PertCF

PertCF is a perturbation-based counterfactual explanation method that combines SHAP feature attribution with nearest-neighbour search to generate high-quality, stable counterfactuals for tabular classification models.

What is a counterfactual explanation?
Given a model's prediction for an instance x, a counterfactual x' is the minimal change to x that would flip the prediction. For example: "If Leo earned $500 more per month, his loan application would be accepted."

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Why PertCF?

Feature	PertCF	DiCE	CF-SHAP
Multi-class support	✅	❌	❌
SHAP-weighted distance	✅	❌	Partial
Custom domain knowledge	✅	❌	❌
Works with sklearn, PyTorch, Keras	✅	Partial	❌
No external server needed	✅	✅	✅

PertCF outperforms DiCE and CF-SHAP on dissimilarity and instability across both benchmark datasets (South German Credit, User Knowledge Modeling). See the paper for full results.

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Installation

pip install pertcf

For PyTorch or Keras model support:

pip install pertcf[torch]      # + PyTorch adapter
pip install pertcf[tensorflow] # + Keras/TF adapter
pip install pertcf[viz]        # + matplotlib/seaborn for plots

Requirements: Python ≥ 3.9, numpy, pandas, scikit-learn, shap.
No Java. No REST server. No external frameworks.

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Quick Start (30 seconds)

import pandas as pd
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.model_selection import train_test_split
from pertcf import PertCFExplainer

# 1. Load data and train a model (example: German Credit dataset)
df = pd.read_csv("german_credit.csv")
X = df.drop(columns=["credit_risk"])
y = df["credit_risk"]

X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)
clf = GradientBoostingClassifier(random_state=42).fit(X_train, y_train)

# 2. Create and fit the explainer
explainer = PertCFExplainer(
    model=clf,
    X_train=X_train,
    y_train=y_train,
    categorical_features=["purpose", "personal_status", "housing"],
    label="credit_risk",
    num_iter=5,
    coef=5,
)
explainer.fit()

# 3. Explain a prediction
instance = X_test.iloc[0].copy()
instance["credit_risk"] = clf.predict(X_test.iloc[[0]])[0]

counterfactual = explainer.explain(instance)
print("Original:       ", instance.to_dict())
print("Counterfactual: ", counterfactual.to_dict())

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Feature Highlights

Works with any classifier

# scikit-learn (auto-detected)
from sklearn.ensemble import RandomForestClassifier
explainer = PertCFExplainer(model=RandomForestClassifier().fit(X, y), ...)

# PyTorch
from pertcf import PertCFExplainer
explainer = PertCFExplainer(
    model=my_torch_model,
    class_names=["bad", "good"],
    ...
)

# Keras / TensorFlow
explainer = PertCFExplainer(
    model=my_keras_model,
    class_names=["bad", "good"],
    ...
)

# Any callable
explainer = PertCFExplainer(
    model=my_model,
    predict_fn=lambda X: my_model.predict(X),
    predict_proba_fn=lambda X: my_model.predict_proba(X),
    class_names=["bad", "good"],
    ...
)

Domain knowledge via custom similarity matrices

# Model the relationship between credit purposes
explainer = PertCFExplainer(
    model=clf,
    ...
    similarity_matrices={
        "purpose": {
            ("car", "furniture"): 0.7,   # similar purposes
            ("car", "education"): 0.2,   # less similar
        }
    }
)

Pre-computed SHAP values (for large datasets)

import shap
# Compute SHAP once, reuse across experiments
shap_exp = shap.TreeExplainer(clf)
shap_vals = shap_exp.shap_values(X_train)
# … build shap_df with shape (n_classes, n_features) …

explainer = PertCFExplainer(
    model=clf, shap_values=shap_df, ...
)
explainer.fit()  # skips SHAP computation

Built-in benchmark

# Reproduce the paper's Table 2 results
results = explainer.benchmark(X_test, n=100, coef=5, verbose=True)
# Results (n=100/100):
#   dissimilarity       : 0.0517
#   sparsity            : 0.7983
#   runtime_mean        : 0.4069

Evaluation metrics

from pertcf import metrics

print(metrics.dissimilarity(query, cf, explainer.sim_fn, cf_class))
print(metrics.sparsity(query, cf))
print(metrics.instability(query, cf, explainer))

# All at once:
results = metrics.evaluate(queries, counterfactuals, explainer)

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How PertCF Works

1. Compute SHAP values per class → class-specific feature importance weights
2. For query x:
   a. Find Nearest Unlike Neighbour (NUN) using SHAP-weighted similarity
   b. Perturb x toward NUN using SHAP weights:
      - Numeric:     p_f = x_f + shap_target_f * (nun_f - x_f)
      - Categorical: p_f = nun_f  if sim(x_f, nun_f) < 0.5  else  x_f
   c. If perturbed instance flips class → refine (approach source)
   d. If not → push harder (approach target)
   e. Terminate when step size < threshold or max iterations reached

See the paper for full algorithmic details.

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Examples

Notebook	Dataset	Description
quickstart_german_credit.ipynb	South German Credit	Basic usage, benchmark, comparison to DiCE
quickstart_knowledge.ipynb	User Knowledge Modeling	Multi-class classification
custom_similarity.ipynb	German Credit	Domain knowledge with custom similarity matrices

Launch in Colab:

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Parameter Guide

Parameter	Default	Description
num_iter	10	Max perturbation iterations. Higher → better quality, slower.
coef	5	Step-size threshold coefficient. Higher → finer convergence.

Recommended settings from the paper:

Dataset	num_iter	coef	Notes
South German Credit	5	5	Most categorical features
User Knowledge Modeling	5	3	All numeric features

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Citation

If you use PertCF in your research, please cite:

@inproceedings{bayrak2023pertcf,
  title     = {PertCF: A Perturbation-Based Counterfactual Generation Approach},
  author    = {Bayrak, Bet{\"u}l and Bach, Kerstin},
  booktitle = {Artificial Intelligence XXXVIII},
  series    = {Lecture Notes in Computer Science},
  volume    = {14381},
  pages     = {174--187},
  year      = {2023},
  publisher = {Springer, Cham},
  doi       = {10.1007/978-3-031-47994-6_13}
}

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License

MIT © Betül Bayrak

This work was supported by the Research Council of Norway through the EXAIGON project (ID 304843).