Multi-and many-objective optimization: present and future in de novo drug design

de novo Drug Design (dnDD) aims to create new molecules that satisfy multiple conflicting objectives. Since several desired properties can be considered in the optimization process, dnDD is naturally categorized as a many-objective optimization problem (ManyOOP), where more than three objectives must be simultaneously optimized. However, a large number of objectives typically pose several challenges that affect the choice and the design of optimization methodologies. Herein, we cover the application of multi- and many-objective optimization methods, particularly those based on Evolutionary Computation and Machine Learning techniques, to enlighten their potential application in dnDD. Additionally, we comprehensively analyze how molecular properties used in the optimization process are applied as either objectives or constraints to the problem. Finally, we discuss future research in many-objective optimization for dnDD, highlighting two important possible impacts: i) its integration with the development of multi-target approaches to accelerate the discovery of innovative and more efficacious drug therapies and ii) its role as a catalyst for new developments in more fundamental and general methodological frameworks in the field.

A New Many-Objective Evolutionary Algorithm Based on Generalized Pareto Dominance

In the past several years, it has become apparent that the effectiveness of Pareto-dominance-based multiobjective evolutionary algorithms deteriorates progressively as the number of objectives in the problem, given by M , grows. This is mainly due to the poor discriminability of Pareto optimality in many-objective spaces (typically M ≥ 4 ). As a consequence, research efforts have been driven in the general direction of developing solution ranking methods that do not rely on Pareto dominance (e.g., decomposition-based techniques), which can provide sufficient selection pressure. However, it is still a nontrivial issue for many existing non-Pareto-dominance-based evolutionary algorithms to deal with unknown irregular Pareto front shapes. In this article, a new many-objective evolutionary algorithm based on the generalization of Pareto optimality (GPO) is proposed, which is simple, yet effective, in addressing many-objective optimization problems. The proposed algorithm used an "( M-1 ) + 1" framework of GPO dominance, ( M-1 )-GPD for short, to rank solutions in the environmental selection step, in order to promote convergence and diversity simultaneously. To be specific, we apply M symmetrical cases of ( M-1 )-GPD, where each enhances the selection pressure of M-1 objectives by expanding the dominance area of solutions, while remaining unchanged for the one objective left out of that process. Experiments demonstrate that the proposed algorithm is very competitive with the state-of-the-art methods to which it is compared, on a variety of scalable benchmark problems. Moreover, experiments on three real-world problems have verified that the proposed algorithm can outperform the others on each of these problems.

Semi-Automatic Ontology Matching Based on Interactive Compact Genetic Algorithm

Ontology matching is able to identify the entity correspondences between two heterogeneous ontologies, which is an effective method to solve the data heterogeneous problem on the Semantic Web. Traditional fully-automatic ontology matching techniques suffer from the limitation of similarity measure, whose alignment’s quality cannot be ensured. To overcome this drawback, in this work, an Interactive Compact Genetic Algorithm (ICGA)-based ontology matching technique is proposed, which utilizes both the compact encoding mechanism and expert interacting mechanism to improve the algorithm’s performance and the alignment’s quality. In addition, an optimization model is established to formally define the ontology entity matching problem, and an efficient interacting strategy is proposed, which is able to reduce the expert’s workload and maximize his working value. The experiment uses Ontology Alignment Evaluation Initiative (OAEI)’s benchmark to test our proposal’s performance. The experimental results show that our approach is able to make use of the expert knowledge to improve the alignment’s quality, and it also outperforms OAEI’s participants.

A Reference Point Selection and Direction Guidance-Based Algorithm for Large-Scale Multi-Objective Optimization

Designing efficient algorithms for the large-scale multi-objective problems (LSMOPs) is a very challenging problem currently. To tackle LSMOPs, we first design a new reference points selection strategy to enhance the diversity of algorithms and avoid the algorithm falling into local minima. The strategy selects not only a part of nondominated solutions with the largest crowding distance, but also a part of relatively uniformly distributed solutions as the reference points. In this way, much better diversity and convergence can be obtained. Second, we propose a direction-guided offspring generation strategy, where a type of potential directions is designed to generate the promising solutions which can balance the convergence and diversity of the obtained solutions and improve the effectiveness of the algorithm significantly. Based on the two proposed strategies, we propose a new effective algorithm for LSMOPs. Numerical experiments are executed on two widely used large-scale multi-objective benchmark problem sets with 200, 500 and 1000 decision variables and a comparison with five state-of-the-art algorithms is made. The experimental results show that our proposed algorithm is effective and can obtain significantly better solutions than the compared algorithms.