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@@ -11,7 +11,8 @@ DATE: September 4-8, 2023
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* Recommended Reading: Hastie et al chapter 3, see URL:"https://link.springer.com/book/10.1007/978-0-387-84858-7"
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* Presentation and discussion of first project
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* Material for the lecture on Thursday September 7
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* Linear Regression and links with Statistics, Resampling methods
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* Technicalities related to scaling and other issues with data handling
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* Linear Regression and links with Statistics
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* Recommended Reading: Goodfellow et al chapter 3 on probability theory, see URL:""
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* See also Murphy, sections 2.4 (Gaussian distributions) and 3.2 (Bayesian Statistics, basis)
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@@ -923,6 +924,499 @@ plt.show()
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===== Material for lecture Thursday September 7 =====
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===== Important technicalities: More on Rescaling data =====
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When you are comparing your own code with for example _Scikit-Learn_'s
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library, there are some technicalities to keep in mind. The examples
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here demonstrate some of these aspects with potential pitfalls.
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The discussion here focuses on the role of the intercept, how we can
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set up the design matrix, what scaling we should use and other topics
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which tend confuse us.
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The intercept can be interpreted as the expected value of our
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target/output variables when all other predictors are set to zero.
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Thus, if we cannot assume that the expected outputs/targets are zero
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when all predictors are zero (the columns in the design matrix), it
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may be a bad idea to implement a model which penalizes the intercept.
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Furthermore, in for example Ridge and Lasso regression, the default solutions
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from the library _Scikit-Learn_ (when not shrinking $\beta_0$) for the unknown parameters
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$\bm{\beta}$, are derived under the assumption that both $\bm{y}$ and
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$\bm{X}$ are zero centered, that is we subtract the mean values.
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If our predictors represent different scales, then it is important to
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standardize the design matrix $\bm{X}$ by subtracting the mean of each
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column from the corresponding column and dividing the column with its
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standard deviation. Most machine learning libraries do this as a default. This means that if you compare your code with the results from a given library,
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the results may differ.
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The
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"Standardscaler":"https://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.StandardScaler.html"
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function in _Scikit-Learn_ does this for us. For the data sets we
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have been studying in our various examples, the data are in many cases
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already scaled and there is no need to scale them. You as a user of different machine learning algorithms, should always perform a
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survey of your data, with a critical assessment of them in case you need to scale the data.
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If you need to scale the data, not doing so will give an *unfair*
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penalization of the parameters since their magnitude depends on the
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scale of their corresponding predictor.
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Suppose as an example that you
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you have an input variable given by the heights of different persons.
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Human height might be measured in inches or meters or
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kilometers. If measured in kilometers, a standard linear regression
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model with this predictor would probably give a much bigger
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coefficient term, than if measured in millimeters.
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This can clearly lead to problems in evaluating the cost/loss functions.
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Keep in mind that when you transform your data set before training a model, the same transformation needs to be done
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on your eventual new data set before making a prediction. If we translate this into a Python code, it would could be implemented as
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!bc pycod
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"""
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#Model training, we compute the mean value of y and X
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y_train_mean = np.mean(y_train)
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X_train_mean = np.mean(X_train,axis=0)
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X_train = X_train - X_train_mean
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y_train = y_train - y_train_mean
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# The we fit our model with the training data
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trained_model = some_model.fit(X_train,y_train)
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#Model prediction, we need also to transform our data set used for the prediction.
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X_test = X_test - X_train_mean #Use mean from training data
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y_pred = trained_model(X_test)
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y_pred = y_pred + y_train_mean
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"""
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!ec
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Let us try to understand what this may imply mathematically when we
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subtract the mean values, also known as *zero centering*. For
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simplicity, we will focus on ordinary regression, as done in the above example.
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The cost/loss function for regression is
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!bt
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\[
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C(\beta_0, \beta_1, ... , \beta_{p-1}) = \frac{1}{n}\sum_{i=0}^{n} \left(y_i - \beta_0 - \sum_{j=1}^{p-1} X_{ij}\beta_j\right)^2,.
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\]
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!et
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Recall also that we use the squared value. This expression can lead to an
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increased penalty for higher differences between predicted and
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output/target values.
