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OPEN Predictive modeling for breast

cancer classification in the context
of Bangladeshi patients by use
of machine learning approach
with explainable AI
Taminul Islam 1, Md. Alif Sheakh 2, Mst. Sazia Tahosin 2, Most. Hasna Hena 2, Shopnil Akash 3,
Yousef A. Bin Jardan 4, Gezahign FentahunWondmie 5*, Hiba‑Allah Nafidi 6 &
Mohammed Bourhia 7*

Breast cancer has rapidly increased in prevalence in recent years, making it one of the leading causes
of mortality worldwide. Among all cancers, it is by far the most common. Diagnosing this illness
manually requires significant time and expertise. Since detecting breast cancer is a time-consuming
process, preventing its further spread can be aided by creating machine-based forecasts. Machine
learning and Explainable AI are crucial in classification as they not only provide accurate predictions
but also offer insights into how the model arrives at its decisions, aiding in the understanding and
trustworthiness of the classification results. In this study, we evaluate and compare the classification
accuracy, precision, recall, and F1 scores of five different machine learning methods using a primary
dataset (500 patients from Dhaka Medical College Hospital). Five different supervised machine
learning techniques, including decision tree, random forest, logistic regression, naive bayes, and
XGBoost, have been used to achieve optimal results on our dataset. Additionally, this study applied
SHAP analysis to the XGBoost model to interpret the model’s predictions and understand the impact
of each feature on the model’s output. We compared the accuracy with which several algorithms
classified the data, as well as contrasted with other literature in this field. After final evaluation, this
study found that XGBoost achieved the best model accuracy, which is 97%.

Keywords Breast cancer prediction, Machine learning, Cancer prediction, Hyperparameter tuning,
Explainable AI

Breast cancer begins when some cells in the breast start to grow uncontrollably, forming a mass called a t­ umor1.
A breast cancer diagnosis typically falls into one of two main categories—benign (non-cancerous) or malignant
(cancerous). Malignant tumors are dangerous as they can spread to distant sites in the body through the blood-
stream or lymph system, a process known as ­metastasis2,3. Figure 1a illustrates the distinction between benign
and malignant tumors in terms of the normal cells and tumor cells, and (b) shows the benign and malignant
masses. Benign tumors generally stay localized in one area and do not metastasize. Breast cancer manifests
through several symptoms—a noticeable lump or mass in the breast, changes in breast size or shape compared
to the other breast, alterations in the skin overlying the breast like dimpling or puckering, newly inverted nipple,
redness or scaliness of breast skin, breast pain, and nipple discharge other than breast m ­ ilk4.
Breast cancer is the second largest killer of women after cardiovascular disease. And more than 8% of women
will experience it. Every year, more than 500,000 women are diagnosed with breast cancer, as stated in the

1
School of Computing, Southern Illinois University Carbondale, Carbondale, IL, USA. 2Department of Computer
Science and Engineering, Daffodil International University, Dhaka, Bangladesh. 3Department of Pharmacy, Faculty
of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh. 4Department of Pharmaceutics,
College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia. 5Department of Biology, Bahir
Dar University, P.O. Box 79, Bahir Dar, Ethiopia. 6Department of Food Science, Faculty of Agricultural and Food
Sciences, Laval University, 2325, Quebec City, QC G1V 0A6, Canada. 7Laboratory of Biotechnology and Natural
Resources Valorization, Ibn Zohr University, 80060 Agadir, Morocco. *email: [email protected]

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Figure 1.  Visualization of breast cancer: (a) benign and malignant tumor cells, (b) benign and malignant
masses.

World Health Organization’s annual r­ eport5. In developing countries, due to a lack of screening programs and
awareness, women often present at an advanced stage where treatment options are limited. Known risk factors
for breast cancer include genetic mutations in BRCA genes, reproductive history (nulliparity, early menarche,
late menopause), hormonal factors (use of hormone replacement therapy, oral contraceptives), obesity, alcohol
consumption, smoking, radiation exposure at a young age and family h ­ istory6.
Many people were affected by cancer during this period. We can’t pinpoint the origin of the sickness since it’s
tied to factors beyond our control. This is also a screening technique for identifying the cancer’s aggressiveness.
Several assessment items are connected to cancer detection, including clamp thickness, cell size consistency,
and shape regularity. The outcome is difficult even for those tasked with inspiring others to take action, and yet
the use of machine learning and other computer science techniques as general diagnostic tools has expanded
in recent years. Countless numbers of people’s lives have been saved by computer diagnostic programs that use
diseases that have killed millions. In the realm of surgery, robotics is indispensable. Aside from other artificial
intelligence’s widespread usage in cancer detection, the system deployed in the intensive care unit is highly
­effective7. One in eight American females may get cancer between the ages of 15 and 1­ 98. Breast cancer is the
result of unchecked cell division, which can also cause breasts to sag (called tumors)9. In most cases, the tumor
poses no health risk. The necessity for precise categorization in the clinic may be a severe challenge for doctors
and health workers, especially when the correct identification of the determinants might contribute to survival,
regardless of whether the condition is benign or malignant.
The diagnosis of breast cancer involves a step-wise approach starting with a thorough clinical examination and
radiological tests like mammograms and breast ultrasounds. This may be followed by tissue sampling through
fine needle aspiration cytology (FNAC) or biopsy from suspicious areas and microscopic assessment to confirm
­malignancy10. As symptoms of breast cancer can be non-specific with wide variation across patients, the combina-
tion of these investigations is needed for accurate diagnosis in the majority of cases. So, to monitor and diagnose
diseases, a human observer must be able to pick out very particular signal features. Due to the large number of
patients in the critical care unit and the need for round-the-clock monitoring, several CAD a­ pproaches11 for
computer-aided medical systems have emerged in the recent decade to meet this issue. With these strategies, the
challenge of classifying quantitative features may be posed rather than relying on qualitative diagnostic criteria.
Machine learning algorithms can predict breast cancer diagnosis and p ­ rognosis12. The purpose of this work is
to evaluate the efficacy and performance of these algorithms in terms of their accuracy, sensitivity, range, and
precision. In the past 25 years, the importance of artificial intelligence has i­ ncreased13. As scientists realize the
importance of making firm decisions about how to treat certain diseases, the use of computers and machine learn-
ing as diagnostic tools has become deadly, which is the most serious disease screening task in the medical ­field14.
One of the most important functions of disease is the definition of cancer. Using machine learning technology,
doctors can detect, identify, and classify tumors as benign or malignant. There are some challenges in analyzing
patient data and choosing doctors and specialists, but cognitive systems and computational methods (such as ML
for classification) will ultimately help doctors and ­professionals15. However, as machine learning models become
more complex, there is a need for Explainable AI (XAI) techniques to interpret these models and understand how
they arrive at their predictions. Explainable AI methods like SHAP (SHapley Additive exPlanations) can shed
light on how different features contribute to a model’s output, increasing trust and transparency in the model’s
decision-making ­process16. In this study, we employ SHAP analysis on our best performing XGBoost model to
explain its predictions and understand which factors have the greatest impact on determining if a patient has
early-stage breast cancer or not. This study makes several key contributions to the prediction of early-stage breast
cancer using supervised machine learning approaches:

