropout\n",
+    "from keras import optimizers, callbacks\n",
+    "from keras.layers import Dense, Flatten, TimeDistributed, Dropout\n",
     "from keras import Input, Model\n",
     "from keras.layers import add, Activation\n",
     "#from keras.utils import plot_model  # Needs pydot.\n",
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Create pocket lists\n",
-    "4 pockets are created :\n",
-    "  + control\n",
-    "  + steroid\n",
-    "  + heme\n",
-    "  + nucleotide"
+    "### used to store model prediction in order to plot roc curve"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "''"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "with open(\"control.list\", \"r\") as filin:\n",
-    "    control = filin.read()\n",
-    "control = control.split(\"\\n\")\n",
-    "control.pop()\n",
-    "\n",
-    "with open(\"steroid.list\", \"r\") as filin:\n",
-    "    steroid = filin.read()\n",
-    "steroid = steroid.split(\"\\n\")\n",
-    "steroid.pop()\n",
-    "\n",
-    "with open(\"heme.list\", \"r\") as filin:\n",
-    "    heme = filin.read()\n",
-    "heme = heme.split(\"\\n\")\n",
-    "heme.pop()\n",
-    "\n",
-    "with open(\"nucleotide.list\", \"r\") as filin:\n",
-    "    nucleotide = filin.read()\n",
-    "nucleotide = nucleotide.split(\"\\n\")\n",
-    "nucleotide.pop()"
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "class prediction_history(callbacks.Callback):\n",
+    "    def __init__(self):\n",
+    "        self.predhis = []\n",
+    "    def on_epoch_end(self, epoch, logs={}):\n",
+    "        self.predhis.append(model.predict(predictor_train))"
    ]
   },
   {
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "data_onehot = np.ndarray(shape=(2219, 14, 32, 32, 32)) # initializing empty array\n",
-    "indices = np.random.permutation(2219)\n",
-    "output = np.ndarray(shape=(2219, 3)) # softmax 3, {steroid=1, heme=1, nucleotide=1}\n",
-    "lmin = len(steroid)\n",
-    "lmid = len(heme)\n",
-    "lmax = len(nucleotide)"
+    "def in_out_lists(size=1000):\n",
+    "    \"\"\"\n",
+    "    returns a tuple of array used as input and output for the model\n",
+    "    Arguments:\n",
+    "        - size, int: default 1000, size of the lists to be created\n",
+    "        \n",
+    "    Returns:\n",
+    "        - tuple (data_onehot, output):\n",
+    "            -data_onehot, ndarray: containing one-hot encoded pockets\n",
+    "            -output, ndarray: containing size-3 vectors for classification\n",
+    "    \"\"\"\n",
+    "    with open(\"control.list\", \"r\") as filin:\n",
+    "        control = filin.read()\n",
+    "        control = control.split(\"\\n\")\n",
+    "        control.pop()\n",
+    "\n",
+    "    with open(\"steroid.list\", \"r\") as filin:\n",
+    "        steroid = filin.read()\n",
+    "        steroid = steroid.split(\"\\n\")\n",
+    "        steroid.pop()\n",
+    "\n",
+    "    with open(\"heme.list\", \"r\") as filin:\n",
+    "        heme = filin.read()\n",
+    "        heme = heme.split(\"\\n\")\n",
+    "        heme.pop()\n",
+    "\n",
+    "    with open(\"nucleotide.list\", \"r\") as filin:\n",
+    "        nucleotide = filin.read()\n",
+    "        nucleotide = nucleotide.split(\"\\n\")\n",
+    "        nucleotide.pop()\n",
+    "    \n",
+    "    lmin = len(heme)\n",
+    "    lmid = len(nucleotide)\n",
+    "    lmax = len(control)\n",
+    "    tot_size = lmin + lmid + lmax\n",
+    "    data_onehot = np.ndarray(shape=(size, 14, 32, 32, 32)) # initializing empty array\n",
+    "\n",
+    "    np.random.seed(9001)\n",
+    "    indices = np.random.permutation(tot_size)\n",
+    "    indices = indices[:size]\n",
+    "    output = np.ndarray(shape=(size, 3)) # softmax 3, {steroid=1, heme=1, nucleotide=1}\n",
+    "\n",
+    "    n = -1\n",
+    "    for i in indices:\n",
+    "        n += 1\n",
+    "        if i < lmin:\n",
+    "            data_onehot[n,] = np.load(\"deepdrug3d_voxel_data/\"+heme[i]+\".npy\")\n",
+    "            output[n,] = [1,0,0]\n",
+    "        elif i > lmin and i < (lmin + lmid):\n",
