TITLE: Data Analysis and Machine Learning: Preprocessing and Dimensionality Reduction AUTHOR: Morten Hjorth-Jensen {copyright, 1999-present|CC BY-NC} at Department of Physics, University of Oslo & Department of Physics and Astronomy and National Superconducting Cyclotron Laboratory, Michigan State University DATE: today !split ===== Reducing the number of degrees of freedom, overarching view ===== !bblock Many Machine Learning problems involve thousands or even millions of features for each training instance. Not only does this make training extremely slow, it can also make it much harder to find a good solution, as we will see. This problem is often referred to as the curse of dimensionality. Fortunately, in real-world problems, it is often possible to reduce the number of features considerably, turning an intractable problem into a tractable one. Here we will discuss some of the most popular dimensionality reduction techniques: the principal component analysis PCA, Kernel PCA, and Locally Linear Embedding (LLE). Furthermore, we will start by looking at some simple preprocessing of the data which allow us to rescale the data. !eblock !split ===== Preprocessing our data ===== !bblock Before we proceed however, we will discuss how to preprocess our data. Till now and in connection with our previous examples we have not met so many cases where we are too sensitive to the scaling of our data. Normally the data may need a rescaling and/or may be sensitive to extreme values. Scaling the data renders our inputs much more suitable for the algorithms we want to employ. _Scikit-Learn_ has several functions which allow us to rescale the data, normally resulting in much better results in terms of various accuracy scores. The _StandardScaler_ function in _Scikit-Learn_ ensures that for each feature/predictor we study the mean value is zero and the variance is one (every column in the design/feature matrix). This scaling has the drawback that it does not ensure that we have a particular maximum or minimum in our data set. Another function included in _Scikit-Learn_ is the _MinMaxScaler_ which ensures that all features are exactly between $0$ and $1$. The !split ===== More preprocessing ===== The _Normalizer_ scales each data point such that the feature vector has a euclidean length of one. In other words, it projects a data point on the circle (or sphere in the case of higher dimensions) with a radius of 1. This means every data point is scaled by a different number (by the inverse of it’s length). This normalization is often used when only the direction (or angle) of the data matters, not the length of the feature vector. The _RobustScaler_ works similarly to the StandardScaler in that it ensures statistical properties for each feature that guarantee that they are on the same scale. However, the RobustScaler uses the median and quartiles, instead of mean and variance. This makes the RobustScaler ignore data points that are very different from the rest (like measurement errors). These odd data points are also called outliers, and might often lead to trouble for other scaling techniques. !eblock !split ===== Simple preprocessing examples, Franke function and regression ===== !bc pycod # Common imports import os import numpy as np import pandas as pd import matplotlib.pyplot as plt import sklearn.linear_model as skl from sklearn.metrics import mean_squared_error from sklearn.model_selection import train_test_split from sklearn.preprocessing import MinMaxScaler, StandardScaler, Normalizer from sklearn.svm import SVR # Where to save the figures and data files PROJECT_ROOT_DIR = "Results" FIGURE_ID = "Results/FigureFiles" DATA_ID = "DataFiles/" if not os.path.exists(PROJECT_ROOT_DIR): os.mkdir(PROJECT_ROOT_DIR) if not os.path.exists(FIGURE_ID): os.makedirs(FIGURE_ID) if not os.path.exists(DATA_ID): os.makedirs(DATA_ID) def image_path(fig_id): return os.path.join(FIGURE_ID, fig_id) def data_path(dat_id): return os.path.join(DATA_ID, dat_id) def save_fig(fig_id): plt.savefig(image_path(fig_id) + ".png", format='png') def FrankeFunction(x,y): term1 = 0.75*np.exp(-(0.25*(9*x-2)**2) - 0.25*((9*y-2)**2)) term2 = 0.75*np.exp(-((9*x+1)**2)/49.0 - 0.1*(9*y+1)) term3 = 0.5*np.exp(-(9*x-7)**2/4.0 - 0.25*((9*y-3)**2)) term4 = -0.2*np.exp(-(9*x-4)**2 - (9*y-7)**2) return term1 + term2 + term3 + term4 def create_X(x, y, n ): if len(x.shape) > 1: x = np.ravel(x) y = np.ravel(y) N = len(x) l = int((n+1)*(n+2)/2) # Number of elements in beta X = np.ones((N,l)) for i in range(1,n+1): q = int((i)*(i+1)/2) for k in range(i+1): X[:,q+k] = (x**(i-k))*(y**k) return X # Making meshgrid of datapoints and compute Franke's function n = 5 N = 1000 x = np.sort(np.random.uniform(0, 1, N)) y = np.sort(np.random.uniform(0, 1, N)) z = FrankeFunction(x, y) X = create_X(x, y, n=n) # split in training and test data X_train, X_test, y_train, y_test = train_test_split(X,z,test_size=0.2) svm = SVR(gamma='auto',C=10.0) svm.fit(X_train, y_train) # The mean squared error and R2 score print("MSE before scaling: {:.2f}".format(mean_squared_error(svm.predict(X_test), y_test))) print("R2 score before scaling {:.2f}".format(svm.score(X_test,y_test))) scaler = StandardScaler() scaler.fit(X_train) X_train_scaled = scaler.transform(X_train) X_test_scaled = scaler.transform(X_test) print("Feature min values before scaling:\n {}".format(X_train.min(axis=0))) print("Feature max values before scaling:\n {}".format(X_train.max(axis=0))) print("Feature min values after scaling:\n {}".format(X_train_scaled.min(axis=0))) print("Feature max values after scaling:\n {}".format(X_train_scaled.max(axis=0))) svm = SVR(gamma='auto',C=10.0) svm.fit(X_train_scaled, y_train) print("MSE after scaling: {:.2f}".format(mean_squared_error(svm.predict(X_test_scaled), y_test))) print("R2 score for scaled data: {:.2f}".format(svm.score(X_test_scaled,y_test))) !ec !split ===== Simple preprocessing examples, breast cancer data and classification, Support Vector Machines ===== We show here how we can use a simple regression case on the breast cancer data using support vector machines (SVM) as algorithm for classification. !bc pycod import matplotlib.pyplot as plt import numpy as np from sklearn.model_selection import train_test_split from sklearn.datasets import load_breast_cancer from sklearn.svm import SVC cancer = load_breast_cancer() X_train, X_test, y_train, y_test = train_test_split(cancer.data,cancer.target,random_state=0) print(X_train.shape) print(X_test.shape) svm = SVC(C=100) svm.fit(X_train, y_train) print("Test set accuracy: {:.2f}".format(svm.score(X_test,y_test))) from sklearn.preprocessing import MinMaxScaler, StandardScaler scaler = MinMaxScaler() scaler.fit(X_train) X_train_scaled = scaler.transform(X_train) X_test_scaled = scaler.transform(X_test) print("Feature min values before scaling:\n {}".format(X_train.min(axis=0))) print("Feature max values before scaling:\n {}".format(X_train.max(axis=0))) print("Feature min values before scaling:\n {}".format(X_train_scaled.min(axis=0))) print("Feature max values before scaling:\n {}".format(X_train_scaled.max(axis=0))) svm.fit(X_train_scaled, y_train) print("Test set accuracy scaled data with Min-Max scaling: {:.2f}".format(svm.score(X_test_scaled,y_test))) scaler = StandardScaler() scaler.fit(X_train) X_train_scaled = scaler.transform(X_train) X_test_scaled = scaler.transform(X_test) svm.fit(X_train_scaled, y_train) print("Test set accuracy scaled data with Standar Scaler: {:.2f}".format(svm.score(X_test_scaled,y_test))) !ec !split ===== More on Cancer Data, now with Logistic Regression ===== !bc pycod import matplotlib.pyplot as plt import numpy as np from sklearn.model_selection import train_test_split from sklearn.datasets import load_breast_cancer from sklearn.linear_model import LogisticRegression cancer = load_breast_cancer() # Set up training data X_train, X_test, y_train, y_test = train_test_split(cancer.data,cancer.target,random_state=0) logreg = LogisticRegression() logreg.fit(X_train, y_train) print("Test set accuracy: {:.2f}".format(logreg.score(X_test,y_test))) # Scale data from sklearn.preprocessing import StandardScaler scaler = StandardScaler() scaler.fit(X_train) X_train_scaled = scaler.transform(X_train) X_test_scaled = scaler.transform(X_test) logreg.fit(X_train_scaled, y_train) print("Test set accuracy scaled data: {:.2f}".format(logreg.score(X_test_scaled,y_test))) !ec !split ===== Why should we think of reducing the dimensionality ===== In addition to the plot of the features, we study now also the covariance (or rather the correlation matrix). We use also _Pandas_ to compute the correlation matrix. !bc pycod import matplotlib.pyplot as plt import numpy as np from sklearn.model_selection import train_test_split from sklearn.datasets import load_breast_cancer from sklearn.linear_model import LogisticRegression cancer = load_breast_cancer() import pandas as pd # Making a data frame cancerpd = pd.DataFrame(cancer.data, columns=cancer.feature_names) fig, axes = plt.subplots(15,2,figsize=(10,20)) malignant = cancer.data[cancer.target == 0] benign = cancer.data[cancer.target == 1] ax = axes.ravel() for i in range(30): _, bins = np.histogram(cancer.data[:,i], bins =50) ax[i].hist(malignant[:,i], bins = bins, alpha = 0.5) ax[i].hist(benign[:,i], bins = bins, alpha = 0.5) ax[i].set_title(cancer.feature_names[i]) ax[i].set_yticks(()) ax[0].set_xlabel("Feature magnitude") ax[0].set_ylabel("Frequency") ax[0].legend(["Malignant", "Benign"], loc ="best") fig.tight_layout() plt.show() import seaborn as sns correlation_matrix = cancerpd.corr().round(1) # use the heatmap function from seaborn to plot the correlation matrix # annot = True to print the values inside the square sns.heatmap(data=correlation_matrix, annot=True) plt.show() #print eigvalues of correlation matrix EigValues, EigVectors = np.linalg.eig(correlation_matrix) print(EigValues) !ec In the above example we note two things. In the first plot we display the overlap of benign and malignant tumors as functions of the various features in the Wisconsing breast cancer data set. We see that for some of the features we can distinguish clearly the benign and malignant cases while for other features we cannot. This can point to us which features may be of greater interest when we wish to classify a benign or not benign tumour. In the second figure we have computed the so-called correlation matrix, which in our case with thirty features becomes a $30\times 30$ matrix. We constructed this matrix using _pandas_ via the statements !bc pycod cancerpd = pd.DataFrame(cancer.data, columns=cancer.feature_names) !ec and then !bc pycod correlation_matrix = cancerpd.corr().round(1) !ec Diagonalizing this matrix we can in turn say something about which features are of relevance and which are not. But before we proceed we need to define