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Learning machine learning with Yellowbrick


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Yellowbrick is an open source Python library that provides visual diagnostic tools called “Visualizers” that extend the Scikit-Learn API to allow human steering of the model selection process. For teachers and students of machine learning, Yellowbrick can be used as a framework for teaching and understanding a large variety of algorithms and methods.

Published in: Data & Analytics
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Learning machine learning with Yellowbrick

  1. 1. Learning machine learning with Yellowbrick
  2. 2. The Model Selection Triple Arun Kumar Feature Analysis Algorithm Selection Hyperparameter Tuning
  3. 3. Feature Analysis
  4. 4. Use radviz or parallel coordinates to look for class separability Yellowbrick Feature Visualizers
  5. 5. ● Based on spring tension minimization algorithm. ● Features equally spaced on a unit circle, instances dropped into circle. ● Features pull instances towards their position on the circle in proportion to their normalized numerical value for that instance. ● Classification coloring based on labels in data. Radial Visualization
  6. 6. Before and after standardization Parallel Coordinates
  7. 7. Parallel Coordinates ● Visualize clusters in data. ● Points represented as connected line segments. ● Each vertical line represents one attribute (x-axis units not meaningful). ● One set of connected line segments represents one instance. ● Points that tend to cluster will appear closer together.
  8. 8. Use Rank2D for pairwise feature analysis, find strong correlations (potential collinearity?) Rank2D
  9. 9. Rank2D ● Feature engineering requires understanding of the relationships between features ● Visualize pairwise relationships as a heatmap ● Pearson shows us strong correlations, potential collinearity ● Covariance helps us understand the sequence of relationships
  10. 10. PCA Projection Plots ● Uses PCA to decompose high dimensional data into two or three dimensions ● Each instance plotted in a scatter plot. ● Projected dataset can be analyzed along axes of principle variation ● Can be interpreted to determine if spherical distance metrics can be utilized.
  11. 11. PCA Projection Plots Can also plot in 3D to visualize more components & get a better sense of distribution in high dimensions
  12. 12. Visualize top tokens, document distribution & part-of-speech tagging Feature Visualizers for Text
  13. 13. How do I select the right features?
  14. 14. Feature Importance Plot ● Need to select the minimum required features to produce a valid model. ● The more features a model contains, the more complex it is (sparse data, errors due to variance). ● This visualizer ranks and plots underlying impact of features relative to each other.
  15. 15. Recursive Feature Elimination
  16. 16. Recursive Feature Elimination ● Recursive feature elimination fits a model and removes the weakest feature(s) until the specified number is reached. ● Features are ranked by internal model’s coef_ or feature_importances_ ● Attempts to eliminate dependencies and collinearity that may exist in the model.
  17. 17. Model Evaluation
  18. 18. Evaluating Classifiers ● How well did predicted values match actual labeled values? ● In a 2-class problem, there are two ways to be “right”: ○ Classifier correctly identifies cases (aka “True Positives”) ○ Classifier correctly identifies non-cases (aka “True Negatives”) ● ...and two ways to be “wrong”: ○ Classifier incorrectly identifies a non-case as a case (aka “False Positive” or “Type I Error”) ○ Classifier incorrectly identifies a case as a non-case (aka “False Negative” or “Type II Error”)
  19. 19. Metrics for Classification Metric Measures In Scikit-learn Precision How many selected are relevant? from sklearn.metrics import precision_score Recall How many relevant were selected? from sklearn.metrics import recall_score F1 Weighted average of precision & recall from sklearn.metrics import f1_score Confusion Matrix True positives, true negatives, false positives, false negatives from sklearn.metrics import confusion_matrix ROC True positive rate vs. false positive rate, as classification threshold varies from sklearn.metrics import roc AUC Aggregate accuracy, as classification threshold varies from sklearn.metrics import auc
  20. 20. accuracy = true positives + true negatives / total precision = true positives / (true positives + false positives) recall = true positives / (false negatives + true positives) F1 score = 2 * ((precision * recall) / (precision + recall))
  21. 21. Visualize accuracy and begin to diagnose problems Yellowbrick Score Visualizers
  22. 22. Classification Report from sklearn.metrics import classification_report as cr print(cr(y, yhat, target_names=target_names)) ● includes same basic info as confusion matrix ● 3 different evaluation metrics: precision, recall, F1 score ● includes class labels for interpretability
  23. 23. Classification Heatmaps Precision: of those labelled edible, how many actually were?Is it better to have false positives here or here? Recall: how many of the poisonous ones did our model find?
