diff options
| author | Christoph Helma <helma@in-silico.ch> | 2021-02-10 19:14:47 +0100 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2021-02-10 19:14:47 +0100 |
| commit | 3bfc5bfb57e8f130b1b3d9a90fc34744278ef6b5 (patch) | |
| tree | 2641524a1496a2746f36b20684a947e956713416 /pyrrolizidine-alkaloids/mp2d | |
| parent | 771a2381ae0fd5e352f23d7223baeb26e8bb4e02 (diff) | |
new confusion matrix locations, PA prediction figures, pandoc-placetable removed, shell.nix updated, PA scripts updated, jupyter notebooks updated
Diffstat (limited to 'pyrrolizidine-alkaloids/mp2d')
| -rw-r--r-- | pyrrolizidine-alkaloids/mp2d/lazar/pa-mp2d-predictions.csv | 603 | ||||
| -rw-r--r-- | pyrrolizidine-alkaloids/mp2d/tensorflow/prediction-v5-ext-ext-Padel-2D.ipynb | 1066 |
2 files changed, 1066 insertions, 603 deletions
diff --git a/pyrrolizidine-alkaloids/mp2d/lazar/pa-mp2d-predictions.csv b/pyrrolizidine-alkaloids/mp2d/lazar/pa-mp2d-predictions.csv index a036b2f..e69de29 100644 --- a/pyrrolizidine-alkaloids/mp2d/lazar/pa-mp2d-predictions.csv +++ b/pyrrolizidine-alkaloids/mp2d/lazar/pa-mp2d-predictions.csv @@ -1,603 +0,0 @@ -ID,SMILES,experimental,classification,probability(0),probability(1),max_similarity,nr_neighbors -1,O=C1O[C@@H]2CCN3[C@@H]2C(=CC3)COC(=O)[C@]([C@]([C@H]1C)(C)O)(C)O,,0,1.0,0.0,1.0,2 -2,C/C=C\1/C[C@@H](C)[C@](O)(CO)C(=O)OCC2=CCN3[C@H]2[C@H](OC1=O)CC3,,1,0.4648450527368263,0.5351549472631738,1.0,7 -3,O[C@@H]1CCN2[C@@H]1C(=CC2)COC(=O)[C@]([C@@H](O)C)(C(C)C)O,,0,0.6641118430278771,0.33588815697212293,1.0,17 -4,CC([C@H]1C(=O)O[C@@H]2CCN3[C@@H]2C(=CC3)COC(=O)[C@]([C@]1(C)O)(C)O)C,,0,0.8000000000000002,0.0,0.8,2 -5,O[C@@H]1CC[N+]2([C@@H]1C(=CC2)COC(=O)[C@]([C@@H](O)C)(C(C)C)O)[O-],,0,0.392514075111411,0.044985924888589046,0.4375,6 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import optimizers, regularizers\n", + "from keras.layers import Dense, Dropout, Input\n", + "from keras.models import Model, Sequential\n", + "from random import shuffle\n", + "from scipy import interp\n", + "from sklearn.linear_model import LogisticRegression\n", + "from scipy.stats.mstats import gmean\n", + "from sklearn.ensemble import RandomForestClassifier\n", + "from sklearn.metrics import roc_curve, auc\n", + "from sklearn.model_selection import StratifiedKFold, train_test_split\n", + "from sklearn.preprocessing import QuantileTransformer\n", + "import contextlib\n", + "import glob\n", + "import gzip\n", + "import h5py\n", + "import keras\n", + "import numpy as np\n", + "import os\n", + "import pandas as pd\n", + "import pylab as plt\n", + "import random\n", + "import scipy\n", + "import sklearn\n", + "import tensorflow as tf\n", + "from sklearn.ensemble import RandomForestClassifier\n", + "from sklearn.datasets import make_classification\n", + "from sklearn.svm import SVC\n", + "\n", + "\n", + "\n", + "random_state = np.random.RandomState(0)\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [], + "source": [ + "X_f_ext = '/home/drewe/notebooks/genotox/mutagenicity-fingerprints.csv'\n", + "\n", + "X = pd.read_csv(X_f_ext,sep=',')\n", + "X['Mutagenicity_bin'] = np.int32(X['Mutagenicity'] == 'mutagenic')\n", + "del X['Mutagenicity']\n", + "\n", + "\n", + "y = X['Mutagenicity_bin'].values\n", + "del X['Mutagenicity_bin']\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(8309, 9638)\n", + "(8309,)\n", + "(602, 9638)\n" + ] + } + ], + "source": [ + "\n", + "\n", + "'''\n", + "X_f_ext = '/home/drewe/notebooks/genotox/mutagenicity-mod-2.csv'\n", + "X = pd.read_csv(X_f_ext,sep=',')\n", + "\n", + "y = np.int32(X['Mutagenicity'] == 'mutagenic')\n", + "del X['Mutagenicity']\n", + "\n", + "'''\n", + "\n", + "x_pad = pd.read_csv('/home/drewe/notebooks/genotox/pa-fingerprints.csv', sep=',', decimal='.')