• Employing hyperparameter tuning to optimize each machine learning algorithm and enhance performance.

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• Utilizing a primary dataset for algorithm evaluation.

• Demonstrating that XGBoost achieved the highest accuracy of 97% and F1 score of 0.96, surpassing other
algorithms.
• Conducting SHAP analysis on the XGBoost model to interpret its predictions and comprehend the impact
of each feature on the model’s output.

Literature review
Every day, the medical sector discovers new machine learning applications. The development is beneficial to
scientific research. There is an abundance of research being conducted on this topic. Several research articles
pertinent to our study have been uncovered. This project aims to provide a mechanism for predicting breast
cancer. The majority of the dataset was obtained from the Dhaka Medical College Hospital. During this study,
we were exposed to a few novel methodologies. Not a straightforward undertaking on our end. This notion will
be discussed in further detail in the next chapter. To completely apply this study and to learn this new term, we
examined prior research about the prediction of heart attacks.
Using their model, V. Chaurasia and T. Pal determined which machine learning algorithms performed the
best in predicting breast cancer. In their study, they used Support Vector Machine (SVM), Naive Bayes (NB),
Radial basis function Neural Networks (RBF NN), Decision Tree (DT), and a simplified version of Classification
and Regression Trees (CART)17. After adopting their successful model, they obtained the highest Area Under
the Curve (AUC) (96.84%) using Support Vector Machine on the original Wisconsin Breast Cancer datasets.
Djebbari et al.18 evaluated if a machine learning ensemble might predict breast cancer survival time. Their
breast cancer dataset they achieve a greater rate of accuracy using their technique than was seen in previous
studies. S. Aruna and L. Nandakishore examine the performance of Decision Tree, Support Vector Machine,
Naive Bayes, and K-Nearest Neighbors (K-NN) for classifying White Blood Cell (WBC)19. Their top Support
Vector Machine classifier AUC was 96.99%.
M. Angrap used six machine learning techniques to categorize tumor cells. Gated Recurrent Unit, a variant
of the long short-term memory neural network, was created and implemented Gated recurrent unit (GRU). The
SoftMax layer of the neural network was switched out for a layer of Support Vector Machine. With an accuracy of
99.04%, GRU Support Vector Machine performed best in that ­study20. Cross-validation was used by Karabatak
et al.21 to improve the accuracy of a model trained with association rules and a neural network to 95.6%. Naive
Bayes classifiers were utilized, using a novel weight adjustment method.
Mohebian et al.22 looked at the feasibility of using ensemble learning to foretell cancer recurrence. Three
machine learning models that performed very well when fed a relevance vector were compared and contrasted
by Gayathri et al.23. Payam et al.24 employed a number of methods for preprocessing and data reduction, includ-
ing a radial basis function network (RBFN), to achieve their goals.
Using information from breast cancer studies reported i­ n25, researchers created survival prediction models.
In this study, they have used survival prediction methods to both benign and malignant tumor of breast cancers.
Extensive historical research shows that machine learning algorithms for breast cancer diagnosis have been
investigated at length, as illustrated ­in26. They suggested that data augmentation strategies might help address
the problem of having insufficient data. I­ n27, the authors showed how to automatically detect and identify cell
structure using features of computer-aided mammography images. Many different methods of categorization
and clustering have been evaluated, as reported ­in28.
Fatih Muhammed and ­Ak29 compared detection and diagnosis of breast cancer using data visualization and
machine learning. Using Dr. William H. Walberg’s breast tumor data, they used a variety of techniques includ-
ing Logistic Regression (LR), nearest neighbor (NN), Support Vector Machine, simple Bayes, Decision Tree,
random forest (RF), and convolutional forest using R, Minitab, and Python. Logistic regression with all features
achieved the highest accuracy (98.1%), indicating high performance. Their research showed the benefits of data
visualization and machine learning in cancer diagnosis, opening up new opportunities for cancer diagnosis.
Md. Islam et al.30 compared five supervised machine learning methods for breast cancer prediction using the
Wisconsin Breast Cancer Database. These methods include Support Vector Machine, Nearest Neighbor, Random
Forest, Artificial neural networks (ANN), and Logistic regression. ANNs outperformed others by achieving the
highest accuracy (98.57%), precision (97.82%) and F1 score (0.9890). The researchers concluded that machine
learning for disease detection could provide medical staff with reliable and rapid responses to reduce the risk
of death.
Vikas Chaurasia and Saurabh ­Pal31 used machine learning to predict breast cancer using the Wisconsin Diag-
nostic Breast Cancer Database. They compared six algorithms, reduced features to 12 using statistical methods,
and used ensemble methods to combine models. The results show that all the algorithms performed well, with
a test accuracy of over 90%, especially in the refined feature section. His contributions include the use of feature
selection and ensemble methods to improve breast cancer prediction accuracy.
Kabiraj et al.32 Creating a breast cancer risk prediction model using Extreme Gradient Boosting (XGBoost)
and Random Forest algorithms. The dataset used is from the UCI Machine Learning Repository. This approach
includes the use of Random Forest and XGBoost methods, and the model achieves a classification accuracy of
74.73%.
Meerja Jabbar et al.33 proposed a new ensemble method using Bayesian Network and Radial Basis function
to classify breast cancer data. This method achieves 97% accuracy, better than existing approaches. The trial was
conducted on the Wisconsin Breast Cancer Dataset (WBCD) using a variety of metrics to measure performance.
The proposed ensemble study can help cancer specialists make accurate tumor diagnoses and support patients
in making treatment decisions.