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What we have done is to single out the $\beta_0$ term in the
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definition of the mean squared error (MSE). The design matrix $X$
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does in this case not contain any intercept column. When we take the
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derivative with respect to $\beta_0$, we want the derivative to obey
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!bt
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\[
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\frac{\partial C}{\partial \beta_j} = 0,
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\]
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!et
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for all $j$. For $\beta_0$ we have
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!bt
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\[
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\frac{\partial C}{\partial \beta_0} = -\frac{2}{n}\sum_{i=0}^{n-1} \left(y_i - \beta_0 - \sum_{j=1}^{p-1} X_{ij} \beta_j\right).
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\]
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!et
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Multiplying away the constant $2/n$, we obtain
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!bt
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\[
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\sum_{i=0}^{n-1} \beta_0 = \sum_{i=0}^{n-1}y_i - \sum_{i=0}^{n-1} \sum_{j=1}^{p-1} X_{ij} \beta_j.
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\]
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!et
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Let us specialize first to the case where we have only two parameters $\beta_0$ and $\beta_1$.
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Our result for $\beta_0$ simplifies then to
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!bt
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\[
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n\beta_0 = \sum_{i=0}^{n-1}y_i - \sum_{i=0}^{n-1} X_{i1} \beta_1.
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\]
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!et
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We obtain then
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!bt
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\[
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\beta_0 = \frac{1}{n}\sum_{i=0}^{n-1}y_i - \beta_1\frac{1}{n}\sum_{i=0}^{n-1} X_{i1}.
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\]
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!et
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If we define
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!bt
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\[
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\mu_{\bm{x}_1}=\frac{1}{n}\sum_{i=0}^{n-1} X_{i1},
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\]
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!et
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and the mean value of the outputs as
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!bt
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\[
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\mu_y=\frac{1}{n}\sum_{i=0}^{n-1}y_i,
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\]
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!et
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we have
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!bt
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\[
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\beta_0 = \mu_y - \beta_1\mu_{\bm{x}_1}.
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\]
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!et
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In the general case with more parameters than $\beta_0$ and $\beta_1$, we have
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!bt
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\[
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\beta_0 = \frac{1}{n}\sum_{i=0}^{n-1}y_i - \frac{1}{n}\sum_{i=0}^{n-1}\sum_{j=1}^{p-1} X_{ij}\beta_j.
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\]
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!et
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We can rewrite the latter equation as
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!bt
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\[
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\beta_0 = \frac{1}{n}\sum_{i=0}^{n-1}y_i - \sum_{j=1}^{p-1} \mu_{\bm{x}_j}\beta_j,
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\]
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!et
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where we have defined
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!bt
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\[
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\mu_{\bm{x}_j}=\frac{1}{n}\sum_{i=0}^{n-1} X_{ij},
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\]
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!et
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the mean value for all elements of the column vector $\bm{x}_j$.
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Replacing $y_i$ with $y_i - y_i - \overline{\bm{y}}$ and centering also our design matrix results in a cost function (in vector-matrix disguise)
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!bt
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\[
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C(\boldsymbol{\beta}) = (\boldsymbol{\tilde{y}} - \tilde{X}\boldsymbol{\beta})^T(\boldsymbol{\tilde{y}} - \tilde{X}\boldsymbol{\beta}).
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\]
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!et
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If we minimize with respect to $\bm{\beta}$ we have then
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!bt
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\[
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\hat{\bm{\beta}} = (\tilde{X}^T\tilde{X})^{-1}\tilde{X}^T\boldsymbol{\tilde{y}},
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\]
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!et
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where $\boldsymbol{\tilde{y}} = \boldsymbol{y} - \overline{\bm{y}}$
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and $\tilde{X}_{ij} = X_{ij} - \frac{1}{n}\sum_{k=0}^{n-1}X_{kj}$.
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For Ridge regression we need to add $\lambda \boldsymbol{\beta}^T\boldsymbol{\beta}$ to the cost function and get then
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!bt
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\[
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\hat{\bm{\beta}} = (\tilde{X}^T\tilde{X} + \lambda I)^{-1}\tilde{X}^T\boldsymbol{\tilde{y}}.
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\]
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!et
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What does this mean? And why do we insist on all this? Let us look at some examples.
