DoC: Introduction to Machine Learning
Decision Tree Coursework
Instructions for setting up the repo are outlined below.
The report named Intro_to_ML_Report.pdf can also be found in the repo.
This library supports the training, pruning, and evaluation of decision trees, as well as cross-validation. The data is assumed to be in numpy integer format, with the last column representing class labels.
Clone the repo onto the lab machine using the following command.
git clone https://github.com/IshaanReni/IML_CW1.gitThe files run.py and run_cross_val.py are examples of how to interface with the classes and functions in the library.
Load other datasets into intro2ML-coursework1/wifi_db/. All datasets must be in .txt format.
In order to run training, pruning, and evaluation once, use the following command in the IML_CW1 directory:
python3 run.py [dataset-filename]The optional argument [dataset-filename] replaces the default .txt file with the specified .txt file (in intro2ML-coursework1/wifi_db/ directory). The .txt file extension must be mentioned.
Alternatively, the default file_name variable in run.py can be changed.
Similarly, cross-validation can be performed using the command:
python3 run_cross_val.py [dataset-filename]In the case that a new top-level script is to be made, the key functions are described below.
(The library stores nodes and trees as objects, as OOP is used. Classifier denotes the class in which the class method resides.)
from prepare_data import prepare_data
training_data, validation_data, test_data = prepare_data(full_dataset, test_prop=0.1, val_prop=0.1, random_gen=np.random.default_rng(8), save_name=None)This function splits the full dataset (numpy array) into usable training, validation, and test data numpy arrays, in the proportions specified. The random generator can be overwritten if a different seed is desired.
If the save_name variable is a string, the function will also save the output arrays as txt files in intro2ML-coursework1/wifi_db/.
from decision_tree import Classifier
tree = Classifier.fit(training_data, max_depth=999)Returns a tree trained on the input training data (numpy array). Optional maximum depth can be specified for early stopping regularisation, debugging, or simpler graphs.
from decision_tree import Classifier
pruned_tree, depth = Classifier.prune(tree, validation_data)Returns a copy of the input tree which is pruned using validation data, along with its depth (tuple).
from decision_tree import Classifier
predictions = Classifier.predict(tree, test_data[:,:-1])Returns an array of predictions by the input tree, for each test in a test set. The function will work regardless of if the test class labels are sent into the function.
import evaluation
confusion_matrix = evaluation.calc_confusion_matrix(test_data, predictions)
accuracy = evaluation.calc_accuracy(test_data, predictions)
precisions = evaluation.calc_precision(confusion_matrix)
recalls = evaluation.calc_recall(confusion_matrix)
f1s = evaluation.calc_F1(precisions, recalls)calc_confusion_matrix returns an N×N confusion matrix, where N is the number of unique classes.
The accuracy function doesn't use the confusion matrix to preclude the matrix needing to be made every fold in cross-validation (optimisation).
Other evaluation functions use the matrix to return a per-class list of values.
from decision_tree import Classifier
nodes, leaves, depth = tree.tree_properties(tree.root)
nodes = tree.get_nodes()
leaves = tree.get_leaves()
depth = tree.get_depth()Getter functions for obtaining tree statistics
from prepare_data_cross_val import prepare_data_cross_val
test_folds, val_folds, train_folds = prepare_data_cross_val(full_dataset, random_gen=np.random.default_rng(8), outer_folds=10, inner_folds=9)Creates lists of data to be used in folds. test_folds is outer_folds long whereas val_folds and train_folds is outer_folds×inner_folds long.
Defaults to 10:10:80 split (90 folds in total).
from cross_validation import cross_validation
cross_validation(test_folds, val_folds, train_folds, outer_folds, inner_folds)Runs outer_folds×inner_folds cross-validation on the data. Prints metrics every fold (pre- and post-pruning), and gives overall metrics at the end.
from decision_tree import Classifier
tree.print_tree()Creates a matplotlib visualisation of the tree. Usually run last, as it halts the program while the graph window is open.