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Shalini and R ­ adhika34 are working to predict breast cancer using different machine learning techniques.
They use the UCI machine learning database and use artificial neural networks, Decision Tree, Support Vector
Machine and Naive Bayes algorithms. As a result, a classification accuracy of 86% was found.
Naji et al.35 Machine learning algorithms are used to predict and diagnose breast cancer. They compared five
different algorithms, including Support Vector Machine, Random Forest, Logistic regression, Decision Tree
(C4.5), and KNN, using the Wisconsin breast cancer diagnostic database. The main goal is to determine the
best algorithm for breast cancer diagnosis. The results revealed that the support vector machine outperformed
the other classifiers and achieved the highest accuracy of 97.2%. Research conducted with the Scikit learning
library in the Anaconda Python environment contributes important insights to update breast cancer therapy
and improve patient safety standards.
Puja Gupta and Shruti ­Garg36 investigated breast cancer prognosis using six supervised machine learning
algorithms and deep learning. The study includes a parametric analysis of each algorithm to achieve greater
accuracy. The data set used in the study is not mentioned. The article describes data pre-processing, machine
learning algorithms and their key parameters. Their research results show that deep learning using Human Gra-
dient Descent Learning is the most accurate with an accuracy rate of 98.24%. The paper concludes that proper
hyperparameter machine learning tools can help identify tumors effectively.

Methodology
This research aims to anticipate breast cancer and achieve the highest level of precision possible. To run the
model, we first build the dataset and choose which methods to employ. Supervised ­Learning37 and Unsupervised
­Learning38 are two techniques to develop a method in machine learning algorithms. We employed supervised
machine learning methods in this study. In supervised learning, some classification methods are utilized to
address classification issues. We employed the Decision Tree, Random Forest, Logistic Regression, Naïve Bayes,
and XGBoost method in this study. In the forthcoming part on the suggested technique, we will explore all of
the algorithms, how they function, and which one is the best, and we will attempt to determine which algorithm
produces the best results based on the data set we gathered. After the model demonstrated robust predictive
accuracy and generalization capability, we performed explainable AI using SHAP to interpret the model’s predic-
tions and understand the impact of each feature on the model’s output.

Dataset description
In this research, we have gathered a total of 500 patient’s information from a government hospital in Bangladesh
known as Dhaka Medical College Hospital. In this dataset, seven features were extracted from the image by
Dhaka Medical College Hospital experts. The data has been used in this research with the consent of all patients.
The dataset features are given below with a short description in Table 1. According to Fig. 2, the data shows
254 noncancerous cases, while the remaining 246 cases are considered to be cancerous. Table 1, shows a short
description of our dataset:
In this research we considered geometric features and age for the classification because geometric features,
such as shape irregularity and size, play a crucial role in identifying abnormal growth patterns associated with
malignant tumors. On the other hand, Age is a significant factor as breast cancer incidence increases with age,

Label of the Dataset Description

age From 22 to 55 years women data is collected here
mean_radius The average of the radius of the tumor cells
mean_texture The average of the gray-scale values in the texture of the tumor cells
mean_perimeter The average size of the tumor cell’s boundary
mean_area The average area of the tumor cells
mean_smoothness The average smoothness of the tumor cell’s surface
diagnosis The classification of the breast tissue as benign is 0 or malignant is 1

Table 1.  Short description of our dataset.

Figure 2.  Ratio of malignant and benign data based on overall dataset.

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and the disease can manifest differently in younger versus older patients. By incorporating these features into our
classification model, we aim to capture the distinct characteristics of benign and malignant tumors, improving the
accuracy of our predictions. The full dataset was considered throughout the analysis of the dataset. It is seen in
Fig. 3 that the mean radius of the dataset is a counterpoint. Patients believed to have cancer have a radius bigger
than 1, whereas those without symptoms have a radius nearer to 1. The full dataset was considered throughout
the analysis of the dataset. It is seen in Fig. 3 that the mean radius of the dataset is a counterpoint. Patients
believed to have cancer have a radius bigger than 1, whereas those without symptoms have a radius nearer to 1.

