scholarly journals mRNA codon optimization with quantum computers

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259101
Author(s):  
Dillion M. Fox ◽  
Kim M. Branson ◽  
Ross C. Walker
Keyword(s):  
Optimization Problem ◽  
Codon Optimization ◽  
Future Generation ◽  
Combinatorial Optimization Problem ◽  
Quantum Computers ◽  
Optimal Solutions ◽  
Computing Technology ◽  
Reverse Translation ◽  
Potential Impact ◽  
Standard Genetic Algorithm

Reverse translation of polypeptide sequences to expressible mRNA constructs is a NP-hard combinatorial optimization problem. Each amino acid in the protein sequence can be represented by as many as six codons, and the process of selecting the combination that maximizes probability of expression is termed codon optimization. This work investigates the potential impact of leveraging quantum computing technology for codon optimization. A Quantum Annealer (QA) is compared to a standard genetic algorithm (GA) programmed with the same objective function. The QA is found to be competitive in identifying optimal solutions. The utility of gate-based systems is also evaluated using a simulator resulting in the finding that while current generations of devices lack the hardware requirements, in terms of both qubit count and connectivity, to solve realistic problems, future generation devices may be highly efficient.

scholarly journals mRNA codon optimization on quantum computers

2021 ◽  
Author(s):  
Dillion M. Fox ◽  
Kim M. Branson ◽  
Ross C. Walker
Keyword(s):  
Optimization Problem ◽  
Quantum Computer ◽  
Codon Optimization ◽  
Future Generation ◽  
Quantum Computers ◽  
Computing Technology ◽  
Reverse Translation ◽  
Classical Gas ◽  
Potential Impact ◽  
Standard Genetic Algorithm

AbstractReverse translation of polypeptide sequences to expressible mRNA constructs is a NP-hard combinatorial optimization problem. Each amino acid in the protein sequence can be represented by as many as six codons, and the process of selecting the combination that maximizes probability of expression is termed codon optimization. This work investigates the potential impact of leveraging quantum computing technology for codon optimization. An adiabatic quantum computer (AQC) is compared to a standard genetic algorithm (GA) programmed with the same objective function. The AQC is found to be competitive in identifying optimal solutions and future generations of AQCs may be able to outperform classical GAs. The utility of gate-based systems is also evaluated using a simulator resulting in the finding that while current generations of devices lack the hardware requirements, in terms of both qubit count and connectivity, to solve realistic problems, future generation devices may be highly efficient.

scholarly journals A Fast and Exact Greedy Algorithm for the Core–Periphery Problem

Symmetry ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 94 ◽  
Author(s):  
Dario Fasino ◽  
Franca Rinaldi
Keyword(s):  
Structural Analysis ◽  
Optimization Problem ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Combinatorial Optimization Problem ◽  
Connected Subgraph ◽  
Optimal Solutions ◽  
The Core ◽  
Core Set ◽  
Key Concepts

The core–periphery structure is one of the key concepts in the structural analysis of complex networks. It consists of a partitioning of the node set of a given graph or network into two groups, called core and periphery, where the core nodes induce a well-connected subgraph and share connections with peripheral nodes, while the peripheral nodes are loosely connected to the core nodes and other peripheral nodes. We propose a polynomial-time algorithm to detect core–periphery structures in networks having a symmetric adjacency matrix. The core set is defined as the solution of a combinatorial optimization problem, which has a pleasant symmetry with respect to graph complementation. We provide a complete description of the optimal solutions to that problem and an exact and efficient algorithm to compute them. The proposed approach is extended to networks with loops and oriented edges. Numerical simulations are carried out on both synthetic and real-world networks to demonstrate the effectiveness and practicability of the proposed algorithm.

Inverse version of the kth maximization combinatorial optimization problem

2018 ◽  
Vol 54(5) ◽  
pp. 72
Author(s):  
Quoc, H.D. ◽  
Kien, N.T. ◽  
Thuy, T.T.C. ◽  
Hai, L.H. ◽  
Thanh, V.N.
Keyword(s):  
Combinatorial Optimization ◽  
Optimization Problem ◽  
Combinatorial Optimization Problem

scholarly journals Quit When You Can: Efficient Evaluation of Ensembles by Optimized Ordering

2021 ◽  
Vol 17 (4) ◽  
pp. 1-20
Author(s):  
Serena Wang ◽  
Maya Gupta ◽  
Seungil You
Keyword(s):  
Optimization Problem ◽  
Optimal Solution ◽  
Combinatorial Optimization Problem ◽  
Joint Optimization ◽  
Early Stopping ◽  
Time Approximation ◽  
Approximation Bound ◽  
Evaluation Time ◽  
Speed Up ◽  
Real World Problems

