# sklearn logistic regression coefficients

- December 2, 2020
- Uncategorized

However, if the coefficients are too large, it can lead to model over-fitting on the training dataset. Cranking out numbers without thinking is dangerous. I knew the log odds were involved, but I couldn't find the words to explain it. Returns the probability of the sample for each class in the model, For machine learning Engineers or data scientists wanting to test their understanding of Logistic regression or preparing for interviews, these concepts and related quiz questions and answers will come handy. Maximum number of iterations taken for the solvers to converge. Let me give you an example, since I’m near the beach this week… suppose you have low mean squared error in predicting the daily mean tide height… this might seem very good, and it is very good if you are a cartographer and need to figure out where to put the coastline on your map… but if you are a beach house owner, what matters is whether the tide is 36 inches above your living room floor. intercept_ is of shape (1,) when the given problem is binary. Such a book, while of interest to pure mathematicians would undoubtedly be taken as a bible for practical applied problems, in a mistaken way. n_features is the number of features. In this module, we will discuss the use of logistic regression, what logistic regression is, the confusion matrix, and the ROC curve. used if penalty='elasticnet'. initialization, otherwise, just erase the previous solution. (Note: you will need to use.coef_ for logistic regression to put it into a dataframe.) This can be achieved by specifying a class weighting configuration that is used to influence the amount that logistic regression coefficients … I mean in the sense of large sample asymptotics. outcome 0 (False). I’m using Scikit-learn version 0.21.3 in this analysis. In the post, W. D. makes three arguments. In short, adding more animals to your experiment is fine. From probability to odds to log of odds. Joined: Oct 2019. Someone learning from this tutorial who also learned about logistic regression in a stats or intro ML class would have no idea that the default options for sklearn’s LogisticRegression class are wonky, not scale invariant, and utilizing untuned hyperparameters. liblinear solver), no regularization is applied. And choice of hyperprior, but that’s usually less sensitive with lots of groups or lots of data per group. 219 1 1 gold badge 3 3 silver badges 11 11 bronze badges. This is the most straightforward kind of classification problem. In this tutorial, we use Logistic Regression to predict digit labels based on images. from sklearn.linear_model import LinearRegression regressor = LinearRegression() regressor.fit(X_train, y_train) As said earlier, in case of multivariable linear regression, the regression model has to find the most optimal coefficients for all the attributes. In this page, we will walk through the concept of odds ratio and try to interpret the logistic regression results using the concept of odds ratio in a couple of examples. How to interpret Logistic regression coefficients using scikit learn. Ridge regression … Note Good day, I'm using the sklearn LogisticRegression class for some data analysis and am wondering how to output the coefficients for the … 0. Someone pointed me to this post by W. D., reporting that, in Python’s popular Scikit-learn package, the default prior for logistic regression coefficients is normal (0,1)—or, as W. D. puts it, L2 penalization with a lambda of 1. scikit-learn returns the regression's coefficients of the independent variables, but it does not provide the coefficients' standard errors. There’s simply no accepted default approach to logistic regression in the machine learning world or in the stats world. Returns the log-probability of the sample for each class in the I am using Python's scikit-learn to train and test a logistic regression. it returns only 1 element. with primal formulation, or no regularization. as all other features. and sparse input. w is the regression co-efficient.. I was recently asked to interpret coefficient estimates from a logistic regression model. schemes. Weirdest of all is that rescaling everything by 2*SD and then regularizing with variance 1 means the strength of the implied confounder adjustment will depend on whether you chose to restrict the confounder range or not.”