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This code shows a simple first-order fit to a data set using the above transformed data, where we consider the role of the intercept first, by either excluding it or including it (*code example thanks to Øyvind Sigmundson Schøyen*). Here our scaling of the data is done by subtracting the mean values only.
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Note also that we do not split the data into training and test.
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!bc pycod
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import numpy as np
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import matplotlib.pyplot as plt
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from sklearn.linear_model import LinearRegression
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np.random.seed(2021)
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def MSE(y_data,y_model):
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n = np.size(y_model)
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return np.sum((y_data-y_model)**2)/n
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def fit_beta(X, y):
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return np.linalg.pinv(X.T @ X) @ X.T @ y
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true_beta = [2, 0.5, 3.7]
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x = np.linspace(0, 1, 11)
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y = np.sum(
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np.asarray([x ** p * b for p, b in enumerate(true_beta)]), axis=0
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) + 0.1 * np.random.normal(size=len(x))
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degree = 3
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X = np.zeros((len(x), degree))
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# Include the intercept in the design matrix
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for p in range(degree):
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X[:, p] = x ** p
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beta = fit_beta(X, y)
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# Intercept is included in the design matrix
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skl = LinearRegression(fit_intercept=False).fit(X, y)
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print(f"True beta: {true_beta}")
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print(f"Fitted beta: {beta}")
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print(f"Sklearn fitted beta: {skl.coef_}")
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ypredictOwn = X @ beta
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ypredictSKL = skl.predict(X)
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print(f"MSE with intercept column")
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print(MSE(y,ypredictOwn))
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print(f"MSE with intercept column from SKL")
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print(MSE(y,ypredictSKL))
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plt.figure()
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plt.scatter(x, y, label="Data")
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plt.plot(x, X @ beta, label="Fit")
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plt.plot(x, skl.predict(X), label="Sklearn (fit_intercept=False)")
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# Do not include the intercept in the design matrix
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X = np.zeros((len(x), degree - 1))
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for p in range(degree - 1):
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X[:, p] = x ** (p + 1)
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# Intercept is not included in the design matrix
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skl = LinearRegression(fit_intercept=True).fit(X, y)
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# Use centered values for X and y when computing coefficients
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y_offset = np.average(y, axis=0)
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X_offset = np.average(X, axis=0)
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beta = fit_beta(X - X_offset, y - y_offset)
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intercept = np.mean(y_offset - X_offset @ beta)
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print(f"Manual intercept: {intercept}")
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print(f"Fitted beta (wiothout intercept): {beta}")
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print(f"Sklearn intercept: {skl.intercept_}")
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print(f"Sklearn fitted beta (without intercept): {skl.coef_}")
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ypredictOwn = X @ beta
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ypredictSKL = skl.predict(X)
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print(f"MSE with Manual intercept")
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print(MSE(y,ypredictOwn+intercept))
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print(f"MSE with Sklearn intercept")
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print(MSE(y,ypredictSKL))
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plt.plot(x, X @ beta + intercept, "--", label="Fit (manual intercept)")
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plt.plot(x, skl.predict(X), "--", label="Sklearn (fit_intercept=True)")
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plt.grid()
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plt.legend()
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plt.show()
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!ec
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The intercept is the value of our output/target variable
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when all our features are zero and our function crosses the $y$-axis (for a one-dimensional case).
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Printing the MSE, we see first that both methods give the same MSE, as
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they should. However, when we move to for example Ridge regression,
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the way we treat the intercept may give a larger or smaller MSE,
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meaning that the MSE can be penalized by the value of the
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intercept. Not including the intercept in the fit, means that the
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regularization term does not include $\beta_0$. For different values
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of $\lambda$, this may lead to different MSE values.
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To remind the reader, the regularization term, with the intercept in Ridge regression, is given by
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!bt
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\[
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\lambda \vert\vert \bm{\beta} \vert\vert_2^2 = \lambda \sum_{j=0}^{p-1}\beta_j^2,
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\]
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!et
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but when we take out the intercept, this equation becomes
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!bt
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\[
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\lambda \vert\vert \bm{\beta} \vert\vert_2^2 = \lambda \sum_{j=1}^{p-1}\beta_j^2.