covariance and correlation matrices. This leads us to the classical Principal Component Analysis (PCA) theorem with applications. !split ===== Basic ideas of the Principal Component Analysis (PCA) ===== We have a data set defined by a design/feature matrix $\bm{X}$ (see below for its definition) * Each data point is determined by $p$ extrinsic (measurement) variables * We may want to ask the following question: Are there fewer intrinsic variables (say $d << p$) that still approximately describe the data? * If so, these intrinsic variables may tell us something important and finding these intrinsic variables is what dimension reduction methods do. !split ===== Introducing the Covariance and Correlation functions ===== Before we discuss the PCA theorem, we need to remind ourselves about the definition of the covariance and the correlation function. Suppose we have defined two vectors $\hat{x}$ and $\hat{y}$ with $n$ elements each. The covariance matrix $\bm{C}$ is defined as !bt \[ \bm{C}[\bm{x},\bm{y}] = \begin{bmatrix} \mathrm{cov}[\bm{x},\bm{x}] & \mathrm{cov}[\bm{x},\bm{y}] \\ \mathrm{cov}[\bm{y},\bm{x}] & \mathrm{cov}[\bm{y},\bm{y}] \\ \end{bmatrix}, \] !et where for example !bt \[ \mathrm{cov}[\bm{x},\bm{y}] =\frac{1}{n} \sum_{i=0}^{n-1}(x_i- \overline{x})(y_i- \overline{y}). \] !et With this definition and recalling that the variance is defined as !bt \[ \mathrm{var}[\bm{x}]=\frac{1}{n} \sum_{i=0}^{n-1}(x_i- \overline{x})^2, \] !et we can rewrite the covariance matrix as !bt \[ \bm{C}[\bm{x},\bm{y}] = \begin{bmatrix} \mathrm{var}[\bm{x}] & \mathrm{cov}[\bm{x},\bm{y}] \\ \mathrm{cov}[\bm{x},\bm{y}] & \mathrm{var}[\bm{y}] \\ \end{bmatrix}, \] !et The covariance takes values between zero and infinity and may thus lead to problems with loss of numerical precision for particularly large values. It is common to scale the covariance matrix by introducing instead the correlation matrix defined via the so-called correlation function !bt \[ \mathrm{corr}[\bm{x},\bm{y}]=\frac{\mathrm{cov}[\bm{x},\bm{y}]}{\sqrt{\mathrm{var}[\bm{x}] \mathrm{var}[\bm{y}]}}. \] !et The correlation function is then given by values $\mathrm{corr}[\bm{x},\bm{y}] \in [-1,1]$. This avoids eventual problems with too large values. We can then define the correlation matrix for the two vectors $\bm{x}$ and $\bm{y}$ as !bt \[ \bm{K}[\bm{x},\bm{y}] = \begin{bmatrix} 1 & \mathrm{corr}[\bm{x},\bm{y}] \\ \mathrm{corr}[\bm{y},\bm{x}] & 1 \\ \end{bmatrix}, \] !et In the above example this is the function we constructed using _pandas_. !split ===== Correlation Function and Design/Feature Matrix ===== In our derivation of the various regression algorithms like Ordinary Least Squares or Ridge regression we defined the design/feature matrix $\bm{X}$ as !bt \[ \bm{X}=\begin{bmatrix} x_{0,0} & x_{0,1} & x_{0,2}& \dots & \dots x_{0,p-1}\\ x_{1,0} & x_{1,1} & x_{1,2}& \dots & \dots x_{1,p-1}\\ x_{2,0} & x_{2,1} & x_{2,2}& \dots & \dots x_{2,p-1}\\ \dots & \dots & \dots & \dots \dots & \dots \\ x_{n-2,0} & x_{n-2,1} & x_{n-2,2}& \dots & \dots x_{n-2,p-1}\\ x_{n-1,0} & x_{n-1,1} & x_{n-1,2}& \dots & \dots x_{n-1,p-1}\\ \end{bmatrix}, \] !et with $\bm{X}\in {\mathbb{R}}^{n\times p}$, with the predictors/features $p$ refering to the column numbers and the entries $n$ being the row elements. We can rewrite the design/feature matrix in terms of its column vectors as !bt \[ \bm{X}=\begin{bmatrix} \bm{x}_0 & \bm{x}_0 & \bm{x}_0 & \dots & \dots & \bm{x}_{p-1}\end{bmatrix}, \] !et with a given vector !bt \[ \bm{x}_i^T = \begin{bmatrix}x_{0,i} & x_{1,i} & x_{2,i}& \dots & \dots x_{n-1,i}\end{bmatrix}. \] !et With