\n", + "selected_cols = list(set(x_pad.columns.tolist()).intersection(set(X.columns.tolist())))\n", + "selected_cols.remove('Canonical SMILES')\n", + "X = np.float64(X[selected_cols].values)\n", + "x_pad = np.float64(x_pad[selected_cols].values)\n", + "print(X.shape)\n", + "print(y.shape)\n", + "print(x_pad.shape)\n", + "\n", + "names =pd.read_csv('/home/drewe/notebooks/genotox/pa-fingerprints.csv', sep=',', decimal='.')['Canonical SMILES'].values\n", + "#X_norm = QuantileTransformer(output_distribution='uniform').fit_transform(X.values.T).T\n", + "\n", + "\n", + "#X = pd.merge(X_ext,X[['Canonical SMILES','Mutagenicity_bin']], right_on='Canonical SMILES', left_on='Name')\n", + "#X = np.float64(X.values[:,1:])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + ">>\n", + ".\n", + ">>\n", + ".\n", + ">>\n", + ".\n", + ">>\n", + ".\n", + ">>\n", + ".\n" + ] + } + ], + "source": [ + "cv = StratifiedKFold(n_splits=10)\n", + "results = np.zeros_like(y, dtype=float)\n", + "\n", + "tprs = []\n", + "aucs = []\n", + "mean_fpr = np.linspace(0, 1, 100)\n", + "\n", + "i = 0\n", + "\n", + "keras.backend.clear_session()\n", + "prbs=[]\n", + "for mod in range(5):\n", + " print('>>')\n", + " curr_try = 0\n", + " while curr_try <10:\n", + " print('.')\n", + "\n", + " model = Sequential()\n", + " model.add(Dense(64, input_dim=X.shape[1], activation='relu'))\n", + " model.add(Dense(64, activation='relu'))\n", + " model.add(Dense(64, activation='relu'))\n", + " model.add(Dense(64, activation='relu'))\n", + " model.add(Dense(1, activation='sigmoid'))\n", + " # Compile model\n", + " opt = keras.optimizers.Adam(epsilon=None, amsgrad=True)\n", + " model.compile(loss='binary_crossentropy', optimizer=opt, metrics=['accuracy'])\n", + "\n", + " # Fit the model\n", + " history = model.fit(X, y, epochs=50, batch_size=64, verbose=0)\n", + " if history.history['acc'][-1] > 0.53:\n", + " break\n", + " else:\n", + " curr_try += 1\n", + "\n", + " # Fit the model\n", + " probas_ = model.predict(x_pad)\n", + " prbs.append(probas_)\n", + "# Average the predictions\n", + "probas_ = np.mean(np.hstack(prbs), axis=1)\n", + "results = probas_\n", + "\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [], + "source": [ + "df_results = pd.DataFrame(data={\"name\": names, 'pred': results})\n", + "df_results.to_csv('/home/drewe/notebooks/genotox/pred.nn.v5-ext-ext-Padel-2D.csv', index=None)" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "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" + } + ], + "source": [ + "plt.hist(results,100, color='red', alpha=0.5)\n", + "plt.show()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + ">>\n", + ".\n", + "Epoch 1/50\n", + "8309/8309 [==============================] - 1s 162us/step - loss: 0.2378 - acc: 0.9183\n", + "Epoch 2/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2365 - acc: 0.9184\n", + "Epoch 3/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2351 - acc: 0.9189\n", + "Epoch 4/50\n", + "8309/8309 [==============================] - 1s 166us/step - loss: 0.2337 - acc: 0.9200\n", + "Epoch 5/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2325 - acc: 0.9210\n", + "Epoch 6/50\n", + "8309/8309 [==============================] - 1s 162us/step - loss: 0.2312 - acc: 0.9215\n", + "Epoch 7/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2300 - acc: 0.9224\n", + "Epoch 8/50\n", + "8309/8309 [==============================] - 1s 162us/step - loss: 0.2288 - acc: 0.9235\n", + "Epoch 