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\]
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!et
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For Lasso regression we have
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!bt
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\[
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\lambda \vert\vert \bm{\beta} \vert\vert_1 = \lambda \sum_{j=1}^{p-1}\vert\beta_j\vert.
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\]
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!et
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It means that, when scaling the design matrix and the outputs/targets,
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by subtracting the mean values, we have an optimization problem which
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is not penalized by the intercept. The MSE value can then be smaller
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since it focuses only on the remaining quantities. If we however bring
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back the intercept, we will get a MSE which then contains the
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intercept.
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Armed with this wisdom, we attempt first to simply set the intercept equal to _False_ in our implementation of Ridge regression for our well-known vanilla data set.
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!bc pycod
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import numpy as np
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import pandas as pd
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import matplotlib.pyplot as plt
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from sklearn.model_selection import train_test_split
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from sklearn import linear_model
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def MSE(y_data,y_model):
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n = np.size(y_model)
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return np.sum((y_data-y_model)**2)/n
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# A seed just to ensure that the random numbers are the same for every run.
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# Useful for eventual debugging.
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np.random.seed(3155)
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n = 100
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x = np.random.rand(n)
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y = np.exp(-x**2) + 1.5 * np.exp(-(x-2)**2)
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Maxpolydegree = 20
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X = np.zeros((n,Maxpolydegree))
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#We include explicitely the intercept column
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for degree in range(Maxpolydegree):
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X[:,degree] = x**degree
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# We split the data in test and training data
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X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)
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p = Maxpolydegree
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I = np.eye(p,p)
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# Decide which values of lambda to use
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nlambdas = 6
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MSEOwnRidgePredict = np.zeros(nlambdas)
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MSERidgePredict = np.zeros(nlambdas)
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lambdas = np.logspace(-4, 2, nlambdas)
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for i in range(nlambdas):
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lmb = lambdas[i]
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OwnRidgeBeta = np.linalg.pinv(X_train.T @ X_train+lmb*I) @ X_train.T @ y_train
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# Note: we include the intercept column and no scaling
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RegRidge = linear_model.Ridge(lmb,fit_intercept=False)
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RegRidge.fit(X_train,y_train)
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# and then make the prediction
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ytildeOwnRidge = X_train @ OwnRidgeBeta
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ypredictOwnRidge = X_test @ OwnRidgeBeta
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ytildeRidge = RegRidge.predict(X_train)
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ypredictRidge = RegRidge.predict(X_test)
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MSEOwnRidgePredict[i] = MSE(y_test,ypredictOwnRidge)
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MSERidgePredict[i] = MSE(y_test,ypredictRidge)
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print("Beta values for own Ridge implementation")
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print(OwnRidgeBeta)
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print("Beta values for Scikit-Learn Ridge implementation")
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print(RegRidge.coef_)
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print("MSE values for own Ridge implementation")
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print(MSEOwnRidgePredict[i])
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print("MSE values for Scikit-Learn Ridge implementation")
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print(MSERidgePredict[i])
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# Now plot the results
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plt.figure()
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plt.plot(np.log10(lambdas), MSEOwnRidgePredict, 'r', label = 'MSE own Ridge Test')
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plt.plot(np.log10(lambdas), MSERidgePredict, 'g', label = 'MSE Ridge Test')
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plt.xlabel('log10(lambda)')
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plt.ylabel('MSE')
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plt.legend()
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plt.show()
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!ec
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The results here agree when we force _Scikit-Learn_'s Ridge function to include the first column in our design matrix.
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We see that the results agree very well. Here we have thus explicitely included the intercept column in the design matrix.
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What happens if we do not include the intercept in our fit?
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Let us see how we can change this code by zero centering.
|
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!bc pycod
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import numpy as np
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import pandas as pd
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import matplotlib.pyplot as plt
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||||
from sklearn.model_selection import train_test_split
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from sklearn import linear_model
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||||
from sklearn.preprocessing import StandardScaler
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||||
|
||||
def MSE(y_data,y_model):
|
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n = np.size(y_model)
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return np.sum((y_data-y_model)**2)/n
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# A seed just to ensure that the random numbers are the same for every run.