these definitions, we can now rewrite our $2\times 2$ correaltion/covariance matrix in terms of a moe general design/feature matrix $\bm{X}\in {\mathbb{R}}^{n\times p}$. This leads to a $p\times p$ covariance matrix for the vectors $\bm{x}_i$ with $i =0,1,\dots,p-1$ !bt \[ \bm{C}[\bm{x}] = \begin{bmatrix} \mathrm{var}[\bm{x}_0] & \mathrm{cov}[\bm{x}_0,\bm{x}_1] & \mathrm{cov}[\bm{x}_0,\bm{x}_2] & \dots & \dots & \mathrm{cov}[\bm{x}_0,\bm{x}_{p-1}]\\ \mathrm{cov}[\bm{x}_1,\bm{x}_0] & \mathrm{var}[\bm{x}_1] & \mathrm{cov}[\bm{x}_1,\bm{x}_2] & \dots & \dots & \mathrm{cov}[\bm{x}_1,\bm{x}_{p-1}]\\ \mathrm{cov}[\bm{x}_2,\bm{x}_0] & \mathrm{cov}[\bm{x}_2,\bm{x}_1] & \mathrm{var}[\bm{x}_2] & \dots & \dots & \mathrm{cov}[\bm{x}_2,\bm{x}_{p-1}]\\ \dots & \dots & \dots & \dots & \dots & \dots \\ \dots & \dots & \dots & \dots & \dots & \dots \\ \mathrm{cov}[\bm{x}_{p-1},\bm{x}_0] & \mathrm{cov}[\bm{x}_{p-1},\bm{x}_1] & \mathrm{cov}[\bm{x}_{p-1},\bm{x}_{2}] & \dots & \dots & \mathrm{var}[\bm{x}_{p-1}]\\ \end{bmatrix}, \] !et and the correlation matrix !bt \[ \bm{K}[\bm{x}] = \begin{bmatrix} 1 & \mathrm{corr}[\bm{x}_0,\bm{x}_1] & \mathrm{corr}[\bm{x}_0,\bm{x}_2] & \dots & \dots & \mathrm{corr}[\bm{x}_0,\bm{x}_{p-1}]\\ \mathrm{corr}[\bm{x}_1,\bm{x}_0] & 1 & \mathrm{corr}[\bm{x}_1,\bm{x}_2] & \dots & \dots & \mathrm{corr}[\bm{x}_1,\bm{x}_{p-1}]\\ \mathrm{corr}[\bm{x}_2,\bm{x}_0] & \mathrm{corr}[\bm{x}_2,\bm{x}_1] & 1 & \dots & \dots & \mathrm{corr}[\bm{x}_2,\bm{x}_{p-1}]\\ \dots & \dots & \dots & \dots & \dots & \dots \\ \dots & \dots & \dots & \dots & \dots & \dots \\ \mathrm{corr}[\bm{x}_{p-1},\bm{x}_0] & \mathrm{corr}[\bm{x}_{p-1},\bm{x}_1] & \mathrm{corr}[\bm{x}_{p-1},\bm{x}_{2}] & \dots & \dots & 1\\ \end{bmatrix}, \] !et !split ===== Covariance Matrix Examples ===== The Numpy function _np.cov_ calculates the covariance elements using the factor $1/(n-1)$ instead of $1/n$ since it assumes we do not have the exact mean values. The following simple function uses the _np.vstack_ function which takes each vector of dimension $1\times n$ and produces a $2\times n$ matrix $\bm{W}$ !bt \[ \bm{W} = \begin{bmatrix} x_0 & y_0 \\ x_1 & y_1 \\ x_2 & y_2\\ \dots & \dots \\ x_{n-2} & y_{n-2}\\ x_{n-1} & y_{n-1} & \end{bmatrix}, \] !et which in turn is converted into into the $2\times 2$ covariance matrix $\bm{C}$ via the Numpy function _np.cov()_. We note that we can also calculate the mean value of each set of samples $\bm{x}$ etc using the Numpy function _np.mean(x)_. We can also extract the eigenvalues of the covariance matrix through the _np.linalg.eig()_ function. !bc pycod # Importing various packages import numpy as np n = 100 x = np.random.normal(size=n) print(np.mean(x)) y = 4+3*x+np.random.normal(size=n) print(np.mean(y)) W = np.vstack((x, y)) C = np.cov(W) print(C) !ec !split ===== Correlation Matrix ===== The previous example can be converted into the correlation matrix by simply scaling the matrix elements with the variances. We should also subtract the mean values for each column. This leads to the following code which sets up the correlations matrix for the previous example in a more brute force way. Here we scale the mean values for each column of the design matrix, calculate the relevant mean values and variances and then finally set up the $2\times 2$ correlation matrix (since we have only two vectors). !bc pycod import numpy as np n = 100 # define two vectors x = np.random.random(size=n) y = 4+3*x+np.random.normal(size=n) #scaling the x and y vectors x = x - np.mean(x) y = y - np.mean(y) variance_x = np.sum(x@x)/n variance_y = np.sum(y@y)/n