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Task Oriented AutoML

Overview

flaml.AutoML is a class for task-oriented AutoML. It can be used as a scikit-learn style estimator with the standard fit and predict functions. The minimal inputs from users are the training data and the task type.

  • Training data:
    • numpy array. When the input data are stored in numpy array, they are passed to fit() as X_train and y_train.
    • pandas dataframe. When the input data are stored in pandas dataframe, they are passed to fit() either as X_train and y_train, or as dataframe and label.
  • Tasks (specified via task):
    • 'classification': classification.
    • 'regression': regression.
    • 'ts_forecast': time series forecasting.
    • 'ts_forecast_classification': time series forecasting for classification.
    • 'rank': learning to rank.
    • 'seq-classification': sequence classification.
    • 'seq-regression': sequence regression.
    • 'summarization': text summarization.
    • 'token-classification': token classification.
    • 'multichoice-classification': multichoice classification.

An optional input is time_budget for searching models and hyperparameters. When not specified, a default budget of 60 seconds will be used.

A typical way to use flaml.AutoML:

# Prepare training data
# ...
from flaml import AutoML
automl = AutoML()
automl.fit(X_train, y_train, task="regression", time_budget=60, **other_settings)
# Save the model
with open("automl.pkl", "wb") as f:
pickle.dump(automl, f, pickle.HIGHEST_PROTOCOL)

# At prediction time
with open("automl.pkl", "rb") as f:
automl = pickle.load(f)
pred = automl.predict(X_test)

If users provide the minimal inputs only, AutoML uses the default settings for time budget, optimization metric, estimator list etc.

Customize AutoML.fit()

Optimization metric

The optimization metric is specified via the metric argument. It can be either a string which refers to a built-in metric, or a user-defined function.

  • Built-in metric.
    • 'accuracy': 1 - accuracy as the corresponding metric to minimize.
    • 'log_loss': default metric for multiclass classification.
    • 'r2': 1 - r2_score as the corresponding metric to minimize. Default metric for regression.
    • 'rmse': root mean squared error.
    • 'mse': mean squared error.
    • 'mae': mean absolute error.
    • 'mape': mean absolute percentage error.
    • 'roc_auc': minimize 1 - roc_auc_score. Default metric for binary classification.
    • 'roc_auc_ovr': minimize 1 - roc_auc_score with multi_class="ovr".
    • 'roc_auc_ovo': minimize 1 - roc_auc_score with multi_class="ovo".
    • 'f1': minimize 1 - f1_score.
    • 'micro_f1': minimize 1 - f1_score with average="micro".
    • 'macro_f1': minimize 1 - f1_score with average="macro".
    • 'ap': minimize 1 - average_precision_score.
    • 'ndcg': minimize 1 - ndcg_score.
    • 'ndcg@k': minimize 1 - ndcg_score@k. k is an integer.
  • User-defined function. A customized metric function that requires the following (input) signature, and returns the input config’s value in terms of the metric you want to minimize, and a dictionary of auxiliary information at your choice:
def custom_metric(
X_val, y_val, estimator, labels,
X_train, y_train, weight_val=None, weight_train=None,
config=None, groups_val=None, groups_train=None,
):
return metric_to_minimize, metrics_to_log

For example,

def custom_metric(
X_val, y_val, estimator, labels,
X_train, y_train, weight_val=None, weight_train=None,
**args,
):
from sklearn.metrics import log_loss
import time

start = time.time()
y_pred = estimator.predict_proba(X_val)
pred_time = (time.time() - start) / len(X_val)
val_loss = log_loss(y_val, y_pred, labels=labels, sample_weight=weight_val)
y_pred = estimator.predict_proba(X_train)
train_loss = log_loss(y_train, y_pred, labels=labels, sample_weight=weight_train)
alpha = 0.5
return val_loss * (1 + alpha) - alpha * train_loss, {
"val_loss": val_loss,
"train_loss": train_loss,
"pred_time": pred_time,
}

It returns the validation loss penalized by the gap between validation and training loss as the metric to minimize, and three metrics to log: val_loss, train_loss and pred_time. The arguments config, groups_val and groups_train are not used in the function.