Proposed model workflow

The model workflow proposed in Fig. 4 includes several steps, such as collecting the dataset, performing data
preprocessing, splitting the data into 80% training and 20% testing sets, selecting the most relevant features,
selecting a suitable supervised machine learning algorithm, classifying the samples into benign tumor or malig-
nant tumor classes, and evaluating the model’s performance. The initial step is to obtain the dataset needed to
train the model. Once we obtain the dataset, we preprocess it by cleaning and translating the raw data into a
machine-learning-friendly format. Following that, we divided the preprocessed dataset into two subsets: one for
training and another for testing the model. After splitting, we select the most appropriate supervised machine
learning method, which is a Random Forest classifier, Decision Tree, XGBoost, Naive Bayes, and Logistic Regres-
sion, and train this on the features. After training the model, we use it to categorize new samples into benign or
malignant groups. Finally, we test the model’s performance using several measures like AUC, precision, recall,
F1 score, and accuracy. During the training process, the model acquired the ability to identify and differentiate
patterns and features that are indicative of malignant and benign instances of breast cancer, thereby enhancing

Figure 3.  Mean radius of this work on our dataset.

Figure 4.  Visualizing the workflow of the proposed model.

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its predictive capability. The performance of the model on the validation set was consistently monitored, and
iterative fine-tuning was conducted until satisfactory results were achieved. After the model demonstrated robust
predictive accuracy and generalization capability, we performed explainable AI using SHAP to interpret the
model’s predictions and understand the impact of each feature on the model’s output. Additionally, we proceeded
to implement the k-fold cross-validation technique. This proposed method ensures that the model is well-trained,
correctly classifies samples, and performs optimally.

Data preprocessing
To make it suitable for machine learning we do cleaning and transforming raw data. This includes handling null
values, scaling features using a standard scaler, encoding categorical variables, and normalizing data. The goal is
to prepare data by improving the performance and efficiency of machine learning models.

Data splitting
After preprocessing we divided the dataset into a training set and a testing set. Here we use a common split
ratio of 80:20, where 80% of the data is used to train the model and 20% is reserved for evaluating the model’s
performance. This ensures that the generalization ability of the model can be evaluated and prevents overfitting
of the training data.

Machine learning model

Machine learning is the most practical way of predicting breast cancer sickness. Reading through the literature
review, it becomes clear that the bulk of the work has been accomplished using machine learning and deep
learning techniques. It is often understood that deep learning falls within the umbrella of machine learning. Five
separate machine learning methods were used to this new dataset to find the most accurate method. Decision
Tree, XGBoost, Logistic regression, Naive Bayes, and Random Forest are the categories used to organize these
­methods39. In this section, we’ll get a brief overview of a few of these designs.

Decision tree (DT)

Decision trees are widely used in machine learning for data classification and prediction. It can have different
structures depending on the application. Although they work well for some classifiers, they can struggle with a
large number of classes and limited training data. The resulting decision tree is easy to understand for domain
experts, making it valuable for problem solving. In addition, it can be combined with ensemble methods to fur-
ther improve performance. In summary, Decision trees are versatile and effective in many industries, including
­finance40. Decision trees classifier can be written as –

f� (x) = θℓ Tℓ (x)
(1)
ℓǫleaves(T )

In Eq. 1, f� (x) represents the model’s final estimated for input vector x. T denotes the decision tree, θℓ is the
weight associated with leaf node l, and Tℓ (x) denotes an indicator function that returns 1 if x falls within the
region defined by leaf node l and 0 otherwise. The total of all the leaves in the tree ensures that the final predic-
tion includes contributions from all of the different trees in the ­ensemble41.

Random forest (RF)

Random Forest is a popular machine-learning technique used for both classification and regression tasks. It cre-
ates multiple decision trees from different parts of the training data. Each tree classifies the data separately and
the final prediction is the sum of all the individual forecasts. This approach reduces the risk of over fitting, leading
to more accurate and reliable predictions. Additionally, as the number of trees increases, the method becomes
more robust to noise and outliers in the data. However, there is a trade-off between accuracy and computational
efficiency, as training more trees requires more time and resources. These algorithms divide the data r­ ecursively42.
The Random Forest algorithm is provided below—

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Node t, randomly selection v of the p independent variables.

∀of the k=1, …, vis the variable that was sampled; for each possible split of kth, determine the
optimal split sk.

In s*, gain the optimal splitting k from k=1 to k=m; Determine the optimal split sk for splitting
node t; jth variable is defined cut point cs* that is used for splitting node t.

The data is separated here, with the i=1, …, n; observation with xij<cs* going to the left
descending node and all other observations going to the right descending node.

To grow a tree of maximum size Tb, simply repeat steps 1–4 for each node in the tree's
descendent set.

Algorithm 1.  Random Forest classifier.

XGBoost (XGB)
XGBoost (Extreme Gradient Boosting) is a widely used method for building robust predictive models, especially
in machine l­earning39. It uses aggregated decision trees to make accurate predictions from complex datasets.
Although decision trees are easy to interpret, XGBoost can be difficult to understand at first glance. However,
data scientists and machine learning experts prefer XGBoost because it efficiently processes large datasets and
quickly builds accurate models. This powerful and versatile tool strikes a balance between model complexity
and prediction accuracy using gradient descent and regularization techniques. It is highly adaptable, making it
valuable for extracting insights from complex datasets. However, careful optimization of the hyperparameters is
necessary to achieve the best results. With the right approach, XGBoost enables data scientists to build accurate
­ atasets43. XGBoost algorithm can be written as –
and reliable models that offer valuable insights into complex d
m
 m
  
Obj = l yi , 
yi + �(fk ) (2)
i=1 k=1
 
where fk is the leaf node’s regular term of the kth classification tree, l yi , 
yi is the training error of sample xi,
and Obj is the objective ­function44.

