Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Improving KNN by Gases Brownian Motion Optimization Algorithm to Breast Cancer Detection

In the last decade, the application of information technology and artificial intelligence algorithms are widely developed in collecting information of cancer patients and detecting them based on proposing various detection algorithms. The K-Nearest-Neighbor classification algorithm (KNN) is one of the most popular of detection algorithms, which has two challenges in determining the value of k and the volume of computations proportional to the size of the data and sample selected for training. In this paper, the Gaussian Brownian Motion Optimization (GBMO) algorithm is utilized for improving the KNN performance to breast cancer detection. To achieve to this aim, each gas molecule contains the information such as a selected subset of features to apply the KNN and k value. The GBMO has lower time-complexity order than other algorithms and has also been observed to perform better than other optimization algorithms in other applications. The algorithm and three well-known meta-heuristic algorithms such as Genetic Algorithm (GA), Particle Swarm Optimization (PSO) and Imperialist Competitive Algorithm (ICA) have been implemented on five benchmark functions and compared the obtained results. The GBMO+KNN performed on three benchmark datasets of breast cancer from UCI and the obtained results are compared with other existing cancer detection algorithms. These comparisons show significantly improves this classification accuracy with the proposed detection algorithm

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

Methods to Improve the Prediction Accuracy and Performance of Ensemble Models

The application of ensemble predictive models has been an important research area in predicting medical diagnostics, engineering diagnostics, and other related smart devices and related technologies. Most of the current predictive models are complex and not reliable despite numerous efforts in the past by the research community. The performance accuracy of the predictive models have not always been realised due to many factors such as complexity and class imbalance. Therefore there is a need to improve the predictive accuracy of current ensemble models and to enhance their applications and reliability and non-visual predictive tools. The research work presented in this thesis has adopted a pragmatic phased approach to propose and develop new ensemble models using multiple methods and validated the methods through rigorous testing and implementation in different phases. The first phase comprises of empirical investigations on standalone and ensemble algorithms that were carried out to ascertain their performance effects on complexity and simplicity of the classifiers. The second phase comprises of an improved ensemble model based on the integration of Extended Kalman Filter (EKF), Radial Basis Function Network (RBFN) and AdaBoost algorithms. The third phase comprises of an extended model based on early stop concepts, AdaBoost algorithm, and statistical performance of the training samples to minimize overfitting performance of the proposed model. The fourth phase comprises of an enhanced analytical multivariate logistic regression predictive model developed to minimize the complexity and improve prediction accuracy of logistic regression model. To facilitate the practical application of the proposed models; an ensemble non-invasive analytical tool is proposed and developed. The tool links the gap between theoretical concepts and practical application of theories to predict breast cancer survivability. The empirical findings suggested that: (1) increasing the complexity and topology of algorithms does not necessarily lead to a better algorithmic performance, (2) boosting by resampling performs slightly better than boosting by reweighting, (3) the prediction accuracy of the proposed ensemble EKF-RBFN-AdaBoost model performed better than several established ensemble models, (4) the proposed early stopped model converges faster and minimizes overfitting better compare with other models, (5) the proposed multivariate logistic regression concept minimizes the complexity models (6) the performance of the proposed analytical non-invasive tool performed comparatively better than many of the benchmark analytical tools used in predicting breast cancers and diabetics ailments. The research contributions to ensemble practice are: (1) the integration and development of EKF, RBFN and AdaBoost algorithms as an ensemble model, (2) the development and validation of ensemble model based on early stop concepts, AdaBoost, and statistical concepts of the training samples, (3) the development and validation of predictive logistic regression model based on breast cancer, and (4) the development and validation of a non-invasive breast cancer analytic tools based on the proposed and developed predictive models in this thesis. To validate prediction accuracy of ensemble models, in this thesis the proposed models were applied in modelling breast cancer survivability and diabetics’ diagnostic tasks. In comparison with other established models the simulation results of the models showed improved predictive accuracy. The research outlines the benefits of the proposed models, whilst proposes new directions for future work that could further extend and improve the proposed models discussed in this thesis

The Combination of Mammography and MRI for Diagnosing Breast Cancer Using Fuzzy NN and SVM

Breast cancer is one of the common cancers among women so that early diagnosing of it can effectively help its treatment in this study, considering combination of Mammography and MRI pictures, we will try to recognize glands in existing pictures which identify all around of gland complete and precisely and separate it completely. In this method using artificial intelligence algorithm such as Affine transformation, Gabor filter, neural network, and support vector machine, image analysis will be carried out. The accuracy of proposed method is 98.14. In this work a special framework is presented which simplifies cancer diagnosis. The algorithm of proposed method is tested on z16 images. High speed and lack of human error are the most important factors in proposed intelligent system