Estimator and search space

The estimator list can contain one or more estimator names, each corresponding to a built-in estimator or a custom estimator. Each estimator has a search space for hyperparameter configurations. FLAML supports both classical machine learning models and deep neural networks.

Estimator

  • Built-in estimator.
    • 'lgbm': LGBMEstimator for task "classification", "regression", "rank", "ts_forecast" and "ts_forecast_classification". Hyperparameters: n_estimators, num_leaves, min_child_samples, learning_rate, log_max_bin (logarithm of (max_bin + 1) with base 2), colsample_bytree, reg_alpha, reg_lambda.
    • 'xgboost': XGBoostSkLearnEstimator for task "classification", "regression", "rank", "ts_forecast" and "ts_forecast_classification". Hyperparameters: n_estimators, max_leaves, max_depth, min_child_weight, learning_rate, subsample, colsample_bylevel, colsample_bytree, reg_alpha, reg_lambda.
    • 'rf': RandomForestEstimator for task "classification", "regression", "ts_forecast" and "ts_forecast_classification". Hyperparameters: n_estimators, max_features, max_leaves, criterion (for classification only).
    • 'extra_tree': ExtraTreesEstimator for task "classification", "regression", "ts_forecast" and "ts_forecast_classification". Hyperparameters: n_estimators, max_features, max_leaves, criterion (for classification only).
    • 'lrl1': LRL1Classifier (sklearn.LogisticRegression with L1 regularization) for task "classification". Hyperparameters: C.
    • 'lrl2': LRL2Classifier (sklearn.LogisticRegression with L2 regularization) for task "classification". Hyperparameters: C.
    • 'catboost': CatBoostEstimator for task "classification" and "regression". Hyperparameters: early_stopping_rounds, learning_rate, n_estimators.
    • 'kneighbor': KNeighborsEstimator for task "classification" and "regression". Hyperparameters: n_neighbors.
    • 'prophet': Prophet for task "ts_forecast". Hyperparameters: changepoint_prior_scale, seasonality_prior_scale, holidays_prior_scale, seasonality_mode.
    • 'arima': ARIMA for task "ts_forecast". Hyperparameters: p, d, q.
    • 'sarimax': SARIMAX for task "ts_forecast". Hyperparameters: p, d, q, P, D, Q, s.
    • 'transformer': Huggingface transformer models for task "seq-classification", "seq-regression", "multichoice-classification", "token-classification" and "summarization". Hyperparameters: learning_rate, num_train_epochs, per_device_train_batch_size, warmup_ratio, weight_decay, adam_epsilon, seed.
  • Custom estimator. Use custom estimator for:
    • tuning an estimator that is not built-in;
    • customizing search space for a built-in estimator.

To tune a custom estimator that is not built-in, you need to:

  1. Build a custom estimator by inheritting flaml.model.BaseEstimator or a derived class. For example, if you have a estimator class with scikit-learn style fit() and predict() functions, you only need to set self.estimator_class to be that class in your constructor.
from flaml.model import SKLearnEstimator
# SKLearnEstimator is derived from BaseEstimator
import rgf

class MyRegularizedGreedyForest(SKLearnEstimator):
def __init__(self, task="binary", **config):
super().__init__(task, **config)

if task in CLASSIFICATION:
from rgf.sklearn import RGFClassifier

self.estimator_class = RGFClassifier
else:
from rgf.sklearn import RGFRegressor

self.estimator_class = RGFRegressor

@classmethod
def search_space(cls, data_size, task):
space = {
"max_leaf": {
"domain": tune.lograndint(lower=4, upper=data_size),
"low_cost_init_value": 4,
},
"n_iter": {
"domain": tune.lograndint(lower=1, upper=data_size),
"low_cost_init_value": 1,
},
"learning_rate": {"domain": tune.loguniform(lower=0.01, upper=20.0)},
"min_samples_leaf": {
"domain": tune.lograndint(lower=1, upper=20),
"init_value": 20,
},
}
return space

In the constructor, we set self.estimator_class as RGFClassifier or RGFRegressor according to the task type. If the estimator you want to tune does not have a scikit-learn style fit() and predict() API, you can override the fit() and predict() function of flaml.model.BaseEstimator, like XGBoostEstimator.

