iANP-EC: Identifying Anticancer Natural Products Using Ensemble Learning Incorporated with Evolutionary Computation.

Cancer is one of the most deadly diseases that annually kills millions of people worldwide. The investigation on anticancer medicines has never ceased to seek better and more adaptive agents with fewer side effects. Besides chemically synthetic anticancer compounds, natural products are scientifically proved as a highly potential alternative source for anticancer drug discovery. Along with experimental approaches being used to find anticancer drug candidates, computational approaches have been developed to virtually screen for potential anticancer compounds. In this study, we construct an ensemble computational framework, called iANP-EC, using machine learning approaches incorporated with evolutionary computation. Four learning algorithms (k-NN, SVM, RF, and XGB) and four molecular representation schemes are used to build a set of classifiers, among which the top-four best-performing classifiers are selected to form an ensemble classifier. Particle swarm optimization (PSO) is used to optimise the weights used to combined the four top classifiers. The models are developed by a set of curated 997 compounds which are collected from the NPACT and CancerHSP databases. The results show that iANP-EC is a stable, robust, and effective framework that achieves an AUC-ROC value of 0.9193 and an AUC-PR value of 0.8366. The comparative analysis of molecular substructures between natural anticarcinogens and nonanticarcinogens partially unveils several key substructures that drive anticancerous activities. We also deploy the proposed ensemble model as an online web server with a user-friendly interface to support the research community in identifying natural products with anticancer activities.

A Hybrid Evolutionary Computation Approach to Inducing Transfer Classifiers for Domain Adaptation.

Domain adaptation utilizes learned knowledge from an existing domain (source domain) to improve the classification performance of another related, but not identical, domain (target domain). Most existing domain adaptation methods first perform domain alignment, then apply standard classification algorithms. Transfer classifier induction is an emerging domain adaptation approach that incorporates the domain alignment into the process of building an adaptive classifier instead of using a standard classifier. Although transfer classifier induction approaches have achieved promising performance, they are mainly gradient-based approaches which can be trapped at local optima. In this article, we propose a transfer classifier induction algorithm based on evolutionary computation to address the above limitation. Specifically, a novel representation of the transfer classifier is proposed which has much lower dimensionality than the standard representation in existing transfer classifier induction approaches. We also propose a hybrid process to optimize two essential objectives in domain adaptation: 1) the manifold consistency and 2) the domain difference. Particularly, the manifold consistency is used in the main fitness function of the evolutionary search to preserve the intrinsic manifold structure of the data. The domain difference is reduced via a gradient-based local search applied to the top individuals generated by the evolutionary search. The experimental results show that the proposed algorithm can achieve better performance than seven state-of-the-art traditional domain adaptation algorithms and four state-of-the-art deep domain adaptation algorithms.

A New Binary Particle Swarm Optimization Approach: Momentum and Dynamic Balance Between Exploration and Exploitation.

Particle swarm optimization (PSO) is a heuristic optimization algorithm generally applied to continuous domains. Binary PSO is a form of PSO applied to binary domains but uses the concepts of velocity and momentum from continuous PSO, which leads to its limited performance. In our previous work, we reformulated momentum as a stickiness property and velocity as a flipping probability to develop sticky binary PSO. The initial design provides a good base, but many key factors need to be investigated. In this article, we propose a new algorithm called dynamic sticky binary PSO by developing a dynamic parameter control strategy based on an investigation of exploration and exploitation in the binary search spaces. The proposed algorithm is compared with four state-of-the-art dynamic binary algorithms on two types of binary problems: 1) knapsack and 2) feature selection. The experimental results on the knapsack datasets show that the new velocity and momentum assist sticky binary PSO in evolving better solutions than the benchmark algorithms. On feature selection, the dynamic strategy takes the advantages of these two newly defined movement concepts to help the proposed algorithm to produce smaller feature subsets with higher classification performance. This is the first time in the binary PSO, the four important concepts, that is, velocity, momentum, exploration, and exploitation, are investigated systematically to capture the properties of the binary search spaces to evolve better solutions for binary problems.