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

Breast Cancer Classification by Gene Expression Analysis using Hybrid Feature Selection and Hyper-heuristic Adaptive Universum Support Vector Machine

Comprehensive assessments of the molecular characteristics of breast cancer from gene expression patterns can aid in the early identification and treatment of tumor patients. The enormous scale of gene expression data obtained through microarray sequencing increases the difficulty of training the classifier due to large-scale features. Selecting pivotal gene features can minimize high dimensionality and the classifier complexity with improved breast cancer detection accuracy. However, traditional filter and wrapper-based selection methods have scalability and adaptability issues in handling complex gene features. This paper presents a hybrid feature selection method of Mutual Information Maximization - Improved Moth Flame Optimization (MIM-IMFO) for gene selection along with an advanced Hyper-heuristic Adaptive Universum Support classification model Vector Machine (HH-AUSVM) to improve cancer detection rates. The hybrid gene selection method is developed by performing filter-based selection using MIM in the first stage followed by the wrapper method in the second stage, to obtain the pivotal features and remove the inappropriate ones. This method improves standard MFO by a hybrid exploration/exploitation phase to accomplish a better trade-off between exploration and exploitation phases. The classifier HH-AUSVM is formulated by integrating the Adaptive Universum learning approach to the hyper- heuristics-based parameter optimized SVM to tackle the class samples imbalance problem. Evaluated on breast cancer gene expression datasets from Mendeley Data Repository, this proposed MIM-IMFO gene selection-based HH-AUSVM classification approach provided better breast cancer detection with high accuracies of 95.67%, 96.52%, 97.97% and 95.5% and less processing time of 4.28, 3.17, 9.45 and 6.31 seconds, respectively

A data mining framework based on boundary-points for gene selection from DNA-microarrays: Pancreatic Ductal Adenocarcinoma as a case study

[EN] Gene selection (or feature selection) from DNA-microarray data can be focused on different techniques, which generally involve statistical tests, data mining and machine learning. In recent years there has been an increasing interest in using hybrid-technique sets to face the problem of meaningful gene selection; nevertheless, this issue remains a challenge. In an effort to address the situation, this paper proposes a novel hybrid framework based on data mining techniques and tuned to select gene subsets, which are meaningfully related to the target disease conducted in DNA-microarray experiments. For this purpose, the framework above deals with approaches such as statistical significance tests, cluster analysis, evolutionary computation, visual analytics and boundary points. The latter is the core technique of our proposal, allowing the framework to define two methods of gene selection. Another novelty of this work is the inclusion of the age of patients as an additional factor in our analysis, which can leading to gaining more insight into the disease. In fact, the results reached in this research have been very promising and have shown their biological validity. Hence, our proposal has resulted in a methodology that can be followed in the gene selection process from DNA-microarray data

Examining applying high performance genetic data feature selection and classification algorithms for colon cancer diagnosis

Background and Objectives: This paper examines the accuracy and efficiency (time complexity) of high performance genetic data feature selection and classification algorithms for colon cancer diagnosis. The need for this research derives from the urgent and increasing need for accurate and efficient algorithms. Colon cancer is a leading cause of death worldwide, hence it is vitally important for the cancer tissues to be expertly identified and classified in a rapid and timely manner, to assure both a fast detection of the disease and to expedite the drug discovery process. Methods: In this research, a three-phase approach was proposed and implemented: Phases One and Two examined the feature selection algorithms and classification algorithms employed separately, and Phase Three examined the performance of the combination of these. Results: It was found from Phase One that the Particle Swarm Optimization (PSO) algorithm performed best with the colon dataset as a feature selection (29 genes selected) and from Phase Two that the Sup- port Vector Machine (SVM) algorithm outperformed other classifications, with an accuracy of almost 86%. It was also found from Phase Three that the combined use of PSO and SVM surpassed other algorithms in accuracy and performance, and was faster in terms of time analysis (94%). Conclusions: It is concluded that applying feature selection algorithms prior to classification algorithms results in better accuracy than when the latter are applied alone. This conclusion is important and significant to industry and society