. If not given, all classes are supposed to have weight one. it could be very sensitive to the strength of one particular connection. Question closed notifications experiment results and graduation. Part of that has to do with my recent focus on prediction accuracy rather than inference. coef_ is of shape (1, n_features) when the given problem is binary. combination of L1 and L2. The returned estimates for all classes are ordered by the Too often statisticians want to introduce such defaults to avoid having to delve into context and see what that would demand. Imagine if a computational fluid mechanics program supplied defaults for density and viscosity and temperature of a fluid. It seems like just normalizing the usual way (mean zero and unit scale), you can choose priors that work the same way and nobody has to remember whether they should be dividing by 2 or multiplying by 2 or sqrt(2) to get back to unity. I was recently asked to interpret coefficient estimates from a logistic regression model. Which would mean the prior SD for the per-year age effect would vary by peculiarities like age restriction even if the per-year increment in outcome was identical across years of age and populations. Useful only when the solver ‘liblinear’ is used The two parametrization are equivalent. If not provided, then each sample is given unit weight. This class implements logistic regression using liblinear, newton-cg, sag of lbfgs optimizer. The questions can be good to have an answer to because it lets you do some math, but the problem is people often reify it as if it were a very very important real world condition. The best possible score is 1.0 and it can be negative (because the model can be arbitrarily worse). Instead, the training algorithm used to fit the logistic regression model must be modified to take the skewed distribution into account. Maybe you are thinking of descriptive surveys with precisely pre-specified sampling frames. across the entire probability distribution, even when the data is set to ‘liblinear’ regardless of whether ‘multi_class’ is specified or (and copied). With the clean data we can start training the model. Again, 0.05 is the poster child for that kind of abuse, and at this point I can imagine parallel strong (if even more opaque) distortions from scaling of priors being driven by a 2*SD covariate scaling. so the problem is hopeless… the “optimal” prior is the one that best describes the actual information you have about the problem. Feb-21-2020, 08:36 PM . Below I have repeated the table to reduce the amount of time you need to spend scrolling when reading this post. For ‘multinomial’ the loss minimised is the multinomial loss fit not. (Currently the ‘multinomial’ option is supported only by the ‘lbfgs’, I think it makes good sense to have defaults when it comes to computational decisions, because the computational people tend to know more about how to compute numbers than the applied people do. -1 means using all processors. A note on standardized coefficients for logistic regression. Viewed 3k times 2 $\begingroup$ I have created a model using Logistic regression with 21 features, most of which is binary. The confidence score for a sample is the signed distance of that Sander said “It is then capable of introducing considerable confounding (e.g., shrinking age and sex effects toward zero and thus reducing control of distortions produced by their imbalances). – Vivek … But the applied people know more about the scientific question than the computing people do, and so the computing people shouldn’t implicitly make choices about how to answer applied questions. You will get to know the coefficients and the correct feature. r is the regression result (the sum of the variables weighted by the coefficients) ... Logistic regression is similar to linear regression, with the only difference being the y data, which should contain integer values indicating the class relative to the observation. In this exercise you will explore how the decision boundary is represented by the coefficients. (such as pipelines). I also think the default I recommend, or other similar defaults, are safer than a default of no regularization, as this leads to problems with separation. added to the decision function. hstack ((bias, features)) # initialize the weight coefficients weights = np. Changed in version 0.22: Default changed from ‘ovr’ to ‘auto’ in 0.22. If ‘none’ (not supported by the New in version 0.17: Stochastic Average Gradient descent solver. intercept_scaling is appended to the instance vector. Imagine failure of a bridge. So it seems here: Regularizing by a prior with variance 1 after rescaling by 2*SD means extending the arbitrariness to made-up prior information and can be pretty strong for a default, adding a substantial amount of pseudo-information centered on the null without any connection to an appropriate loss function. In my opinion this is problematic, because real world conditions often have situations where mean squared error is not even a good approximation of the real world practical utility. I apologize for the … A rule of thumb is that the number of zero elements, which can For non-sparse models, i.e. This library contains many models and is updated constantly making it very useful. Considerate Swedes only die during the week. Reputation: 0 #1. Like in support vector machines, smaller values specify stronger For multiclass problems, only ‘newton-cg’, ‘sag’, ‘saga’ and ‘lbfgs’ If you are using a normal distribution in your likelihood, this would reduce mean squared error to its minimal value… But if you have an algorithm for discovering the exact true parameter values in your problem without even seeing data (ie. Apparently some of the discussion of this default choice revolved around whether the routine should be considered “statistics” (where primary goal is typically parameter estimation) or “machine learning” (where the primary goal is