In the recent few years, an increasing number of studies have shown that microRNAs (miRNAs) play critical roles in many fundamental and important biological processes. As one of pathogenetic factors, the molecular mechanisms underlying human complex diseases still have not been completely understood from the perspective of miRNA. Predicting potential miRNA-disease associations makes important contributions to understanding the pathogenesis of diseases, developing new drugs, and formulating individualized diagnosis and treatment for diverse human complex diseases. Instead of only depending on expensive and time-consuming biological experiments, computational prediction models are effective by predicting potential miRNA-disease associations, prioritizing candidate miRNAs for the investigated diseases, and selecting those miRNAs with higher association probabilities for further experimental validation. In this study, Path-Based MiRNA-Disease Association (PBMDA) prediction model was proposed by integrating known human miRNA-disease associations, miRNA functional similarity, disease semantic similarity, and Gaussian interaction profile kernel similarity for miRNAs and diseases. This model constructed a heterogeneous graph consisting of three interlinked sub-graphs and further adopted depth-first search algorithm to infer potential miRNA-disease associations. As a result, PBMDA achieved reliable performance in the frameworks of both local and global LOOCV (AUCs of 0.8341 and 0.9169, respectively) and 5-fold cross validation (average AUC of 0.9172). In the cases studies of three important human diseases, 88% (Esophageal Neoplasms), 88% (Kidney Neoplasms) and 90% (Colon Neoplasms) of top-50 predicted miRNAs have been manually confirmed by previous experimental reports from literatures. Through the comparison performance between PBMDA and other previous models in case studies, the reliable performance also demonstrates that PBMDA could serve as a powerful computational tool to accelerate the identification of disease-miRNA associations. Identification of miRNA-disease associations is considered as a key way for the development of pathology, diagnose and therapy. Computational prediction models contribute to discovering the underlying disease-related miRNAs on a large scale. Based on the assumption that functionally related miRNAs tend to be involved in phenotypically similar disease and vice versa, the model of PBMDA was developed to prioritize the underlying miRNA-disease associations by adopting a special depth-first search algorithm in a heterogeneous graph, which was composed of known miRNA-disease association network, miRNA similarity network, and disease similarity network. Through leave-one-out cross validation and 5-fold cross validation, the promising results demonstrated the effectiveness of the proposed model. We further implemented the case studies of three important human complex diseases, 88%, 88% and 90% of top-50 predicted miRNA-disease associations have been manually confirmed based on recent experimental reports. It is anticipated that PBMDA could prioritize the most potential miRNA-disease associations on a large scale for advancing the progress of biological experiment validation in the future, which could further contribute to the understanding of complex disease mechanisms.

The first cooperative co-evolutionary algorithm (CCEA) was proposed by Potter and De Jong in 1994 and since then many CCEAs have been proposed and successfully applied to solving various complex optimization problems. In applying CCEAs, the complex optimization problem is decomposed into multiple subproblems, and each subproblem is solved with a separate subpopulation, evolved by an individual evolutionary algorithm (EA). Through cooperative co-evolution of multiple EA subpopulations, a complete problem solution is acquired by assembling the representative members from each subpopulation. The underlying divide-and-conquer and collaboration mechanisms enable CCEAs to tackle complex optimization problems efficiently, and hence CCEAs have been attracting wide attention in the EA community. This paper presents a comprehensive survey of these CCEAs, covering problem decomposition, collaborator selection, individual fitness evaluation, subproblem resource allocation, implementations, benchmark test problems, control parameters, theoretical analyses, and applications. The unsolved challenges and potential directions for their solutions are discussed.