Naive Bayes (NB)

Naive Bayes is a classification algorithm that assumes that features are conditionally independent, given class
labels. Although this assumption is often violated in real databases, it is still useful in practical applications.
Although not independent, classification can derive information from features. For high-dimensional data, is fast
and efficient with less training data than complicated and complex models because it estimates the probability of
each feature separately. It can handle both discrete and continuous data, making it versatile for different databases.
In natural language processing, it is essential for text categorization and spam filtering. Overall, Naive Bayes is
a useful machine learning tool for solving classification p­ roblems45. Naive Bayes classifier can be written as –
n  
fcNB (x) = P Xj = xj |C = c)P(C = c (3)
j=1

In Eq. 3, Naive Bayes(x) is the

 probability that observation
 x is in class c, fc is the class-c observations, and n
is the number f observations. P Xj = xj |C = c)P(C = c is the conditional probability of seeing feature j in class
c. Divide class c’s observations by feature j’s xj usage. Training data can be used to calculate P(C = c). Multiplying
feature conditional probabilities and prior probabilities classifies new data into the most likely ­class46.

Logistic regression (LR)

Using labeled data, we train our model in supervised learning. Logistic regression is used for categorization
problems in supervised learning. Logistic regression’s discrete output variable (y) is usually 0 or 1. A sigmoid
function simulates X’s effect on the output variable. This function provides a probability between 0 and 1 indicat-
ing the input’s likelihood of being positive (1). Finance, marketing, and healthcare use logistic regression. Based
on medical history and demographic data, logistic regression can estimate patients’ cancer risk. Logistic regres-
sion handles nonlinear input–output relationships. For massive datasets, it requires fewer computing resources.
Logistic regression’s simplicity and effectiveness make it a common classification problem solution. Logistic
regression can also provide relative relevance information for feature selection and model i­ nterpretation47. Logis-
tic regression classifier can be written as –

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π(x)
g(x) = ln = β0 + β0 x1 + · · · + βm xm (4)
1 − π(x)
where π(x) denotes the probability of a binary outcome (such as success or failure) given the values in the
predictor vector x. The log odds are predicted as a linear combination of the predictor variables, and the coef-
ficients β0, β1, …, βm show the impacts of each predictor on the log chances. Exponentiating the equation allows
one to determine the odds of a successful outcome given specific values of the p­ redictors48.

Ethical approval
The current research is approved by the Dhaka Medical College Hospital Cancer Sample & Research Center
Informed consent was obtained, and ethical guidelines were followed. The approval letter confirms that all nec-
essary precautions were taken to ensure the protection of human subjects and adherence to ethical standards.

Experimental result
A lot of people make blunders in training or when extrapolating their results. Because the training error rate
decreases with increasing model complexity, increasing the model’s complexity can assist reduce training mis-
takes. The Bias-Variance Decomposition (Bias + Variance) method can be used to reduce the number of incorrect
generalizations. Over fitting occurs when a reduction in training error results in an in-crease in test error rates.
Each classification method may be judged by its accuracy, precision, recall, and F1 score.
When gauging the success of their models, writers used a wide range of techniques. While most studies
looked at a combination of markers to determine how well they did, some just used one. The work is evaluated
here using the criteria of accuracy, precision, recall, and the F1 score. For analyzing prediction data, this four-
factor system is ideal. The capacity to appropriately recognize and categorize incidents is related to accuracy.
Equation 549 shows the formula of accuracy.
TruePositive + TrueNegative
Accuracy = (5)
TruePositive + FalsePositive + TrueNegative + FalseNegative
Specifically, accuracy in statistics is defined as the ratio of actual positive occurrences to the total predicted
positive events. The mathematical expression of accuracy is given by Eq. 650.
TruePositive
Precision = (6)
TruePositive + FalsePositive
The term "harmonic mean" describes this method since it balances accuracy and memory. A version of the
mathematical equation for the F1 score is given by Eq. 751.
 
Precision × Recall
F1 score = 2 (7)
Precision + Recall

Result analysis
Table 2 provides information on hyperparameter tuning and each metric for different machine learning algo-
rithms: Decision Tree, Random Forest, XGBoost, Naive Bayes, and Logistic regression. Hyperparameter tuning
is an important step to improve the performance of machine learning models and involves finding the best
combination of hyperparameters to achieve the highest precision, accuracy, recall, and F1 score. Three hyperpa-
rameters are set for the decision tree algorithm: max_depth, min_samples_leaf, and min_samples_split. The best

Algorithms Hyperparameter tuning Range Best Accuracy Precision Recall F 1 Score

max_depth None, 5, 10 5
Decision tree min_samples_leaf 2, 5, 10 4 0.91 0.94 0.89 0.9
min_samples_split 1, 2, 2004 5
max_depth None, 5, 10, 20 None
min_samples_leaf 1, 2, 2004 1
Random forest 0.96 0.93 0.95 0.94
min_samples_split 2, 5, 10 5
n_estimators 100, 300, 500 300
learning_rate 0.01, 0.1, 0.3 0.01
max_depth 3, 5, 2007 3
XGBoost 0.97 0.94 0.95 0.96
n_estimators 100, 300, 500 500
subsample 0.8, 1.0 1
Naive Bayes No 0.94 0.99 0.9 0.94
Logistic Regression Regularization strength 0.001, 0.01, 0.1, 1, 10 10 0.93 0.93 0.93 0.93

Table 2.  Hyperparameter tuning with performance metrics for all algorithms. E.g. Significant values are in
[bold]

