Feature Selection via Swarm Intelligence for Determining Protein Essentiality

Binary Horse Optimization Algorithm for Feature Selection

The bio-inspired research field has evolved greatly in the last few years due to the large number of novel proposed algorithms and their applications. The sources of inspiration for these novel bio-inspired algorithms are various, ranging from the behavior of groups of animals to the properties of various plants. One problem is the lack of one bio-inspired algorithm which can produce the best global solution for all types of optimization problems. The presented solution considers the proposal of a novel approach for feature selection in classification problems, which is based on a binary version of a novel bio-inspired algorithm. The principal contributions of this article are: (1) the presentation of the main steps of the original Horse Optimization Algorithm (HOA), (2) the adaptation of the HOA to a binary version called the Binary Horse Optimization Algorithm (BHOA), (3) the application of the BHOA in feature selection using nine state-of-the-art datasets from the UCI machine learning repository and the classifiers Random Forest (RF), Support Vector Machines (SVM), Gradient Boosted Trees (GBT), Logistic Regression (LR), K-Nearest Neighbors (K-NN), and Naïve Bayes (NB), and (4) the comparison of the results with the ones obtained using the Binary Grey Wolf Optimizer (BGWO), Binary Particle Swarm Optimization (BPSO), and Binary Crow Search Algorithm (BCSA). The experiments show that the BHOA is effective and robust, as it returned the best mean accuracy value and the best accuracy value for four and seven datasets, respectively, compared to BGWO, BPSO, and BCSA, which returned the best mean accuracy value for four, two, and two datasets, respectively, and the best accuracy value for eight, seven, and five datasets, respectively.

A Novel Collaborative Filtering Model-Based Method for Identifying Essential Proteins

Considering that traditional biological experiments are expensive and time consuming, it is important to develop effective computational models to infer potential essential proteins. In this manuscript, a novel collaborative filtering model-based method called CFMM was proposed, in which, an updated protein–domain interaction (PDI) network was constructed first by applying collaborative filtering algorithm on the original PDI network, and then, through integrating topological features of PDI networks with biological features of proteins, a calculative method was designed to infer potential essential proteins based on an improved PageRank algorithm. The novelties of CFMM lie in construction of an updated PDI network, application of the commodity-customer-based collaborative filtering algorithm, and introduction of the calculation method based on an improved PageRank algorithm, which ensured that CFMM can be applied to predict essential proteins without relying entirely on known protein–domain associations. Simulation results showed that CFMM can achieve reliable prediction accuracies of 92.16, 83.14, 71.37, 63.87, 55.84, and 52.43% in the top 1, 5, 10, 15, 20, and 25% predicted candidate key proteins based on the DIP database, which are remarkably higher than 14 competitive state-of-the-art predictive models as a whole, and in addition, CFMM can achieve satisfactory predictive performances based on different databases with various evaluation measurements, which further indicated that CFMM may be a useful tool for the identification of essential proteins in the future.

A novel scheme for essential protein discovery based on multi-source biological information

Mining essential protein is crucial for discovering the process of cellular organization and viability. At present, there are many computational methods for essential proteins detecting. However, these existing methods only focus on the topological information of the networks and ignore the biological information of proteins, which lead to low accuracy of essential protein identification. Therefore, this paper presents a new essential proteins prediction strategy, called DEP-MSB which integrates a variety of biological information including gene expression profiles, GO annotations, and Domain interaction strength. In order to evaluate the performance of DEP-MSB, we conduct a series of experiments on the yeast PPI network and the experimental results have shown that the proposed algorithm DEP-MSB is more superior to the other existing traditional methods and has obviously improvement in prediction accuracy.