Classification with Tabular Data using Scikit-Learn and Cleanlab

In this 5-minute quickstart tutorial, we use cleanlab with scikit-learn models to find potential label errors in a classification dataset with tabular (numeric/categorical) features. Tabular (or structured) data are typically organized in a row/column format and stored in a SQL database or file types like: CSV, Excel, or Parquet. Here we study the German Credit dataset which contains 1,000 individuals described by 20 features, each labeled as either “good” or “bad” credit risk. cleanlab automatically shortlists hundreds of examples from this dataset that confuse our ML model; many of which are potential label errors (due to annotator mistakes), edge cases, and otherwise ambiguous examples.

Overview of what we’ll do in this tutorial:

• Build a simple credit risk classifier with scikit-learn’s HistGradientBoostingClassifier.

• Use this classifier to compute out-of-sample predicted probabilities, pred_probs, via cross validation.

• Identify potential label errors in the data with cleanlab’s find_label_issues method.

• Train a robust version of the same histogram-based gradient boosting model via cleanlab’s CleanLearning wrapper.

Quickstart

Already have an sklearn compatible model, tabular data and given labels? Run the code below to train your model and get label issues.

from cleanlab.classification import CleanLearning

cl = CleanLearning(model)
_ = cl.fit(train_data, labels)
label_issues = cl.get_label_issues()
preds = cl.predict(test_data) # predictions from a version of your model
                              # trained on auto-cleaned data

Is your model/data not compatible with CleanLearning? You can instead run cross-validation on your model to get out-of-sample pred_probs. Then run the code below to get label issue indices ranked by their inferred severity.

from cleanlab.filter import find_label_issues

ranked_label_issues = find_label_issues(
    labels,
    pred_probs,
    return_indices_ranked_by="self_confidence",
)

1. Install required dependencies

You can use pip to install all packages required for this tutorial as follows:

!pip install sklearn
!pip install cleanlab
# Make sure to install the version corresponding to this tutorial
# E.g. if viewing master branch documentation:
#     !pip install git+https://github.com/cleanlab/cleanlab.git

import random
import numpy as np

SEED = 100

np.random.seed(SEED)
random.seed(SEED)

2. Load and process the data

We first load the data features and labels (which are possibly noisy).

from sklearn.datasets import fetch_openml

data = fetch_openml("credit-g", version=1)  # get the credit data from OpenML
X_raw = data.data  # features (pandas DataFrame)
labels_raw = data.target  # labels (pandas Series)

/opt/hostedtoolcache/Python/3.10.10/x64/lib/python3.10/site-packages/sklearn/datasets/_openml.py:968: FutureWarning: The default value of `parser` will change from `'liac-arff'` to `'auto'` in 1.4. You can set `parser='auto'` to silence this warning. Therefore, an `ImportError` will be raised from 1.4 if the dataset is dense and pandas is not installed. Note that the pandas parser may return different data types. See the Notes Section in fetch_openml's API doc for details.
  warn(

Next we preprocess the data. Here we apply one-hot encoding to features with categorical data, and standardize features with numeric data. We also perform label encoding on the labels — “bad” is encoded as 0 and “good” is encoded as 1.

import pandas as pd
from sklearn.preprocessing import StandardScaler

cat_features = X_raw.select_dtypes("category").columns
X_encoded = pd.get_dummies(X_raw, columns=cat_features, drop_first=True)

num_features = X_raw.select_dtypes("float64").columns
scaler = StandardScaler()
X_scaled = X_encoded.copy()
X_scaled[num_features] = scaler.fit_transform(X_encoded[num_features])

labels = labels_raw.map({"bad": 0, "good": 1})  # encode labels as integers

Bringing Your Own Data (BYOD)?

You can easily replace the above with your own tabular dataset, and continue with the rest of the tutorial.

Your classes (and entries of labels) should be represented as integer indices 0, 1, …, num_classes - 1.

For example, if your dataset has 7 examples from 3 classes, labels might look like: np.array([2,0,0,1,2,0,1])

3. Select a classification model and compute out-of-sample predicted probabilities

Here we use a simple histogram-based gradient boosting model (similar to XGBoost), but you can choose any suitable scikit-learn model for this tutorial.

from sklearn.ensemble import HistGradientBoostingClassifier

clf = HistGradientBoostingClassifier()

To find potential labeling errors, cleanlab requires a probabilistic prediction from your model for every datapoint. However, these predictions will be overfitted (and thus unreliable) for examples the model was previously trained on. cleanlab is intended to only be used with out-of-sample predicted probabilities, i.e., on examples held out from the model during the training.

