Iterative Tuning of Tree-Ensemble-Based Models' parameters Using Bayesian Optimization for Breast Cancer Prediction

Finding breast cancer early and accurately is very important for helping patients live longer. We use the Wisconsin Diagnostic Breast Cancer (WDBC) dataset to look at two popular machine learning classifiers: Support Vector Machines (SVM) and k-nearest neighbors (KNN). Our work combines theory with practice by including things like data preprocessing exploratory feature evaluation, model configuration, hyperparameter, and validation through cross-validation techniques. We use common evaluation metrics like accuracy, precision, recall, F1-score, and Area Under the Curve (AUC) to judge performance. When we did experiments with both a 70:30 train-test split and 10-fold cross-validation, we found that SVM did a little better (~96.3% accuracy) than compared to KNN, which has an accuracy of about 96.5% and AUC values of about 0.96 and 0.968, respectively. SVM is better at dealing with high-dimensional data and making maximum-margin decision boundaries, but KNN is still appealing because it is simple and works well on datasets of moderate size. Even though both methods have their pros and cons, they also have some problems that are talked about, as well as ways they could be improved and how they could be used in the clinic. This paper evaluates and compares the theoretical and practical performance of SVM and KNN using the WDBC dataset. We include preprocessing, careful evaluation metrics, and hyperparameter optimization to provide an empirical comparison of both models. The study also discusses important trade-offs and real-world factors for using these algorithms in medical screening contexts.

Breast cancer death rates are higher than any other cancer in American women. Machine learning-based predictive models promise earlier detection techniques for breast cancer diagnosis. However, making an evaluation for models that efficiently diagnose cancer is still challenging. In this work, we proposed data exploratory techniques (DET) and developed four different predictive models to improve breast cancer diagnostic accuracy. Prior to models, four-layered essential DET, e.g., feature distribution, correlation, elimination, and hyperparameter optimization, were deep-dived to identify the robust feature classification into malignant and benign classes. These proposed techniques and classifiers were implemented on the Wisconsin Diagnostic Breast Cancer (WDBC) and Breast Cancer Coimbra Dataset (BCCD) datasets. Standard performance metrics, including confusion matrices and K-fold cross-validation techniques, were applied to assess each classifier’s efficiency and training time. The models’ diagnostic capability improved with our DET, i.e., polynomial SVM gained 99.3%, LR with 98.06%, KNN acquired 97.35%, and EC achieved 97.61% accuracy with the WDBC dataset. We also compared our significant results with previous studies in terms of accuracy. The implementation procedure and findings can guide physicians to adopt an effective model for a practical understanding and prognosis of breast cancer tumors.

Currently, as governments across the world attempt to halt the spread of COVID-19, many of their efforts are being hampered by shortages of crucial testing kits. Even in many developed countries, the health system has come to the point of standstill due to the increasing demand for intensive care units. One study reveals that 40,000 women die in a year from breast cancer, which is one woman every 13 minutes dying from this disease every day. Breast cancer remains the number one form of cancer that women are diagnosed with around the world. Any hospital in the world will have a multidisciplinary team of experts including radiologists, oncologists, surgeons, and other respiratory physicians and consultants. This multidisciplinary team uses a wide variety of data taken from CT scans, x-rays, PET scans, biopsies, clinical examination, imaging mammography, ultrasound (sonography), pathology biopsy, and fine-needle aspiration to identify whether a patient has cancer. Individuals with cancer, particularly those who are receiving systemic anticancer treatments, have been postulated to be at increased risk of mortality from COVID-19. Therefore, it is the need of an hour to implement an early detection of cancer that will prevent patients from COVID-19 and due treatment will be provided. Breast cancer that is detected early is far easier to cure, but at the same time it is difficult to detect. An accurate breast cancer staging is an essential task performed by pathologists (experts who examine the laboratory samples) to inform clinical management for the appropriate treatment. For instance, evaluation of the extent of cancer spread by histopathologic analysis or microscopic examination is an important part of breast cancer staging, and the process involves the decision-making of human behavior with time-consuming and costly sample examination and a period of more than one month to have breast cancer type, stage, etc., to decide the appropriate therapy to patients by the time it can affect the results of therapeutic treatments and survival of patients. The application of artificial intelligence (AI) machine learning technology with deep learning algorithms to whole-slide pathology images can potentially improve the diagnostic accuracy of breast cancer at a very early stage. I have developed a simple machine-learning model using the Python programming language and neural network, inspired by the structure of the human brain, with 12 attributes, out of which 10 real-valued features from each cell nucleus obtained from the Wisconsin diagnostic breast cancer dataset available in public domain for the education capacity that explains about the stage of breast cancer M (Malignant) and B (Benign). This model predicts the presence of breast cancer with an accuracy of 98.8% at a very early stage. The continuous development of technology in the medical field will save countless lives and the overall quality of human life will continue to improve over time. Citation Format: Subash Kumar. Early detection of breast cancer during the Covid-19 pandemic using artificial intelligence neural networks [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2020 Jul 20-22. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(18_Suppl):Abstract nr PO-003.

