Xiufen Zou

Xiangzheng Cheng, Haili Huang, Ye Su et al.

In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which are crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics technologies provide unprecedented opportunities to systematically infer and analyze CCC from these omics data, either by integrating prior knowledge of ligand-receptor interactions (LRIs) or through de novo approaches. A variety of computational methods have been developed, focusing on methodological innovations, accurate modeling of complex signaling mechanisms, and investigation of broader biological questions. These advances have greatly enhanced our ability to analyze CCC and generate biological hypotheses. Here, we introduce the biological mechanisms and modeling strategies of CCC, and provide a focused overview of more than 140 computational methods for inferring CCC from single-cell and spatial transcriptomic data, emphasizing the diversity in methodological frameworks and biological questions. Finally, we discuss the current challenges and future opportunities in this rapidly evolving field.

Cong Wang, Jun He, Yu Chen et al.

Although differential evolution (DE) algorithms perform well on a large variety of complicated optimization problems, only a few theoretical studies are focused on the working principle of DE algorithms. To make the first attempt to reveal the function of binomial crossover, this paper aims to answer whether it can reduce the approximation error of evolutionary algorithms. By investigating the expected approximation error and the probability of not finding the optimum, we conduct a case study comparing two evolutionary algorithms with and without binomial crossover on two classical benchmark problems: OneMax and Deceptive. It is proven that using binomial crossover leads to the dominance of transition matrices. As a result, the algorithm with binomial crossover asymptotically outperforms that without crossover on both OneMax and Deceptive, and outperforms on OneMax, however, not on Deceptive. Furthermore, an adaptive parameter strategy is proposed which can strengthen the superiority of binomial crossover on Deceptive.

Yu Chen, Yuanyuan Yang, Yaochu Jin et al.

Motivation: Identifying interaction clusters of large gene regulatory networks (GRNs) is critical for its further investigation, while this task is very challenging, attributed to data noise in experiment data, large scale of GRNs, and inconsistency between gene expression profiles and function modules, etc. It is promising to semi-supervise this process by prior information, but shortage of prior information sometimes make it very challenging. Meanwhile, it is also annoying, and sometimes impossible to discovery gold standard for evaluation of clustering results.\\ Results: With assistance of an online enrichment tool, this research proposes a semi-supervised hierarchical clustering method via deconvolved correlation matrix~(SHC-DC) to discover interaction clusters of large-scale GRNs. Three benchmark networks including a \emph{Ecoli} network and two \emph{Yeast} networks are employed to test semi-supervision scheme of the proposed method. Then, SHC-DC is utilized to cluster genes in sleep study. Results demonstrates it can find interaction modules that are generally enriched in various signal pathways. Besides the significant influence on blood level of interleukins, impact of sleep on important pathways mediated by them is also validated by the discovered interaction modules.

Yu Chen, Xiufen Zou

Inference of gene regulatory networks (GRNs) based on experimental data is a challenging task in bioinformatics. In this paper, we present a bi-objective minimization model (BoMM) for inference of GRNs, where one objective is the fitting error of derivatives, and the other is the number of connections in the network. To solve the BoMM efficiently, we propose a multi-objective evolutionary algorithm (MOEA), and utilize the separable parameter estimation method (SPEM) decoupling the ordinary differential equation (ODE) system. Then, the Akaike Information Criterion (AIC) is employed to select one inference result from the obtained Pareto set. Taking the S-system as the investigated GRN model, our method can properly identify the topologies and parameter values of benchmark systems. There is no need to preset problem-dependent parameter values to obtain appropriate results, and thus, our method could be applicable to inference of various GRNs models.

Yu Chen, Weicheng Xie, Xiufen Zou

Although real-coded differential evolution (DE) algorithms can perform well on continuous optimization problems (CoOPs), it is still a challenging task to design an efficient binary-coded DE algorithm. Inspired by the learning mechanism of particle swarm optimization (PSO) algorithms, we propose a binary learning differential evolution (BLDE) algorithm that can efficiently locate the global optimal solutions by learning from the last population. Then, we theoretically prove the global convergence of BLDE, and compare it with some existing binary-coded evolutionary algorithms (EAs) via numerical experiments. Numerical results show that BLDE is competitive to the compared EAs, and meanwhile, further study is performed via the change curves of a renewal metric and a refinement metric to investigate why BLDE cannot outperform some compared EAs for several selected benchmark problems. Finally, we employ BLDE solving the unit commitment problem (UCP) in power systems to show its applicability in practical problems.