  24. 24. ROC-AUC from sklearn.metrics import roc_curve, auc fpr, tpr, thresholds = roc_curve(y,yhat) roc_auc = auc(fpr, tpr) Visualize tradeoff between classifier's sensitivity (how well it finds true positives) and specificity (how well it avoids false positives) ● straight horizontal line -> perfect classifier ● pulling a lot toward the upper left corner -> good accuracy ● exactly aligned with the diagonal -> coin toss
  25. 25. Getting more right comes at the expense of getting more wrong ROC-AUC
  26. 26. ROC-AUC for Multiclass Classification ROC curves are typically used in binary classification,, but Yellowbrick allows for multiclass classification evaluation by binarizing output (per-class) or using one-vs-rest (micro score) or one-vs-all (macro score) strategies of classification.
  27. 27. Confusion Matrix ● takes as an argument actual values and predicted values generated by the fitted model ● outputs a confusion matrix from sklearn.metrics import confusion_matrix
  28. 28. I have a lot of classes; how does my model perform on each? Do I care about certain classes more than others? Confusion Matrix
  29. 29. Class Prediction Error Plot Similar to confusion matrix, but sometimes more interpretable
  30. 30. Discrimination Threshold Visualizer * for binary classification only ● Probability or score at which positive class is chosen over negative. ● Generally set to 50% ● Can be adjusted to increase/decrease sensitivity to false positives or other application factors ● Cases that require special treatment?
  31. 31. Evaluating Regressors ● How well does the model describe the training data? ● How well does the model predict out-of-sample data? ○ Goodness-of-fit ○ Randomness of residuals ○ Prediction error
  32. 32. Metrics for Regression Metric Measures In Scikit-learn Mean Square Error (MSE, RMSE) distance between predicted values and actual values (more sensitive to outliers) from sklearn.metrics import mean_squared_error Absolute Error (MAE, RAE) distance between predicted values and actual values (less sensitive to outliers) from sklearn.metrics import mean_absolute_error, median_absolute_error Coefficient of Determination (R- Squared) % of variance explained by the regression; how well future samples are likely to be predicted by the model from sklearn.metrics import r2_score
  33. 33. Visualize the distribution of error to diagnose heteroscedasticity Yellowbrick Score Visualizers
  34. 34. Prediction Error Plots from sklearn.model_selection import cross_val_predict ● Cross-validation is a way of measuring model performance. ● Divide data into training and test splits; fit model on training, predict on test. ● Use cross_val_predict to visualize prediction errors as a scatterplot of the predicted and actual values.
  35. 35. Prediction Error Plots
  36. 36. Plotting Residuals ● Standardized y-axis ● Model prediction on x-axis. ● Model accuracy on y-axis; distance from line at 0 indicates how good/bad the prediction was for that value. ● Check whether residuals are consistent with random error; data points should appear evenly dispersed around the plotted line. Should not be able to predict error. ● Visualize train and test data with different colors.
  37. 37. Plotting Residuals
  38. 38. Metrics for Clustering ...
  39. 39. Maybe? ● Silhouette scores ● Elbow curves Metrics for Clustering ...
  40. 40. Why is my F1/R2 so low?
  41. 41. ● What to do with a low- accuracy classifier? ● Check for class imbalance. ● Visual cue that we might try stratified sampling, oversampling, or getting more data. Class Balance
  42. 42. Cross Validation Scores ● Real world data are often distributed somewhat unevenly; the fitted model likely to perform better on some sections of data than others. ● See cross-validated scores as a bar chart (one bar for each fold) with average score across all folds plotted as dotted line. ● Explore variations in performance using different cross validation strategies.
  43. 43. Learning Curve ● Relationship of the training score vs. the cross validated test score for an estimator. ● Do we need more data? If the scores converge together, then probably not. If the training score is much higher than the validation score, then yes. ● Is the estimator more sensitive to error due to variance or error due to bias?