+    "            data_onehot[n,] = np.load(\"deepdrug3d_voxel_data/\"+nucleotide[i - lmin]+\".npy\")\n",
+    "            output[n,] = [0,1,0]\n",
+    "        else:\n",
+    "            data_onehot[n,] = np.load(\"deepdrug3d_voxel_data/\"+control[i - (lmin+lmid) - 1]+\".npy\")\n",
+    "            output[n,] = [0,0,1]\n",
+    "    \n",
+    "    return (data_onehot, output)"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 4,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "n = -1\n",
-    "for i in indices:\n",
-    "    n += 1\n",
-    "    if i < lmin:\n",
-    "        data_onehot[n,] = np.load(\"deepdrug3d_voxel_data/\"+steroid[i]+\".npy\")\n",
-    "        output[n,] = [1,0,0]\n",
-    "    elif i > lmin and i < (lmin + lmid):\n",
-    "        data_onehot[n,] = np.load(\"deepdrug3d_voxel_data/\"+heme[i - lmin]+\".npy\")\n",
-    "        output[n,] = [0,1,0]\n",
-    "    else:\n",
-    "        data_onehot[n,] = np.load(\"deepdrug3d_voxel_data/\"+nucleotide[i - (lmin+lmid) - 1]+\".npy\")\n",
-    "        output[n,] = [0,0,1]"
+    "### Defining different model to test and compare"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "X_train = data_onehot[0:1664,]\n",
-    "Y_train = output[0:1664,]\n",
-    "X_test = data_onehot[1664:,]\n",
-    "Y_test = output[1664:,]"
+    "def model_heavy(): # créer un objet modèle\n",
+    "    \"\"\"\n",
+    "    Return a simple sequentiel model\n",
+    "    \n",
+    "    Returns :\n",
+    "        - model : keras.Model\n",
+    "    \"\"\"\n",
+    "    inputs = Input(shape=(14,32,32,32))\n",
+    "    conv_1 = Conv3D(64, (28, 28, 28), padding=\"same\", activation=\"relu\", kernel_initializer=\"he_normal\")(inputs)\n",
+    "    conv_2 = Conv3D(64, (26, 26, 26), padding=\"same\", activation=\"relu\", kernel_initializer=\"he_normal\")(conv_1)\n",
+    "    drop_1 = Dropout(0.2)(conv_2)\n",
+    "    maxpool = MaxPooling3D()(drop_1)\n",
+    "    drop_2 = Dropout(0.4)(maxpool)\n",
+    "    dense = Dense(512)(drop_2)\n",
+    "    drop_3 = Dropout(0.4)(dense)\n",
+    "    flatters = Flatten()(drop_3)\n",
+    "    #output = TimeDistributed(Dense(3, activation='softmax'))(drop_3)\n",
+    "    output = Dense(3, activation='softmax')(flatters)\n",
+    "    model = Model(inputs=inputs, outputs=output)\n",
+    "    my_opt = optimizers.Adam(learning_rate=0.000001, beta_1=0.9, beta_2=0.999, amsgrad=False)\n",
+    "    print(model.summary)\n",
+    "    model.compile(optimizer=my_opt, loss=\"categorical_crossentropy\",\n",
+    "                  metrics=[\"accuracy\"])\n",
+    "    return model"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "(1, 14, 32, 32, 32)"
-      ]
-     },
-     "execution_count": 14,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "def model_sequential(): # créer un objet modèle\n",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def model_light(): # créer un objet modèle\n",
     "    \"\"\"\n",
     "    Return a simple sequentiel model\n",
     "    \n",
     "    Returns :\n",
     "        - model : keras.Model\n",
     "    \"\"\"\n",
-    "    inputs = Input(shape=(32,32,32,14)) # 759 aa, 21 car onehot\n",
-    "    conv_1 = Conv3D(64, (28, 28, 28), padding=\"same\", activation=\"LeakyReLU\",\n",
-    "                        kernel_initializer=\"he_normal\")(inputs)\n",
-    "    conv_2 = Conv3D(64, (26, 26, 26), padding=\"same\", activation=\"LeakyReLU\",\n",
-    "                        kernel_initializer=\"he_normal\")(conv_1)\n",
+    "    inputs = Input(shape=(14,32,32,32))\n",
+    "    conv_1 = Conv3D(32, (28, 28, 28), padding=\"same\", activation=\"relu\", kernel_initializer=\"he_normal\")(inputs)\n",
+    "    conv_2 = Conv3D(64, (26, 26, 26), padding=\"same\", activation=\"relu\", kernel_initializer=\"he_normal\")(conv_1)\n",
     "    drop_1 = Dropout(0.2)(conv_2)\n",
     "    maxpool = MaxPooling3D()(drop_1)\n",
-    "    drop_2 = Dropout(0.4)(maxpool)\n",
-    "    dense = Dense(512)(drop_2)\n",
-    "    drop_3 = Dropout(0.4)(dense)\n",
-    "    output = TimeDistributed(Dense(3, activation='softmax'))(drop_3)\n",
+    "    drop_2 = Dropout(0.3)(maxpool)\n",
