Biomedical Data Classification Research Articles

Evolutionary optimisation with outlier detection-based deep learning model for biomedical data classification

Evolutionary optimisation with outlier detection-based deep learning model for biomedical data classification

A Hybrid Feature Selection Method for Improve the Accuracy of Medical Classification Process

Generally, medical dataset classification has become one of the biggest problems in data mining research. Every database has a given number of features but it is observed that some of these features can be redundant and can be harmful as well as disrupt the process of classification and this problem is known as a high dimensionality problem. Dimensionality reduction in data preprocessing is critical for increasing the performance of machine learning algorithms. Besides the contribution of feature subset selection in dimensionality reduction gives a significant improvement in classification accuracy. In this paper, we proposed a new hybrid feature selection approach based on (GA assisted by KNN) to deal with issues of high dimensionality in biomedical data classification. The proposed method first applies the combination between GA and KNN for feature selection to find the optimal subset of features where the classification accuracy of the k-Nearest Neighbor (kNN) method is used as the fitness function for GA. After selecting the best-suggested subset of features, Support Vector Machine (SVM) are used as the classifiers. The proposed method experiments on five medical datasets of the UCI Machine Learning Repository. It is noted that the suggested technique performs admirably on these databases, achieving higher classification accuracy while using fewer features.

Ten simple rules for reporting machine learning methods implementation and evaluation on biomedical data

AbstractThere is a huge discrepancy in how researchers implement, evaluate, and report the performance of a machine learning method for classification or segmentation of biomedical data. Poor reporting and inadequate inferences are, however, not unusual to see in current literature. More specifically, vague aims and scope, missing details about the data, ambiguous preprocessing procedures, lack of clarity regarding the method's implementation, poor validation and testing, invalid comparisons between methods, and the absence of a clear rationale for performance metric choices are making it difficult to draw the right conclusions from many studies in the field. This report suggests 10 guidelines and principles that should be followed when reporting the implementation of a method and the evaluation of its performance in order to make the study transparent, interpretable, replicable, and useful. All stages of data processing and method's performance evaluation should be clearly described, and parameters and metric choices must be justified in order to aid readers in appreciating the performance of the method or in comparing it with other relevant methods. We feel that these guidelines are important for clear scientific communication in the field of biomedical data processing.

A Master-Slave Binary Grey Wolf Optimizer for Optimal Feature Selection in Biomedical Data Classification.

A new master-slave binary grey wolf optimizer (MSBGWO) is introduced. A master-slave learning scheme is introduced to the grey wolf optimizer (GWO) to improve its ability to explore and get better solutions in a search space. Five high-dimensional biomedical datasets are used to test the ability of MSBGWO in feature selection. The experimental results of MSBGWO are superior in terms of classification accuracy, precision, recall, F-measure, and number of features selected when compared to those of the binary grey wolf optimizer version 2 (BGWO2), binary genetic algorithm (BGA), binary particle swarm optimization (BPSO), differential evolution (DE) algorithm, and sine-cosine algorithm (SCA).

A hybrid feature selection model based on improved squirrel search algorithm and rank aggregation using fuzzy techniques for biomedical data classification.

Feature selection has gained its importance due to the voluminous nature of the data. Owing to the computational complexity of wrapper approaches, the poor performance of filtering techniques, and the classifier dependency of embedded approaches, hybrid approaches are more commonly used in feature selection. Hybrid approaches use filtering metrics to reduce the computational complexity of wrapper algorithms and are proved to yield better feature subset. Though filtering metrics select the features based on their significance, most of them are unstable and biased towards the metric used. Moreover, the choice of filtering metrics depends largely on the distribution of data and data types. Biomedical datasets contain features with different distribution and types adding to the complexity in the choice of filtering metric. We address this problem by proposing a stable filtering method based on rank aggregation in hybrid feature selection model with Improved Squirrel search algorithm for biomedical datasets. Our proposed model is compared with other well-known and state-of-the-art methods and the results prove that our model exhibited superior performance in terms of classification accuracy and computational time. The robustness of our proposed model is proved by conducting experiments on nine biomedical datasets and with three different classifiers.