A multifactorial evolutionary algorithm (MFEA) is a recently proposed algorithm for evolutionary multitasking, which optimizes multiple optimization tasks simultaneously. With the design of knowledge transfer among different tasks, MFEA has demonstrated the capability to outperform its single-task counterpart in terms of both convergence speed and solution quality. In MFEA, the knowledge transfer across tasks is realized via the crossover between solutions that possess different skill factors. This crossover is thus essential to the performance of MFEA. However, we note that the present MFEA and most of its existing variants only employ a single crossover for knowledge transfer, and fix it throughout the evolutionary search process. As different crossover operators have a unique bias in generating offspring, the appropriate configuration of crossover for knowledge transfer in MFEA is necessary toward robust search performance, for solving different problems. Nevertheless, to the best of our knowledge, there is no effort being conducted on the adaptive configuration of crossovers in MFEA for knowledge transfer, and this article thus presents an attempt to fill this gap. In particular, here, we first investigate how different types of crossover affect the knowledge transfer in MFEA on both single-objective (SO) and multiobjective (MO) continuous optimization problems. Furthermore, toward robust and efficient multitask optimization performance, we propose a new MFEA with adaptive knowledge transfer (MFEA-AKT), in which the crossover operator employed for knowledge transfer is self-adapted based on the information collected along the evolutionary search process. To verify the effectiveness of the proposed method, comprehensive empirical studies on both SO and MO multitask benchmarks have been conducted. The experimental results show that the proposed MFEA-AKT is able to identify the appropriate knowledge transfer crossover for different optimization problems and even at different optimization stages along the search, which thus leads to superior or competitive performances when compared to the MFEAs with fixed knowledge transfer crossover operators.

This paper suggests a multimodal multi-objective evolutionary algorithm with dual clustering in decision and objective spaces. One clustering is run in decision space to gather nearby solutions, which will classify solutions into multiple local clusters. Non-dominated solutions within each local cluster are first selected to maintain local Pareto sets, and the remaining ones with good convergence in objective space are also selected, which will form a temporary population with more than N solu-tions (N is the population size). After that, a second clustering is run in objective space for this temporary population to get N final clusters with good diversity in objective space. Finally, a pruning process is repeatedly run on the above clusters until each cluster has only one solution, which removes the most crowded solution in decision space from the most crowded cluster in objective space each time. This way, the clustering in decision space can distinguish all Pareto sets and avoid the loss of local Pareto sets,while that in objective space can maintain diversity in objective space. When solving all the benchmark problems from the competition of multimodal multi-objective optimization in IEEE Congress on Evolutionary Computation 2019, the experi-ments validate our advantages to maintain diversity in both objective and decision spaces.

Tchebycheff decomposition represents one of the most widely used decomposition approaches that can convert a multiobjective optimization problem into a set of scalar optimization subproblems. Nevertheless, the geometric properties of the subproblem objective functions in Tchebycheff decomposition have not been explicitly studied. This paper proposes a Tchebycheff decomposition with lp-norm constraint on direction vectors in which the subproblem objective functions are endowed with clear geometric property. Especially, the Tchebycheff decomposition with l ₂ -norm constraint on direction vectors is taken as an example to illustrate its advantage. A new unary R ₂ indicator is also introduced to approximate the hyper-volume metric and justify the efficiency of the proposed Tchebycheff decomposition. A resultant Tchebycheff decomposition-based multiobjective evolutionary algorithm (MOEA) with l ₂ -norm constraint and a new population update strategy is proposed to solve multiobjective optimization problems. The experimental results on both benchmark and real-world multiobjective optimization problems show that the proposed algorithm is capable of obtaining high quality solutions compared with other state-of-the-art MOEAs.

With the increasing prevalence of autism spectrum disorder (ASD), it is important to identify ASD patients for effective treatment and intervention, especially in early childhood. Neuroimaging techniques have been used to characterize the complex biomarkers based on the functional connectivity anomalies in the ASD. However, the diagnosis of ASD still adopts the symptom-based criteria by clinical observation. The existing computational models tend to achieve unreliable diagnostic classification on the large-scale aggregated data sets. In this work, we propose a novel graph-based classification model using the deep belief network (DBN) and the Autism Brain Imaging Data Exchange (ABIDE) database, which is a worldwide multisite functional and structural brain imaging data aggregation. The remarkable connectivity features are selected through a graph extension of K-nearest neighbors and then refined by a restricted path-based depth-first search algorithm. Thanks to the feature reduction, lower computational complexity could contribute to the shortening of the training time. The automatic hyperparameter-tuning technique is introduced to optimize the hyperparameters of the DBN by exploring the potential parameter space. The simulation experiments demonstrate the superior performance of our model, which is 6.4% higher than the best result reported on the ABIDE database. We also propose to use the data augmentation and the oversampling technique to identify further the possible subtypes within the ASD. The interpretability of our model enables the identification of the most remarkable autistic neural correlation patterns from the data-driven outcomes.