scholarly journals JuPOETs: A Constrained Multiobjective Optimization Approach to Estimate Biochemical Model Ensembles in the Julia Programming Language

2016 ◽  
Author(s):  
David Bassen ◽  
Michael Vilkhovoy ◽  
Mason Minot ◽  
Jonathan T Butcher ◽  
Jeffrey D. Varner
Keyword(s):  
Programming Language ◽  
Optimization Problems ◽  
Training Data ◽  
Optimization Approach ◽  
Proof Of Concept ◽  
Test Functions ◽  
Biochemical Model ◽  
Constrained Problems ◽  
Optimal Ensemble ◽  
Model Ensembles

AbstractEnsemble modeling is a well established approach for obtaining robust predictions and for simulating course grained population behavior in deterministic mathematical models. In this study, we present a multiobjective based technique to estimate model ensembles, the Pareto Optimal Ensemble Technique in the Julia programming language (JuPOETs). JuPOETs integrates simulated annealing with Pareto optimality to estimate parameter ensembles on or near the optimal tradeoff surface between competing training objectives. We demonstrated JuPOETs on a suite of multiobjective problems, including test functions with parameter bounds and system constraints as well as for the identification of a proof-of-concept biochemical model with four conflicting training objectives. JuPOETs identified optimal or near optimal solutions approximately six-fold faster than a corresponding implementation in Octave for the suite of test functions. For the proof-of-concept biochemical model, JuPOETs produced an ensemble of parameters that gave both the mean of the training data for conflicting data sets, while simultaneously estimating parameter sets that performed well on each of the individual objective functions. JuPOETs can be adapted to solve many problem types, including mixed binary and continuous variable types, bilevel optimization problems and constrained problems without altering the base algorithm. JuPOETs can be installed using the Julia package manager from the JuPOETs GitHub repository at https://github.com/varnerlab/POETs.jl.

Multi-Objective Surrogate-Assisted Stochastic Optimization for Engine Calibration

2021 ◽  
Author(s):  
Anuj Pal ◽  
Yan Wang ◽  
Ling Zhu ◽  
Guoming George Zhu
Keyword(s):  
Optimization Problems ◽  
Fuel Efficiency ◽  
Optimization Approach ◽  
Engine Fuel ◽  
Practical Applications ◽  
Engine Calibration ◽  
Constrained Problems ◽  
Calibration Problem ◽  
Uniform Noise ◽  
Measurement Noises

Abstract A surrogate assisted optimization approach is an attractive way to reduce the total computational budget for obtaining optimal solutions. This makes it special for its application to practical optimization problems requiring a large number of expensive evaluations. Unfortunately, all practical applications are affected by measurement noises, and not much work has been done to address the issue of handling stochastic problems with multiple objectives and constraints. This work tries to bridge the gap by demonstrating three different frameworks for performing surrogate assisted optimization on multiobjective constrained problems with stochastic measurements. To make the algorithms applicable to real-world problems, heteroscedastic (non-uniform) noise is considered for all frameworks. The proposed algorithms are first validated on several multiobjective numerical problems (unconstrained and constrained) to verify their effectiveness, and then applied to the diesel engine calibration problem, which is expensive to perform and has measurement noises. A GT-SUITE model is used to perform the engine calibration study. Three control parameters, namely variable geometry turbocharger vane position, exhaust-gas-recirculating valve position, and the start of injection, are calibrated to obtain the trade-off between engine fuel efficiency performance (brake specific fuel consumption) and NOx emissions within the constrained design space. The results show that all three proposed extensions can handle the problems well with different measurement noise levels at a reduced evaluation budget. For the engine calibration problem, a good approximation of the optimal region is observed with more than 80\% reduction in evaluation budget for all the proposed methodologies.