According to the WHO, the cases of Breast Cancer are now a global issue as the cases are increasing day by day globally. Hence the early detection of malignant tumor is utmost important to prevent patient’s early demise due to patient’s ignorance. If patient comes to doctor and their application detects the tumor is non cancerous or it is just a benign tumor but actually it is malignant tumor then early detection alone can not play such an important role for cancer prevention. So, It is equally important to use best Machine Learning model, which surely detects malignant as malignant tumor and benign as benign tumor. Such accurate model is also highly required along with early detection of Breast Cancer disease. Our work is dedicated in this direction that our suggested model predicts malignant tumor as malignant and benign as benign tumor with high accuracy than existing model is providing. This paper suggests an architecture which produces high accuracy of the model when applied on Wisconsin Diagnostic Breast Cancer (WDBC) dataset obtained by digitized fine needle aspirate images. Our suggested model is the modified version of SVM. It is providing 63% accuracy when data points are not scaled, 98% when date is correctly scaled and 99% when the data points are correctly scaled with appropriate regularization and K fold validation techniques are applied on Support Vector Machine (SVM) instead of simply using default SVM with default parameters. Evidently, our suggested SVM provides 99% accuracy for detecting tumor as benign or malignant over WDBC dataset obtained by digitized fine needle aspirate images.

Breast cancer has been one of the leading causes of death among women in the world. Early detection of this disease can save patient’s lives and reduce mortality. Due to the large number of features involved in the diagnosis of this disease, the breast cancer diagnosis process can be time consuming. To reduce cost and time and improving accuracy of breast cancer diagnosis, this paper propose a feature selection algorithm based on particle swarm optimization (PSO) combined with machine learning methods for selection the most effective features for breast cancer diagnosis among all features. In order to evaluate the efficiency of the proposed feature selection method, it was tested on three most common breast cancer datasets available in the University of California, Irvine (UCI) repository named: Coimbra dataset (CD), Wisconsin Diagnostic Breast Cancer dataset (WDBC) and Wisconsin Prognostic Breast Cancer dataset (WPBC). In the Coimbra dataset with all its 9 features and without PSO feature selection algorithm the highest obtained accuracy was 87% by Support Vector Machine method, while with PSO feature selection algorithm the accuracy reached to 91% and the number of features was reduced from 9 to 4. In the WDBC dataset with all its 30 features and without PSO feature selection algorithm the highest obtained accuracy was 99% by Random Forest method, while with PSO feature selection algorithm the accuracy reached to 100% and the number of features was reduced from 30 to 19. In the WPBC dataset with all its 33 features and without PSO feature selection algorithm the highest obtained accuracy was 94% by Support Vector Machine method, while with PSO feature selection algorithm the accuracy reached to 96% and the number of features was reduced from 33 to 17. The results of this paper indicated that the proposed feature selection algorithm based on PSO algorithm can improve the accuracy of breast cancer diagnosis. While it has selected fewer and more effective features than the total number of features in the original datasets.

Breast cancer is a disease that causes excessive fear in women around the world. The number of high death rates by breast cancer can be reduced by early detection. This can make breast cancer a disease that is easy to cure. A collection of datasets about breast cancer is used in the process of early detection. Early detection is carried out to analyze the state of the early stages of breast cancer patients. This research paper proposes machine learning methods, namely Generalized Linear Model, Logistic Regression, and Gradient Boosted Decision Tree to enhance the classification performance of Wisconsin Diagnostic Breast Cancer Data. The diagnosis results in two classes of cancer decisions which are malignant and benign by looking at evaluating the accuracy of the data classification test. The result shows that the Generalized Linear Model achieves the accuracy of 99.4%, which is higher than the accuracies of the previous studies for classifying the Wisconsin Diagnostic Breast Cancer dataset.