Data-driven mechanism based on fuzzy Lagrangian twin parametric-margin support vector machine for biomedical data analysis

This paper proposes a fuzzy-based Lagrangian twin parametric-margin support vector machine (FLTPMSVM) to reduce the effect of the outliers presented in biomedical data. The proposed FLTPMSVM assigns the weights to each data sample on the basis of fuzzy membership values to reduce the effect of outliers. This paper also adopts the square of the 2-norm of slack variables to make the objective function more convex. The proposed FLTPMSVM solves simple linearly convergent iterative schemes instead of solving a pair of quadratic programming problems. No external toolbox is required for the proposed FLTPMSVM as compared to the other methods. To establish the applicability of the proposed FLTPMSVM in the area of biomedical data classification, numerical experiments are performed on several biomedical datasets. The proposed FLTPMSVM gives an improved generalization performance and reduced training cost as compared to support vector machine (SVM), twin support vector machine (TWSVM), fuzzy twin support vector machine (FTSVM), twin parametric-margin support vector machine (TPMSVM) and new fuzzy twin support vector machine (NFTSVM).

Optimal Fuzzy Cluster Partitioning by Crow Search Meta-Heuristic for Biomedical Data Analysis

Biomedical data is often more unstructured in nature, and biomedical data processing task is becoming more complex day by day. Thus, biomedical informatics requires competent data analysis and data mining techniques for designing decision support system's framework to solve clinical and heathcare-related issues. Due to increasingly large and complex data sets and demand of biomedical informatics research, researchers are attracted towards automated machine learning models. This paper is proposed to design an efficient machine learning model based on fuzzy c-means with meta-heuristic optimizations for biomedical data analysis and clustering. The main contributions of this paper are 1) projecting an efficient machine learning model based on fuzzy c-means and meta-heuristic optimization for biomedical data classification, 2) employing benchmark validation techniques and critical hypothesises testing, and 3) providing a background for biomedical data processing with a view of data processing and mining.

1D convolutional neural networks and applications: A survey

During the last decade, Convolutional Neural Networks (CNNs) have become the de facto standard for various Computer Vision and Machine Learning operations. CNNs are feed-forward Artificial Neural Networks (ANNs) with alternating convolutional and subsampling layers. Deep 2D CNNs with many hidden layers and millions of parameters have the ability to learn complex objects and patterns providing that they can be trained on a massive size visual database with ground-truth labels. With a proper training, this unique ability makes them the primary tool for various engineering applications for 2D signals such as images and video frames. Yet, this may not be a viable option in numerous applications over 1D signals especially when the training data is scarce or application specific. To address this issue, 1D CNNs have recently been proposed and immediately achieved the state-of-the-art performance levels in several applications such as personalized biomedical data classification and early diagnosis, structural health monitoring, anomaly detection and identification in power electronics and electrical motor fault detection. Another major advantage is that a real-time and low-cost hardware implementation is feasible due to the simple and compact configuration of 1D CNNs that perform only 1D convolutions (scalar multiplications and additions). This paper presents a comprehensive review of the general architecture and principals of 1D CNNs along with their major engineering applications, especially focused on the recent progress in this field. Their state-of-the-art performance is highlighted concluding with their unique properties. The benchmark datasets and the principal 1D CNN software used in those applications are also publicly shared in a dedicated website. While there has not been a paper on the review of 1D CNNs and its applications in the literature, this paper fulfills this gap.

FR–KDE: A Hybrid Fuzzy Rule-Based Information Fusion Method with its Application in Biomedical Classification

Granular computing (GrC) is an essential tool to solve human real problem since the information granules is close to human perception schemes. In GrC, both classification accuracy and interpretability play significant roles. Fuzzy rule (FR) based classification systems are effective methods solving this problem. However, the accuracy of FR may be decreased when solving some complex application. In this paper, a novel model called FR–KDE integrating the FR and kernel density estimation (KDE) in the framework of Dempster–Shafer evidence theory is proposed to deal with the classification problem. By fusing the result of FR and KDE via the Dempster’s combination rule, it can reduce the uncertainty of FR and obtain better accuracy. To illustrate the effect of the FR–KDE approach, it is applied to the medical data classification problem. Experimentally, the results demonstrate that the FR–KDE method is effective in handling biomedical data classification problems.

