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Training

The training phase is where the models are fitted on the training data. After this, you can use the plots and prediction methods to evaluate the results. The training applies the following steps for all models:

  1. Use hyperparameter tuning to select the optimal hyperparameters for the model (optional).
  2. The model is fitted on the training set using the best combination of hyperparameters found. After that, the model is evaluated on the tes set.
  3. Calculate various scores on the test set using a bootstrap algorithm (optional).

There are three approaches to run the training.

The direct fashion repeats the aforementioned steps only once, while the other two approaches repeats them more than once. Just like the data cleaning and feature engineering classes, it's discouraged to use these classes directly. Instead, every approach can be called directly from atom through the run, successive_halving and train_sizing methods respectively.

Models are called through their acronyms, e.g. atom.run(models="RF") will train a RandomForest. If you want to run the same model multiple times, add a tag after the acronym to differentiate them.

>>> atom.run(
...     models=["RF1", "RF2"],
...     est_params={
...         "RF1": {"n_estimators": 100},
...         "RF2": {"n_estimators": 200},
...     }
... )

For example, this pipeline fits two Random Forest models, one with 100 and the other with 200 decision trees. The models can be accessed through atom.rf1 and atom.rf2. Use tagged models to test how the same model performs when fitted with different parameters or on different data sets. See the Imbalanced datasets example.

Additional things to take into account:

  • If an exception is encountered while fitting an estimator, the pipeline will automatically jump to the next model. The exceptions are stored in the errors attribute. Note that when a model is skipped, there is no model subclass for that estimator.
  • When showing the final results, a ! indicates the highest score and a ~ indicates that the model is possibly overfitting (training set has a score at least 20% higher than the test set).


Metric

ATOM uses sklearn's scorers for model evaluation. A scorer consists of a metric function and some parameters that define the scorer's properties , such as if a higher or lower score is better (score or loss function) or if the function needs probability estimates or rounded predictions (see the make_scorer function). The metric parameter accepts three ways of defining the scorer:

  • Using the name of one of the predefined scorers.
  • Using a function with signature function(y_true, y_pred) -> score. In this case, ATOM uses make_scorer with default parameters.
  • Using a scorer object.

Note that all scorers follow the convention that higher return values are better than lower return values. Thus, metrics which measure the distance between the model and the data (i.e. loss functions), like max_error or mean_squared_error, will return the negated value of the metric.


Predefined scorers

ATOM accepts all sklearn's scorers as well as some custom acronyms and custom scorers. Since some of sklearn's scorers have quite long names and ATOM is all about lazyfast experimentation, the package provides acronyms for some of the most commonly used ones. These acronyms are case-insensitive and can be used in the metric parameter instead of the scorer's full name, e.g. atom.run("LR", metric="BA") uses balanced_accuracy. The available acronyms are:

  • "AP" for "average_precision"
  • "BA" for "balanced_accuracy"
  • "AUC" for "roc_auc"
  • "LogLoss" for "neg_log_loss"
  • "EV" for "explained_variance"
  • "ME" for "max_error"
  • "MAE" for "neg_mean_absolute_error"
  • "MSE" for "neg_mean_squared_error"
  • "RMSE" for "neg_root_mean_squared_error"
  • "MSLE" for "neg_mean_squared_log_error"
  • "MEDAE" for "neg_median_absolute_error"
  • "MAPE" for "neg_mean_absolute_percentage_error"
  • "POISSON" for "neg_mean_poisson_deviance"
  • "GAMMA" for "neg_mean_gamma_deviance"

ATOM also provides some extra common metrics for binary classification tasks.

  • "TN" for True Negatives
  • "FP" for False Positives
  • "FN" for False Negatives
  • "TP" for True Positives
  • "FPR" for False Positive rate (fall-out)
  • "TPR" for True Positive Rate (sensitivity, recall)
  • "TNR" for True Negative Rate (specificity)
  • "FNR" for False Negative Rate (miss rate)
  • "MCC" for Matthews Correlation Coefficient (also for multiclass classification)


Multi-metric runs

Sometimes it is useful to measure the performance of the models in more than one way. ATOM lets you run the pipeline with multiple metrics at the same time. To do so, provide the metric parameter with a list of desired metrics, e.g. atom.run("LDA", metric=["r2", "mse"]).

When fitting multi-metric runs, the resulting scores will return a list of metrics. For example, if you provided three metrics to the pipeline, atom.knn.score_train could return [0.8734, 0.6672, 0.9001]. Only the first metric of a multi-metric run (this metric is called the main metric) is used to select the winning model.

Info

  • The winning model is retrieved comparing only the main metric.
  • Some plots let you choose which of the metrics in a multi-metric run to show using the metric parameter, e.g. plot_results.