In the presented study, the authors have compared the performances of various machine learning and deep learning algorithms on two separate datasets: the Wisconsin Diagnostic Breast Cancer dataset and the Wisconsin Breast Cancer Dataset. We evaluated the extent of their ability to correctly classify the samples as “malignant” or “benign”. The respective performances of these algorithms were judged on the grounds of various evaluation metrics such as accuracy, precision, recall, specificity, and the AUC-ROC curve for both datasets. From the experimental results, we concluded that the deep learning approaches have provided better results on evaluation grounds than the machine learning ones. In quantitative terms, ANN performed most consistently among all the considered approaches for either dataset with an accuracy of 100% and 98% respectively.KeywordsConvolutional neural networksClassificationMachine learning algorithmsDecision boundaryDeep learningArtificial neural networks

Breast cancer is one of the leading causes of increasing deaths in women worldwide. The complex nature (microcalcification and masses) of breast cancer cells makes it quite difficult for radiologists to diagnose it properly. Subsequently, various computer-aided diagnosis (CAD) systems have previously been developed and are being used to aid radiologists in the diagnosis of cancer cells. However, due to intrinsic risks associated with the delayed and/or incorrect diagnosis, it is indispensable to improve the developed diagnostic systems. In this regard, machine learning has recently been playing a potential role in the early and precise detection of breast cancer. This paper presents a new machine learning-based framework that utilizes the Random Forest, Gradient Boosting, Support Vector Machine, Artificial Neural Network, and Multilayer Perception approaches to efficiently predict breast cancer from the patient data. For this purpose, the Wisconsin Diagnostic Breast Cancer (WDBC) dataset has been utilized and classified using a hybrid Multilayer Perceptron Model (MLP) and 5-fold cross-validation framework as a working prototype. For the improved classification, a connection-based feature selection technique has been used that also eliminates the recursive features. The proposed framework has been validated on two separate datasets, i.e., the Wisconsin Prognostic dataset (WPBC) and Wisconsin Original Breast Cancer (WOBC) datasets. The results demonstrate improved accuracy of 99.12% due to efficient data preprocessing and feature selection applied to the input data.

Data mining is a technique to extracts some meaningful information from large amount of data. Nowadays In healthcare sector data mining is come out important field from all the fields for providing accurate prediction of diseases and deeper study of medical data. Authors are using different data mining techniques to identification of various diseases such as stoke, diabetes, cancer, hypothyroid and heart disease etc. This paper discussed the literature study of various data mining techniques in section two. In this paper, we used two disease dataset breast cancer and diabetes dataset from the UCI machine learning repository. We classified the five classification algorithms on WEKA Explorer and WEKA Experimenter interface. WEKA tool is a good classification tool used in this paper. Naïve bayes, SMO, REP Tree, J48 and MLP algorithms are used to classify breast cancer and diabetes dataset on WEKA interface. The performances of these five algorithms have been analyzed on breast cancer and diabetes dataset using training data testing mode. After analyzing the performances of all algorithm, found that naïve bayes gives 72.70%accuracy on breast cancer dataset and SMO gives 76.80%accuracy on diabetes dataset.

The purpose of the proposed study was to provide a solution to the Wisconsin Diagnostic Breast Cancer (WDBC) classification problem. The WDBC dataset, provided by the University of Wisconsin Hospital, was derived from a group of images using Fine Needle Aspiration (biopsies) of the breast. An ensemble of Support Vector Machines (SVM's) was employed in this study. Support vectors with linear, polynomial and RBF kernel functions were trained using a fraction of the WDBC dataset as a training set. The five top performing models were recruited into the ensemble. The classification was then carried out using the majority opinion of the ensemble. The SVM ensemble successfully classified more than 99 percent of the testing data and in the process yielded 100 percent benign tumor prediction accuracy. Keywords: Support Vector Machines; Breast Cancer; Machine Learning, Ensemble, Classifiers