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combination of hyperparameters that resulted in the highest F1 score of 0.90 was a max_depth of 5, min_samples_
leaf of 4, and min_samples_split of 5. Next, the Random Forest algorithm was tuned with four hyperparameters:
max_depth, min_samples_leaf, min_samples_split, and n_estimators. The best combination of hyperparameters,
which resulted in an impressive F1score of 0.94, included a min_samples_leaf of 1, min_samples_split of 5,
and n_estimators of 300. The max_depth hyperparameter was not specified, indicating that the default value or
automatic selection method might have been used. For the XGBoost algorithm, four hyperparameters were tuned:
learning_rate, max_depth, n_estimators, and subsample. The best combination of hyperparameters achieved
the highest F1 score of 0.96, with a learning_rate of 0.01, max_depth of 3, n_estimators of 500, and subsample
of 1.0. The Naive Bayes algorithm did not require hyperparameter tuning, and its default settings were used. It
still achieved a respectable F1 score of 0.94. Finally, the Logistic Regression algorithm was tuned for the hyper-
parameters regularization strength, max_iter, and penalty. The best combination of hyperparameters resulted
in an F1 score of 0.93, with a regularization strength of 10, max_iter of 100, and penalty using L2 regularization.
In terms of performance metrics, the XGBoost algorithm outperformed others with an effective precision of
0.97 and high precision, recall, and F1 scores. The random forest algorithm also performed well with an accuracy
of 0.96 and a balanced accuracy trade-off. The decision tree algorithm achieved good results with an accuracy of
0.91 and a balanced F1 score of 0.90. Naive Bayes and Logistic regression show competitive performance with F1
scores of 0.94 and 0.93, respectively. Overall, hyper-parameter tuning plays an important role in improving the
performance of the model, and the choice of algorithm significantly influenced the final result, with XGBoost
and Random Forest standing out as high-performance models.
As can be seen in Table 2, it is evident that the accuracy of Random Forest and XGB is significantly greater
than that of the other five machine-learning methods. When compared to the other algorithms that were used,
the results of the Decision Tree method are significantly inferior to those of the Naive Bayes and Logistic Regres-
sion algorithms. In terms of the AUC comparison, the best results were achieved by Random Forest and XGB.
Confusion matrices (CM) can be used to rapidly and easily summarize a classification system’s efficacy. When
the quantity of observations across categories differs significantly, even when there are only two categories in the
dataset, the categorization may be incorrect. For more insight into the precision of the classification approach,
we can compute a CM (Fig. 5, 6, 7, 8 and 9).
Additionally, receiver operating characteristic (ROC) curves illustrate the diagnostic ability of a binary clas-
sifier as its discrimination threshold is varied. The area under the ROC curve (AUC) provides an aggregate
measure across all possible classification thresholds. For our XGBoost model, the ROC AUC was 0.98, indicating
excellent overall performance in distinguishing between the two classes shown in Fig. 10. This high ROC AUC
means the model is reliably assigning higher scores to positive instances than negative instances. We can have
increased confidence in its ability to generalize well to new data. Further analysis into the confusion matrix for
specific probability thresholds would provide deeper insight into preferred operating points along the ROC curve.

Performance analysis using explainable AI

Here we perform SHAP analysis on our best performing XGBoost model.
In Fig. 11, the SHAP summary plot shows the impact of each feature on the model’s output. The x-axis repre-
sents the SHAP value, where higher positive values indicate a higher probability of predicting early-stage breast
cancer, and lower negative values indicate a lower probability. The features are ordered by their importance,
with the most important features at the top. From the plot, we can observe that the mean_perimeter feature has
the highest positive SHAP values, indicating that higher values of mean_perimeter contribute significantly to
predicting early-stage breast cancer. On the other hand, the mean_radius feature has predominantly negative
SHAP values, suggesting that lower values of mean_radius are associated with a higher likelihood of early-stage
breast cancer.

Figure 5.  CM of DT.

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Figure 6.  CM of RF.

Figure 7.  CM of NB.

Figure 8.  CM of XGB.

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Figure 9.  CM of LR.

Figure 10.  ROC Curve of XGBoost Model.

Figure 11.  SHAP Summary Plot for XGBoost Model.

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Figure 12 presents the SHAP dependence plots for various feature pairs, illustrating the relationship between
the SHAP values and the feature values. In Fig. 12a, the dependence plot for mean_perimeter shows a weak posi-
tive correlation with the SHAP value, indicating that higher mean_perimeter values contribute to a higher prob-
ability of predicting early-stage breast cancer. The scatter plot for mean_smoothness and mean_texture in Fig. 12b
suggests a weak positive correlation, implying that as mean_smoothness increases, mean_texture also tends to
increase. Figure 12c shows the plot for mean_area and mean_smoothness, which exhibits no clear linear relation-
ship, with data points scattered throughout the area, suggesting no strong correlation or causation. Interestingly,
the data points for mean_smoothness and mean_area in Fig. 12d appear to exhibit a weak positive correlation,
indicating that smoother surfaces tend to have larger areas, but with a fair amount of variation. Finally, Fig. 12e

Figure 12.  SHAP Dependence Plot for XGBoost Model.

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displays the scatter plot for the SHAP value and mean_radius, which shows no discernible relationship, with data
points scattered throughout the area, suggesting no strong correlation or causation between these two variables.

Performance analysis using cross‑validation

When evaluating the transferability of statistical findings to a new dataset, researchers often employ a model
validation technique known as cross-validation52. The result was calculated using K-fold cross-validation in this
study. Using k-fold cross-validation, the dataset is split up into k smaller subsets. The remaining k1 subsets are
combined for use as training samples, while the remaining subset is utilized to validate the others. The optimal
value of k is dependent on the number of variables and the nature of the predictor, according to statistical theory.
The sole adjustable aspect of the method is the number of subsamples (K) into which each data sample is divided.
This method is typically referred to as k-fold cross-validation. For instance, k = 10 would be referred to be tenfold
cross-validation if used in the model reference. Accuracy for all of the models in this study is shown in Table 3
using k-fold cross-validation.
In this study, five machine learning algorithms were implemented to determine the optimal model perfor-
mance. Based on the findings presented in the results section, the XGBoost method generated the highest model
accuracy of 97%. To assess the performance, the k-fold cross-validation technique was employed in this study.
The detailed outcome can be observed in Table 3. The accuracy cross-validation revealed that five algorithms,
namely Decision Tree, Random Forest, Logistic regression, Naive Bayes, and XGBoost, exhibited strong perfor-
mance. A 90% mean accuracy score was obtained through tenfold cross-validation for the Decision Tree model,
while the Random Forest model achieved a 95% mean accuracy score. In contrast, XGBoost exhibits superior
performance compared to alternative algorithms. A tenfold cross-validation mean score of 97% was obtained
from the algorithm, while Naive Bayes achieved a score of 92%. In the tenfold cross-validation, Logistic regres-
sion achieved a mean score of 92%. The results of the accuracy tenfold cross-validation score indicate that the
quality of the model employed in this research is satisfactory.