9/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2277 - acc: 0.9244\n", + "Epoch 10/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2265 - acc: 0.9242\n", + "Epoch 11/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2254 - acc: 0.9249\n", + "Epoch 12/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2243 - acc: 0.9253\n", + "Epoch 13/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2232 - acc: 0.9251\n", + "Epoch 14/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2222 - acc: 0.9256\n", + "Epoch 15/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2212 - acc: 0.9256\n", + "Epoch 16/50\n", + "8309/8309 [==============================] - 1s 159us/step - loss: 0.2202 - acc: 0.9265\n", + "Epoch 17/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2192 - acc: 0.9259\n", + "Epoch 18/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2182 - acc: 0.9266\n", + "Epoch 19/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2173 - acc: 0.9266\n", + "Epoch 20/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2164 - acc: 0.9267\n", + "Epoch 21/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2154 - acc: 0.9267\n", + "Epoch 22/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2146 - acc: 0.9269\n", + "Epoch 23/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2137 - acc: 0.9268\n", + "Epoch 24/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2128 - acc: 0.9271\n", + "Epoch 25/50\n", + "8309/8309 [==============================] - 1s 159us/step - loss: 0.2120 - acc: 0.9275\n", + "Epoch 26/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2112 - acc: 0.9274\n", + "Epoch 27/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2104 - acc: 0.9279\n", + "Epoch 28/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2096 - acc: 0.9282\n", + "Epoch 29/50\n", + "8309/8309 [==============================] - 1s 159us/step - loss: 0.2088 - acc: 0.9282\n", + "Epoch 30/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2080 - acc: 0.9275\n", + "Epoch 31/50\n", + "8309/8309 [==============================] - 1s 159us/step - loss: 0.2073 - acc: 0.9288\n", + "Epoch 32/50\n", + "8309/8309 [==============================] - 1s 158us/step - loss: 0.2065 - acc: 0.9291\n", + "Epoch 33/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2058 - acc: 0.9292\n", + "Epoch 34/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2050 - acc: 0.9296\n", + "Epoch 35/50\n", + "8309/8309 [==============================] - 1s 159us/step - loss: 0.2043 - acc: 0.9296\n", + "Epoch 36/50\n", + "8309/8309 [==============================] - 1s 158us/step - loss: 0.2037 - acc: 0.9309\n", + "Epoch 37/50\n", + "8309/8309 [==============================] - 1s 161us/step - loss: 0.2030 - acc: 0.9303\n", + "Epoch 38/50\n", + "8309/8309 [==============================] - 1s 160us/step - loss: 0.2023 - acc: 0.9309\n", + "Epoch 39/50\n", + "8309/8309 [==============================] - 1s 158us/step - loss: 0.2016 - acc: 0.9306\n", + 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0.1961 - acc: 0.9328\n", + "Epoch 49/50\n", + "8309/8309 [==============================] - 1s 159us/step - loss: 0.1955 - acc: 0.9332\n", + "Epoch 50/50\n", + "8309/8309 [==============================] - 1s 159us/step - loss: 0.1950 - acc: 0.9333\n", + ">>\n", + ".