# Development of Symbolic Expressions Ensemble for Breast Cancer Type Classification Using Genetic Programming Symbolic Classifier and Decision Tree Classifier

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## Abstract

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## Simple Summary

## Abstract

## 1. Introduction

- Is it possible to apply dataset balancing methods to equalize the number of samples per class and in the end improve the classification accuracy of obtaining SEs?
- Is it possible to use GPSC with the random hyperparameter value selection (RHVS) method, and train using 5-fold cross validation (5CV) to obtain a set of SEs with high classification accuracy for each dataset class?
- Is it possible to combine obtained SEs to create a robust system with high classification accuracy?
- Is it possible to combine the SEs with the decision tree classifier to achieve high classification accuracy?

## 2. Materials and Methods

#### 2.1. Research Methodology

- Dimensionality reduction using PCA—reduction in the number of input variables.
- Application of different oversampling methods—the creation of datasets with an equal number of class samples.
- Application of GPSC with RHVS and training using 5CV—using each dataset in GPSC and trained using 5CV to obtain the set of SEs for each class; the RHVS method is used to find the optimal combination of hyperparameters with which the GPSC will generate SEs with high classification accuracy.
- Customized set of SEs—evaluation of the best SEs and creating a robust set of SEs.
- Final evaluation—application of customized set of SEs and SEs + DTC and evaluation on the original dataset.

#### 2.2. Dataset Description

- Large number of input variables (54,676 genes);
- Small number of dataset samples (151 samples);
- Large imbalance between class samples.

#### 2.2.1. PCA

#### 2.2.2. Target Variable Description and Transformation into Numerical Form

#### 2.3. Oversampling Methods

#### 2.3.1. BorderlineSMOTE

#### 2.3.2. SMOTE

#### 2.3.3. SVM SMOTE

#### 2.4. GPSC with RHVS

- The output of each population member has to be computed by providing values of input variables;
- The previous output is used in the sigmoid function to compute the output. The sigmoid function can be written in the following form:$$Sig\left(x\right)=\frac{1}{1+exp(-x)}.$$
- After the sigmoid output is computed, then the LogLoss function is used as the evaluation metric. The LogLoss function can be written as$$LogLoss=-\frac{1}{N}\sum _{i=1}^{N}\left({y}_{i}log{p}_{i}+(1-{y}_{i})log(1-{p}_{i})\right)$$

Hyperparameter Name | Range |
---|---|

SizePop | 1000–2000 |

DepthInit | 3–18 |

GenNum | 200–300 |

RangeConst | −10,000–10,000 |

SizeTour | 100–500 |

CritStop | ${10}^{-6}$–${10}^{-3}$ |

CrossValue | 0.001–0.3 |

HoistMute | 0.001–0.3 |

SubMute | 0.9–1.0 |

PointMute | 0.001–0.3 |

ParsCoef | ${10}^{-5}$–${10}^{-4}$ |

#### 2.5. Decision Tree Classifier

#### 2.6. Training Procedure

## 3. Results

#### 3.1. The Best Set of SEs Obtained on Dataset Balanced with BorderlineSMOTE

^{−5}); however, the parsimony pressure method has a different influence on these cases. For example, the parsimony coefficient ($4.08\times {10}^{-5}$) in the case of class 5 has a large influence since it generates the smallest SEs (average SE size 26.8). However, in the case of class 4, the parsimony coefficient ($3.98\times {10}^{-5}$) has a lower influence, generating larger SEs (average length 135.2). The largest range of constants is in the case of class 4 ($-3011.14$ and 9994.33). The four simple SEs obtained for class 5 (normal) in the 5CV process are written as

#### 3.2. The Best Set of SEs Obtained on Dataset Balanced with SMOTE

^{−5}) is very low to enable the growth of SEs during GPSC execution. However, in the case of class 4, the bloat phenomenon does occur since the GPSC generates a set of large SEs. The bloat also occurs for the first SE in the case of class 0. The problem with these two classes is that the GPSC execution is terminated after a maximum number of generations is reached and due to small parsimony pressure, the population members grow in size without any significant benefit to the fitness function.

#### 3.3. The Best Set of SEs Obtained on Dataset Balanced with SVMSMOTE

#### 3.4. Final Evaluation on the Original Dataset

- First approach—using sets of the best SEs to create an ensemble.
- Second approach—combine the outputs of the best SEs with the original dataset and use the dataset to train the decision tree classifier.

