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A large number of clinical observations have showed that metabolites are involved in a variety of important human diseases in the recent years. Nonetheless, the inherent noise and incompleteness in the existing biological datasets are tough factors which limit the prediction accuracy of current computational methods. To solve this problem, in this paper, a prediction method, IBNPLNSMDA, is proposed which uses the improved bipartite network projection method to predict latent metabolite-disease associations based on linear neighborhood similarity. Specifically, liner neighborhood similarity matrix about metabolites (diseases) is reconstructed according to the new feature which is gained by the known metabolite-disease associations and relevant integrated similarities. The improved bipartite network projection method is adopted to infer the potential associations between metabolites and diseases. At last, IBNPLNSMDA achieves a reliable performance in LOOCV (AUC of 0.9634) outperforming the compared methods. In addition, in case studies of four common human diseases, simulation results confirm the utility of our method in discovering latent metabolite-disease pairs. Thus, we believe that IBNPLNSMDA could serve as a reliable computational tool for metabolite-disease associations prediction.

The circular RNAs (circRNAs) have significant effects on a variety of biological processes, the dysfunction of which is closely related to the emergence and development of diseases. Therefore, identification of circRNA-disease associations will contribute to analysing the pathogenesis of diseases. Here, we present a computational model called BRWSP to predict circRNA-disease associations, which searches paths on a multiple heterogeneous network based on biased random walk. Firstly, BRWSP constructs a multiple heterogeneous network by using circRNAs, diseases, and genes. Then, the biased random walk algorithm runs on the multiple heterogeneous network to search paths between circRNAs and diseases. Finally, the performance of BRWSP is significantly better than the state-of-the-art algorithms. Furthermore, BRWSP further contributes to the discovery of novel circRNA-disease associations.

Brain storm optimization (BSO) algorithm is a simple and effective evolutionary algorithm. Some multiobjective brain storm optimization algorithms have low search efficiency. This paper combines the decomposition technology and multiobjective brain storm optimization algorithm (MBSO/D) to improve the search efficiency. Given weight vectors transform a multiobjective optimization problem into a series of subproblems. The decomposition technology determines the neighboring clusters of each cluster. Solutions of adjacent clusters generate new solutions to update population. An adaptive selection strategy is used to balance exploration and exploitation. Besides, MBSO/D compares with three efficient state-of-the-art algorithms, e.g., NSGAII and MOEA/D, on twenty-two test problems. The experimental results show that MBSO/D is more efficient than compared algorithms and can improve the search efficiency for most test problems.

Recently, decomposition-based multiobjective evolutionary algorithms have good performances in the field of multiobjective optimization problems (MOPs) and have been paid attention by many scholars. Generally, a MOP is decomposed into a number of subproblems through a set of weight vectors with good uniformly and aggregate functions. The main role of weight vectors is to ensure the diversity and convergence of obtained solutions. However, these algorithms with uniformity of weight vectors cannot obtain a set of solutions with good diversity on some MOPs with complex Pareto optimal fronts (PFs) (i.e., PFs with a sharp peak or low tail or discontinuous PFs). To deal with this problem, an improved decomposition-based multiobjective evolutionary algorithm with adaptive weight adjustment (IMOEA/DA) is proposed. Firstly, a new method based on uniform design and crowding distance is used to generate a set of weight vectors with good uniformly. Secondly, according to the distances of obtained nondominated solutions, an adaptive weight vector adjustment strategy is proposed to redistribute the weight vectors of subobjective spaces. Thirdly, a selection strategy is used to help each subobjective space to obtain a nondominated solution (if have). Comparing with six efficient state-of-the-art algorithms, for example, NSGAII, MOEA/D, MOEA/D-AWA, EMOSA, RVEA, and KnEA on some benchmark functions, the proposed algorithm is able to find a set of solutions with better diversity and convergence.

Protein complexes play a critical role in understanding the biological processes and the functions of cellular mechanisms. Most existing protein complex detection algorithms cannot reflect dynamics of protein complexes. In this paper, a novel algorithm named Improved Cuckoo Search Clustering (ICSC) algorithm is proposed to detect protein complexes in weighted dynamic protein-protein interaction (PPI) networks. First, we constructed weighted dynamic PPI networks and detected protein complex cores in each dynamic subnetwork. Then, ICSC algorithm was used to cluster the protein attachments to the cores. The experimental results on both DIP dataset and Krogan dataset demonstrated that ICSC algorithm is more effective in identifying protein complexes than other competing methods.