Automated feature scaling

Models that require feature scaling will automatically do so before training, unless the data is sparse or already scaled. The data is considered scaled if it has one of the following prerequisites:

  • The mean value over the mean of all columns lies between -0.05 and 0.05 and the mean of the standard deviation over all columns lies between 0.85 and 1.15. Categorical and binary columns (only 0s and 1s) are excluded from the calculation.
  • There is a transformer in the pipeline whose __name__ contains the word scaler.

The scaling is applied using a Scaler with default parameters. It can be accessed from the model through the scaler attribute. The scaled dataset can be examined through the model's data attributes. Use the available_models method to see which models require feature scaling. See here an example.


In-training validation

Some predefined models allow in-training validation. This means that the estimator is evaluated (using only the main metric) on the train and test set after every round of the training (a round can be an iteration for linear models or an added tree for boosted tree models). The validation scores are stored in the evals attribute, a dictionary of the train and test performances per round (also when pruning isn't applied). Click here for an example using in-training validation.

The predefined models that support in-training validation are:

To apply in-training validation to a custom model, use the has_validation parameter when creating the custom model.

Warning

In-training validation is not calculated during hyperparameter tuning.

Tip

Use the plot_evals method to visualize the in-training validation on the train and test sets.


Parameter customization

By default, every estimator uses the default parameters they get from their respective packages. To select different ones, use the est_params. parameter of the run method. There are two ways to add custom parameters to the models: adding them directly to the dictionary as key-value pairs or through dictionaries.

Adding the parameters directly to est_params (or using a dict with the key 'all') shares them across all models in the trainer. In this example, both the XGBoost and the LightGBM model use 200 boosted trees. Make sure all the models do have the specified parameters or an exception will be raised!

>>> atom.run(models=["XGB", "LGB"], est_params={"n_estimators": 200})

To specify parameters per model, use the model name as key and a dict of the parameters as value. In this example, the XGBoost model uses n_estimators=200 and the MultiLayerPerceptron uses one hidden layer with 75 neurons.

>>> atom.run(
...     models=["XGB", "MLP"],
...     est_params={
...         "XGB": {"n_estimators": 200},
...         "MLP": {"hidden_layer_sizes": (75,)},
...     }
... )

Some estimators allow you to pass extra parameters to the fit method (besides X and y). This can be done adding _fit at the end of the parameter. For example, to change XGBoost's verbosity, we can run:

>>> atom.run(models="XGB", est_params={"verbose_fit": True})

Note

If a parameter is specified through est_params, it's ignored by the study, even if it's added manually to ht_params["distributions"].

Info

The estimator's n_jobs and random_state parameters adopt atom's values (when available), unless specified through est_params.


Hyperparameter tuning

In order to achieve maximum performance, it's important to tune an estimator's hyperparameters before training it. ATOM provides hyperparameter tuning through the optuna package. Just like optuna, we use the terms study and trial as follows:

  • Study: optimization based on an objective function.
  • Trial: a single execution of the objective function.

Each trial is either computed by cross-validation on the complete training set or by randomly splitting the training set every iteration into a (sub)training and validation set. This process can create some minimum data leakage towards specific parameters (since the estimator is evaluated on data that is used to train the next estimator), but it ensures maximal use of the provided data. However, the leakage is not present in the independent test set, thus the final score of every model is unbiased. Note that, if the dataset is relatively small, the tuning's best score can consistently be lower than the final score on the test set due to the considerable lower fraction of instances on which it is trained. After finishing the study, the parameters that resulted in the best score are used to fit the final model on the complete training set.

Info

There are many possibilities to tune the study to your liking. The main parameter is n_trials, which determine the number of trials that are performed.

Extra things to take into account:

  • The train/validation splits are different per trial but equal for all models.
  • Re-evaluating the objective function at the same point (with the same hyperparameters) automatically skips the calculation and returns the same score as the equivalent trial.

Tip

The hyperparameter tuning output can become quite wide for models with many hyperparameters. If you are working in a Jupyter Notebook, you can change the output's width running the following code in a cell: 

>>> from IPython.display import display, HTML
>>> display(HTML("<style>.container { width:100% !important; }</style>"))

Other settings can be changed through the ht_params parameter, a dictionary where every key-value combination can be used to further customize the optimization.

By default, which hyperparameters are tuned and their corresponding distributions are predefined by ATOM. Use the 'distributions' key to customize these. Just like with est_params, it's possible to share the same parameters across models or use a dictionary with the model name as key to specify the parameters for every individual model. Use the key 'all' to tune some hyperparameters for all models when you also want to tune other parameters only for specific ones. The following example tunes the n_estimators parameter for both models but the max_depth parameter only for the RandomForest.

