matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2

Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the COVID-19 pandemic. One transformative approach, online phylogenetics, aims to incrementally add samples to an ever-growing phylogeny, but there are no previously-existing approaches that can efficiently optimize this vast phylogeny under the time constraints of the pandemic. Here, we present matOptimize, a fast and memory-efficient phylogenetic tree optimization tool based on parsimony that can be parallelized across multiple CPU threads and nodes, and provides orders of magnitude improvement in runtime and peak memory usage compared to existing state-of-the-art methods. We have developed this method particularly to address the pressing need during the COVID-19 pandemic for daily maintenance and optimization of a comprehensive SARS-CoV-2 phylogeny. Thus, our approach addresses an important need for daily maintenance and refinement of a comprehensive SARS-CoV-2 phylogeny.

Energy-Efficient Adaptive Sensing Scheduling in Wireless Sensor Networks Using Fibonacci Tree Optimization Algorithm

Wireless sensor networks are appealing, largely because they do not need wired infrastructure, but it is precisely this feature that renders them energy-constrained. The duty cycle scheduling is perceived as a contributor to the energy efficiency of sensing. This paper developed a novel paradigm for modeling wireless sensor networks; in this context, an adaptive sensing scheduling strategy is proposed depending on event occurrence behavior, and the scheduling problem is framed as an optimization problem. The optimization objectives include reducing energy depletion and optimizing detection accuracy. We determine the explicit form of the objective function by numerical fitting and found that the objective function aggregated by the fitting functions is a bivariate multimodal function that favors the Fibonacci tree optimization algorithm. Then, with the optimal parameters optimized by the Fibonacci tree optimization algorithm, the scheduling scheme can be easily deployed, and it behaves consistently in the coming hours. The proposed “Fibonacci Tree Optimization Strategy” (“FTOS”) outperforms lightweight deployment-aware scheduling (LDAS), balanced-energy scheduling (BS), distributed self-spreading algorithm (DSS) and probing environment and collaborating adaptive sleeping (PECAS) in achieving the aforementioned scheduling objectives. The Fibonacci tree optimization algorithm has attained a better optimistic effect than the artificial bee colony (ABC) algorithm, differential evolution (DE) algorithm, genetic algorithm (GA) algorithm, particle swarm optimization (PSO) algorithm, and comprehensive learning particle swarm optimization (CLPSO) algorithm in multiple runs.

Energy-Efficient Adaptive Sensing Scheduling in Wireless Sensor Networks using Fibonacci Tree Optimization Algorithm

Wireless sensor networks are attractive largely because they need no wired infrastructure. But precisely this feature makes them energy constrained. Recent studies find that sensing behaviors that are otherwise deemed efficient consume comparable energy with communication. The duty cycle scheduling is perceived as contributing to achieving energy efficiency of sensing. Because of different research assumptions and objectives, various scheduling schemes have various emphases. This paper designed an adaptive sensing scheduling strategy. The objective function of the scheduling strategy includes minimizing average energy expenditure and maximizing sensing coverage (reducing event miss-rate), and it requires relatively loose assumptions. We determine the functional relationship between the variables of the objective function and the step-size parameters of the proposed strategy through the numerical fitting. We found that the objective function aggregated by the fitting functions is a bivariate multi-peak function that favors the Fibonacci tree optimization algorithm. Once the optimization of parameters is done, the strategy can be easily deployed and behaves consistently in the coming hours. We name the proposed strategy as “FTOS”. The experimental results show that the Fibonacci tree optimization algorithm gets a better optimistic effect than the comprehensive learning particle swarm optimization (CLPSO) algorithm and differential evolution (DE) algorithm. The FTOS strategy is superior to the fixed time scheduling strategy in achieving the scheduling objectives. It also outperforms other strategies with the same scheduling objectives such as LDAS, BS, DSS and PECAS.