Wavelet feature extraction and genetic algorithm for biomarker detection in colorectal cancer data

Biomarkers which predict patient’s survival can play an important role in medical diagnosis and treatment. How to select the significant biomarkers from hundreds of protein markers is a key step in survival analysis. In this paper a novel method is proposed to detect the prognostic biomarkers ofsurvival in colorectal cancer patients using wavelet analysis, genetic algorithm, and Bayes classifier. One dimensional discrete wavelet transform (DWT) is normally used to reduce the dimensionality of biomedical data. In this study one dimensional continuous wavelet transform (CWT) was proposed to extract the features of colorectal cancer data. One dimensional CWT has no ability to reduce dimensionality of data, but captures the missing features of DWT, and is complementary part of DWT. Genetic algorithm was performed on extracted wavelet coefficients to select the optimized features, using Bayes classifier to build its fitness function. The corresponding protein markers were located based on the position of optimized features. Kaplan-Meier curve and Cox regression model 2 were used to evaluate the performance of selected biomarkers. Experiments were conducted on colorectal cancer dataset and several significant biomarkers were detected. A new protein biomarker CD46 was found to significantly associate with survival time

A new model for large dataset dimensionality reduction based on teaching learning-based optimization and logistic regression

One of the human diseases with a high rate of mortality each year is breast cancer (BC). Among all the forms of cancer, BC is the commonest cause of death among women globally. Some of the effective ways of data classification are data mining and classification methods. These methods are particularly efficient in the medical field due to the presence of irrelevant and redundant attributes in medical datasets. Such redundant attributes are not needed to obtain an accurate estimation of disease diagnosis. Teaching learning-based optimization (TLBO) is a new metaheuristic that has been successfully applied to several intractable optimization problems in recent years. This paper presents the use of a multi-objective TLBO algorithm for the selection of feature subsets in automatic BC diagnosis. For the classification task in this work, the logistic regression (LR) method was deployed. From the results, the projected method produced better BC dataset classification accuracy (classified into malignant and benign). This result showed that the projected TLBO is an efficient features optimization technique for sustaining data-based decision-making systems

Breast Tumor Classification Using an Ensemble Machine Learning Method

Breast cancer is the most common cause of death for women worldwide. Thus, the ability of artificial intelligence systems to detect possible breast cancer is very important. In this paper, an ensemble classification mechanism is proposed based on a majority voting mechanism. First, the performance of different state-of-the-art machine learning classification algorithms were evaluated for the Wisconsin Breast Cancer Dataset (WBCD). The three best classifiers were then selected based on their F3 score. F3 score is used to emphasize the importance of false negatives (recall) in breast cancer classification. Then, these three classifiers, simple logistic regression learning, support vector machine learning with stochastic gradient descent optimization and multilayer perceptron network, are used for ensemble classification using a voting mechanism. We also evaluated the performance of hard and soft voting mechanism. For hard voting, majority-based voting mechanism was used and for soft voting we used average of probabilities, product of probabilities, maximum of probabilities and minimum of probabilities-based voting methods. The hard voting (majority-based voting) mechanism shows better performance with 99.42%, as compared to the state-of-the-art algorithm for WBCD

An improvement in support vector machine classification model using grey relational analysis for cancer diagnosis

To further improve the accuracy of classifier for cancer diagnosis, a hybrid model called GRA-SVM which comprises Support Vector Machine classifier and filter feature selection Grey Relational Analysis is proposed and tested against Wisconsin Breast Cancer Dataset (WBCD) and BUPA Disorder Dataset. The performance of GRA-SVM is compared to SVM’s in terms of accuracy, sensitivity, specificity and Area under Curve (AUC). The experimental results reveal that GRA-SVM improves the SVM accuracy of about 0.48 by using only two features for the WBCD dataset. For BUPA dataset, GRA-SVM improves the SVM accuracy of about 0.97 by using four features. Besides improving the accuracy performance, GRA-SVM also produces a ranking scheme that provides information about the priority of each feature. Therefore, based on the benefits gained, GRA-SVM is recommended as a new approach to obtain a better and more accurate result for cancer diagnosis