Discussion
Accurately predicting breast cancer development is a critical objective in current research efforts. However, the
current utilization of data in this particular field is still limited. ML techniques have been employed to improve
the accuracy of cancer prediction. The efficiency of the categorization method employed in this study justifies its
comparison with other research attempts to evaluate its public importance. The primary goal of this study was
to determine the most effective machine learning methodologies for accurately evaluating breast cancer risk. It
acknowledges the potentially surprising effects of the predictive capabilities within this domain.
While most research in this field focuses on a limited amount of publicly accessible datasets, resulting in com-
parable evaluations of algorithms, the current study aims to explore new data sources. Out of the five machine
learning methods utilized in this dataset, XGBoost and RF demonstrated exceptional performance, achieving 97%
and 96% accuracy. Significantly, XGBoost demonstrated superior effectiveness in handling a recently produced
dataset. It is reasonable to consider that a more extensive and equally distributed dataset may result in even higher
levels of precision in the long term. The Random Forest algorithm showed significant capability by achieving the
second-highest accuracy in performance. The Random Forest algorithm demonstrates its superiority in managing
intricate interactions and mitigating the issue of overfitting. On the other hand, XGBoost exhibits remarkable
abilities in enhancing model performance by utilizing gradient-boosting approaches. Upon evaluating their
respective performances within the context of our study, it is evident that both algorithms contribute substan-
tially to the accuracy of predictions. The ability of Random Forest to effectively handle different data features
is a valuable complement to XGBoost’s capability to capture complicated patterns. These unique traits improve
our comprehension of breast cancer prediction. However, it is essential to acknowledge that these methods have
certain disadvantages, including sensitivity to noisy data and computational complexity. When considering the
broader effects of a study, it is essential to acknowledge that the generalizability of the results may be influenced
in ways such as the size and diversity of the dataset. Reliability could be enhanced by ensuring a more bal-
anced and broader dataset. This discourse highlights the considerable prospects of these algorithms while also
acknowledging their limitations and recognizing the need for further refinement of prediction models in Table 4.
Table 4 summarizes several research papers related to the prediction and diagnosis of breast cancer using
various machine learning and deep learning techniques. Each paper addresses different aspects of breast cancer
detection and prediction, and they vary in terms of accuracy, applied algorithms, and limitations.
Yu et al. introduce a nine-layer Convolutional Neural Network (CNN) for identifying abnormal breast tis-
sue in mammography images. Their method achieves a sensitivity of 93.4% and specificity of 94.6%, showing
good performance for image-based breast cancer detection. The limitation mentioned is a potential for further
enhancing the method’s performance. Parampreet et al. propose a Bayesian hyperparameter optimization tech-
nique for stacked ensemble models, achieving good Area under the Curve (AUC) scores for various datasets.
They use machine learning models like Deep Neural Network (DNN), Gradient Boosting Machine (GBM), and
Distributed Random Forest (DRF). The limitation here is the availability of a limited dataset. Alessandro et al.
focus on automated image analysis of breast ultrasound images, achieving an accuracy of 91% using ensemble
methods with CNN architectures. The limitation is the potential for improving accuracy. Hiba et al. primarily
employ machine learning algorithms for breast cancer risk prediction and diagnosis, with SVM yielding the
highest accuracy of 97.13%. They also use DT, NB, and KNN. A limitation mentioned is data pre-processing.
Puja et al. use deep learning with Adam Gradient Descent Learning, achieving a high accuracy of 98.24%. They
also employ various traditional machine learning models. The sources do not mention any specific limitations.
Comparing this work to the others, the novelty lies in the application of multiple supervised machine learning
algorithms for early-stage breast cancer prediction, providing a comprehensive approach. While the accuracy is

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Algorithm cv = 10 cv_score cv_score (mean)

1 0.917718
2 0.923146
3 0.894783
4 0.899032
5 0.924925
Decision tree 0.907497
6 0.90834
7 0.895156
8 0.913099
9 0.895104
10 0.903675
1 0.919113
2 0.972991
3 0.951697
4 0.940283
5 0.957985
Random forest 0.955505
6 0.95892
7 0.97818
8 0.957673
9 0.932415
10 0.981293
1 0.972403
2 0.976671
3 0.98727
4 0.969338
5 0.967068
XGBoost 0.973807
6 0.968395
7 0.963595
8 0.981956
9 0.988937
10 0.962441
1 0.915354
2 0.917053
3 0.950712
4 0.914418
5 0.923784
Naive Bayes 0.925651
6 0.908685
7 0.913652
8 0.921779
9 0.949879
10 0.941254
1 0.917948
2 0.917869
3 0.93195
4 0.929658
5 0.939511
Logistic regression 0.927323
6 0.924365
7 0.918985
8 0.935196
9 0.936036
10 0.921721

Table 3.  Evaluation of machine learning algorithms (accuracy) using k-fold cross-validation.

competitive, the acknowledgment of potential for improvement shows a commitment to enhancing the model’s
performance. Additionally, by leveraging various algorithms, this research showcases versatility and adaptability,