K-fold cross-validation is a straightforward way to produce out-of-sample predicted probabilities for every datapoint in the dataset by training K copies of our model on different data subsets and using each copy to predict on the subset of data it did not see during training. An additional benefit of cross-validation is that it provides a more reliable evaluation of our model than a single training/validation split. We can obtain cross-validated out-of-sample predicted probabilities from any classifier via a simple scikit-learn wrapper:

from sklearn.model_selection import cross_val_predict

num_crossval_folds = 3  # for efficiency; values like 5 or 10 will generally work better
pred_probs = cross_val_predict(
    clf,
    X_scaled,
    labels,
    cv=num_crossval_folds,
    method="predict_proba",
)

4. Use cleanlab to find label issues

Based on the given labels and out-of-sample predicted probabilities, cleanlab can quickly help us identify poorly labeled instances in our data table. For a dataset with N examples from K classes, the labels should be a 1D array of length N and predicted probabilities should be a 2D (N x K) array. Here we request that the indices of the identified label issues be sorted by cleanlab’s self-confidence score, which measures the quality of each given label via the probability assigned to it in our model’s prediction.

from cleanlab.filter import find_label_issues

ranked_label_issues = find_label_issues(
    labels=labels, pred_probs=pred_probs, return_indices_ranked_by="self_confidence"
)

print(f"Cleanlab found {len(ranked_label_issues)} potential label errors.")

Cleanlab found 195 potential label errors.

Let’s review some of the most likely label errors:

X_raw.iloc[ranked_label_issues].assign(label=labels_raw.iloc[ranked_label_issues]).head()

	checking_status	duration	credit_history	purpose	credit_amount	savings_status	employment	installment_commitment	personal_status	other_parties	...	property_magnitude	age	other_payment_plans	housing	existing_credits	job	num_dependents	own_telephone	foreign_worker	label
949	no checking	24.0	existing paid	radio/tv	3621.0	100<=X<500	>=7	2.0	male single	none	...	car	31.0	none	own	2.0	skilled	1.0	none	yes	bad
175	no checking	30.0	all paid	used car	7485.0	no known savings	unemployed	4.0	female div/dep/mar	none	...	real estate	53.0	bank	own	1.0	high qualif/self emp/mgmt	1.0	yes	yes	bad
647	no checking	12.0	existing paid	new car	1386.0	500<=X<1000	1<=X<4	2.0	female div/dep/mar	none	...	life insurance	26.0	none	own	1.0	skilled	1.0	none	yes	bad
278	no checking	6.0	existing paid	furniture/equipment	4611.0	<100	<1	1.0	female div/dep/mar	none	...	life insurance	32.0	none	own	1.0	skilled	1.0	none	yes	bad
424	0<=X<200	12.0	existing paid	furniture/equipment	2762.0	no known savings	>=7	1.0	female div/dep/mar	none	...	life insurance	25.0	bank	own	1.0	skilled	1.0	yes	yes	bad

5 rows × 21 columns

These examples appear the most suspicious to our model and should be carefully re-examined. Perhaps the original annotators missed something when deciding on the labels for these individuals. This is a straightforward approach to visualize the rows in a data table that might be mislabeled.

5. Train a more robust model from noisy labels

Following proper ML practice, let’s split our data into train and test sets.

from sklearn.model_selection import train_test_split

X_train, X_test, labels_train, labels_test = train_test_split(
    X_encoded,
    labels,
    test_size=0.25,
    random_state=SEED,
)

We again standardize the numeric features, this time fitting the scaling parameters solely on the training set.

scaler = StandardScaler()
X_train[num_features] = scaler.fit_transform(X_train[num_features])
X_test[num_features] = scaler.transform(X_test[num_features])

X_train = X_train.to_numpy()
labels_train = labels_train.to_numpy()
X_test = X_test.to_numpy()
labels_test = labels_test.to_numpy()

Let’s now train and evaluate the original gradient boosting model.

from sklearn.metrics import accuracy_score

clf.fit(X_train, labels_train)
acc_og = clf.score(X_test, labels_test)
print(f"Test accuracy of original model: {acc_og}")

Test accuracy of original model: 0.748

cleanlab provides a wrapper class that can be easily applied to any scikit-learn compatible model. Once wrapped, the resulting model can still be used in the exact same manner, but it will now train more robustly if the data have noisy labels.

from cleanlab.classification import CleanLearning

clf = HistGradientBoostingClassifier()  # Note we first re-initialize clf
cl = CleanLearning(clf)  # cl has same methods/attributes as clf

The following operations take place when we train the cleanlab-wrapped model: The original model is trained in a cross-validated fashion to produce out-of-sample predicted probabilities. Then, these predicted probabilities are used to identify label issues, which are then removed from the dataset. Finally, the original model is trained on the remaining clean subset of the data once more.

_ = cl.fit(X_train, labels_train)

We can get predictions from the resulting model and evaluate them, just like how we did it for the original scikit-learn model.

preds = cl.predict(X_test)
acc_cl = accuracy_score(labels_test, preds)
print(f"Test accuracy of cleanlab-trained model: {acc_cl}")

Test accuracy of cleanlab-trained model: 0.752

We can see that the test set accuracy slightly improved as a result of the data cleaning. Note that this will not always be the case, especially when we evaluate on test data that are themselves noisy. The best practice is to run cleanlab to identify potential label issues and then manually review them, before blindly trusting any accuracy metrics. In particular, the most effort should be made to ensure high-quality test data, which is supposed to reflect the expected performance of our model during deployment.