typically prediction). Take the absolute values to rank. For a multi_class problem, if multi_class is set to be “multinomial” And most of our users don’t understand the details (even I don’t understand the dual averaging tuning parameters for setting step size—they seem very robust, so I’ve never bothered). In R, SAS, and Displayr, the coefficients appear in the column called Estimate, in Stata the column is labeled as Coefficient, in SPSS it is called simply B. The default warmup in Stan is a mess, but we’re working on improvements, so I hope the new version will be more effective and also better documented. ‘saga’ are faster for large ones. The constraint is that the selected features are the same for all the regression problems, also called tasks. Based on a given set of independent variables, it is used to estimate discrete value (0 or 1, yes/no, true/false). Advertisements. Used when solver == ‘sag’, ‘saga’ or ‘liblinear’ to shuffle the You can take in-sample CV MSE or expected out of sample MSE as the objective. Threads: 4. I don’t recommend no regularization over weak regularization, but problems like separation are fixed by even the weakest priors in use. Convert coefficient matrix to dense array format. http://users.iems.northwestern.edu/~nocedal/lbfgsb.html, https://www.csie.ntu.edu.tw/~cjlin/liblinear/, Minimizing Finite Sums with the Stochastic Average Gradient data. By the end of the article, you’ll know more about logistic regression in Scikit-learn and not sweat the solver stuff. Train a classifier using logistic regression: Finally, we are ready to train a classifier. The newton-cg, sag and lbfgs solvers support only L2 regularization with primal formulation. shape [0], 1)) features = np. Fit the model according to the given training data. Logistic regression is used to describe data and to explain the relationship between one dependent binary … Everything starts with the concept of … For 0 < l1_ratio <1, the penalty is a It happens that the approaches presented here sometimes results in para… Logistic regression is the appropriate regression an a lysis to conduct when the dependent variable is dichotomous (binary). Why transform to mean zero and scale two? What is Logistic Regression using Sklearn in Python - Scikit Learn Logistic regression is a predictive analysis technique used for classification problems. Sander disagreed with me so I think it will be valuable to share both perspectives. The default prior for logistic regression coefficients in Scikit-learn. Multinomial logistic regression yields more accurate results and is faster to train on the larger scale dataset. Dual or primal formulation. The logistic regression model is Where X is the vector of observed values for an observation (including a constant), β is the vector of coefficients, and σ is the sigmoid function above. weights inversely proportional to class frequencies in the input data As far as I’m concerned, it doesn’t matter: I’d prefer a reasonably strong default prior such as normal(0,1) both for parameter estimation and for prediction. If you want to reuse the coefficients later you can also put them in a dictionary: coef_dict = {} context. As for “poorer parameter estimates” that is extremely dependent on the performance criteria one uses to gauge “poorer” (bias is often minimized by the Jeffreys prior which is too weak even for me – even though it is not as weak as a Cauchy prior). If binary or multinomial, Of course high-dimensional exploratory settings may call for quite a bit of shrinkage, but then there is a huge volume of literature on that and none I’ve seen supports anything resembling assigning a prior based on 2*SD rescaling, so if you have citations showing it is superior to other approaches in comparative studies, please send them along! and otherwise selects ‘multinomial’. is suggesting the common practice of choosing the penalty scale to optimize some end-to-end result (typically, but not always predictive cross-validation). Note that ‘sag’ and ‘saga’ fast convergence is only guaranteed on It would absolutely be a mistake to spend a bunch of time thinking up a book full of theory about how to “adjust penalties” to “optimally in predictive MSE” adjust your prediction algorithms. No matter which software you use to perform the analysis you will get the same basic results, although the name of the column changes. Naufal Khalid Naufal Khalid. It is a simple optimization problem in quadratic programming where your constraint is that all the coefficients(a.k.a weights) should be positive. I agree with two of them. Weirdest of all is that rescaling everything by 2*SD and then regularizing with variance 1 means the strength of the implied confounder adjustment will depend on whether you chose to restrict the confounder range or not. The problem is in using statistical significance to make decisions about what to conclude from your data. For example, your inference model needs to make choices about what factors to include in the model or not, which requires decisions, but then your decisions for which you plan to use the predictions also need to be made, like whether to invest in something, or build