\n", + "Epoch 1/50\n", + "8309/8309 [==============================] - 1s 163us/step - loss: 0.2377 - acc: 0.9189\n", + "Epoch 2/50\n", + "8309/8309 [==============================] - 1s 164us/step - loss: 0.2363 - acc: 0.9190\n", + "Epoch 3/50\n", + "8309/8309 [==============================] - 1s 164us/step - loss: 0.2350 - acc: 0.9197\n", + "Epoch 4/50\n", + "8309/8309 [==============================] - 1s 164us/step - loss: 0.2337 - acc: 0.9197\n", + "Epoch 5/50\n", + "8309/8309 [==============================] - 1s 164us/step - loss: 0.2324 - acc: 0.9214\n", + "Epoch 6/50\n", + "8309/8309 [==============================] - 1s 163us/step - loss: 0.2312 - acc: 0.9219\n", + "Epoch 7/50\n", + "8309/8309 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0.9196\n", + "Epoch 4/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2338 - acc: 0.9200\n", + "Epoch 5/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2325 - acc: 0.9209\n", + "Epoch 6/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2312 - acc: 0.9210\n", + "Epoch 7/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2300 - acc: 0.9224\n", + "Epoch 8/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2289 - acc: 0.9229\n", + "Epoch 9/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2277 - acc: 0.9232\n", + "Epoch 10/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2265 - acc: 0.9239\n", + "Epoch 11/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2254 - acc: 0.9243\n", + "Epoch 12/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2243 - acc: 0.9249\n", + "Epoch 13/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2232 - acc: 0.9254\n", + "Epoch 14/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2222 - acc: 0.9251\n", + "Epoch 15/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2212 - acc: 0.9253\n", + "Epoch 16/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2201 - acc: 0.9261\n", + "Epoch 17/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2191 - acc: 0.9261\n", + "Epoch 18/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2182 - acc: 0.9259\n", + "Epoch 19/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2173 - acc: 0.9268\n", + "Epoch 20/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2164 - acc: 0.9271\n", + "Epoch 21/50\n", + "8309/8309 [==============================] - 1s 156us/step - loss: 0.2154 - acc: 0.9267\n", + "Epoch 22/50\n", + "8309/8309 [==============================] - 1s 159us/step - loss: 0.2146 - acc: 0.9271\n", + "Epoch 23/50\n", + "8309/8309 [==============================] - 1s 152us/step - loss: 0.2137 - acc: 0.9277\n", + "Epoch 24/50\n", + "8309/8309 [==============================] - 1s 169us/step - loss: 0.2128 - acc: 0.9267\n", + "Epoch 25/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2120 - acc: 0.9273\n", + "Epoch 26/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2112 - acc: 0.9272\n", + "Epoch 27/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2104 - acc: 0.9278\n", + "Epoch 28/50\n", + "8309/8309 [==============================] - 1s 150us/step - loss: 0.2096 - acc: 0.9280\n", + "Epoch 29/50\n", + "8309/8309 [==============================] - 1s 150us/step - loss: 0.2088 - acc: 0.9290\n", + "Epoch 30/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2080 - acc: 0.9291\n", + "Epoch 31/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2073 - acc: 0.9291\n", + "Epoch 32/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2065 - acc: 0.9296\n", + "Epoch 33/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2058 - acc: 0.9300\n", + "Epoch 34/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2051 - acc: 0.9297\n", + "Epoch 35/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2044 - acc: 0.9301\n", + "Epoch 36/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2037 - acc: 0.9301\n", + "Epoch 37/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2030 - acc: 0.9313\n", + "Epoch 