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Ref. Main idea of the paper Accuracy Applied algorithms Limitations

Decision Tree
Proposed supervised machine learning Decision Tree: 91%, Random Forest: Random Forest
This Work algorithms to predict early-stage breast 96%, XGBoost:97%, Naïve Bayes: 94%, XGBoost Need more analysis with models
cancer Logistic Regression: 93% Naïve Bayes
Logistic Regression
The paper proposes an improved nine-
The proposed method achieved a
layer convolutional neural network
53 sensitivity of 93.4%, specificity of 94.6%, Could enhance the performance of the
(CNN) for identifying abnormal breast Convolutional neural network (CNN)
precision of 94.5%, and accuracy of proposed method
in mammography using the open-access
94.0% on the test set
mini MIAS dataset
Proposed a parallel Bayesian hyperpa- BSense model 83.9%, 87.3%, 91.1%, and Stacking of machine learning models,
54 rameter to optimize stacked ensemble 80.1% Area Under Curve (AUC) for i.e., Deep Neural Network (DNN), Gra-
Limited dataset
models for breast cancer survival TCGA, METABRIC, Metabolomics, and dient Boosting Machine (GBM), and
prediction RNA-seq dataset, respectively Distributed Random Forest (DRF)
Outline a complete automated process
Ensembles methods to combine the
55 using advanced computer techniques to Achieved 91% accuracy in the clas-
performance of the individual CNNs Accuracy could be better
identify and categorize structures within sification
architectures
breast ultrasound images
The paper focuses on using machine Support Vector Machine (SVM), Deci-
56 SVM has the highest accuracy of 97.13%
learning algorithms for breast cancer sion Tree (C4.5), Naive Bayes (NB), and Data Pre-Processing
with the lowest error rate
risk prediction and diagnosis k Nearest Neighbors (k-NN) algorithms
The paper focuses on predicting breast k-Nearest Neighborhood, Logistic
36 Deep learning using Adam Gradient The provided sources do not mention
cancer using machine learning models Regression, Decision Tree, Random
Descent Learning is 98.24% any specific limitations of the paper
and varying parameters Forest, Support Vector Machine

Table 4.  Comparative analysis of different published studies.

which can be advantageous in real-world clinical settings where different types of data may be available. This
approach makes it a robust and promising breast cancer prediction and diagnosis solution. However, it’s essential
to continue refining the model to achieve even higher accuracy rates and overcome its limitations.

Limitations and future work

The study although presents a promising result, but it has several limitations. As we have already discussed, the
dataset has used here was limited in size and diversity, potentially limiting the generalizability of the findings. Due
to the sensitive nature of patient data and the challenges associated with data collection, we were constrained in
the amount of data we could gather for this study. Additionally, the features provided in the dataset were extracted
image properties rather than raw scans, restricting direct image-based analysis. In future we are aiming to col-
lect a large number of patient dataset from Bangladesh and United States and applying our method to get the
comparative result. We plan to collaborate with multiple healthcare institutions to gather a more extensive and
diverse dataset, incorporating data from different demographics and regions to improve model generalizability.
Additionally, we will explore newer machine learning algorithms, deep learning techniques, or ensemble meth-
ods to enhance the accuracy and efficiency of our models. Conducting in-depth analyses on feature importance
and selection methods will provide valuable insights into the key factors influencing breast cancer prediction.
Furthermore, we intend to validate our models in real clinical settings through prospective studies, working
closely with healthcare professionals for validation.

Conclusion
This study demonstrates the potential of using supervised machine learning algorithms for early prediction of
breast cancer. This research has collected 500 patients primary data from Dhaka Medical College Hospital and
applied five supervised machine learning algorithms. In the evaluation this research found that XGBoost achieved
the highest accuracy of 97%. XGBoost also achieved the highest precision (0.94), recall (0.95), and F1 score (0.96)
rather than other algorithms. However, some limitations need to be acknowledged. More extensive real-world
data is required to confirm the model’s generalization capability across larger populations. Furthermore, the
dataset only included derived picture attributes rather than raw scans, which limited the possibility of conducting
direct image-based analysis. Despite these constraints, this work illustrates an important proof-of-concept for
leveraging artificial intelligence to improve breast cancer diagnosis. The model can enable clinicians to rapidly
screen patients and identify high-risk cases needing further examination. This would significantly impact early
intervention and tailored treatment planning to improve survival outcomes. As next steps, integrating medical
imagery into the pipeline and validating performance over larger multi-center datasets could help strengthen
model robustness. It would also be valuable to experiment with combining machine predictions with expertise
of oncologists to develop an augmented diagnostics system. Such human-AI collaboration can lead to more
accurate and transparent cancer care.

Data availability
The data that support the findings of this study are available from the corresponding author upon reasonable
request.

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Received: 12 September 2023; Accepted: 21 March 2024

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Acknowledgements
The authors would like to extend their sincere appreciation to the Researchers Supporting Project, King Saud
University, Riyadh, Saudi Arabia for funding this work through the project number (RSP-2024R457)

Author contributions
Conceptualization: T.I., M.A.S., M.S.T., and S.A. Methodology: T.I., M.A.S., M.S.T. Validation: T.I., M.A.S.,
and Y.A.B.J. Formal analysis: T.I., Y.A.B.J., G.F.W., and H.A.N. Writing—original draft preparation: T.I., M.A.S.,
and M.S.T. Writing—review and editing: T.I., M.A.S, M.S.T., Y.A.B.J., M.B., and G.F.W. Supervision: M.H.H.,
and M.B. Resources: T.I., M.A.S., M.H.H. Project administration: M.B., and T.I.

Competing interests
The authors declare no competing interests.

Additional information
Correspondence and requests for materials should be addressed to G.F. or M.B.
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