  44. 44. Validation Curve ● Plot the influence of a single hyperparameter on the training and test data. ● Is the estimator under- or over- fitting for some hyperparameter values? For SVC, gamma is the coefficient of the RBF kernel. The larger gamma is, the tighter the support vector is around single points (e.g. overfitting). Here around gamma=0.1 the SVC memorizes the data.
  45. 45. Hyperparameter Tuning
  46. 46. Hyperparameters ● When we call fit() on an estimator, it learns the parameters of the algorithm that make it fit the data best. ● However, some parameters are not directly learned within an estimator. These are the ones we provide when we instantiate the estimator. ○ alpha for LASSO or Ridge ○ C, kernel, and gamma for SVC ● These parameters are often referred to as hyperparameters.
  47. 47. Examples: ● Alpha/penalty for regularization ● Kernel function in support vector machine ● Leaves or depth of a decision tree ● Neighbors used in a nearest neighbor classifier ● Clusters in a k-means clustering Hyperparameters
  48. 48. How to pick the best hyperparameters? ● Use the defaults ● Pick randomly ● Search parameter space for the best score (e.g. grid search) … Except that hyperparameter space is large and gridsearch is slow if you don’t know already what you’re looking for. Hyperparameters
  49. 49. How do I tune this model?
  50. 50. Should I use Lasso, Ridge, or ElasticNet? Is regularlization even working? More alpha => less complexity Reduced bias, but increased variance Alpha selection with Yellowbrick
  51. 51. ● How many clusters do you see? ● How do you pick an initial value for k in k- means clustering? ● How do you know whether to increase or decrease k? ● Is partitive clustering the right choice? What’s the right k?
  52. 52. higher silhouette scores mean denser, more separate clusters The elbow shows the best value of k… Or suggests a different algorithm K-selection with Yellowbrick
  53. 53. Manifold Visualization ● Embed instances described by many dimensions into 2. ● Look for latent structures in the data, noise, separability. ● Is it possible to create a decision space in the data? ● Unlike PCA or SVD, manifolds use nearest neighbors, can capture non- linear structures.
  54. 54. Using Yellowbrick
  55. 55. Install: $ pip install yellowbrick Upgrade: $ pip install -U yellowbrick Anaconda: $ conda install -c districtdatalabs yellowbrick Quickstart
  56. 56. # Import the estimator from sklearn.linear_model import Lasso # Instantiate the estimator model = Lasso() # Fit the data to the estimator, y_train) # Generate a prediction model.predict(X_test) Scikit-Learn Estimator Interface
  57. 57. # Import the model and visualizer from sklearn.linear_model import Lasso from yellowbrick.regressor import PredictionError # Instantiate the visualizer visualizer = PredictionError(Lasso()) # Fit, y_train) # Score and visualize visualizer.score(X_test, y_test) visualizer.poof() Yellowbrick Visualizer Interface
  58. 58. The main API implemented by Scikit-Learn is that of the estimator. An estimator is any object that learns from data; it may be a classification, regression or clustering algorithm, or a transformer that extracts/filters useful features from raw data. class Estimator(object): def fit(self, X, y=None): """ Fits estimator to data. """ # set state of self return self def predict(self, X): """ Predict response of X """ # compute predictions pred return pred Scikit-learn Estimators
  59. 59. Transformers are special cases of Estimators -- instead of making predictions, they transform the input dataset X to a new dataset X′. class Transformer(Estimator): def transform(self, X): """ Transforms the input data. """ # transform X to X_prime return X_prime Scikit-learn Transformers
  60. 60. A visualizer is an estimator that produces visualizations based on data rather than new datasets or predictions. Visualizers are intended to work in concert with Transformers and Estimators to shed light onto the modeling process. class Visualizer(Estimator): def draw(self): """ Draw the data """ def finalize(self): """ Complete the figure """ def poof(self): """ Show the figure """ Yellowbrick Visualizers
  61. 61. Contributing
  62. 62. Yellowbrick is an open source project that is supported by a community who will gratefully and humbly accept any contributions you might make to the project. Large or small, any contribution makes a big difference; and if you’ve never contributed to an open source project before, we hope you will start with Yellowbrick!
  63. 63. Please star Yellowbrick on GitHub!