Elucidating transcriptomic profiles from single-cell RNA sequencing data using nature-inspired compressed sensing.

Gene-expression profiling can define the cell state and gene-expression pattern of cells at the genetic level in a high-throughput manner. With the development of transcriptome techniques, processing high-dimensional genetic data has become a major challenge in expression profiling. Thanks to the recent widespread use of matrix decomposition methods in bioinformatics, a computational framework based on compressed sensing was adopted to reduce dimensionality. However, compressed sensing requires an optimization strategy to learn the modular dictionaries and activity levels from the low-dimensional random composite measurements to reconstruct the high-dimensional gene-expression data. Considering this, here we introduce and compare four compressed sensing frameworks coming from nature-inspired optimization algorithms (CSCS, ABCCS, BACS and FACS) to improve the quality of the decompression process. Several experiments establish that the three proposed methods outperform benchmark methods on nine different datasets, especially the FACS method. We illustrate therefore, the robustness and convergence of FACS in various aspects; notably, time complexity and parameter analyses highlight properties of our proposed FACS. Furthermore, differential gene-expression analysis, cell-type clustering, gene ontology enrichment and pathology analysis are conducted, which bring novel insights into cell-type identification and characterization mechanisms from different perspectives. All algorithms are written in Python and available at https://github.com/Philyzh8/Nature-inspired-CS.

An Enhanced Food Digestion Algorithm for Mobile Sensor Localization.

Mobile sensors can extend the range of monitoring and overcome static sensors' limitations and are increasingly used in real-life applications. Since there can be significant errors in mobile sensor localization using the Monte Carlo Localization (MCL), this paper improves the food digestion algorithm (FDA). This paper applies the improved algorithm to the mobile sensor localization problem to reduce localization errors and improve localization accuracy. Firstly, this paper proposes three inter-group communication strategies to speed up the convergence of the algorithm based on the topology that exists between groups. Finally, the improved algorithm is applied to the mobile sensor localization problem, reducing the localization error and achieving good localization results.

A Multi-Objective Sine Cosine Algorithm Based on a Competitive Mechanism and Its Application in Engineering Design Problems.

There are a lot of multi-objective optimization problems (MOPs) in the real world, and many multi-objective evolutionary algorithms (MOEAs) have been presented to solve MOPs. However, obtaining non-dominated solutions that trade off convergence and diversity remains a major challenge for a MOEA. To solve this problem, this paper designs an efficient multi-objective sine cosine algorithm based on a competitive mechanism (CMOSCA). In the CMOSCA, the ranking relies on non-dominated sorting, and the crowding distance rank is utilized to choose the outstanding agents, which are employed to guide the evolution of the SCA. Furthermore, a competitive mechanism stemming from the shift-based density estimation approach is adopted to devise a new position updating operator for creating offspring agents. In each competition, two agents are randomly selected from the outstanding agents, and the winner of the competition is integrated into the position update scheme of the SCA. The performance of our proposed CMOSCA was first verified on three benchmark suites (i.e., DTLZ, WFG, and ZDT) with diversity characteristics and compared with several MOEAs. The experimental results indicated that the CMOSCA can obtain a Pareto-optimal front with better convergence and diversity. Finally, the CMOSCA was applied to deal with several engineering design problems taken from the literature, and the statistical results demonstrated that the CMOSCA is an efficient and effective approach for engineering design problems.

X-architecture Steiner minimal tree algorithm based on multi-strategy optimization discrete differential evolution.

Global routing is an important link in very large scale integration (VLSI) design. As the best model of global routing, X-architecture Steiner minimal tree (XSMT) has a good performance in wire length optimization. XSMT belongs to non-Manhattan structural model, and its construction process cannot be completed in polynomial time, so the generation of XSMT is an NP hard problem. In this paper, an X-architecture Steiner minimal tree algorithm based on multi-strategy optimization discrete differential evolution (XSMT-MoDDE) is proposed. Firstly, an effective encoding strategy, a fitness function of XSMT, and an initialization strategy of population are proposed to record the structure of XSMT, evaluate the cost of XSMT and obtain better initial particles, respectively. Secondly, elite selection and cloning strategy, multiple mutation strategies, and adaptive learning factor strategy are presented to improve the search process of discrete differential evolution algorithm. Thirdly, an effective refining strategy is proposed to further improve the quality of the final Steiner tree. Finally, the results of the comparative experiments prove that XSMT-MoDDE can get the shortest wire length so far, and achieve a better optimization degree in the larger-scale problem.

Multilayer obstacle-avoiding x-architecture steiner minimal tree construction based on particle swarm optimization.

As the basic model for very large scale integration routing, the Steiner minimal tree (SMT) can be used in various practical problems, such as wire length optimization, congestion, and time delay estimation. In this paper, an effective algorithm based on particle swarm optimization is presented to construct a multilayer obstacle-avoiding X-architecture SMT (ML-OAXSMT). First, a pretreatment strategy is presented to reduce the total number of judgments for the routing conditions around obstacles and vias. Second, an edge transformation strategy is employed to make the particles have the ability to bypass the obstacles while the union-find partition is used to prevent invalid solutions. Third, according to the feature of ML-OAXSMT problem, we design an edge-vertex encoding strategy, which has the advantage of simple and effective. Moreover, a penalty mechanism is proposed to help the particle bypass the obstacles, and reduce the generation of via at the same time. Experimental results show that our algorithm from a global perspective of multilayer structure can achieve the best solution quality among the existing algorithms. Finally, to our best knowledge, we redefine the edge cost and then construct the obstacle-avoiding preferred direction X-architecture Steiner tree, which is the first work to address this problem and can offer the theory supports for chip design based on non-Manhattan architecture.