+    "    maxpool_2 = MaxPooling3D()(drop_2)\n",
+    "    drop_3 = Dropout(0.3)(maxpool_2)\n",
+    "    dense = Dense(256)(drop_3)\n",
+    "    drop_4 = Dropout(0.4)(dense)\n",
+    "    flatters = Flatten()(drop_4)\n",
+    "    output = Dense(3, activation='softmax')(flatters)\n",
     "    model = Model(inputs=inputs, outputs=output)\n",
     "    my_opt = optimizers.Adam(learning_rate=0.000001, beta_1=0.9, beta_2=0.999, amsgrad=False)\n",
     "    print(model.summary)\n",
     "    return model"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Create pocket lists\n",
+    "4 lists are created :\n",
+    "  + control\n",
+    "  + steroid\n",
+    "  + heme\n",
+    "  + nucleotide"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = in_out_lists(1400)\n",
+    "pockets = np.cumsum(data[1], axis=0)[-1]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(\"with random seed=9001 and a 1400 pockets dataset the rates are:\\n\\\n",
+    "      {} heme, {} nucleotide, {} control\\n\\\n",
+    "      Total avaible dataset are composed of the following proportions:\\n\\\n",
+    "      {} heme, {} nucleotide, {} control\".format(pockets[0]/1400, pockets[1]/1400,pockets[2]/1400,\n",
+    "                                                0.145, 0.380, 0.475))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data_onehot = data[0]\n",
+    "output = data[1]\n",
+    "X_train = data_onehot[0:1000,]\n",
+    "Y_train = output[0:1000,]\n",
+    "X_test = data_onehot[1000:,]\n",
+    "Y_test = output[1000:,]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "my_model = model_light()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tf.test.is_gpu_available()\n",
+    "#my_model.fit(X_train, Y_train, epochs=50, batch_size=30)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "history_mild_2mp = mild_model.fit(X_train, Y_train, validation_data=(X_test, Y_test), epochs=30, batch_size=32)\n",
+    "my_model.save('light_model_2mp_e30_b32.h5')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#predictions=prediction_history()"
+   ]
   }
  ],
  "metadata": {

DeepDrug.py

+#!/usr/bin/env python
+# coding: utf-8
+
+# # DeepDrug3D
+
+# ## Importing library
+
+# In[ ]:
+
+
+import numpy as np
+import tensorflow as tf
+from sklearn.preprocessing import LabelEncoder
+from keras.models import Sequential
+from keras import optimizers, callbacks
+from keras.layers import Dense, Flatten, TimeDistributed, Dropout
+from keras import Input, Model
+from keras.layers import add, Activation
+#from keras.utils import plot_model  # Needs pydot.
+from keras.layers import Conv3D, MaxPooling3D
+
+
+# ### used to store model prediction in order to plot roc curve
+
+# In[ ]:
+
+
+class prediction_history(callbacks.Callback):
+    def __init__(self):
+        self.predhis = []
+    def on_epoch_end(self, epoch, logs={}):
+        self.predhis.append(model.predict(predictor_train))
+
+
+# ### Creating input and ouputs
+
+# In[ ]:
+
+
+def in_out_lists(size=1000):
+    """
+    returns a tuple of array used as input and output for the model
+    Arguments:
+        - size, int: default 1000, size of the lists to be created
+        
+    Returns:
+        - tuple (data_onehot, output):
+            -data_onehot, ndarray: containing one-hot encoded pockets
+            -output, ndarray: containing size-3 vectors for classification
+    """
+    with open("control.list", "r") as filin:
+        control = filin.read()
+        control = control.split("\n")
+        control.pop()
+
+    with open("steroid.list", "r") as filin:
+        steroid = filin.read()
+        steroid = steroid.split("\n")
+        steroid.pop()
+
+    with open("heme.list", "r") as filin:
+        heme = filin.read()
+        heme = heme.split("\n")
+        heme.pop()
+
+    with open("nucleotide.list", "r") as filin:
+        nucleotide = filin.read()
+        nucleotide = nucleotide.split("\n")
+        nucleotide.pop()
+    
+    lmin = len(heme)
+    lmid = len(nucleotide)
+    lmax = len(control)
+    tot_size = lmin + lmid + lmax
+    data_onehot = np.ndarray(shape=(size, 14, 32, 32, 32)) # initializing empty array