something, or change a regulation etc. this may actually increase memory usage, so use this method with L1 Penalty and Sparsity in Logistic Regression¶ Comparison of the sparsity (percentage of zero coefficients) of solutions when L1, L2 and Elastic-Net penalty are used for different values of C. We can see that large values of C give more freedom to the model. The following sections of the guide will discuss the various regularization algorithms. https://hal.inria.fr/hal-00860051/document, SAGA: A Fast Incremental Gradient Method With Support In this article we’ll use pandas and Numpy for wrangling the data to our liking, and matplotlib … in the narrative documentation. But no stronger than that, because a too-strong default prior will exert too strong a pull within that range and thus meaningfully favor some stakeholders over others, as well as start to damage confounding control as I described before. Browse other questions tagged scikit-learn logistic-regression or ask your own question. When you call fit with scikit-learn, the logistic regression coefficients are automatically learned from your dataset. for Non-Strongly Convex Composite Objectives i.e. Finding a linear model with scikit-learn. Predict output may not match that of standalone liblinear in certain Logistic Regression - Coefficients have p-value more than alpha(0.05) 2. Setting l1_ratio=0 is equivalent Next Page . n_samples > n_features. logreg = LogisticRegression () The intercept becomes intercept_scaling * synthetic_feature_weight. … But there’s a tradeoff: once we try to make a good default, it can get complicated (for example, defaults for regression coefficients with non-binary predictors need to deal with scaling in some way). Do you not think the variance of these default priors should scale inversely with the number of parameters being estimated? l2 penalty with liblinear solver. In this case, x becomes the softmax function is used to find the predicted probability of The latter have parameters of the form Array of weights that are assigned to individual samples. each class. When the number of predictors increases in this way, you’ll want to fit a hierarchical model in which the amount of partial pooling is a hyperparameter that is estimated from the data. Another default with even larger and more perverse biasing effects uses k*SE as the prior scale unit with SE=the standard error of the estimated confounder coefficient: The bias that produces increases with sample size (note that the harm from bias increases with sample size as bias comes to dominate random error). The coefficient R^2 is defined as (1 - u/v), where u is the residual sum of squares ((y_true - y_pred) ** 2).sum() and v is the total sum of squares ((y_true - y_true.mean()) ** 2).sum(). Specifies if a constant (a.k.a. The two parametrization are equivalent. New in version 0.17: warm_start to support lbfgs, newton-cg, sag, saga solvers. https://discourse.datamethods.org/t/what-are-credible-priors-and-what-are-skeptical-priors/580. Part of that has to do with my recent focus on prediction accuracy rather than … Then we’ll manually compute the coefficients ourselves to convince ourselves of what’s happening. Machine Learning 85(1-2):41-75. Given my sense of the literature, that will often be just overlooked so “warnings” that it shouldn’t be, should be given. On logistic regression. Logistic Regression (aka logit, MaxEnt) classifier. My reply regarding Sander’s first paragraph is that, yes, different goals will correspond to different models, and that can make sense. select features when fitting the model. Return the coefficient of determination R^2 of the prediction. When you call fit with scikit-learn, the logistic regression coefficients are automatically learned from your dataset. Logistic regression is similar to linear regression, with the only difference being the y data, which should contain integer values indicating the class relative to the observation. Multiclass sparse logisitic regression on newgroups20¶ Comparison of multinomial logistic L1 vs one-versus-rest L1 logistic regression to classify documents from the newgroups20 dataset. to outcome 1 (True) and -coef_ corresponds to outcome 0 (False). this method is only required on models that have previously been Also, Wald’s theorem shows that you might as well look for optimal decision rules inside the class of Bayesian rules, but obviously, the truly optimal decision rule would be the one that puts a delta-function prior on the “real” parameter values. only supported by the ‘saga’ solver. sklearn.linear_model.Ridge is the module used to solve a regression model where loss function is the linear least squares function and regularization is L2. To see what coefficients our regression model has chosen, … UPDATE December 20, 2019 : I made several edits to this article after helpful feedback from Scikit-learn core developer and maintainer, Andreas Mueller. In order to train the model we will indicate which are the variables that predict and the predicted variable. I don’t get the scaling by two standard deviations. 2. n_features is the number of features. 