  1. Give the custom estimator a name and add it in AutoML. E.g.,
from flaml import AutoML
automl = AutoML()
automl.add_learner("rgf", MyRegularizedGreedyForest)

This registers the MyRegularizedGreedyForest class in AutoML, with the name "rgf".

  1. Tune the newly added custom estimator in either of the following two ways depending on your needs:
  • tune rgf alone: automl.fit(..., estimator_list=["rgf"]); or
  • mix it with other built-in learners: automl.fit(..., estimator_list=["rgf", "lgbm", "xgboost", "rf"]).

Search space

Each estimator class, built-in or not, must have a search_space function. In the search_space function, we return a dictionary about the hyperparameters, the keys of which are the names of the hyperparameters to tune, and each value is a set of detailed search configurations about the corresponding hyperparameters represented in a dictionary. A search configuration dictionary includes the following fields:

  • domain, which specifies the possible values of the hyperparameter and their distribution. Please refer to more details about the search space domain.
  • init_value (optional), which specifies the initial value of the hyperparameter.
  • low_cost_init_value(optional), which specifies the value of the hyperparameter that is associated with low computation cost. See cost related hyperparameters or FAQ for more details.

In the example above, we tune four hyperparameters, three integers and one float. They all follow a log-uniform distribution. "max_leaf" and "n_iter" have "low_cost_init_value" specified as their values heavily influence the training cost.

To customize the search space for a built-in estimator, use a similar approach to define a class that inherits the existing estimator. For example,

from flaml.model import XGBoostEstimator

def logregobj(preds, dtrain):
labels = dtrain.get_label()
preds = 1.0 / (1.0 + np.exp(-preds)) # transform raw leaf weight
grad = preds - labels
hess = preds * (1.0 - preds)
return grad, hess

class MyXGB1(XGBoostEstimator):
"""XGBoostEstimator with logregobj as the objective function"""

def __init__(self, **config):
super().__init__(objective=logregobj, **config)

We override the constructor and set the training objective as a custom function logregobj. The hyperparameters and their search range do not change. For another example,

class XGBoost2D(XGBoostSklearnEstimator):
@classmethod
def search_space(cls, data_size, task):
upper = min(32768, int(data_size))
return {
"n_estimators": {
"domain": tune.lograndint(lower=4, upper=upper),
"low_cost_init_value": 4,
},
"max_leaves": {
"domain": tune.lograndint(lower=4, upper=upper),
"low_cost_init_value": 4,
},
}

We override the search_space function to tune two hyperparameters only, "n_estimators" and "max_leaves". They are both random integers in the log space, ranging from 4 to data-dependent upper bound. The lower bound for each corresponds to low training cost, hence the "low_cost_init_value" for each is set to 4.

Constraint

There are several types of constraints you can impose.

  1. End-to-end constraints on the AutoML process.
  • time_budget: constrains the wall-clock time (seconds) used by the AutoML process. We provide some tips on how to set time budget.

  • max_iter: constrains the maximal number of models to try in the AutoML process.

  1. Constraints on the (hyperparameters of) the estimators.

Some constraints on the estimator can be implemented via the custom learner. For example,

class MonotonicXGBoostEstimator(XGBoostSklearnEstimator):
@classmethod
def search_space(**args):
return super().search_space(**args).update({"monotone_constraints": "(1, -1)"})

It adds a monotonicity constraint to XGBoost. This approach can be used to set any constraint that is a parameter in the underlying estimator's constructor.

  1. Constraints on the models tried in AutoML.

Users can set constraints such as the maximal number of models to try, limit on training time and prediction time per model.

  • train_time_limit: training time in seconds.
  • pred_time_limit: prediction time per instance in seconds.

For example,

automl.fit(X_train, y_train, max_iter=100, train_time_limit=1, pred_time_limit=1e-3)
  1. Constraints on the metrics of the ML model tried in AutoML.