>>> atom.run(
...    models=["ET", "RF"],
...    n_trials=30,
...    ht_params={"distributions": {"all": "n_estimators", "RF": "max_depth"}},
... )

Like the columns parameter in atom's methods, you can exclude parameters from the optimization adding ! before its name. It's possible to exclude multiple parameters, but not to combine inclusion and exclusion for the same model. For example, to optimize a RandomForest using all its predefined parameters except n_estimators, run:

>>> atom.run(
... models="ET",
... n_trials=15,
... ht_params={"distributions": "!n_estimators"},
... )

If just the parameter name is provided, the predefined distribution is used. It's also possible to provide custom distributions spaces, but make sure they are compliant with optuna's API. See every model's individual documentation in ATOM's API section for an overview of their hyperparameters and distributions.

>>> from optuna.distributions import (
...    IntDistribution, FloatDistribution, CategoricalDistribution
... )

>>> atom.run(
...     models=["ET", "RF"],
...     n_trials=30,
...     ht_params={
...         "dimensions": {
...             "all": {"n_estimators": IntDistribution(10, 100, step=10),
...             "RF": {
...                 "max_depth": IntDistribution(1, 10),
...                 "max_features": CategoricalDistribution(["sqrt", "log2"]),
...            },
...         },
...     },
... )

Parameters for optuna's study and the study's optimize method can be added as kwargs to ht_params. For example, to use a different sampler or add a custom callback.

>>> from optuna.samplers import RandomSampler

>>> atom.run(
...     models="LR",
...     n_trials=30,
...     ht_params={
...         "sampler": RandomSampler(seed=atom.random_state),
...         "callbacks": custom_callback(),
...     },
... )

Note

  • If you use the default sampler, it’s recommended to consider setting larger n_trials to make full use of the characteristics of TPESampler because TPESampler uses some (by default, 10) trials for its startup.
  • When specifying distributions manually, make sure to import the distribution types from optuna: from optuna.distributions import ....

Warning

Keras' models can only use hyperparameter tuning when n_jobs=1 or ht_params={"cv": 1}. Using n_jobs > 1 and cv > 1 raises a PicklingError due to incompatibilities of the APIs. Read here more about deep learning models.

Tip

ATOM has several plots that can help you examine a model's study and trials. Have a look at them here.


Pruning

During hyperparameter tuning, pruning stops unpromising trials at the early stages of the training (a.k.a., automated early-stopping). This can save the pipeline much time that would otherwise be wasted on an estimator that is unlikely to yield the best results. A pruned trial can't be selected as best_trial. Click here to see an example that uses pruning.

The study uses MedianPruner as default pruner. You can use any other of optuna's pruners through the ht_params parameter.

>>> from optuna.pruners import HyperbandPruner

>>> atom.run("SGD", n_trials=30, ht_params={"pruner": HyperbandPruner()})

Warning


Bootstrapping

After fitting the estimator, you can assess the robustness of the model using the bootstrap technique. This technique creates several new data sets selecting random samples from the training set (with replacement) and evaluates them on the test set. This way you can get a distribution of the performance of the model. The sets are the same for every model. The number of sets can be chosen through the n_bootstrap parameter.

Tip

Use the plot_results method to plot the boostrap scores in a boxplot.


Successive halving

Successive halving is a bandit-based algorithm that fits N models to 1/N of the data. The best half are selected to go to the next iteration where the process is repeated. This continues until only one model remains, which is fitted on the complete dataset. Beware that a model's performance can depend greatly on the amount of data on which it is trained. For this reason, we recommend only to use this technique with similar models, e.g. only using tree-based models.

Run successive halving from atom via the successive_halving method. Consecutive runs of the same model are saved with the model's acronym followed by the number of models in the run. For example, a RandomForest in a run with 4 models would become model RF4.

See here a successive halving example.

Tip

Use the plot_successive_halving method to see every model's performance per iteration of the successive halving.


Train sizing

When training models, there is usually a trade-off between model performance and computation time, that is regulated by the number of samples in the training set. Train sizing can be used to create insights in this trade-off, and help determine the optimal size of the training set. The models are fitted multiple times, ever-increasing the number of samples in the training set.

Run train sizing from atom via the train_sizing method. The number of iterations and the number of samples per training can be specified with the train_sizes parameter. Consecutive runs of the same model are saved with the model's acronym followed by the fraction of rows in the training set (the . is removed from the fraction!). For example, a RandomForest in a run with 80% of the training samples would become model RF08.

See here a train sizing example.

Tip

Use the plot_learning_curve method to see the model's performance per size of the training set.