From 3697cce4d80a8de3a1e9ef241eb961d024e9e6e8 Mon Sep 17 00:00:00 2001 From: samoturk Date: Wed, 29 Nov 2017 11:33:50 +0100 Subject: [PATCH 1/3] Classification example --- data/ames.sdf | 288860 +++++++++++++++ ...mutagenicity_data_set_classification.ipynb | 488 + 2 files changed, 289348 insertions(+) create mode 100644 data/ames.sdf create mode 100644 notebooks/006_Ames_mutagenicity_data_set_classification.ipynb diff --git a/data/ames.sdf b/data/ames.sdf new file mode 100644 index 0000000..7054616 --- /dev/null +++ b/data/ames.sdf @@ -0,0 +1,288860 @@ +2475-33-4 + RDKit 2D + + 50 60 0 0 0 0 0 0 0 0999 V2000 + 5.2375 -5.0866 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.3943 -3.5948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.7646 -2.9847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 7.9781 -3.8664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.3484 -3.2563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 9.5052 -1.7645 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 8.2917 -0.8828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.9214 -1.4929 0.0000 C 0 0 0 0 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cheminformatics. Morgan fingerprints will be used to featurize the molecules. Features will be then used to train random forest models which will be validated within 4-fold cross validation." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "@TAGS: #advanced #sklearn #Classification #RandomForest" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from __future__ import print_function\n", + "% matplotlib inline" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "import pandas as pd\n", + "from rdkit import Chem\n", + "from rdkit.Chem import PandasTools\n", + "from rdkit.Chem.Draw import IPythonConsole" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Load the pre-processed [Ames mutagenicity data set](http://pubs.acs.org/doi/suppl/10.1021/ci900161g)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "df = PandasTools.LoadSDF('../data/ames.sdf')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
IDROMolclass
02475-33-4\"Mol\"/0
" + ], + "text/plain": [ + " ID ROMol class\n", + "0 2475-33-4 \"Mol\"/ 0" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "6506" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(df)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Featurization" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Helper classes and functions" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "from rdkit import DataStructs\n", + "from rdkit.Chem import AllChem\n", + "\n", + "class FP:\n", + " \"\"\"\n", + " Molecular fingerprint class, useful to pack features in pandas df\n", + " \n", + " Parameters \n", + " ---------- \n", + " fp : np.array\n", + " Features stored in numpy array\n", + " names : list, np.array\n", + " Names of the features\n", + " \"\"\"\n", + " def __init__(self, fp, names):\n", + " self.fp = fp\n", + " self.names = names\n", + " def __str__(self):\n", + " return \"%d bit FP\" % len(self.fp)\n", + " def __len__(self):\n", + " return len(self.fp)\n", + "\n", + "def get_cfps(mol, radius=2, nBits=1024, useFeatures=False, counts=False, dtype=np.float32):\n", + " \"\"\"Calculates circural (Morgan) fingerprint. \n", + " http://rdkit.org/docs/GettingStartedInPython.html#morgan-fingerprints-circular-fingerprints \n", + " \n", + " Parameters\n", + " ----------\n", + " mol : rdkit.Chem.rdchem.Mol\n", + " radius : float \n", + " Fingerprint radius, default 2\n", + " nBits : int \n", + " Length of hashed fingerprint (without descriptors), default 1024\n", + " useFeatures : bool \n", + " To get feature fingerprints (FCFP) instead of normal ones (ECFP), defaults to False\n", + " counts : bool\n", + " If set to true it returns for each bit number of appearances of each substructure (counts). Defaults to false (fingerprint is binary)\n", + " dtype : np.dtype\n", + " Numpy data type for the array. Defaults to np.float32 because it is the default dtype for scikit-learn\n", + " \n", + " Returns\n", + " -------\n", + " ML.FP\n", + " Fingerprint (feature) object\n", + " \"\"\"\n", + " arr = np.zeros((1,), dtype)\n", + " \n", + " if