When users provide a custom metric function, which returns a primary optimization metric and a dictionary of additional metrics (typically also about the model) to log, users can also specify constraints on one or more of the metrics in the dictionary of additional metrics.

Users need to provide a list of such constraints in the following format: Each element in this list is a 3-tuple, which shall be expressed in the following format: the first element of the 3-tuple is the name of the metric, the second element is the inequality sign chosen from ">=" and "<=", and the third element is the constraint value. E.g., ('val_loss', '<=', 0.1).

For example,

metric_constraints = [("train_loss", "<=", 0.1), ("val_loss", "<=", 0.1)]
automl.fit(X_train, y_train, max_iter=100, train_time_limit=1, metric_constraints=metric_constraints)

Ensemble

To use stacked ensemble after the model search, set ensemble=True or a dict. When ensemble=True, the final estimator and passthrough in the stacker will be automatically chosen. You can specify customized final estimator or passthrough option:

  • "final_estimator": an instance of the final estimator in the stacker.
  • "passthrough": True (default) or False, whether to pass the original features to the stacker.

For example,

automl.fit(
X_train, y_train, task="classification",
"ensemble": {
"final_estimator": LogisticRegression(),
"passthrough": False,
},
)

Resampling strategy

By default, flaml decides the resampling automatically according to the data size and the time budget. If you would like to enforce a certain resampling strategy, you can set eval_method to be "holdout" or "cv" for holdout or cross-validation.

For holdout, you can also set:

  • split_ratio: the fraction for validation data, 0.1 by default.
  • X_val, y_val: a separate validation dataset. When they are passed, the validation metrics will be computed against this given validation dataset. If they are not passed, then a validation dataset will be split from the training data and held out from training during the model search. After the model search, flaml will retrain the model with best configuration on the full training data. You can setretrain_full to be False to skip the final retraining or "budget" to ask flaml to do its best to retrain within the time budget.

For cross validation, you can also set n_splits of the number of folds. By default it is 5.

Data split method

By default, flaml uses the following method to split the data:

  • stratified split for classification;
  • uniform split for regression;
  • time-based split for time series forecasting;
  • group-based split for learning to rank.

The data split method for classification can be changed into uniform split by setting split_type="uniform". The data are shuffled when split_type in ("uniform", "stratified"). For both classification and regression, time-based split can be enforced if the data are sorted by timestamps, by setting split_type="time".

When eval_method="cv", split_type can also be set as a custom splitter. It needs to be an instance of a derived class of scikit-learn KFold and have split and get_n_splits methods with the same signatures.

Parallel tuning

When you have parallel resources, you can either spend them in training and keep the model search sequential, or perform parallel search. Following scikit-learn, the parameter n_jobs specifies how many CPU cores to use for each training job. The number of parallel trials is specified via the parameter n_concurrent_trials. By default, n_jobs=-1, n_concurrent_trials=1. That is, all the CPU cores (in a single compute node) are used for training a single model and the search is sequential. When you have more resources than what each single training job needs, you can consider increasing n_concurrent_trials.

To do parallel tuning, install the ray and blendsearch options:

pip install flaml[ray,blendsearch]

ray is used to manage the resources. For example,

ray.init(n_cpus=16)

allocates 16 CPU cores. Then, when you run:

automl.fit(X_train, y_train, n_jobs=4, n_concurrent_trials=4)

flaml will perform 4 trials in parallel, each consuming 4 CPU cores. The parallel tuning uses the BlendSearch algorithm.

Warm start

We can warm start the AutoML by providing starting points of hyperparameter configurstions for each estimator. For example, if you have run AutoML for one hour, after checking the results, you would like to run it for another two hours, then you can use the best configurations found for each estimator as the starting points for the new run.

automl1 = AutoML()
automl1.fit(X_train, y_train, time_budget=3600)
automl2 = AutoML()
automl2.fit(X_train, y_train, time_budget=7200, starting_points=automl1.best_config_per_estimator)

starting_points is a dictionary. The keys are the estimator names. If you do not need to specify starting points for an estimator, exclude its name from the dictionary. The value for each key can be either a dictionary of a list of dictionaries, corresponding to one hyperparameter configuration, or multiple hyperparameter configurations, respectively.