- For each SE in the ensemble provides input variable values to calculate the output. Use this output in the Sigmoid function (Equation (2)) to determine the binary value (0 or 1).
- Combines the output of all SEs for a class into one output. If there are 40 SEs for one class, i.e., 30 output values of at least half of the generated output values must be the same value so that the final output is correctly classified.
- After the combination of all ensemble SE outputs into one output array, apply ACC, AUC, precision, recall, and F1-score to compute the evaluation metric performance.

## 4. Discussion

## 5. Conclusions

- The dimensionality reduction method (PCA) can greatly reduce the number of input dataset variables.
- The oversampling methods have a great influence on the performance of the GPSC since high accuracy of the obtained SEs was achieved.
- The proposed methodology of training using the 5CV method generated a large set of SEs, and in combination with the decision tree, the classifier contributed to the robust system, which could be used for the accurate classification of the breast cancer type.
- The application of the developed RHVS method proved to be crucial in finding the optimal hyperparameter combination on each oversampled dataset and obtaining SEs obtained with this combination of GPSC hyperparameters achieved high classification accuracy.

- The method is great for solving datasets with a large number of input variables and a small number of samples.
- The benefit of utilizing the GPSC method is that after each training round, a SE is obtained that is easier to understand and process, i.e., requires low computational resources.
- The benefit of utilizing different oversampling methods is to obtain multiple sets of symbolic expressions, which could potentially solve overfitting that can occur due to the small number of dataset samples.

- Although the number of input dataset variables is reduced, the large number of dataset oversampling variations can prolong the time required to train GPSC on each dataset.
- The RHVS method found the optimal combination of GPSC hyperparameters on each oversampled dataset variation, which means each time a new dataset variation was utilized, a RHVS method was used to find the combination of hyperparameters for that dataset variation.
- Generally, a long time was required to find the optimal combination of GPSC hyperparameters using the RHVS method.

## Author Contributions

## Funding

## Institutional Review Board Statement

## Informed Consent Statement

## Data Availability Statement

## Conflicts of Interest

## Appendix A. Modification of Mathematical Functions

## Appendix B. SEs Obtained in This Research

- Use the initial dataset, perform standard scaling and the PCA dimensionality reduction method to obtain 144 input variables. Transform the target variable from string to integer form using ordinal encoder and then one-hot encoder to binarize each class integer, creating one array for each class (one-versus-rest approach).
- Use the dataset to calculate the output for each SE and use that output as the input value in the sigmoid function (Equation (2)) to determine the output class (0 or 1).

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**Figure 3.**The flowchart of the training and testing process using the GPSC algorithm with RHVS and 5CV method.

**Figure 4.**The mean and $\sigma $ evaluation metric values for best SEs sets obtained on each dataset class. The $\sigma $ values are shown as error bars.

**Figure 5.**The mean and $\sigma $ evaluation metric values of best sets of SEs obtained for each dataset class on dataset balanced with SMOTE method. The $\sigma $ values are shown as error bars.

**Figure 6.**The mean and $\sigma $ evaluation metric values of best sets of SEs obtained for each dataset class on the dataset balanced with SVMSMOTE method. The $\sigma $ values are shown as error bars.

**Figure 8.**Confusion matrix plots for each class. (

**a**) Confusion matrix of SEs ensemble for class 0 (HER). (

**b**) Confusion matrix of SEs ensemble for class 1 (basal). (

**c**) Confusion matrix of SEs ensemble for class 2 (cell line). (

**d**) Confusion matrix of SEs ensemble for class 3 (luminal A). (

**e**) Confusion matrix of SEs ensemble for class 4 (luminal B). (

**f**) Confusion matrix of SEs ensemble for class 5 (normal).

**Figure 9.**The DTC performance on the original imbalanced dataset in terms of evaluation metric values.

**Figure 10.**Confusion matrix plots for each class. (

**a**) Confusion matrix of DTC for class 0 (HER). (

**b**) Confusion matrix of DTC for class 1 (basal). (

**c**) Confusion matrix of DTC for class 2 (cell line). (

**d**) Confusion matrix of DTC for class 3 (luminal A). (

**e**) Confusion matrix of DTC for class 4 (luminal B). (

**f**) Confusion matrix of DTC for class 5 (normal).

Reference | Reduction Methods | AI Methods | Results |
---|---|---|---|

[4] | ACOC5 | DT, SVM, KNN, RF | ACC: 0.954 |

[5] | IGAG | FLNN | ACC: 0.856 |

[6] | MRMD, PCA | RFC | ACC: 0.913 |

[7] | CFS-PSO | Naive-Bayes | ACC: 0.927 |

[8] | CMIM-AGA | ELM, SVM, KNN | ACC:0.903 |

[9] | MIMAGA | ELM | ACC:0.952 |

[10] | MCSO | RR, OSRR, SVMRBF, SVM Poly, and KRR | ACC: 0.966 |

[11] | SUF-HSA | IBL | ACC: 0.833 |

[12] | hybrid Feature Selection sequential framework consisting of minimum Redundancy-Maximum Relevance, two-tailed unpaired t-test, and meta-heuristics | SVM, KNN, ANN, NB, DT, XGBoost | ACC: 0.976 |