counts is True:\n", + " info = {}\n", + " fp = AllChem.GetMorganFingerprintAsBitVect(mol, radius, nBits=nBits, useFeatures=useFeatures, bitInfo=info)\n", + " DataStructs.ConvertToNumpyArray(fp, arr)\n", + " arr = np.array([len(info[x]) if x in info else 0 for x in range(nBits)], dtype)\n", + " else:\n", + " DataStructs.ConvertToNumpyArray(AllChem.GetMorganFingerprintAsBitVect(mol, radius, nBits=nBits, useFeatures=useFeatures), arr)\n", + " return FP(arr, range(nBits))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Calculate Morgan fingerprints and store them as FP objects in the data frame" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
IDROMolclassFP
02475-33-4\"Mol\"/01024 bit FP
" + ], + "text/plain": [ + " ID ROMol class FP\n", + "0 2475-33-4 \"Mol\"/ 0 1024 bit FP" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df['FP'] = df['ROMol'].map(get_cfps)\n", + "df.head(1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Extract the features (X) and target values (y) from the data frame" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "X = np.array([x.fp for x in df['FP']])\n", + "y = np.array(df['class'], int)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Cross validation" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "from sklearn.model_selection import StratifiedKFold\n", + "from sklearn.ensemble import RandomForestClassifier" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "To validate a machine learning approach cross validation (CV) is common strategy since all available data is used to obtain performance metrics of your selected method. It is a good practice to keep class ratios (stratification) and shuffle samples so we will use [stratified K-fold](http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.StratifiedKFold.html) CV with shuffling." + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [], + "source": [ + "kf = StratifiedKFold(n_splits=4, shuffle=True, random_state=0)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Random forest classifier with 10 estimators is the selected machine learning method" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "clf = RandomForestClassifier(n_estimators=10, random_state=0)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "4-fold CV" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [], + "source": [ + "y_values = []\n", + "predictions = []\n", + "probas = []\n", + "for train, test in kf.split(X, y):\n", + " clf.fit(X[train], y[train])\n", + " predictions.append(clf.predict(X[test]))\n", + " probas.append(clf.predict_proba(X[test]).T[1]) # Probabilities for class 1\n", + " y_values.append(y[test])" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Check the performance of the models using receiver operating characteristic (ROC) curve and area under ROC curve (ROC AUC)." + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [ + "from matplotlib import pyplot as plt\n", + "from sklearn.metrics import roc_curve, roc_auc_score" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [], + "source": [ + "aucs = [roc_auc_score(y, proba) for y, proba in zip(y_values, probas)]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Performance metrics" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "ROC AUC gives an indication how well the probabilities of the two classes are separated. Range for the ROC AUC is between 0 and 1 where 0.5 represents random selection and 1 means perfect separation." + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Mean AUC: 0.84 +- 0.01\n" + ] + } + ], + "source": [ + "print('Mean AUC: %0.2f +- %0.2f' % (np.mean(aucs), np.std(aucs)))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Plot the ROC curves" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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ssKAsU4O8NPbL0lebtJ/OH7f1AwDOq2C/LIkjEJLQaLBx8RcJpdFgAwDUMMyS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\n", + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "#doctest: IGNORE\n", + "f, ((p1, p2, p3, p4)) = plt.subplots(1,4, squeeze=True, sharex=True, sharey=True, \n", + " figsize=(12,3))\n", + "\n", + "for y,proba,ax in zip(y_values, probas, (p1,p2,p3,p4)):\n", + " tpr, fpr, _ = roc_curve(y, proba)\n", + " auc = roc_auc_score(y, proba)\n", + " ax.plot(tpr, fpr)\n", + " ax.get_xaxis().set_visible(False)\n", + " ax.get_yaxis().set_visible(False)\n", + " ax.text(0.95, 0.01, u\"%0.2f\" % auc,\n", + " verticalalignment='bottom', horizontalalignment='right',\n", + " transform=ax.transAxes, weight='bold',\n", + " fontsize=10)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The four models from cross validation show very similar performance and thus it seems that our methods is robust. Final model for prospective predictions should be trained on all samples." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "collapsed": true + }, + "source": [ + "Tutorial author: Samo Turk, Nov. 2017" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "anaconda-cloud": {}, + "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": "3.6.3" + } + }, + "nbformat": 4, + "nbformat_minor": 1 +} From dae9c2f3723b02f823e79559cd4b901ef5ecfb0c Mon Sep 17 00:00:00 2001 From: samoturk Date: Mon, 18 Dec 2017 17:47:26 +0100 Subject: [PATCH 2/3] Fix test --- ...mutagenicity_data_set_classification.ipynb | 29 ++++++++++++++----- 1 file changed, 22 insertions(+), 7 deletions(-) diff --git a/notebooks/006_Ames_mutagenicity_data_set_classification.ipynb b/notebooks/006_Ames_mutagenicity_data_set_classification.ipynb index 67472ad..b998a62 100644 --- a/notebooks/006_Ames_mutagenicity_data_set_classification.ipynb +++ b/notebooks/006_Ames_mutagenicity_data_set_classification.ipynb @@ -18,7 +18,9 @@ { "cell_type": "code", "execution_count": 1, - "metadata": {}, + "metadata": { + "collapsed": true + }, "outputs": [], "source": [ "from __future__ import print_function\n", @@ -28,7 +30,9 @@ { "cell_type": "code", "execution_count": 2, - "metadata": {}, + "metadata": { + "collapsed": true + }, "outputs": [], "source": [ "import numpy as np\n", @@ -48,7 +52,9 @@ { "cell_type": "code", "execution_count": 3, - "metadata": {}, + "metadata": { + "collapsed": true + }, "outputs": [], "source": [ "df = PandasTools.LoadSDF('../data/ames.sdf')" @@ -132,7 +138,9 @@ { "cell_type": "code", "execution_count": 6, - "metadata": {}, + "metadata": { + "collapsed": true + }, "outputs": [], "source": [ "from rdkit import DataStructs\n", @@ -291,7 +299,9 @@ { "cell_type": "code", "execution_count": 10, - "metadata": {}, + "metadata": { + "collapsed": true + }, "outputs": [], "source": [ "kf = StratifiedKFold(n_splits=4, shuffle=True, random_state=0)" @@ -325,9 +335,12 @@ { "cell_type": "code", "execution_count": 12, - "metadata": {}, + "metadata": { + "collapsed": true + }, "outputs": [], "source": [ + "#doctest: IGNORE\n", "y_values = []\n", "predictions = []\n", "probas = []\n", @@ -360,7 +373,9 @@ { "cell_type": "code", "execution_count": 14, - "metadata": {}, + "metadata": { + "collapsed": true + }, "outputs": [], "source": [ "aucs = [roc_auc_score(y, proba) for y, proba in zip(y_values, probas)]" From b83c0279e503933c102585ed7cdfb77a2deb612c Mon Sep 17 00:00:00 2001 From: samoturk Date: Mon, 18 Dec 2017 17:57:04 +0100 Subject: [PATCH 3/3] Fix test --- .../006_Ames_mutagenicity_data_set_classification.ipynb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/notebooks/006_Ames_mutagenicity_data_set_classification.ipynb b/notebooks/006_Ames_mutagenicity_data_set_classification.ipynb index b998a62..8006533 100644 --- a/notebooks/006_Ames_mutagenicity_data_set_classification.ipynb +++ b/notebooks/006_Ames_mutagenicity_data_set_classification.ipynb @@ -340,12 +340,11 @@ }, "outputs": [], "source": [ - "#doctest: IGNORE\n", "y_values = []\n", "predictions = []\n", "probas = []\n", "for train, test in kf.split(X, y):\n", - " clf.fit(X[train], y[train])\n", + " _ = clf.fit(X[train], y[train])\n", " predictions.append(clf.predict(X[test]))\n", " probas.append(clf.predict_proba(X[test]).T[1]) # Probabilities for class 1\n", " y_values.append(y[test])" @@ -428,7 +427,7 @@ "data": { "image/png": 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ssKAsU4O8NPbL0lebtJ/OH7f1AwDOq2C/LIkjEJLQaLBx8RcJpdFgAwDUMMyS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\n+APWr1+Phx56SLHPNVb3Lqt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