<p>Breast cancer is the most frequent cancer in women and the second-leading cause of cancer-related deaths globally. The main problems in managing breast cancer are high heterogeneity and the formation of therapeutic resistance. White blood cells, omics and large Wisconsin diagnostic breast cancer datasets present the three-decade genomic revolution and advance the understanding of cellular function. The precision of cancer diagnosis has also increased over the past decades. High throughput sequencing, screening, and artificial intelligence technologies have significantly improved and increased the methodologies used for diagnosis, prognosis, and therapy. This paper follows several phases of breast cancer, studies datasets and evaluate many algorithms of machine learning (ML) used for analysis and feature selection i.e. k-means, similarity correlation, genetic algorithm, and principal component analysis, have been used to recognize the subset of proteins with the highest significance for breast cancer prediction by using different biomarkers. The best correlation, as determined by Pearson correlation, between copy number and protein is 0.014, and the accuracy achieved by the genetic algorithm is 93.5% using multi-omics datasets.</p>

The need for an accurate reasoning algorithm is usually necessitated by the sensitivity of domain of (medicine as example) application of such algorithms. Most reasoning algorithms for medical diagnosis are either limited by their techniques or accuracy and efficiency. Even the Select and Test (ST) algorithm which is considered a more approximate reasoning algorithm is also limited by its approach of using bipartite graph in modeling domain knowledge and making inference through the use of orthogonal vector projection for estimating likelihood of diagnosis at the clinical decision stage (induction). While the bipartite graph knowledge base lacks n-ary use of predicate on concepts, orthogonal vector projection on the other hand has high computation for the inference process. The aim of this paper is to enhance ST algorithm for improved performance and accuracy. First, we propose the use of ontologies and semantic web based rule for knowledge representation so as to provide support for inference making. Furthermore, three major improvements were added to ST algorithm to aid the improvement of its approximation. Secondly, we designed an inference making procedure to enable interaction with the knowledge base mentioned earlier. Thirdly, we model Hill’s Criteria of Causation into clinical decision stage of ST to overcome the limitation of orthogonal vector projection. Lastly, the improved ST algorithm was largely represented and described using set notations (though implemented as linked-list and queues) and mathematical notations. The result of the improved ST algorithm revealed a sensitivity of 0.81 and 0.89 and specificity of 0.82 and 1.0 in the Wisconsin Breast Cancer Database (WBCD) and Wisconsin Diagnostic Breast Cancer (WDBC) datasets respectively. In addition, the accuracy obtained from the proposed algorithm was 86.0% and 88.72% for the Wisconsin Breast Cancer Database (WBCD) and Wisconsin Diagnostic Breast Cancer (WDBC) datasets respectively. This enhancement in accuracy was obtained at a slowdown time due to the reasoning process and ontology parsing task added to the enhanced system. However, there was an improvement in the accuracy and inference power of the resulting system.