A Modified LeNet CNN for Breast Cancer Diagnosis in Ultrasound Images

Convolutional neural networks (CNNs) have been extensively utilized in medical image processing to automatically extract meaningful features and classify various medical conditions, enabling faster and more accurate diagnoses. In this paper, LeNet, a classic CNN architecture, has been successfully applied to breast cancer data analysis. It demonstrates its ability to extract discriminative features and classify malignant and benign tumors with high accuracy, thereby supporting early detection and diagnosis of breast cancer. LeNet with corrected Rectified Linear Unit (ReLU), a modification of the traditional ReLU activation function, has been found to improve the performance of LeNet in breast cancer data analysis tasks via addressing the “dying ReLU” problem and enhancing the discriminative power of the extracted features. This has led to more accurate, reliable breast cancer detection and diagnosis and improved patient outcomes. Batch normalization improves the performance and training stability of small and shallow CNN architecture like LeNet. It helps to mitigate the effects of internal covariate shift, which refers to the change in the distribution of network activations during training. This classifier will lessen the overfitting problem and reduce the running time. The designed classifier is evaluated against the benchmarking deep learning models, proving that this has produced a higher recognition rate. The accuracy of the breast image recognition rate is 89.91%. This model will achieve better performance in segmentation, feature extraction, classification, and breast cancer tumor detection

Multi-Criterion Mammographic Risk Analysis Supported with Multi-Label Fuzzy-Rough Feature Selection

Context and background Breast cancer is one of the most common diseases threatening the human lives globally, requiring effective and early risk analysis for which learning classifiers supported with automated feature selection offer a potential robust solution. Motivation Computer aided risk analysis of breast cancer typically works with a set of extracted mammographic features which may contain significant redundancy and noise, thereby requiring technical developments to improve runtime performance in both computational efficiency and classification accuracy. Hypothesis Use of advanced feature selection methods based on multiple diagnosis criteria may lead to improved results for mammographic risk analysis. Methods An approach for multi-criterion based mammographic risk analysis is proposed, by adapting the recently developed multi-label fuzzy-rough feature selection mechanism. Results A system for multi-criterion mammographic risk analysis is implemented with the aid of multi-label fuzzy-rough feature selection and its performance is positively verified experimentally, in comparison with representative popular mechanisms. Conclusions The novel approach for mammographic risk analysis based on multiple criteria helps improve classification accuracy using selected informative features, without suffering from the redundancy caused by such complex criteria, with the implemented system demonstrating practical efficacy

Classification of microarray gene expression cancer data by using artificial intelligence methods

Günümüzde bilgisayar teknolojilerinin gelişmesi ile birçok alanda yapılan çalışmaları etkilemiştir. Moleküler biyoloji ve bilgisayar teknolojilerinde meydana gelen gelişmeler biyoinformatik adlı bilimi ortaya çıkarmıştır. Biyoinformatik alanında meydana gelen hızlı gelişmeler, bu alanda çözülmeyi bekleyen birçok probleme çözüm olma yolunda büyük katkılar sağlamıştır. DNA mikroarray gen ekspresyonlarının sınıflandırılması da bu problemlerden birisidir. DNA mikroarray çalışmaları, biyoinformatik alanında kullanılan bir teknolojidir. DNA mikroarray veri analizi, kanser gibi genlerle alakalı hastalıkların teşhisinde çok etkin bir rol oynamaktadır. Hastalık türüne bağlı gen ifadeleri belirlenerek, herhangi bir bireyin hastalıklı gene sahip olup olmadığı büyük bir başarı oranı ile tespit edilebilir. Bireyin sağlıklı olup olmadığının tespiti için, mikroarray gen ekspresyonları üzerinde yüksek performanslı sınıflandırma tekniklerinin kullanılması büyük öneme sahiptir. DNA mikroarray’lerini sınıflandırmak için birçok yöntem bulunmaktadır. Destek Vektör Makinaları, Naive Bayes, k-En yakın Komşu, Karar Ağaçları gibi birçok istatistiksel yöntemler yaygın olarak kullanlmaktadır. Fakat bu yöntemler tek başına kullanıldığında, mikroarray verilerini sınıflandırmada her zaman yüksek başarı oranları vermemektedir. Bu yüzden mikroarray verilerini sınıflandırmada yüksek başarı oranları elde etmek için yapay zekâ tabanlı yöntemlerin de kullanılması yapılan çalışmalarda görülmektedir. Bu çalışmada, bu istatistiksel yöntemlere ek olarak yapay zekâ tabanlı ANFIS gibi bir yöntemi kullanarak daha yüksek başarı oranları elde etmek amaçlanmıştır. İstatistiksel sınıflandırma yöntemleri olarak K-En Yakın Komşuluk, Naive Bayes ve Destek Vektör Makineleri kullanılmıştır. Burada Göğüs ve Merkezi Sinir Sistemi kanseri olmak üzere iki farklı kanser veri seti üzerinde çalışmalar yapılmıştır. Sonuçlardan elde edilen bilgilere göre, genel olarak yapay zekâ tabanlı ANFIS tekniğinin, istatistiksel yöntemlere göre daha başarılı olduğu tespit edilmiştir