38/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2023 - acc: 0.9312\n", + "Epoch 39/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2016 - acc: 0.9307\n", + "Epoch 40/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2010 - acc: 0.9309\n", + "Epoch 41/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.2003 - acc: 0.9316\n", + "Epoch 42/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.1997 - acc: 0.9324\n", + "Epoch 43/50\n", + "8309/8309 [==============================] - 1s 152us/step - loss: 0.1991 - acc: 0.9325\n", + "Epoch 44/50\n", + "8309/8309 [==============================] - 1s 153us/step - loss: 0.1985 - acc: 0.9320\n", + "Epoch 45/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.1978 - acc: 0.9327\n", + "Epoch 46/50\n", + "8309/8309 [==============================] - 1s 151us/step - loss: 0.1973 - acc: 0.9324\n", + "Epoch 47/50\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "8309/8309 [==============================] - 1s 150us/step - loss: 0.1967 - acc: 0.9330\n", + "Epoch 48/50\n", + "8309/8309 [==============================] - 1s 150us/step - loss: 0.1961 - acc: 0.9332\n", + "Epoch 49/50\n", + "8309/8309 [==============================] - 1s 150us/step - loss: 0.1955 - acc: 0.9336\n", + "Epoch 50/50\n", + "8309/8309 [==============================] - 1s 150us/step - loss: 0.1950 - acc: 0.9331\n" + ] + } + ], + "source": [ + "#Logistic regression (SGD)\n", + "cv = StratifiedKFold(n_splits=10)\n", + "results = np.zeros_like(y, dtype=float)\n", + "\n", + "tprs = []\n", + "aucs = []\n", + "mean_fpr = np.linspace(0, 1, 100)\n", + "\n", + "i = 0\n", + "keras.backend.clear_session()\n", + "prbs=[]\n", + "for mod in range(5):\n", + " print('>>')\n", + " curr_try = 0\n", + " while curr_try <10:\n", + " print('.')\n", + "\n", + " model = Sequential()\n", + " model.add(Dense(1, activation='sigmoid'))\n", + " # Compile model\n", + " opt = keras.optimizers.Adam(epsilon=None, amsgrad=True)\n", + " model.compile(loss='binary_crossentropy', optimizer=opt, metrics=['accuracy'])\n", + "\n", + " # Fit the model\n", + " history = model.fit(X, y, epochs=50, batch_size=64, verbose=0)\n", + " if history.history['acc'][-1] > 0.53:\n", + " break\n", + " else:\n", + " curr_try += 1\n", + "\n", + " # Fit the model\n", + " model.fit(X, y, epochs=50, batch_size=64, verbose=1)\n", + "\n", + " # evaluate the model\n", + " probas_ = model.predict(x_pad)\n", + " prbs.append(probas_)\n", + "# Average the predictions\n", + "probas_ = np.mean(np.hstack(prbs), axis=1)\n", + "results = probas_" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [], + "source": [ + "df_results = pd.DataFrame(data={\"name\": names, 'pred': results})\n", + "df_results.to_csv('/home/drewe/notebooks/genotox/pred.lr.v5-ext-ext-Padel-2D.csv', index=None)" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "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" + } + ], + "source": [ + "plt.hist(results,100, color='red', alpha=0.5)\n", + "plt.show()" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/fast_data/drewe/software/envs/tf_gpu/lib/python3.6/site-packages/sklearn/linear_model/_logistic.py:940: ConvergenceWarning: lbfgs failed to converge (status=1):\n", + "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n", + "\n", + "Increase the number of iterations (max_iter) or scale the data as shown in:\n", + " https://scikit-learn.org/stable/modules/preprocessing.html\n", + "Please also refer to the documentation for alternative solver options:\n", + " https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n", + " extra_warning_msg=_LOGISTIC_SOLVER_CONVERGENCE_MSG)\n" + ] + } + ], + "source": [ + "#Logistic regression (scikit)\n", + "cv = StratifiedKFold(n_splits=10)\n", + "results = np.zeros_like(y, dtype=float)\n", + "\n", + "tprs = []\n", + "aucs = []\n", + "mean_fpr = np.linspace(0, 1, 100)\n", + "\n", + "i = 0\n", + "keras.backend.clear_session()\n", + "prbs=[]\n", + "model = LogisticRegression(random_state=0)\n", + "model.fit(X, y)\n", + "probas_ = model.predict_proba(x_pad)[:, 1]\n", + "results = probas_\n" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [], + "source": [ + "df_results = pd.DataFrame(data={\"name\": names, 'pred': results})\n", + "df_results.to_csv('/home/drewe/notebooks/genotox/pred.lr2.v5-ext-ext-Padel-2D.csv', index=None)" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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9Pqfa5mFU+08AzgRuTfIQw2OLexo5Wdr3c399Vf2kqv6d4fxJp8+pvlnr0/7LgGsBquqrwDMYzo2yGfTKhiOtp1DvM+3AHuDSbvkNwJeqO5uwwY1se3f44WMMA72lY6owov1V9VhVbamqbVW1jeE5hddV1d61KXeq+nzu/47hiXKSbGF4OObBuVY5O33a/23gPIAkL2YY6ofnWuXa2QO8pRsFcw7wWFUdPOYea332d5kzvf/G8Gz4+7t1f8TwHzAM38zPAg8AXwOev9Y1z7Ht/wQ8Auzrfvasdc3zbP9R295KI6Nfer73AT4M3AfcA1y81jXPuf1nAF9hODJmH/Cata55im3/FHAQ+AnDXvllwNuBtx/x3n+ke23u6fO59xulktSQ9XT4RZI0IUNdkhpiqEtSQwx1SWqIoS5JDTHUJakhhrokNcRQl6SG/C/POGpxQwLyrQAAAABJRU5ErkJggg==\n", + "text/plain": [ + "<Figure size 432x288 with 1 Axes>" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "plt.hist(results,100, color='red', alpha=0.5)\n", + "plt.show()" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [], + "source": [ + "cv = StratifiedKFold(n_splits=10)\n", + "results = np.zeros_like(y, dtype=float)\n", + "\n", + "tprs = []\n", + "aucs = []\n", + "mean_fpr = np.linspace(0, 1, 100)\n", + "\n", + "i = 0\n", + "keras.backend.clear_session()\n", + "prbs=[]\n", + "model = RandomForestClassifier(n_estimators=1000, random_state=0, max_leaf_nodes=200)\n", + "# Fit the model\n", + "model.fit(X, y)\n", + "\n", + "\n", + "probas_ = model.predict_proba(x_pad)[:, 1]\n", + "results = probas_" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [], + "source": [ + "df_results = pd.DataFrame(data={\"name\": names, 'pred': results})\n", + "df_results.to_csv('/home/drewe/notebooks/genotox/pred.rf.v5-ext-ext-Padel-2D.csv', index=None)" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "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" + } + ], + "source": [ + "plt.hist(results,100, color='red', alpha=0.5)\n", + "plt.show()" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [], + "source": [ + "cv = StratifiedKFold(n_splits=10)\n", + "results = np.zeros_like(y, dtype=float)\n", + "\n", + "tprs = []\n", + "aucs = []\n", + "mean_fpr = np.linspace(0, 1, 100)\n", + "\n", + "i = 0\n", + "keras.backend.clear_session()\n", + "prbs=[]\n", + "model = SVC(kernel='rbf', gamma='scale', probability=True)\n", + "# Fit the model\n", + "model.fit(X, y)\n", + "\n", + "\n", + "probas_ = model.predict_proba(x_pad)[:, 1]\n", + "results = probas_" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [], + "source": [ + "df_results = pd.DataFrame(data={\"name\": names, 'pred': results})\n", + "df_results.to_csv('/home/drewe/notebooks/genotox/pred.svm.v5-ext-ext-Padel-2D.csv', index=None)" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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+ "text/plain": [ + "<Figure size 432x288 with 1 Axes>" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "plt.hist(results,100, color='red', alpha=0.5)\n", + "plt.show()" + ] + } + ], + "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": "3.6.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} |