Background Earlier detection of breast cancer through mammography screening has reduced disease-specific mortality; however, confounding issues such as technical challenges, breast density, and tumor size can result in false negatives and ultimately later stage diagnosis. Next generation liquid biopsy has the potential to complement mammography and enable earlier detection for more women. We have previously demonstrated high sensitivity and specificity for early detection of invasive breast cancer (IBC) by utilizing a novel category of cancer-associated small RNAs, termed orphan noncoding RNAs (oncRNAs), through a liquid biopsy platform. Here, we further improve the ability to detect breast cancer in a larger, multi-source cohort through an AI-driven approach and demonstrate potential for detection of ductal carcinoma in-situ (DCIS). Methods We utilized The Cancer Genome Atlas (TCGA) small RNA-seq database to discover a library of 20,538 oncRNAs, through a female-specific analysis, that were significantly enriched among 1,103 breast tumors compared to 349 normal tissue samples spanning multiple tissue sites. The diagnostic performance of these oncRNAs were assessed in an independent cohort of archived serum samples from 663 female individuals, sourced from Indivumed (Hamburg, Germany), Proteogenex (Inglewood, CA), and MT Group (Los Angeles, CA), including 279 breast cancer patients of various stages (221 IBC and 58 DCIS; mean age: 57.0 ± 13.8 years; ever-smoker: 25.8%) and 304 age-matched controls (mean age: 58.5 ± 13.9 years; ever-smoker: 23.4%) without breast cancer. All samples were collected between 2010–2022 at time of diagnosis for breast cancer patients. We sequenced the small RNA content of these samples at an average depth of 25.28 ± 9.37 million 50-bp single-end reads. We detected 18,025 (87.8%) unique breast cancer-specific oncRNA species within at least one sample from the study cohort. We then trained a generative AI model using 5-fold cross-validation to predict cancer status for all samples. Results Our oncRNA-based model achieved an overall AUC of 0.95 (95% CI, 0.93–0.97) for prediction of IBC versus cancer-free controls with a sensitivity of 0.87 (0.82–0.91) at 90% specificity. We observed high sensitivities, also at 90% specificity, across all tumor stages and tumor sizes (Table 1). Sensitivities for the earliest stage and smallest tumor size were 0.87 (0.78–0.93) and 0.81 (0.61–0.93) for Stage I (n=83) and T1a–b ( >1mm to ≤10mm; n=26), respectively. Additionally, in a small single-source cohort, we also saw high model accuracy and sensitivity for DCIS, which we aim to confirm in additional cohorts. While our overall cancer cohort primarily consisted of individuals with luminal breast cancer, our model had high sensitivities across all breast cancer subtypes at 0.90 (0.84–0.94), 0.73 (0.59–0.85), and 0.86 (0.42–1.0) for luminal (n=181), HER2 positive (n=49), and triple negative (n=7), respectively. Conclusions We further demonstrate the potential utility of oncRNAs as a blood-based biomarker using an AI algorithm for sensitive and accurate early detection of breast cancer in a large cohort. Additionally, we have shown that this oncRNA-based assay performs well in detecting small, early-stage invasive breast tumors, with potential to detect precursors of breast cancer. Table 1: Model sensitivity in breast cancer by tumor stage and size For each tumor stage and size, as defined by the AJCC 7th Edition breast cancer staging system, sensitivity and 95% Pearson-Clopper confidence intervals (CI) are reported at 90% specificity for the number of samples (N). Citation Format: Noura Tbeileh, Taylor Cavazos, Mehran Karimzadeh, Jeffrey Wang, Alice Huang, Dung Ngoc Lam, Seda Kilinc, Jieyang Wang, Xuan Zhao, Andy Pohl, Helen Li, Lisa Fish, Kimberly Chau, Marra Francis, Lee Schwartzberg, Patrick Arensdorf, Hani Goodarzi, Fereydoun Hormozdiari, Babak Alipanahi. Cell-free orphan noncoding RNAs and AI enable early detection of invasive breast cancer and ductal carcinoma in-situ [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-13-08.

Due to increased number of breast cancer cases, there is rise in concern about the disease. So, in today’s era, machine learning classification can play a vital role in classifying the degree of malignancy of the cancer. This paper uses four different classifiers such as KNN, logistic regression, naive Bayes and decision tree to classify the cancer into two classes of benign and malignant. The proposed model is simulated over Wisconsin diagnostic breast cancer dataset and evaluated by accuracy metric. The model classifies the disease based on the most accurate classifier. The KNN model shows significantly better result than the other classifier.

<p>Breast cancer is ranked as a significant cause of mortality among females globally. Its complex nature poses principal challenges for physicians and researchers for rapid diagnosis and prognosis. Hence, machine learning algorithms are employed to forecast and identify diseases. This study discusses the comparative analysis of seven machine learning models, e.g., logistic regression (LR), support vector machine (SVM), k-nearest neighbor classifier (KNN), decision tree classifier (DT), random forest classifier (RF), Naïve Bayes (NB), and artificial neural network (ANN) to predict breast cancer using Wisconsin breast cancer and breast cancer datasets. In the Wisconsin breast cancer dataset, KNN depicted 99% accuracy, followed by RF (98%), SVM (96%), NB (96%), LR (96%), ANN (93%), and DT (92%). On the contrary, in the breast cancer (BC) dataset, the highest accuracy was achieved by LR at 83%, and the lowest was achieved by DT (65%), which depicted that the numeric dataset WBC has better accuracy than the breast cancer dataset.</p>