Breast cancer data classification using deep neural network

Artificial neural networks and their variants play an important role in the analysis and classification of different biomedical data. Deep learning is an advanced machine learning approach which has been used in many applications in the last few years. Worldwide breast cancer is a major disease for women; it is one of the most challenging jobs to detect at an early stage. The authors in this work have taken an attempt to classify the breast cancer data collected from the UCI machine learning repository. Malignant and benign two different types of breast cancer tumours are classified using deep neural network (DNN). Before classification two pre-processing steps are done for improving the accuracy. The correlation and one-hot encoding of the dataset was done for getting some relevant features that can be used as the input to the DNN. Around 94% of classification accuracy is achieved by using a six-layer DNN classifier. The result is also compared with some earlier works and it is found that the proposed classifier is providing better results as compared to others.

Breast cancer data classification using deep neural network

Artificial neural networks and their variants play an important role in the analysis and classification of different biomedical data. Deep learning is an advanced machine learning approach which has been used in many applications in the last few years. Worldwide breast cancer is a major disease for women; it is one of the most challenging jobs to detect at an early stage. The authors in this work have taken an attempt to classify the breast cancer data collected from the UCI machine learning repository. Malignant and benign two different types of breast cancer tumours are classified using deep neural network (DNN). Before classification two pre-processing steps are done for improving the accuracy. The correlation and one-hot encoding of the dataset was done for getting some relevant features that can be used as the input to the DNN. Around 94% of classification accuracy is achieved by using a six-layer DNN classifier. The result is also compared with some earlier works and it is found that the proposed classifier is providing better results as compared to others.

A study of data pre-processing techniques for imbalanced biomedical data classification

Biomedical data are widely accepted in developing prediction models for identifying a specific tumor, drug discovery and classification of human cancers. However, previous studies usually focused on different classifiers, and overlook the class imbalance problem in real-world biomedical datasets. There are a lack of studies on evaluation of data pre-processing techniques, such as resampling and feature selection, on imbalanced biomedical data learning. The relationship between data pre-processing techniques and the data distributions has never been analysed in previous studies. This article mainly focuses on reviewing and evaluating some popular and recently developed resampling and feature selection methods for class imbalance learning. We analyse the effectiveness of each technique from data distribution perspective. Extensive experiments have been done based on five classifiers, four performance measures, eight learning techniques across twenty real-world datasets. Experimental results show that: (1) resampling and feature selection techniques exhibit better performance using support vector machine (SVM) classifier. However, resampling and Feature Selection techniques perform poorly when using C4.5 decision tree and Linear discriminant analysis classifiers; (2) for datasets with different distributions, techniques such as Random undersampling and Feature Selection perform better than other data pre-processing methods with T Location-Scale distribution when using SVM and KNN (K-nearest neighbours) classifiers. Random oversampling outperforms other methods on Negative Binomial distribution using Random Forest classifier with lower level of imbalance ratio; (3) Feature Selection outperforms other data pre-processing methods in most cases, thus, Feature Selection with SVM classifier is the best choice for imbalanced biomedical data learning.

A study of data pre-processing techniques for imbalanced biomedical data classification

Biomedical data are widely accepted in developing prediction models for identifying a specific tumour, drug discovery and human cancers detection. However, previous studies usually focused on different classifiers, and overlook the class imbalance problem in real-world biomedical datasets. This paper mainly focuses on reviewing and evaluating some popular and recently developed resampling and feature selection (FS) methods for class imbalance learning with data distribution being considered. Experimental results show that: 1) resampling and FS techniques exhibit better performance using support vector machine (SVM) classifier; 2) techniques such as random undersampling and FS perform better than other data pre-processing methods with T location-scale distribution when using SVM and K-nearest neighbours (KNN) classifiers. Random oversampling outperforms other methods on negative binomial distribution using Random Forest with lower level of imbalance ratio; 3) FS outperforms other data pre-processing methods in most cases, thus, FS with SVM classifier is the best choice for imbalanced biomedical data learning.