+
+    np.random.seed(9001)
+    indices = np.random.permutation(tot_size)
+    indices = indices[:size]
+    output = np.ndarray(shape=(size, 3)) # softmax 3, {steroid=1, heme=1, nucleotide=1}
+
+    n = -1
+    for i in indices:
+        n += 1
+        if i < lmin:
+            data_onehot[n,] = np.load("deepdrug3d_voxel_data/"+heme[i]+".npy")
+            output[n,] = [1,0,0]
+        elif i > lmin and i < (lmin + lmid):
+            data_onehot[n,] = np.load("deepdrug3d_voxel_data/"+nucleotide[i - lmin]+".npy")
+            output[n,] = [0,1,0]
+        else:
+            data_onehot[n,] = np.load("deepdrug3d_voxel_data/"+control[i - (lmin+lmid) - 1]+".npy")
+            output[n,] = [0,0,1]
+    
+    return (data_onehot, output)
+
+
+# ### Defining different model to test and compare
+
+# In[ ]:
+
+
+def model_heavy(): # créer un objet modèle
+    """
+    Return a simple sequentiel model
+    
+    Returns :
+        - model : keras.Model
+    """
+    inputs = Input(shape=(14,32,32,32))
+    conv_1 = Conv3D(64, (28, 28, 28), padding="same", activation="relu", kernel_initializer="he_normal")(inputs)
+    conv_2 = Conv3D(64, (26, 26, 26), padding="same", activation="relu", kernel_initializer="he_normal")(conv_1)
+    drop_1 = Dropout(0.2)(conv_2)
+    maxpool = MaxPooling3D()(drop_1)
+    drop_2 = Dropout(0.4)(maxpool)
+    dense = Dense(512)(drop_2)
+    drop_3 = Dropout(0.4)(dense)
+    flatters = Flatten()(drop_3)
+    #output = TimeDistributed(Dense(3, activation='softmax'))(drop_3)
+    output = Dense(3, activation='softmax')(flatters)
+    model = Model(inputs=inputs, outputs=output)
+    my_opt = optimizers.Adam(learning_rate=0.000001, beta_1=0.9, beta_2=0.999, amsgrad=False)
+    print(model.summary)
+    model.compile(optimizer=my_opt, loss="categorical_crossentropy",
+                  metrics=["accuracy"])
+    return model
+
+
+# In[ ]:
+
+
+def model_light(): # créer un objet modèle
+    """
+    Return a simple sequentiel model
+    
+    Returns :
+        - model : keras.Model
+    """
+    inputs = Input(shape=(14,32,32,32))
+    conv_1 = Conv3D(32, (28, 28, 28), padding="same", activation="relu", kernel_initializer="he_normal")(inputs)
+    conv_2 = Conv3D(64, (26, 26, 26), padding="same", activation="relu", kernel_initializer="he_normal")(conv_1)
+    drop_1 = Dropout(0.2)(conv_2)
+    maxpool = MaxPooling3D()(drop_1)
+    drop_2 = Dropout(0.3)(maxpool)
+    maxpool_2 = MaxPooling3D()(drop_2)
+    drop_3 = Dropout(0.3)(maxpool_2)
+    dense = Dense(256)(drop_3)
+    drop_4 = Dropout(0.4)(dense)
+    flatters = Flatten()(drop_4)
+    output = Dense(3, activation='softmax')(flatters)
+    model = Model(inputs=inputs, outputs=output)
+    my_opt = optimizers.Adam(learning_rate=0.000001, beta_1=0.9, beta_2=0.999, amsgrad=False)
+    print(model.summary)
+    model.compile(optimizer=my_opt, loss="categorical_crossentropy",
+                  metrics=["accuracy"])
+    return model
+
+
+# ## Create pocket lists
+# 4 lists are created :
+#   + control
+#   + steroid
+#   + heme
+#   + nucleotide
+
+# In[ ]:
+
+
+data = in_out_lists(1400)
+pockets = np.cumsum(data[1], axis=0)[-1]
+
+
+# In[ ]:
+
+
+print("with random seed=9001 and a 1400 pockets dataset the rates are:\n      {} heme, {} nucleotide, {} control\n      Total avaible dataset are composed of the following proportions:\n      {} heme, {} nucleotide, {} control".format(pockets[0]/1400, pockets[1]/1400,pockets[2]/1400,
+                                                0.145, 0.380, 0.475))
+
+
+# In[ ]:
+
+
+data_onehot = data[0]
+output = data[1]
+X_train = data_onehot[0:1000,]
+Y_train = output[0:1000,]
+X_test = data_onehot[1000:,]
+Y_test = output[1000:,]
+
+
+# In[ ]:
+
+
+my_model = model_light()
+
+
+# In[ ]:
+
+
+tf.test.is_gpu_available()
+#my_model.fit(X_train, Y_train, epochs=50, batch_size=30)
+
+
+# In[ ]:
+
+
+history_mild_2mp = my_model.fit(X_train, Y_train, validation_data=(X_test, Y_test), epochs=30, batch_size=32)
+my_model.save('light_model_2mp_e30_b32.h5')
+
+
+# In[ ]:
+
+
+#predictions=prediction_history()
+