print(variance_x) print(variance_y) cov_xy = np.sum(x@y)/n cov_xx = np.sum(x@x)/n cov_yy = np.sum(y@y)/n C = np.zeros((2,2)) C[0,0]= cov_xx/variance_x C[1,1]= cov_yy/variance_y C[0,1]= cov_xy/np.sqrt(variance_y*variance_x) C[1,0]= C[0,1] print(C) !ec We see that the matrix elements along the diagonal are one as they should be and that the matrix is symmetric. Furthermore, diagonalizing this matrix we easily see that it is a positive definite matrix. The above procedure with _numpy_ can be made more compact if we use _pandas_. !split ===== Correlation Matrix with Pandas ===== We whow here how we can set up the correlation matrix using _pandas_, as done in this simple code !bc pycod import numpy as np import pandas as pd n = 10 x = np.random.normal(size=n) x = x - np.mean(x) y = 4+3*x+np.random.normal(size=n) y = y - np.mean(y) X = (np.vstack((x, y))).T print(X) Xpd = pd.DataFrame(X) print(Xpd) correlation_matrix = Xpd.corr() print(correlation_matrix) !ec We expand this model to the Franke function discussed above. !split ===== Correlation Matrix with Pandas and the Franke function ===== !bc pycod # Common imports import numpy as np import pandas as pd def FrankeFunction(x,y): term1 = 0.75*np.exp(-(0.25*(9*x-2)**2) - 0.25*((9*y-2)**2)) term2 = 0.75*np.exp(-((9*x+1)**2)/49.0 - 0.1*(9*y+1)) term3 = 0.5*np.exp(-(9*x-7)**2/4.0 - 0.25*((9*y-3)**2)) term4 = -0.2*np.exp(-(9*x-4)**2 - (9*y-7)**2) return term1 + term2 + term3 + term4 def create_X(x, y, n ): if len(x.shape) > 1: x = np.ravel(x) y = np.ravel(y) N = len(x) l = int((n+1)*(n+2)/2) # Number of elements in beta X = np.ones((N,l)) for i in range(1,n+1): q = int((i)*(i+1)/2) for k in range(i+1): X[:,q+k] = (x**(i-k))*(y**k) return X # Making meshgrid of datapoints and compute Franke's function n = 4 N = 100 x = np.sort(np.random.uniform(0, 1, N)) y = np.sort(np.random.uniform(0, 1, N)) z = FrankeFunction(x, y) X = create_X(x, y, n=n) Xpd = pd.DataFrame(X) # subtract the mean values and set up the covariance matrix Xpd = Xpd - Xpd.mean() covariance_matrix = Xpd.cov() print(covariance_matrix) !ec We note here that the covariance is zero for the first rows and columns since all matrix elements in the design matrix were set to one (we are fitting the function in terms of a polynomial of degree $n$). This means that the variance for these elements will be zero and will cause problems when we set up the correlation matrix. We can simply drop these elements as follows and then construct the correlation matrix. !split ===== Classical PCA Theorem ===== !split ===== Prof of the PCA Theorem ===== !split ===== Getting started with PCA ===== !bc pycod # Now add PCA from sklearn.decomposition import PCA pca = PCA(n_components = 2) pca.fit(X_train_scaled) X_pca = pca.transform(X_train_scaled) !ec !split ===== Principal Component Analysis ===== !bblock Principal Component Analysis (PCA) is by far the most popular dimensionality reduction algorithm. First it identifies the hyperplane that lies closest to the data, and then it projects the data onto it. The following Python code uses NumPy’s _svd()_ function to obtain all the principal components of the training set, then extracts the first two principal components !bc pycod X_centered = X - X.mean(axis=0) U, s, V = np.linalg.svd(X_centered) c1 = V.T[:, 0] c2 = V.T[:, 1] !ec PCA assumes that the dataset is centered around the origin. Scikit-Learn’s PCA classes take care of centering the data for you. However, if you implement PCA yourself (as in the preceding example), or if you use other libraries, don’t forget to center the data first. Once you have identified all the principal components, you