Generalized Spectral-Analytical Method and Its Applications in Image Analysis and Pattern Recognition Problems

The generalized spectral-analytical method as a new approach to the processing of information arrays is stated. Some theoretical foundations of this method and its applications in different experimental data analysis problems are given. The method is based on the adaptive expansion of initial arrays in the functional bases belonging to the classical algebraic systems of polynomials and functions of continuous and discrete arguments (Jacobi, Chebyshev, Lagrange, Laguerre, Kravchuk, Charlier, and other polynomials). This approach combines analytical and digital data-processing procedures, thus providing a basis for the universal combined technology for the processing of information arrays. An appreciable part of this review is devoted to video data analysis and pattern-recognition problems. In addition, some relevant applications of this method in biomedical and bioinformation data analysis, recognition, classification, and diagnosis problems are described.

Classification of high dimensional biomedical data based on feature selection using redundant removal.

High dimensional biomedical data contain tens of thousands of features, accurate and effective identification of the core features in these data can be used to assist diagnose related diseases. However, there are often a large number of irrelevant or redundant features in biomedical data, which seriously affect subsequent classification accuracy and machine learning efficiency. To solve this problem, a novel filter feature selection algorithm based on redundant removal (FSBRR) is proposed to classify high dimensional biomedical data in this paper. First of all, two redundant criteria are determined by vertical relevance (the relationship between feature and class attribute) and horizontal relevance (the relationship between feature and feature). Secondly, to quantify redundant criteria, an approximate redundancy feature framework based on mutual information (MI) is defined to remove redundant and irrelevant features. To evaluate the effectiveness of our proposed algorithm, controlled trials based on typical feature selection algorithm are conducted using three different classifiers, and the experimental results indicate that the FSBRR algorithm can effectively reduce the feature dimension and improve the classification accuracy. In addition, an experiment of small sample dataset is designed and conducted in the section of discussion and analysis to clarify the specific implementation process of FSBRR algorithm more clearly.

Private naive bayes classification of personal biomedical data: Application in cancer data analysis

Clinicians would benefit from access to predictive models for diagnosis, such as classification of tumors as malignant or benign, without compromising patients’ privacy. In addition, the medical institutions and companies who own these medical information systems wish to keep their models private when in use by outside parties. Fully homomorphic encryption (FHE) enables computation over encrypted medical data while ensuring data privacy. In this paper we use private-key fully homomorphic encryption to design a cryptographic protocol for private Naive Bayes classification. This protocol allows a data owner to privately classify his or her information without direct access to the learned model. We apply this protocol to the task of privacy-preserving classification of breast cancer data as benign or malignant. Our results show that private-key fully homomorphic encryption is able to provide fast and accurate results for privacy-preserving medical classification.

A new complement naïve Bayesian approach for biomedical data classification

Biomedical data classification tasks are very challenging because data is usually large, noised and imbalanced. Particularly the noise can reduce system performance in terms of classification accuracy, time in building a classifier and the size of the classifier. Accordingly, most existing learning algorithms have integrated various approaches to enhance their learning abilities from noisy environments, but the existence of noise can still introduce serious negative impacts. A more reasonable solution might be to employ some preprocessing mechanisms to handle noisy instances before a learner is formed. Therefore, we introduce a method called double learning to improve the classification performance of our model. As to the author’s knowledge, most of the previous works used the normal (noise free) instances for model construction (training) after the noise instances are isolated. This approach increases computational task on model construction for active learners and total computational time for passive learners. It also ignores minority data instance which leads to miss classification of instances from minority group as test cases. The main idea of this paper is to construct a model using noised instances. This approach minimizes the model construction time by reducing the number of instances and improves classification performance. Therefore, only the identified noised data are used for model construction instead of the normal (noise free) data. Since noised instances are used for model construction, the entire naive Bayesian working logic is reversed. This method is called complement naive Bayesian (CNB) which makes use of the idea of complement based learning to improve the accuracy performance. Finally, the performance of the proposed CNB is compared to naive Bayesian and some other classification algorithms with the single photon emission computed tomography, Indian liver patient dataset, Wilt and Tic-Tac-Toe endgame datasets. The experimental results demonstrated that the proposed approach has shown promising results in terms of computational time and accuracy performance on both balanced and imbalanced datasets used.