|
||||
# Useful for eventual debugging.
|
||||
np.random.seed(315)
|
||||
|
||||
n = 100
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||||
x = np.random.rand(n)
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||||
y = np.exp(-x**2) + 1.5 * np.exp(-(x-2)**2)
|
||||
|
||||
Maxpolydegree = 20
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||||
X = np.zeros((n,Maxpolydegree-1))
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||||
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for degree in range(1,Maxpolydegree): #No intercept column
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||||
X[:,degree-1] = x**(degree)
|
||||
|
||||
# We split the data in test and training data
|
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X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)
|
||||
|
||||
#For our own implementation, we will need to deal with the intercept by centering the design matrix and the target variable
|
||||
X_train_mean = np.mean(X_train,axis=0)
|
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#Center by removing mean from each feature
|
||||
X_train_scaled = X_train - X_train_mean
|
||||
X_test_scaled = X_test - X_train_mean
|
||||
#The model intercept (called y_scaler) is given by the mean of the target variable (IF X is centered)
|
||||
#Remove the intercept from the training data.
|
||||
y_scaler = np.mean(y_train)
|
||||
y_train_scaled = y_train - y_scaler
|
||||
|
||||
p = Maxpolydegree-1
|
||||
I = np.eye(p,p)
|
||||
# Decide which values of lambda to use
|
||||
nlambdas = 6
|
||||
MSEOwnRidgePredict = np.zeros(nlambdas)
|
||||
MSERidgePredict = np.zeros(nlambdas)
|
||||
|
||||
lambdas = np.logspace(-4, 2, nlambdas)
|
||||
for i in range(nlambdas):
|
||||
lmb = lambdas[i]
|
||||
OwnRidgeBeta = np.linalg.pinv(X_train_scaled.T @ X_train_scaled+lmb*I) @ X_train_scaled.T @ (y_train_scaled)
|
||||
intercept_ = y_scaler - X_train_mean@OwnRidgeBeta #The intercept can be shifted so the model can predict on uncentered data
|
||||
#Add intercept to prediction
|
||||
ypredictOwnRidge = X_test_scaled @ OwnRidgeBeta + y_scaler
|
||||
RegRidge = linear_model.Ridge(lmb)
|
||||
RegRidge.fit(X_train,y_train)
|
||||
ypredictRidge = RegRidge.predict(X_test)
|
||||
MSEOwnRidgePredict[i] = MSE(y_test,ypredictOwnRidge)
|
||||
MSERidgePredict[i] = MSE(y_test,ypredictRidge)
|
||||
print("Beta values for own Ridge implementation")
|
||||
print(OwnRidgeBeta) #Intercept is given by mean of target variable
|
||||
print("Beta values for Scikit-Learn Ridge implementation")
|
||||
print(RegRidge.coef_)
|
||||
print('Intercept from own implementation:')
|
||||
print(intercept_)
|
||||
print('Intercept from Scikit-Learn Ridge implementation')
|
||||
print(RegRidge.intercept_)
|
||||
print("MSE values for own Ridge implementation")
|
||||
print(MSEOwnRidgePredict[i])
|
||||
print("MSE values for Scikit-Learn Ridge implementation")
|
||||
print(MSERidgePredict[i])
|
||||
|
||||
|
||||
# Now plot the results
|
||||
plt.figure()
|
||||
plt.plot(np.log10(lambdas), MSEOwnRidgePredict, 'b--', label = 'MSE own Ridge Test')
|
||||
plt.plot(np.log10(lambdas), MSERidgePredict, 'g--', label = 'MSE SL Ridge Test')
|
||||
plt.xlabel('log10(lambda)')
|
||||
plt.ylabel('MSE')
|
||||
plt.legend()
|
||||
plt.show()
|
||||
!ec
|
||||
We see here, when compared to the code which includes explicitely the
|
||||
intercept column, that our MSE value is actually smaller. This is
|
||||
because the regularization term does not include the intercept value
|
||||
$\beta_0$ in the fitting. This applies to Lasso regularization as
|
||||
well. It means that our optimization is now done only with the
|
||||
centered matrix and/or vector that enter the fitting procedure.
|
||||
|
||||
|
||||
!split
|
||||
===== Linking the regression analysis with a statistical interpretation =====
|
||||
|
||||
@@ -1567,3 +2061,5 @@ which is our Lasso cost function!
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user