Log the trials

The trials are logged in a file if a log_file_name is passed. Each trial is logged as a json record in one line. The best trial's id is logged in the last line. For example,

{"record_id": 0, "iter_per_learner": 1, "logged_metric": null, "trial_time": 0.12717914581298828, "wall_clock_time": 0.1728971004486084, "validation_loss": 0.07333333333333332, "config": {"n_estimators": 4, "num_leaves": 4, "min_child_samples": 20, "learning_rate": 0.09999999999999995, "log_max_bin": 8, "colsample_bytree": 1.0, "reg_alpha": 0.0009765625, "reg_lambda": 1.0}, "learner": "lgbm", "sample_size": 150}
{"record_id": 1, "iter_per_learner": 3, "logged_metric": null, "trial_time": 0.07027268409729004, "wall_clock_time": 0.3756711483001709, "validation_loss": 0.05333333333333332, "config": {"n_estimators": 4, "num_leaves": 4, "min_child_samples": 12, "learning_rate": 0.2677050123105203, "log_max_bin": 7, "colsample_bytree": 1.0, "reg_alpha": 0.001348364934537134, "reg_lambda": 1.4442580148221913}, "learner": "lgbm", "sample_size": 150}
{"curr_best_record_id": 1}
  1. iter_per_learner means how many models have been tried for each learner. The reason you see records like iter_per_learner=3 for record_id=1 is that flaml only logs better configs than the previous iters by default, i.e., log_type='better'. If you use log_type='all' instead, all the trials will be logged.
  2. trial_time means the time taken to train and evaluate one config in that trial. total_search_time is the total time spent from the beginning of fit().
  3. flaml will adjust the n_estimators for lightgbm etc. according to the remaining budget and check the time budget constraint and stop in several places. Most of the time that makes fit() stops before the given budget. Occasionally it may run over the time budget slightly. But the log file always contains the best config info and you can recover the best model until any time point using retrain_from_log().

We can also use mlflow for logging:

mlflow.set_experiment("flaml")
with mlflow.start_run():
automl.fit(X_train=X_train, y_train=y_train, **settings)

Extra fit arguments

Extra fit arguments that are needed by the estimators can be passed to AutoML.fit(). For example, if there is a weight associated with each training example, they can be passed via sample_weight. For another example, period can be passed for time series forecaster. For any extra keywork argument passed to AutoML.fit() which has not been explicitly listed in the function signature, it will be passed to the underlying estimators' fit() as is.

Retrieve and analyze the outcomes of AutoML.fit()

Get best model

The best model can be obtained by the model property of an AutoML instance. For example,

automl.fit(X_train, y_train, task="regression")
print(automl.model)
# <flaml.model.LGBMEstimator object at 0x7f9b502c4550>

flaml.model.LGBMEstimator is a wrapper class for LightGBM models. To access the underlying model, use the estimator property of the flaml.model.LGBMEstimator instance.

print(automl.model.estimator)
'''
LGBMRegressor(colsample_bytree=0.7610534336273627,
learning_rate=0.41929025492645006, max_bin=255,
min_child_samples=4, n_estimators=45, num_leaves=4,
reg_alpha=0.0009765625, reg_lambda=0.009280655005879943,
verbose=-1)
'''

Just like a normal LightGBM model, we can inspect it. For example, we can plot the feature importance:

import matplotlib.pyplot as plt
plt.barh(automl.model.estimator.feature_name_, automl.model.estimator.feature_importances_)

png

Get best configuration

We can find the best estimator's name and best configuration by:

print(automl.best_estimator)
# lgbm
print(automl.best_config)
# {'n_estimators': 148, 'num_leaves': 18, 'min_child_samples': 3, 'learning_rate': 0.17402065726724145, 'log_max_bin': 8, 'colsample_bytree': 0.6649148062238498, 'reg_alpha': 0.0009765625, 'reg_lambda': 0.0067613624509965}

