A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies

A hybrid multi-objective whale optimization algorithm for analyzing microarray data based on Apache Spark

A microarray is a revolutionary tool that generates vast volumes of data that describe the expression profiles of genes under investigation that can be qualified as Big Data. Hadoop and Spark are efficient frameworks, developed to store and analyze Big Data. Analyzing microarray data helps researchers to identify correlated genes. Clustering has been successfully applied to analyze microarray data by grouping genes with similar expression profiles into clusters. The complex nature of microarray data obligated clustering methods to employ multiple evaluation functions to ensure obtaining solutions with high quality. This transformed the clustering problem into a Multi-Objective Problem (MOP). A new and efficient hybrid Multi-Objective Whale Optimization Algorithm with Tabu Search (MOWOATS) was proposed to solve MOPs. In this article, MOWOATS is proposed to analyze massive microarray datasets. Three evaluation functions have been developed to ensure an effective assessment of solutions. MOWOATS has been adapted to run in parallel using Spark over Hadoop computing clusters. The quality of the generated solutions was evaluated based on different indices, such as Silhouette and Davies-Bouldin indices. The obtained clusters were very similar to the original classes. Regarding the scalability, the running time was inversely proportional to the number of computing nodes.

A Multi-Objective Optimization Method for Hospital Admission Problem—A Case Study on Covid-19 Patients

The wide spread of Covid-19 has led to infecting a huge number of patients, simultaneously. This resulted in a massive number of requests for medical care, at the same time. During the first wave of Covid-19, many people were not able to get admitted to appropriate hospitals because of the immense number of patients. Admitting patients to suitable hospitals can decrease the in-bed time of patients, which can lead to saving many lives. Also, optimizing the admission process can minimize the waiting time for medical care, which can save the lives of severe cases. The admission process needs to consider two main criteria: the admission time and the readiness of the hospital that will accept the patients. These two objectives convert the admission problem into a Multi-Objective Problem (MOP). Pareto Optimization (PO) is a common multi-objective optimization method that has been applied to different MOPs and showed its ability to solve them. In this paper, a PO-based algorithm is proposed to deal with admitting Covid-19 patients to hospitals. The method uses PO to vary among hospitals to choose the most suitable hospital for the patient with the least admission time. The method also considers patients with severe cases by admitting them to hospitals with the least admission time regardless of their readiness. The method has been tested over a real-life dataset that consisted of 254 patients obtained from King Faisal specialist hospital in Saudi Arabia. The method was compared with the lexicographic multi-objective optimization method regarding admission time and accuracy. The proposed method showed its superiority over the lexicographic method regarding the two criteria, which makes it a good candidate for real-life admission systems.

Influence of the go-based semantic similarity measures in multi-objective gene clustering algorithm performance

Using a prior biological knowledge of relationships and genetic functions for gene similarity, from repository such as the Gene Ontology (GO), has shown good results in multi-objective gene clustering algorithms. In this scenario and to obtain useful clustering results, it would be helpful to know which measure of biological similarity between genes should be employed to yield meaningful clusters that have both similar expression patterns (co-expression) and biological homogeneity. In this paper, we studied the influence of the four most used GO-based semantic similarity measures in the performance of a multi-objective gene clustering algorithm. We used four publicly available datasets and carried out comparative studies based on performance metrics for the multi-objective optimization field and clustering performance indexes. In most of the cases, using Jiang-Conrath and Wang similarities stand in terms of multi-objective metrics. In clustering properties, Resnik similarity allows to achieve the best values of compactness and separation and therefore of co-expression of groups of genes. Meanwhile, in biological homogeneity, the Wang similarity reports greater number of significant GO terms. However, statistical, visual, and biological significance tests showed that none of the GO-based semantic similarity measures stand out above the rest in order to significantly improve the performance of the multi-objective gene clustering algorithm.

Application of Systems Engineering Principles and Techniques in Biological Big Data Analytics: A Review

In the past few decades, we have witnessed tremendous advancements in biology, life sciences and healthcare. These advancements are due in no small part to the big data made available by various high-throughput technologies, the ever-advancing computing power, and the algorithmic advancements in machine learning. Specifically, big data analytics such as statistical and machine learning has become an essential tool in these rapidly developing fields. As a result, the subject has drawn increased attention and many review papers have been published in just the past few years on the subject. Different from all existing reviews, this work focuses on the application of systems, engineering principles and techniques in addressing some of the common challenges in big data analytics for biological, biomedical and healthcare applications. Specifically, this review focuses on the following three key areas in biological big data analytics where systems engineering principles and techniques have been playing important roles: the principle of parsimony in addressing overfitting, the dynamic analysis of biological data, and the role of domain knowledge in biological data analytics.

RoCoLe: A robusta coffee leaf images dataset for evaluation of machine learning based methods in plant diseases recognition

In this article we introduce a robusta coffee leaf images dataset called RoCoLe. The dataset contains 1560 leaf images with visible red mites and spots (denoting coffee leaf rust presence) for infection cases and images without such structures for healthy cases. In addition, the data set includes annotations regarding objects (leaves), state (healthy and unhealthy) and the severity of disease (leaf area with spots). Images were all obtained in real-world conditions in the same coffee plants field using a smartphone camera. RoCoLe data set facilitates the evaluation of the performance of machine learning algorithms used in image segmentation and classification problems related to plant diseases recognition. The current dataset is freely and publicly available at https://doi.org/10.17632/c5yvn32dzg.2.