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Hierarchical Confusion Matrix

This GitHub repository includes the implementation of the hierarchical confusion matrix in Python, that was proposed in [Riehl et al., 2023] Riehl, K., Neunteufel, M., Hemberg, M. (2023). Hierarchical confusion matrix for classification performance evaluation, Journal of the Royal Statistical Society Series C: Applied Statistics, 2023;, qlad057, https://doi.org/10.1093/jrsssc/qlad057

Hierarchical Confusion Matrix Examples

Table of Contents

  • File structure of this GitHub
  • Installation using Pip
  • Exemplary use
  • Citations

File structure of this GitHub

This GitHub consists of following parts...

  • HierarchicalConfusion.py that includes the implementation of hierarchical confusion matrix.
  • Four examples from the paper that show how to use the implementation and calculate evaluation measures based on the hierarchical confusion matrix.
    • Example_Figure4 (Example_Figure4.py)
    • Example_TransposonClassification (Example_TransposonClassification.py)
    • Example_GermEval2019_Task1A (Example_GermEval2019_Task1A.py)
    • Example_GermEval2019_Task1B (Example_GermEval2019_Task1B.py)
    • A folder CaseStudies that include the classification model predictions for the different examples.

Installation using Pip

pip install numpy networkx hierarchical-confusion-matrix

Exemplary use

Let us take the four examples from the figure above that was taken from the paper. The core method of the implementation determineHierarchicalConfusionMatrix(G, trueLabels, P_d) in HierarchicalConfusion.py needs three arguments, a graph, a list of true labels and a list of prediction paths. As a result, it returns a numpy array with four elements, including true positives (TP), true negatives (TN), false positives (FP) and false negatives (FN) in this order. For the first problem shown in Fig.4 (a), in which the true label is node "I", we can calculate the hierarchical confusion matrix for different predictions (x, 1, and 2) as follows:

# Imports
import networkx as nx
from hierarchical_confusion_matrix import determineHierarchicalConfusionMatrix, printHierarchicalConfusionMatrix

# Generate strucutre = tree graph
graph = nx.DiGraph()
graph.add_edges_from([("root", "A"), ("root", "B"), ("A", "C"), ("A", "D"), ("A", "E"), ("C", "H"), ("D","I"), ("D","J"), ("D","K"), ("E","L"), ("E","M"), ("B","F"), ("B","G")])

# Set true label(s)
true_labels = ["I"]

# Set prediction path(s)
p_d0 = [["root","A","D","I"]]
p_d1 = [["root","A","D","J"]]
p_d2 = [["root","A","E","L"]]

# Calculate hierarchical confusion matrix
confusion_matrix_a0 = determineHierarchicalConfusionMatrix(graph, true_labels, p_d0)
confusion_matrix_a1 = determineHierarchicalConfusionMatrix(graph, true_labels, p_d1)
confusion_matrix_a2 = determineHierarchicalConfusionMatrix(graph, true_labels, p_d2)

# Print results
printHierarchicalConfusionMatrix(confusion_matrix_a0, "Problem A, Prediction 0")
printHierarchicalConfusionMatrix(confusion_matrix_a1, "Problem A, Prediction 1")
printHierarchicalConfusionMatrix(confusion_matrix_a2, "Problem A, Prediction 2")

Console Output:

HierarchicalConfusionMatrix  Problem A, Prediction 0
	TP	 3
	TN	 5
	FP	 0
	FN	 0
HierarchicalConfusionMatrix  Problem A, Prediction 1
	TP	 2
	TN	 4
	FP	 1
	FN	 1
HierarchicalConfusionMatrix  Problem A, Prediction 2
	TP	 1
	TN	 2
	FP	 2
	FN	 2

Further examples for the other three problems of the Fig.4 can be found in Example_Figure4. These examples show the calculation of the hierarchical confusion matrix for one single object of a dataset.

Examples for the calculation of the hierarchical confusion matrix for multiple object predictions can be found in Example_TransposonClassification, Example_GermEval2019_Task1A, and Example_GermEval2019_Task1B.

Citations

Please cite our paper if you find hierarchical confusion matrix useful: [Riehl et al., 2023] Riehl, K., Neunteufel, M., Hemberg, M. (2023). Hierarchical confusion matrix for classification performance evaluation, Journal of the Royal Statistical Society Series C: Applied Statistics, 2023;, qlad057, https://doi.org/10.1093/jrsssc/qlad057