We can also find the best configuration per estimator.

print(automl.best_config_per_estimator)
# {'lgbm': {'n_estimators': 148, 'num_leaves': 18, 'min_child_samples': 3, 'learning_rate': 0.17402065726724145, 'log_max_bin': 8, 'colsample_bytree': 0.6649148062238498, 'reg_alpha': 0.0009765625, 'reg_lambda': 0.0067613624509965}, 'rf': None, 'catboost': None, 'xgboost': {'n_estimators': 4, 'max_leaves': 4, 'min_child_weight': 1.8630223791106992, 'learning_rate': 1.0, 'subsample': 0.8513627344387318, 'colsample_bylevel': 1.0, 'colsample_bytree': 0.946138073111236, 'reg_alpha': 0.0018311776973217073, 'reg_lambda': 0.27901659190538414}, 'extra_tree': {'n_estimators': 4, 'max_features': 1.0, 'max_leaves': 4}}

The None value corresponds to the estimators which have not been tried.

Other useful information:

print(automl.best_config_train_time)
# 0.24841618537902832
print(automl.best_iteration)
# 10
print(automl.best_loss)
# 0.15448622217577546
print(automl.time_to_find_best_model)
# 0.4167296886444092
print(automl.config_history)
# {0: ('lgbm', {'n_estimators': 4, 'num_leaves': 4, 'min_child_samples': 20, 'learning_rate': 0.09999999999999995, 'log_max_bin': 8, 'colsample_bytree': 1.0, 'reg_alpha': 0.0009765625, 'reg_lambda': 1.0}, 1.2300517559051514)}
# Meaning: at iteration 0, the config tried is {'n_estimators': 4, 'num_leaves': 4, 'min_child_samples': 20, 'learning_rate': 0.09999999999999995, 'log_max_bin': 8, 'colsample_bytree': 1.0, 'reg_alpha': 0.0009765625, 'reg_lambda': 1.0} for lgbm, and the wallclock time is 1.23s when this trial is finished.

Plot learning curve

To plot how the loss is improved over time during the model search, first load the search history from the log file:

from flaml.data import get_output_from_log

time_history, best_valid_loss_history, valid_loss_history, config_history, metric_history = \
get_output_from_log(filename=settings["log_file_name"], time_budget=120)

Then, assuming the optimization metric is "accuracy", we can plot the accuracy versus wallclock time:

import matplotlib.pyplot as plt
import numpy as np

plt.title("Learning Curve")
plt.xlabel("Wall Clock Time (s)")
plt.ylabel("Validation Accuracy")
plt.step(time_history, 1 - np.array(best_valid_loss_history), where="post")
plt.show()

png

The curve suggests that increasing the time budget may further improve the accuracy.

How to set time budget

  • If you have an exact constraint for the total search time, set it as the time budget.
  • If you have flexible time constraints, for example, your desirable time budget is t1=60s, and the longest time budget you can tolerate is t2=3600s, you can try the following two ways:
  1. set t1 as the time budget, and check the message in the console log in the end. If the budget is too small, you will see a warning like

    WARNING - Time taken to find the best model is 91% of the provided time budget and not all estimators' hyperparameter search converged. Consider increasing the time budget.

  2. set t2 as the time budget, and also set early_stop=True. If the early stopping is triggered, you will see a warning like

    WARNING - All estimator hyperparameters local search has converged at least once, and the total search time exceeds 10 times the time taken to find the best model.

WARNING - Stopping search as early_stop is set to True.

How much time is needed to find the best model

If you want to get a sense of how much time is needed to find the best model, you can use max_iter=2 to perform two trials first. The message will be like:

INFO - iteration 0, current learner lgbm

INFO - Estimated sufficient time budget=145194s. Estimated necessary time budget=2118s.

INFO - at 2.6s, estimator lgbm's best error=0.4459, best estimator lgbm's best error=0.4459

You will see that the time to finish the first and cheapest trial is 2.6 seconds. The estimated necessary time budget is 2118 seconds, and the estimated sufficient time budget is 145194 seconds. Note that this is only an estimated range to help you decide your budget.