**Table 2.**The original class names and their integer representation after application of ordinal encoder.

Class Original Name | Integer Representation |
---|---|

HER | 0 |

basal | 1 |

cell_line | 2 |

luminal A | 3 |

luminal B | 4 |

normal | 5 |

**Table 3.**The class labels in integer form with the number of samples of target variable for that class label created after the application of one-hot encoder.

Class Labels | Label 0 | Label 1 |
---|---|---|

0 | 121 | 30 |

1 | 110 | 41 |

2 | 137 | 14 |

3 | 122 | 29 |

4 | 121 | 30 |

5 | 144 | 7 |

**Table 4.**The comparisons of a number of samples per class before and after the application of oversampling methods.

Oversampling Method | Class 0 vs. Rest | Class 1 vs. Rest | Class 2 vs. Rest | Class 3 vs. Rest | Class 4 vs. Rest | Class 5 vs. Rest |
---|---|---|---|---|---|---|

Original Dataset | 30, 120 | 41, 110 | 14, 137 | 29, 122 | 30, 121 | 7, 144 |

BorderlineSMOTE | 121, 121 | 110, 110 | 14, 137 | 29, 122 | 121, 121 | 141, 141 |

SMOTE | 121, 121 | 110, 110 | 137, 137 | 122, 122 | 121, 121 | 144, 144 |

SVMSMOTE | 121, 121 | 110, 110 | 69, 137 | 71, 122 | 121, 121 | 144, 144 |

DTC Hyperparameter | Value |
---|---|

criterion | ‘gini’ |

splitter | best |

max_depth | None |

min_samples_split | 2 |

**Table 7.**The list of GPSC hyperparameters used to obtain SEs with the SE length and average length for each class on datasets balanced with BorderlineSMOTE.

Dataset Class | GPSC Hyperparameters | SEs Length | Average Length |
---|---|---|---|

0 | 1305, 286, 320, (6, 12), 0.027, 0.92, 0.0034, 0.047, 0.000849, 0.992, ($-8472.53$, 6538.77), $5.84\times {10}^{-5}$ | 57/106/109/61/59 | 78.4 |

1 | 1773, 255,115,(5, 15), 0.028, 0.95, 0.013, 0.001, 0.000761, 0.99, ($-6536.37$, 3.62), $6.18\times {10}^{-5}$ | 51/66/91/100/304 | 122.4 |

4 | 1467, 208, 206, (7, 14), 0.028, 0.95, 0.0067, 0.013, 0.00067, 0.998, ($-3011.14$, 9994.33), $3.98\times {10}^{-5}$ | 86/214/140/92/144 | 135.2 |

5 | 1636, 208, 235, (6, 14), 0.013, 0.95, 0.027, 0.0014, 0.00047, 0.99, ($-2166.54$, 2091.41), $4.08\times {10}^{-5}$ | 74/17/25/11/7 | 26.8 |

**Table 8.**The optimal combination of GPSC hyperparameter values used to obtain the best SEs, their length, and average length for each dataset class balanced with SMOTE.

Dataset Class | GPSC Hyperparameters | SEs Length | Average Length |
---|---|---|---|

0 | 1689, 242, 229, (7, 9), 0.021, 0.95, 0.024, 0.0018, 0.000128, 0.9999, ($-3476.2$, 4881.51), $7.1\times {10}^{-5}$ | 322/99/103/70/28 | 124.4 |

1 | 1333, 238, 492, (5, 18), 0.015, 0.9, 0.058, 0.02, 0.000257, 0.99, ($-3806.57$, 9422.75), $6.96\times {10}^{-5}$ | 68/42/82/34/82 | 61.6 |

2 | 1981, 242, 322, (4, 16), 0.034, 0.9, 0.0036, 0.06, 0.000926, 0.99, ($-6987.74$, 606.08), $6.33\times {10}^{-5}$ | 82/18/21/22/86 | 45.8 |

3 | 1927, 284, 196, (7, 14), 0.18, 0.52, 0.026, 0.25, 0.0009, 0.99, ($-9471.025$, 7889.12) $9.65\times {10}^{-5}$ | 77/128/42/57/33 | 67.4 |

4 | 1587, 285, 170, (7, 10), 0.044, 0.032, 0.095, 0.82, 0.000912, 0.99, ($-3146.31$, 7425.75), $8.62\times {10}^{-5}$ | 391/944/191/155/81 | 352.4 |

5 | 1818, 292, 179, (7, 18), 0.045, 0.93, 0.0084, 0.012, 0.000295, 0.99, ($-8427.52$, 7910.95), $5.0\times {10}^{-5}$ | 27/18/51/18/17 | 26.2 |

**Table 9.**The optimal combination of GPSC hyperparameters used to obtain best SEs with their length and average length for each dataset class balanced with SVMSMOTE.