can reduce the dimensionality of the dataset down to $d$ dimensions by projecting it onto the hyperplane defined by the first $d$ principal components. Selecting this hyperplane ensures that the projection will preserve as much variance as possible. !bc pycod W2 = V.T[:, :2] X2D = X_centered.dot(W2) !ec !split ===== PCA and scikit-learn ===== Scikit-Learn’s PCA class implements PCA using SVD decomposition just like we did before. The following code applies PCA to reduce the dimensionality of the dataset down to two dimensions (note that it automatically takes care of centering the data): !bc pycod from sklearn.decomposition import PCA pca = PCA(n_components = 2) X2D = pca.fit_transform(X) !ec After fitting the PCA transformer to the dataset, you can access the principal components using the components variable (note that it contains the PCs as horizontal vectors, so, for example, the first principal component is equal to !bc pycod pca.components_.T[:, 0]). !ec Another very useful piece of information is the explained variance ratio of each principal component, available via the $explained\_variance\_ratio$ variable. It indicates the proportion of the dataset’s variance that lies along the axis of each principal component. More material to come here. !split ===== More on the PCA ===== Instead of arbitrarily choosing the number of dimensions to reduce down to, it is generally preferable to choose the number of dimensions that add up to a sufficiently large portion of the variance (e.g., 95%). Unless, of course, you are reducing dimensionality for data visualization — in that case you will generally want to reduce the dimensionality down to 2 or 3. The following code computes PCA without reducing dimensionality, then computes the minimum number of dimensions required to preserve 95% of the training set’s variance: !bc pycod pca = PCA() pca.fit(X) cumsum = np.cumsum(pca.explained_variance_ratio_) d = np.argmax(cumsum >= 0.95) + 1 !ec You could then set $n\_components=d$ and run PCA again. However, there is a much better option: instead of specifying the number of principal components you want to preserve, you can set $n\_components$ to be a float between 0.0 and 1.0, indicating the ratio of variance you wish to preserve: !bc pycod pca = PCA(n_components=0.95) X_reduced = pca.fit_transform(X) !ec !split ===== Incremental PCA ===== One problem with the preceding implementation of PCA is that it requires the whole training set to fit in memory in order for the SVD algorithm to run. Fortunately, Incremental PCA (IPCA) algorithms have been developed: you can split the training set into mini-batches and feed an IPCA algorithm one minibatch at a time. This is useful for large training sets, and also to apply PCA online (i.e., on the fly, as new instances arrive). !split ===== Randomized PCA ===== Scikit-Learn offers yet another option to perform PCA, called Randomized PCA. This is a stochastic algorithm that quickly finds an approximation of the first d principal components. Its computational complexity is $O(m \times d^2)+O(d^3)$, instead of $O(m \times n^2) + O(n^3)$, so it is dramatically faster than the previous algorithms when $d$ is much smaller than $n$. !eblock !split ===== Kernel PCA ===== !bblock The kernel trick is a mathematical technique that implicitly maps instances into a very high-dimensional space (called the feature space), enabling nonlinear classification and regression with Support Vector Machines. Recall that a linear decision boundary in the high-dimensional feature space corresponds to a complex nonlinear decision boundary in the