Imbalanced biomedical data classification using self-adaptive multilayer ELM combined with dynamic GAN

BackgroundImbalanced data classification is an inevitable problem in medical intelligent diagnosis. Most of real-world biomedical datasets are usually along with limited samples and high-dimensional feature. This seriously affects the classification performance of the model and causes erroneous guidance for the diagnosis of diseases. Exploring an effective classification method for imbalanced and limited biomedical dataset is a challenging task.MethodsIn this paper, we propose a novel multilayer extreme learning machine (ELM) classification model combined with dynamic generative adversarial net (GAN) to tackle limited and imbalanced biomedical data. Firstly, principal component analysis is utilized to remove irrelevant and redundant features. Meanwhile, more meaningful pathological features are extracted. After that, dynamic GAN is designed to generate the realistic-looking minority class samples, thereby balancing the class distribution and avoiding overfitting effectively. Finally, a self-adaptive multilayer ELM is proposed to classify the balanced dataset. The analytic expression for the numbers of hidden layer and node is determined by quantitatively establishing the relationship between the change of imbalance ratio and the hyper-parameters of the model. Reducing interactive parameters adjustment makes the classification model more robust.ResultsTo evaluate the classification performance of the proposed method, numerical experiments are conducted on four real-world biomedical datasets. The proposed method can generate authentic minority class samples and self-adaptively select the optimal parameters of learning model. By comparing with W-ELM, SMOTE-ELM, and H-ELM methods, the quantitative experimental results demonstrate that our method can achieve better classification performance and higher computational efficiency in terms of ROC, AUC, G-mean, and F-measure metrics.ConclusionsOur study provides an effective solution for imbalanced biomedical data classification under the condition of limited samples and high-dimensional feature. The proposed method could offer a theoretical basis for computer-aided diagnosis. It has the potential to be applied in biomedical clinical practice.

Exploring Active Learning Based on Representativeness and Uncertainty for Biomedical Data Classification.

Nowadays, there is an abundance of biomedical data, such as images and genetic sequences, among others. However, there is a lack of annotation to such volume of data, due to the high costs involved to perform this task. Thus, it is mandatory to develop techniques to ease the burden of human annotation. To reach such goal active learning strategies can be applied. However, the state-of-the-art active learning methods, generally, are not feasible to lead with real-world datasets. Another important issue, that is generally neglected by these methods, is related to the conception that the classifier tends to learn more and more at each iteration. Their adopted selection criteria do not properly exploit the knowledge of the classifier. Therefore, in this paper, we propose the use of an active learning approach, in order to leverage the learning process, including the proposal of a novel active learning strategy. The main difference of our proposed strategy is related to the participation of the classifier in an extremely active way in its learning process. So, we can better maximize and prioritize the knowledge that is obtained by the classifier at each iteration, making use of this knowledge in a more appropriate and useful way when selecting more informative samples. To do so, in our selection criteria, we give significant importance to the classifications suggested by the classifier. In addition, jointly with the participation and the knowledge of the classifier, we consider both uncertainty and representativeness criteria through a fine-grained analysis of the samples. Experimental results show that our novel active learning approach outperforms state-of-the-art active learning methods, considering several supervised classifiers. Hence, dealing with real dataset problems in a better way, equalizing the tradeoff between annotation task and higher accuracy rates.

A Method of Biomedical Information Classification Based on Particle Swarm Optimization with Inertia Weight and Mutation.

With the rapid development of information technology and biomedical engineering, people can get more and more information. At the same time, they begin to study how to apply the advanced technology in biomedical information. The main research of this paper is to optimize the machine learning method by particle swarm optimization (PSO) and apply it in the classification of biomedical data. In order to improve the performance of the classification model, we compared the different inertia weight strategies and mutation strategies and their combinations with PSO, and obtained the best inertia weight strategy without mutation, the best mutation strategy without inertia weight and the best combination of the two. Then, we used the three PSO algorithms to optimize the parameters of support vector machine in the classification of biomedical data. We found that the PSO algorithm with the combination of inertia weight and mutation strategy and the inertia weight strategy that we proposed could improve the classification accuracy. This study has an important reference value for the prediction of clinical diseases.