2. difference between feature interactions and confounding variables. bias or intercept) should be https://stats.stackexchange.com/questions/438173/how-should-regularization-parameters-scale-with-data-size, https://discourse.datamethods.org/t/what-are-credible-priors-and-what-are-skeptical-priors/580, The Shrinkage Trilogy: How to be Bayesian when analyzing simple experiments. Applying logistic regression. contained subobjects that are estimators. Elastic-Net penalty is only supported by … The SAGA solver supports both float64 and float32 bit arrays. I’m curious what Andrew thinks, because he writes that statistics is the science of defaults. W.D., in the original blog post, says. Furthermore, the lambda is never selected using a grid search. The key feature to understand is that logistic regression returns the coefficients of a formula that predicts the logit transformation of the probability of the target we are trying to predict (in the example above, completing the full course). This isn’t usually equivalent to empirical Bayes, because it’s not usually maximizing the marginal. Few of the … Weights associated with classes in the form {class_label: weight}. In the post, W. D. makes three arguments. The what needs to be carefully considered whereas defaults are supposed to be only place holders until that careful consideration is brought to bear. For small datasets, ‘liblinear’ is a good choice, whereas ‘sag’ and class would be predicted. There are several general steps you’ll take when you’re preparing your classification models: Import packages, … Don’t we just want to answer this whole kerfuffle with “use a hierarchical model”? number of iteration across all classes is given. A severe question would be what is “the” population SD? to have slightly different results for the same input data. label of classes. component of a nested object. but because that connection will fail first, it is insensitive to the strength of the over-specced beam. I think that weaker default priors will lead to poorer parameter estimates and poorer predictions–but estimation and prediction are not everything, and I could imagine that for some users, including epidemiology, weaker priors could be considered more acceptable. Algorithm to use in the optimization problem. (There are ways to handle multi-class classific… bias) added to the decision function. https://arxiv.org/abs/1407.0202, methods for logistic regression and maximum entropy models. Even if you cross-validate, there’s the question of which decision rule to use. Informative priors—regularization—makes regression a more powerful tool. Prefer dual=False when Good parameter estimation is a sufficient but not necessary condition for good prediction? https://www.csie.ntu.edu.tw/~cjlin/papers/maxent_dual.pdf. In comparative studies (which I have seen you involved in too), I’m fine with a prior that pulls estimates toward the range that debate takes place among stakeholders, so they can all be comfortable with the results. See the Glossary. It could make for an interesting blog post! Intercept and slopes are also called coefficients of regression The logistic regression model follows a binomial distribution, and the coefficients of regression (parameter estimates) are estimated using the maximum likelihood estimation (MLE). from sklearn import linear_model: import numpy as np: import scipy. In this post, you will learn about Logistic Regression terminologies / glossary with quiz / practice questions. The original year data has 1 by 11 shape. What is Ridge Regularisation. when there are not many zeros in coef_, Used to specify the norm used in the penalization. ‘auto’ selects ‘ovr’ if the data is binary, or if solver=’liblinear’, I think that rstanarm is currently using normal(0,2.5) as a default, but if I had to choose right now, I think I’d go with normal(0,1), actually. I’d say the “standard” way that we approach something like logistic regression in Stan is to use a hierarchical model. But those are a bit different in that we can usually throw diagnostic errors if sampling fails. scikit-learn 0.23.2 That still leaves you choice of prior family, for which we can throw the horseshoe, Finnish horseshoe, and Cauchy (or general Student-t) into the ring. Someone pointed me to this post by W. D., reporting that, in Python’s popular Scikit-learn package, the default prior for logistic regression coefficients is normal(0,1)—or, as W. D. puts it, L2 penalization with a lambda of 1.. Let’s map males to 0, and female to 1, then feed it through sklearn’s logistic regression function to get the coefficients out, for the bias, for the logistic coefficient for sex. Logistic regression models are used when the outcome of interest is binary. To do so, you will change the coefficients manually (instead of with fit), and visualize the resulting classifiers.. A … Find the probability of data samples belonging to a specific class with one of the most popular classification algorithms. How to adjust cofounders in Logistic regression? share | improve this question | follow | edited Nov 15 '17 at 9:58. In the multiclass case, the training algorithm uses the one-vs-rest (OvR) scheme if the ‘multi_class’ option is set to ‘ovr’, and uses the