original space. It turns out that the same trick can be applied to PCA, making it possible to perform complex nonlinear projections for dimensionality reduction. This is called Kernel PCA (kPCA). It is often good at preserving clusters of instances after projection, or sometimes even unrolling datasets that lie close to a twisted manifold. For example, the following code uses Scikit-Learn’s KernelPCA class to perform kPCA with an !bc pycod from sklearn.decomposition import KernelPCA rbf_pca = KernelPCA(n_components = 2, kernel="rbf", gamma=0.04) X_reduced = rbf_pca.fit_transform(X) !ec !eblock !split ===== LLE ===== Locally Linear Embedding (LLE) is another very powerful nonlinear dimensionality reduction (NLDR) technique. It is a Manifold Learning technique that does not rely on projections like the previous algorithms. In a nutshell, LLE works by first measuring how each training instance linearly relates to its closest neighbors (c.n.), and then looking for a low-dimensional representation of the training set where these local relationships are best preserved (more details shortly). !split ===== Other techniques ===== There are many other dimensionality reduction techniques, several of which are available in Scikit-Learn. Here are some of the most popular: * _Multidimensional Scaling (MDS)_ reduces dimensionality while trying to preserve the distances between the instances. * _Isomap_ creates a graph by connecting each instance to its nearest neighbors, then reduces dimensionality while trying to preserve the geodesic distances between the instances. * _t-Distributed Stochastic Neighbor Embedding_ (t-SNE) reduces dimensionality while trying to keep similar instances close and dissimilar instances apart. It is mostly used for visualization, in particular to visualize clusters of instances in high-dimensional space (e.g., to visualize the MNIST images in 2D). * Linear Discriminant Analysis (LDA) is actually a classification algorithm, but during training it learns the most discriminative axes between the classes, and these axes can then be used to define a hyperplane onto which to project the data. The benefit is that the projection will keep classes as far apart as possible, so LDA is a good technique to reduce dimensionality before running another classification algorithm such as a Support Vector Machine (SVM) classifier discussed in the SVM lectures. Here are other examples where we use the _DataFrame_ functionality to handle arrays, now with more interesting features for us, namely numbers. We set up a matrix of dimensionality $10\times 5$ and compute the mean value and standard deviation of each column. Similarly, we can perform mathematial operations like squaring the matrix elements and many other operations. !bc pycod import numpy as np import pandas as pd from IPython.display import display np.random.seed(100) # setting up a 10 x 5 matrix rows = 10 cols = 5 a = np.random.randn(rows,cols) df = pd.DataFrame(a) display(df) print(df.mean()) print(df.std()) display(df**2) !ec Thereafter we can select specific columns only and plot final results !bc pycod df.columns = ['First', 'Second', 'Third', 'Fourth', 'Fifth'] df.index = np.arange(10) display(df) print(df['Second'].mean() ) print(df.info()) print(df.describe()) from pylab import plt, mpl plt.style.use('seaborn') mpl.rcParams['font.family'] = 'serif' df.cumsum().plot(lw=2.0, figsize=(10,6)) plt.show() df.plot.bar(figsize=(10,6), rot=15) plt.show() !ec We can produce a $4\times 4$ matrix !bc pycod b = np.arange(16).reshape((4,4)) print(b) df1 = pd.DataFrame(b) print(df1) !ec and many other operations.