Before doing anything below, you’ll want to install SKLL.


In general, there are four steps to using SKLL:

  1. Get some data in a SKLL-compatible format.

  2. Create a small configuration file describing the machine learning experiment you would like to run.

  3. Run that configuration file with run_experiment.

  4. Examine the results of the experiment.

Titanic Example

Let’s see how we can apply the basic workflow above to a simple example using the Titanic: Machine Learning from Disaster data from Kaggle.

Create virtual environment with SKLL

Before we proceed further, we need to install SKLL. The easiest way to do this is in a virtual environment. For this tutorial, we will use conda for creating our virtual environment as follows:

conda create -n skllenv -c conda-forge -c ets python=3.11 skll

This will create a new virtual environment named skllenv with the latest release of SKLL which you can then activate by running conda activate skllenv. Make sure to create and activate this environment before proceeding further. Once you are done with the tutorial, you may deactivate the virtual environment by running conda deactivate.

Get your data into the correct format

The first step is to get the Titanic data. We have already downloaded the data files from Kaggle and included them in the SKLL repository. Next, we need to get the files and process them to get them in the right shape.

The provided script, make_titanic_example_data.py, will split the train and test data files from Kaggle up into groups of related features and store them in dev, test, train, and train+dev subdirectories. The development set that gets created by the script is 20% of the data that was in the original training set, and train contains the other 80%.

Create a configuration file for the experiment

For this tutorial, we will refer to an “experiment” as having a single data set split into training and testing portions. As part of each experiment, we can train and test several models, either simultaneously or sequentially, depending whether we’re using GridMap or not. This will be described in more detail later on, when we are ready to run our experiment.

You can consult the full list of learners currently available in SKLL to get an idea for the things you can do. As part of this tutorial, we will use the following classifiers:

  • Decision Tree

  • Multinomial Naïve Bayes

  • Random Forest

  • Support Vector Machine

experiment_name = Titanic_Evaluate_Tuned
task = evaluate

# this could also be an absolute path instead (and must be if you're not
# running things in local mode)
train_directory = train
test_directory = dev
featuresets = [["family.csv", "misc.csv", "socioeconomic.csv", "vitals.csv"]]
learners = ["RandomForestClassifier", "DecisionTreeClassifier", "SVC", "MultinomialNB"]
label_col = Survived
id_col = PassengerId

grid_search = true
grid_search_folds = 3
objectives = ['accuracy']

# again, these can be absolute paths
metrics = ['roc_auc']
probability = true
logs = output
results = output
predictions = output
models = output

Let’s take a look at the options specified in titanic/evaluate_tuned.cfg. Here, we are only going to train a model and evaluate its performance on the development set, because in the General section, task is set to evaluate. We will explore the other options for task later.

In the Input section, we have specified relative paths to the training and testing directories via the train_directory and test_directory settings respectively. featuresets indicates the name of both the training and testing files. learners must always be specified in between [ ] brackets, even if you only want to use one learner. This is similar to the featuresets option, which requires two sets of brackets, since multiple sets of different-yet-related features can be provided. We will keep our examples simple, however, and only use one set of features per experiment. The label_col and id_col settings specify the columns in the CSV files that specify the class labels and instances IDs for each example.

The Tuning section defines how we want our model to be tuned. Setting grid_search to True here employs scikit-learn’s GridSearchCV class, which is an implementation of the standard, brute-force approach to hyperparameter optimization.

objectives refers to the desired objective functions; here, accuracy will optimize for overall accuracy. You can see a list of all the available objective functions here.

In the Output section, we first define the additional evaluation metrics we want to compute in addition to the tuning objective via the metrics option. The other options are directories where you’d like all of the relevant output from your experiment to go. results refers to the results of the experiment in both human-readable and JSON forms. logs specifies where to put log files containing any status, warning, or error messages generated during model training and evaluation. predictions refers to where to store the individual predictions generated for the test set. models is for specifying a directory to serialize the trained models.

Running your configuration file through run_experiment

Getting your experiment running is the simplest part of using SKLL, you just need to type the following into a terminal:

$ run_experiment titanic/evaluate_tuned.cfg

Make sure you have the skllenv environment activated before you run this command which should produce output like:

2020-03-10 14:25:23,596 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_RandomForestClassifier - INFO - Task: evaluate
2020-03-10 14:25:23,596 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_RandomForestClassifier - INFO - Training on train, Test on dev, feature set ['family.csv', 'misc.csv', 'socioeconomic.csv', 'vitals.csv'] ...
Loading /Users/nmadnani/work/skll/examples/titanic/train/family.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/train/misc.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/train/socioeconomic.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/train/vitals.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/dev/family.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/dev/misc.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/dev/socioeconomic.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/dev/vitals.csv...           done
2020-03-10 14:25:23,662 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_RandomForestClassifier - INFO - Featurizing and training new RandomForestClassifier model
2020-03-10 14:25:23,663 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_RandomForestClassifier - WARNING - Training data will be shuffled to randomize grid search folds.  Shuffling may yield different results compared to scikit-learn.
2020-03-10 14:25:28,129 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_RandomForestClassifier - INFO - Best accuracy grid search score: 0.798
2020-03-10 14:25:28,130 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_RandomForestClassifier - INFO - Hyperparameters: bootstrap: True, ccp_alpha: 0.0, class_weight: None, criterion: gini, max_depth: 5, max_features: auto, max_leaf_nodes: None, max_samples: None, min_impurity_decrease: 0.0, min_impurity_split: None, min_samples_leaf: 1, min_samples_split: 2, min_weight_fraction_leaf: 0.0, n_estimators: 500, n_jobs: None, oob_score: False, random_state: 123456789, verbose: 0, warm_start: False
2020-03-10 14:25:28,130 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_RandomForestClassifier - INFO - Evaluating predictions
2020-03-10 14:25:28,172 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_RandomForestClassifier - INFO - using probabilities for the positive class to compute "roc_auc" for evaluation.
2020-03-10 14:25:28,178 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_DecisionTreeClassifier - INFO - Task: evaluate
2020-03-10 14:25:28,178 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_DecisionTreeClassifier - INFO - Training on train, Test on dev, feature set ['family.csv', 'misc.csv', 'socioeconomic.csv', 'vitals.csv'] ...
Loading /Users/nmadnani/work/skll/examples/titanic/train/family.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/train/misc.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/train/socioeconomic.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/train/vitals.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/dev/family.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/dev/misc.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/dev/socioeconomic.csv...           done
Loading /Users/nmadnani/work/skll/examples/titanic/dev/vitals.csv...           done
2020-03-10 14:25:28,226 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_DecisionTreeClassifier - INFO - Featurizing and training new DecisionTreeClassifier model
2020-03-10 14:25:28,226 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_DecisionTreeClassifier - WARNING - Training data will be shuffled to randomize grid search folds.  Shuffling may yield different results compared to scikit-learn.
2020-03-10 14:25:28,269 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_DecisionTreeClassifier - INFO - Best accuracy grid search score: 0.754
2020-03-10 14:25:28,269 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_DecisionTreeClassifier - INFO - Hyperparameters: ccp_alpha: 0.0, class_weight: None, criterion: gini, max_depth: None, max_features: None, max_leaf_nodes: None, min_impurity_decrease: 0.0, min_impurity_split: None, min_samples_leaf: 1, min_samples_split: 2, min_weight_fraction_leaf: 0.0, presort: deprecated, random_state: 123456789, splitter: best
2020-03-10 14:25:28,269 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_DecisionTreeClassifier - INFO - Evaluating predictions
2020-03-10 14:25:28,272 - Titanic_Evaluate_Tuned_family.csv+misc.csv+socioeconomic.csv+vitals.csv_DecisionTreeClassifier - INFO - using probabilities for the positive class to compute "roc_auc" for evaluation.

We could squelch the warnings about shuffling by setting shuffle to True in the Input section.

The reason we see the loading messages repeated is that we are running the different learners sequentially, whereas SKLL is designed to take advantage of a cluster to execute everything in parallel via GridMap.

Examine the results

As a result of running our experiment, there will be a whole host of files in our results directory. They can be broken down into three types of files:

  1. .results files, which contain a human-readable summary of the experiment, complete with confusion matrix.

  2. .results.json files, which contain all of the same information as the .results files, but in a format more well-suited to automated processing.

  3. A summary .tsv file, which contains all of the information in all of the .results.json files with one line per file. This is very nice if you’re trying many different learners and want to compare their performance. If you do additional experiments later (with a different config file), but would like one giant summary file, you can use the summarize_results command.

An example of a human-readable results file for our Titanic experiment is:

Experiment Name: Titanic_Evaluate_Tuned
SKLL Version: 2.1
Training Set: train
Training Set Size: 569
Test Set: dev
Test Set Size: 143
Shuffle: False
Feature Set: ["family.csv", "misc.csv", "socioeconomic.csv", "vitals.csv"]
Learner: RandomForestClassifier
Task: evaluate
Feature Scaling: none
Grid Search: True
Grid Search Folds: 3
Grid Objective Function: accuracy
Additional Evaluation Metrics: ['roc_auc']
Scikit-learn Version: 0.22.2.post1
Start Timestamp: 10 Mar 2020 14:25:23.595787
End Timestamp: 10 Mar 2020 14:25:28.175375
Total Time: 0:00:04.579588

Model Parameters: {"bootstrap": true, "ccp_alpha": 0.0, "class_weight": null, "criterion": "gini", "max_depth": 5, "max_features": "auto", "max_leaf_nodes": null, "max_samples": null, "min_impurity_decrease": 0.0, "min_impurity_split": null, "min_samples_leaf": 1, "min_samples_split": 2, "min_weight_fraction_leaf": 0.0, "n_estimators": 500, "n_jobs": null, "oob_score": false, "random_state": 123456789, "verbose": 0, "warm_start": false}
Grid Objective Score (Train) = 0.797874315418175
|    |    0 |    1 |   Precision |   Recall |   F-measure |
|  0 | [79] |    8 |       0.849 |    0.908 |       0.878 |
|  1 |   14 | [42] |       0.840 |    0.750 |       0.792 |
(row = reference; column = predicted)
Accuracy = 0.8461538461538461
Objective Function Score (Test) = 0.8461538461538461

Additional Evaluation Metrics (Test):
 roc_auc = 0.9224137931034483

IRIS Example on Binder

If you prefer using an interactive Jupyter notebook to learn about SKLL, you can do so by clicking the launch button below.