Given a classifier ensemble and a dataset, many examples may be confidently and accurately classified after only a subset of the base models in the ensemble is evaluated. Dynamically deciding to classify early can reduce both mean latency and CPU without harming the accuracy of the original ensemble. To achieve such gains, we propose jointly optimizing the evaluation order of the base models and early-stopping thresholds. Our proposed objective is a combinatorial optimization problem, but we provide a greedy algorithm that achieves a 4-approximation of the optimal solution under certain assumptions, which is also the best achievable polynomial-time approximation bound. Experiments on benchmark and real-world problems show that the proposed Quit When You Can (QWYC) algorithm can speed up average evaluation time by 1.8–2.7 times on even jointly trained ensembles, which are more difficult to speed up than independently or sequentially trained ensembles. QWYC’s joint optimization of ordering and thresholds also performed better in experiments than previous fixed orderings, including gradient boosted trees’ ordering.

Adaptive Grouping Brain Storm Optimization for Multimodal Optimization Problems

2021 ◽  
Vol 12 (4) ◽  
pp. 81-100
Author(s):  
Yao Peng ◽  
Zepeng Shen ◽  
Shiqi Wang
Keyword(s):  
Optimization Problem ◽  
Optimization Problems ◽  
Optimal Algorithm ◽  
Peak Detection ◽  
Multimodal Optimization ◽  
Optimal Solutions ◽  
Grouping Strategy ◽  
Different Dimensions ◽  
Global Optimal ◽  
Localization Ability

Multimodal optimization problem exists in multiple global and many local optimal solutions. The difficulty of solving these problems is finding as many local optimal peaks as possible on the premise of ensuring global optimal precision. This article presents adaptive grouping brainstorm optimization (AGBSO) for solving these problems. In this article, adaptive grouping strategy is proposed for achieving adaptive grouping without providing any prior knowledge by users. For enhancing the diversity and accuracy of the optimal algorithm, elite reservation strategy is proposed to put central particles into an elite pool, and peak detection strategy is proposed to delete particles far from optimal peaks in the elite pool. Finally, this article uses testing functions with different dimensions to compare the convergence, accuracy, and diversity of AGBSO with BSO. Experiments verify that AGBSO has great localization ability for local optimal solutions while ensuring the accuracy of the global optimal solutions.

scholarly journals ANALYSIS AND SYNTHESIS OF ENHANCED ANT COLONY OPTIMIZATION WITH THE TRADITIONAL ANT COLONY OPTIMIZATION TO SOLVE TRAVELLING SALES PERSON PROBLEM

2011 ◽  
Vol 1 (1) ◽  
pp. 88-92
Author(s):  
Pallavi Arora ◽  
Harjeet Kaur ◽  
Prateek Agrawal
Keyword(s):  
Combinatorial Optimization ◽  
Ant Colony Optimization ◽  
Optimization Problem ◽  
Traditional Approach ◽  
Combinatorial Optimization Problem ◽  
Ant Colony ◽  
Ant Colony Optimization Algorithm ◽  
Analysis And Synthesis ◽  
Heuristic Technique ◽  
Travelling Salesperson Problem

Ant Colony optimization is a heuristic technique which has been applied to a number of combinatorial optimization problem and is based on the foraging behavior of the ants. Travelling Salesperson problem is a combinatorial optimization problem which requires that each city should be visited once. In this research paper we use the K means clustering technique and Enhanced Ant Colony Optimization algorithm to solve the TSP problem. We show a comparison of the traditional approach with the proposed approach. The simulated results show that the proposed algorithm is better compared to the traditional approach.

Space Contraction and Partition Algorithm for Combinatorial Optimization

2011 ◽  
Vol 421 ◽  
pp. 559-563
Author(s):  
Yong Chao Gao ◽  
Li Mei Liu ◽  
Heng Qian ◽  
Ding Wang
Keyword(s):  
Combinatorial Optimization ◽  
Optimization Problem ◽  
Optimization Problems ◽  
Solution Space ◽  
Search Space ◽  
Small Scale ◽  
Optimal Solutions ◽  
Solution Quality ◽  
Intelligent Algorithms ◽  
Combinatorial Optimization Problems

The scale and complexity of search space are important factors deciding the solving difficulty of an optimization problem. The information of solution space may lead searching to optimal solutions. Based on this, an algorithm for combinatorial optimization is proposed. This algorithm makes use of the good solutions found by intelligent algorithms, contracts the search space and partitions it into one or several optimal regions by backbones of combinatorial optimization solutions. And optimization of small-scale problems is carried out in optimal regions. Statistical analysis is not necessary before or through the solving process in this algorithm, and solution information is used to estimate the landscape of search space, which enhances the speed of solving and solution quality. The algorithm breaks a new path for solving combinatorial optimization problems, and the results of experiments also testify its efficiency.

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