Dataset Class | GPSC Hyperparameters | SEs Length | Average Length |
---|---|---|---|

0 | 1487, 226, 140, (7, 18), 0.015, 0.95, 0.011, 0.017, 0.000373, 0.99, ($-7056.42$, 2732.52), $9.46\times {10}^{-5}$ | 47/41/58/98/82 | 65.2 |

1 | 1384, 213, 429, (5, 16), 0.013, 0.96, 0.017, 0.003, 0.000193, 0.99, ($-7609.64$, 4173.5), $9.83\times {10}^{-5}$ | 249/66/103/302/185 | 181 |

4 | 1393, 201, 113, (4, 8), 0.017, 0.97, 0.0019, 0.0027, 0.000675, 0.99, ($-2655.73$, 7489.67), $7.48\times {10}^{-5}$ | 138/52/68/294/147 | 138.8 |

5 | 1263, 211, 103, (6, 9), 0.011, 0.92, 0.06, 0.0034, 0.00028, 0.99, ($-5354.17$, 5345.63), $1.409\times {10}^{-5}$ | 96/10/11/91/77 | 57 |

**Table 10.**Final evaluation metric mean values obtained based on values shown in Figure 7.

Evaluation Metric | Value |
---|---|

$\overline{ACC}$ | 0.992 |

$\overline{AUC}$ | 0.995 |

$\overline{Precision}$ | 0.966 |

$\overline{Recall}$ | 1.0 |

$\overline{F1-Score}$ | 0.9825 |

Evaluation Metric | Value |
---|---|

$\overline{ACC}$ | 0.994 |

$\overline{AUC}$ | 0.993 |

$\overline{Precision}$ | 0.984 |

$\overline{Recall}$ | 0.99 |

$\overline{F1-Score}$ | 0.987 |

Reference | Reduction Methods | AI Methods | Results |
---|---|---|---|

[4] | ACOC5 | DT, SVM, KNN, RF | ACC: 0.954 |

[5] | IGAG | FLNN | ACC: 0.856 |

[6] | MRMD, PCA | RFC | ACC: 0.913 |

[7] | CFS-PSO | Naive-Bayes | ACC: 0.927 |

[8] | CMIM-AGA | ELM, SVM, KNN | ACC: 0.903 |

[9] | MIMAGA | ELM | ACC: 0.952 |

[10] | MCSO | RR, OSRR, SVMRBF, SVM Poly, and KRR | ACC: 0.966 |

[11] | SUF-HSA | IBL | ACC: 0.833 |

[12] | hybrid Feature Selection sequential framework consisting of minimum Redundancy-Maximum Relevance, two-tailed unpaired t-test, and meta-heuristics | SVM, KNN, ANN, NB, DT, XGBoost | ACC: 0.976 |

This paper | PCA + oversampling methods (BorderlineSMOTE, SMOTE, and SVMSMOTE) | GPSC GPSC + DTC | ACC: 0.992 ACC: 0.994 |

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## Share and Cite

**MDPI and ACS Style**

Anđelić, N.; Baressi Šegota, S.
Development of Symbolic Expressions Ensemble for Breast Cancer Type Classification Using Genetic Programming Symbolic Classifier and Decision Tree Classifier. *Cancers* **2023**, *15*, 3411.
https://doi.org/10.3390/cancers15133411

**AMA Style**

Anđelić N, Baressi Šegota S.
Development of Symbolic Expressions Ensemble for Breast Cancer Type Classification Using Genetic Programming Symbolic Classifier and Decision Tree Classifier. *Cancers*. 2023; 15(13):3411.
https://doi.org/10.3390/cancers15133411

**Chicago/Turabian Style**

Anđelić, Nikola, and Sandi Baressi Šegota.
2023. "Development of Symbolic Expressions Ensemble for Breast Cancer Type Classification Using Genetic Programming Symbolic Classifier and Decision Tree Classifier" *Cancers* 15, no. 13: 3411.
https://doi.org/10.3390/cancers15133411