cross-entropy loss if the ‘multi_class’ option is set to ‘multinomial’. The MultiTaskLasso is a linear model that estimates sparse coefficients for multiple regression problems jointly: y is a 2D array , of shape (n_samples, n_tasks). Let’s first understand what exactly Ridge regularization:. I disagree with the author that a default regularization prior is a bad idea. Tom, this can only be defined by specifying an objective function. Sander Greenland and I had a discussion of this. model, where classes are ordered as they are in self.classes_. I replied that I think that scaling by population sd is better than scaling by sample sd, and the way I think about scaling by sample sd is as an approximation to scaling by population sd. sklearn.linear_model.LogisticRegressionCV¶ class sklearn.linear_model. corresponds to outcome 1 (True) and -intercept_ corresponds to This makes the interpretation of the regression coefficients somewhat tricky. The logistic regression model the output as the odds, which … Only Conversely, smaller values of C constrain the model more. I agree with W. D. that it … When set to True, reuse the solution of the previous call to fit as Still, it's an important concept to understand and this is a good opportunity to refamiliarize myself with it. Posts: 9. None means 1 unless in a joblib.parallel_backend As a general point, I think it makes sense to regularize, and when it comes to this specific problem, I think that a normal(0,1) prior is a reasonable default option (assuming the predictors have been scaled). It sounds like you would prefer weaker default priors. ‘liblinear’ library, ‘newton-cg’, ‘sag’, ‘saga’ and ‘lbfgs’ solvers. 1. be computed with (coef_ == 0).sum(), must be more than 50% for this These transformed values present the main advantage of relying on an objectively defined scale rather than depending on the original metric of the corresponding predictor. After calling this method, further fitting with the partial_fit Ask Question Asked 1 year, 2 months ago. When to use Logistic Regression… to using penalty='l1'. Many thanks for the link and for elaborating. To overcome this shortcoming, we do regularization which penalizes large coefficients. The Elastic-Net regularization is only supported by the as a prior) what do you need statistics for ;-). [x, self.intercept_scaling], since the objective function changes from problem to problem, there can be no one answer to this question. Release Highlights for scikit-learn 0.23¶, Release Highlights for scikit-learn 0.22¶, Comparison of Calibration of Classifiers¶, Plot class probabilities calculated by the VotingClassifier¶, Feature transformations with ensembles of trees¶, Regularization path of L1- Logistic Regression¶, MNIST classification using multinomial logistic + L1¶, Plot multinomial and One-vs-Rest Logistic Regression¶, L1 Penalty and Sparsity in Logistic Regression¶, Multiclass sparse logistic regression on 20newgroups¶, Restricted Boltzmann Machine features for digit classification¶, Pipelining: chaining a PCA and a logistic regression¶, {‘l1’, ‘l2’, ‘elasticnet’, ‘none’}, default=’l2’, {‘newton-cg’, ‘lbfgs’, ‘liblinear’, ‘sag’, ‘saga’}, default=’lbfgs’, {‘auto’, ‘ovr’, ‘multinomial’}, default=’auto’, ndarray of shape (1, n_features) or (n_classes, n_features). Sander wrote: The following concerns arise in risk-factor epidemiology, my area, and related comparative causal research, not in formulation of classifiers or other pure predictive tasks as machine learners focus on…. The first example is related to a single-variate binary classification problem. handle multinomial loss; ‘liblinear’ is limited to one-versus-rest Logistic regression does not support imbalanced classification directly. I agree with W. D. that it makes sense to scale predictors before regularization. number for verbosity. See Glossary for more details. The logistic regression model the output as the odds, which … where classes are ordered as they are in self.classes_. The Overflow Blog Podcast 287: How do you make software reliable enough for space travel? array([[9.8...e-01, 1.8...e-02, 1.4...e-08], array_like or sparse matrix, shape (n_samples, n_features), {array-like, sparse matrix} of shape (n_samples, n_features), array-like of shape (n_samples,) default=None, array-like of shape (n_samples, n_features), array-like of shape (n_samples, n_classes), array-like of shape (n_samples,) or (n_samples, n_outputs), array-like of shape (n_samples,), default=None, Plot class probabilities calculated by the VotingClassifier, Feature transformations with ensembles of trees, Regularization path of L1- Logistic Regression, MNIST classification using multinomial logistic + L1, Plot multinomial and One-vs-Rest Logistic Regression, L1 Penalty and Sparsity in Logistic Regression, Multiclass sparse logistic regression on 20newgroups, Restricted Boltzmann Machine features for digit classification, Pipelining: chaining a PCA and a logistic regression, http://users.iems.northwestern.edu/~nocedal/lbfgsb.html, https://hal.inria.fr/hal-00860051/document, https://www.csie.ntu.edu.tw/~cjlin/papers/maxent_dual.pdf.

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