scholarly journals Design and Assembly of DNA Molecules Using Multi-Objective Optimisation

2021 ◽  
Author(s):  
Angelo Gaeta ◽  
Valentin Zulkower ◽  
Giovanni Stracquadanio

Abstract Rapid engineering of biological systems is currently hindered by limited integration of manufacturing constraints into the design process, ultimately reducing the yield of many synthetic biology workflows. Here we tackle DNA engineering as a multi-objective optimization problem aiming at finding the best tradeoff between design requirements and manufacturing constraints. We developed a new open-source algorithm for DNA engineering, called Multi-Objective Optimisation algorithm for DNA Design and Assembly (MOODA), available as a Python and Anaconda package, as well as a Docker image. Experimental results show that our method provides near optimal constructs and scales linearly with design complexity, effectively paving the way to rational engineering of DNA molecules from genes to genomes.

2019 ◽  
Author(s):  
Angelo Gaeta ◽  
Valentin Zulkower ◽  
Giovanni Stracquadanio

AbstractRapid engineering of biological systems is currently hindered by limited integration of manufacturing constraints into the design process, ultimately limiting the yield of many synthetic biology workflows.Here we tackle DNA engineering as a multi-objective optimization problem aiming at finding the best tradeoff between design requirements and manufacturing constraints. We developed a new open-source algorithm for DNA engineering, called Multi-Objective Optimisation algorithm for DNA Design and Assembly (MOODA), available as a Python package and web application at http://mooda.stracquadaniolab.org.Experimental results show that our method provides near optimal constructs and scales linearly with design complexity, effectively paving the way to rational engineering of DNA molecules from genes to genomes.


2019 ◽  
Vol 29 (01) ◽  
pp. 2050003
Author(s):  
Lalin L. Laudis ◽  
N. Ramadass

The complexity of any integrated circuit pushes the researchers to optimize the various parameters in the design process. Usually, the Nondeterministic Polynomial problems in the design process of Very Large Scale Integration (VLSI) are considered as a Single Objective Optimization Problem (SOOP). However, due to the increasing demand for the multi-criterion optimization, researchers delve up on Multi-Objective Optimization methodologies to solve a problem with multiple objectives. Moreover, it is evident from the literature that biologically inspired algorithm works very well in optimizing a Multi-Objective Optimization Problem (MOOP). This paper proposes a new Lion’s pride inspired algorithm to solve any MOOP. The methodologies mimic the traits of a Lion which always strives to become the Pride Lion. The Algorithm was tested with VLSI floorplanning problem wherein the area and dead space are the objectives. The algorithm was also tested with several standard test problems. The tabulated results justify the ruggedness of the proposed algorithm in solving any MOOP.


Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2775
Author(s):  
Tsubasa Takano ◽  
Takumi Nakane ◽  
Takuya Akashi ◽  
Chao Zhang

In this paper, we propose a method to detect Braille blocks from an egocentric viewpoint, which is a key part of many walking support devices for visually impaired people. Our main contribution is to cast this task as a multi-objective optimization problem and exploits both the geometric and the appearance features for detection. Specifically, two objective functions were designed under an evolutionary optimization framework with a line pair modeled as an individual (i.e., solution). Both of the objectives follow the basic characteristics of the Braille blocks, which aim to clarify the boundaries and estimate the likelihood of the Braille block surface. Our proposed method was assessed by an originally collected and annotated dataset under real scenarios. Both quantitative and qualitative experimental results show that the proposed method can detect Braille blocks under various environments. We also provide a comprehensive comparison of the detection performance with respect to different multi-objective optimization algorithms.


2021 ◽  
pp. 1-13
Author(s):  
Hailin Liu ◽  
Fangqing Gu ◽  
Zixian Lin

Transfer learning methods exploit similarities between different datasets to improve the performance of the target task by transferring knowledge from source tasks to the target task. “What to transfer” is a main research issue in transfer learning. The existing transfer learning method generally needs to acquire the shared parameters by integrating human knowledge. However, in many real applications, an understanding of which parameters can be shared is unknown beforehand. Transfer learning model is essentially a special multi-objective optimization problem. Consequently, this paper proposes a novel auto-sharing parameter technique for transfer learning based on multi-objective optimization and solves the optimization problem by using a multi-swarm particle swarm optimizer. Each task objective is simultaneously optimized by a sub-swarm. The current best particle from the sub-swarm of the target task is used to guide the search of particles of the source tasks and vice versa. The target task and source task are jointly solved by sharing the information of the best particle, which works as an inductive bias. Experiments are carried out to evaluate the proposed algorithm on several synthetic data sets and two real-world data sets of a school data set and a landmine data set, which show that the proposed algorithm is effective.


Author(s):  
Weijun Wang ◽  
Stéphane Caro ◽  
Fouad Bennis ◽  
Oscar Brito Augusto

For Multi-Objective Robust Optimization Problem (MOROP), it is important to obtain design solutions that are both optimal and robust. To find these solutions, usually, the designer need to set a threshold of the variation of Performance Functions (PFs) before optimization, or add the effects of uncertainties on the original PFs to generate a new Pareto robust front. In this paper, we divide a MOROP into two Multi-Objective Optimization Problems (MOOPs). One is the original MOOP, another one is that we take the Robustness Functions (RFs), robust counterparts of the original PFs, as optimization objectives. After solving these two MOOPs separately, two sets of solutions come out, namely the Pareto Performance Solutions (PP) and the Pareto Robustness Solutions (PR). Make a further development on these two sets, we can get two types of solutions, namely the Pareto Robustness Solutions among the Pareto Performance Solutions (PR(PP)), and the Pareto Performance Solutions among the Pareto Robustness Solutions (PP(PR)). Further more, the intersection of PR(PP) and PP(PR) can represent the intersection of PR and PP well. Then the designer can choose good solutions by comparing the results of PR(PP) and PP(PR). Thanks to this method, we can find out the optimal and robust solutions without setting the threshold of the variation of PFs nor losing the initial Pareto front. Finally, an illustrative example highlights the contributions of the paper.


2014 ◽  
Vol 494-495 ◽  
pp. 1715-1718
Author(s):  
Gui Li Yuan ◽  
Tong Yu ◽  
Juan Du

The classic multi-objective optimization method of sub goals multiplication and division theory is applied to solve optimal load distribution problem in thermal power plants. A multi-objective optimization model is built which comprehensively reflects the economy, environmental protection and speediness. The proposed model effectively avoids the target normalization and weights determination existing in the process of changing the multi-objective optimization problem into a single objective optimization problem. Since genetic algorithm (GA) has the drawback of falling into local optimum, adaptive immune vaccines algorithm (AIVA) is applied to optimize the constructed model and the results are compared with that optimized by genetic algorithm. Simulation shows this method can complete multi-objective optimal load distribution quickly and efficiently.


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