A microbial treatment population dynamics optimization approach

2021 ◽  
pp. 1-15
Author(s):  
Jinding Gao
Keyword(s):  
Population Dynamics ◽  
Information Exchange ◽  
Information Diffusion ◽  
Optimization Problems ◽  
Microbial Control ◽  
Function Optimization ◽  
Optimization Approach ◽  
Dynamics Model ◽  
Population Dynamics Model ◽  
Number Of Individuals

In order to solve some function optimization problems, Population Dynamics Optimization Algorithm under Microbial Control in Contaminated Environment (PDO-MCCE) is proposed by adopting a population dynamics model with microbial treatment in a polluted environment. In this algorithm, individuals are automatically divided into normal populations and mutant populations. The number of individuals in each category is automatically calculated and adjusted according to the population dynamics model, it solves the problem of artificially determining the number of individuals. There are 7 operators in the algorithm, they realize the information exchange between individuals the information exchange within and between populations, the information diffusion of strong individuals and the transmission of environmental information are realized to individuals, the number of individuals are increased or decreased to ensure that the algorithm has global convergence. The periodic increase of the number of individuals in the mutant population can greatly increase the probability of the search jumping out of the local optimal solution trap. In the iterative calculation, the algorithm only deals with 3/500∼1/10 of the number of individual features at a time, the time complexity is reduced greatly. In order to assess the scalability, efficiency and robustness of the proposed algorithm, the experiments have been carried out on realistic, synthetic and random benchmarks with different dimensions. The test case shows that the PDO-MCCE algorithm has better performance and is suitable for solving some optimization problems with higher dimensions.

scholarly journals A Hybrid Whale Optimization Algorithm for Global Optimization

Mathematics ◽  
2021 ◽  
Vol 9 (13) ◽  
pp. 1477
Author(s):  
Chun-Yao Lee ◽  
Guang-Lin Zhuo
Keyword(s):  
Global Optimization ◽  
Optimization Algorithm ◽  
Optimization Problems ◽  
Whale Optimization Algorithm ◽  
Initial Population ◽  
Test Functions ◽  
Benchmark Test ◽  
Thermal Exchange ◽  
Whale Optimization ◽  
Benchmark Test Functions

This paper proposes a hybrid whale optimization algorithm (WOA) that is derived from the genetic and thermal exchange optimization-based whale optimization algorithm (GWOA-TEO) to enhance global optimization capability. First, the high-quality initial population is generated to improve the performance of GWOA-TEO. Then, thermal exchange optimization (TEO) is applied to improve exploitation performance. Next, a memory is considered that can store historical best-so-far solutions, achieving higher performance without adding additional computational costs. Finally, a crossover operator based on the memory and a position update mechanism of the leading solution based on the memory are proposed to improve the exploration performance. The GWOA-TEO algorithm is then compared with five state-of-the-art optimization algorithms on CEC 2017 benchmark test functions and 8 UCI repository datasets. The statistical results of the CEC 2017 benchmark test functions show that the GWOA-TEO algorithm has good accuracy for global optimization. The classification results of 8 UCI repository datasets also show that the GWOA-TEO algorithm has competitive results with regard to comparison algorithms in recognition rate. Thus, the proposed algorithm is proven to execute excellent performance in solving optimization problems.

scholarly journals 630. A 5-mRNA host response whole-blood classifier trained using patients with non-COVID-19 viral infections accurately predicts severity of COVID-19

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S375-S376
Author(s):  
ljubomir Buturovic ◽  
Purvesh Khatri ◽  
Benjamin Tang ◽  
Kevin Lai ◽  
Win Sen Kuan ◽  
...  
Keyword(s):  
Logistic Regression ◽  
Respiratory Failure ◽  
Viral Infections ◽  
Lamp Assay ◽  
Training Data ◽  
Diagnostic Tools ◽  
Severe Respiratory Failure ◽  
Proof Of Concept ◽  
Risk Of Death ◽  
Qpcr Platform

Abstract Background While major progress has been made to establish diagnostic tools for the diagnosis of SARS-CoV-2 infection, determining the severity of COVID-19 remains an unmet medical need. With limited hospital resources, gauging severity would allow for some patients to safely recover in home quarantine while ensuring sicker patients get needed care. We discovered a 5 host mRNA-based classifier for the severity of influenza and other acute viral infections and validated the classifier in COVID-19 patients from Greece. Methods We used training data (N=705) from 21 retrospective clinical studies of influenza and other viral illnesses. Five host mRNAs from a preselected panel were applied to train a logistic regression classifier for predicting 30-day mortality in influenza and other viral illnesses. We then applied this classifier, with fixed weights, to an independent cohort of subjects with confirmed COVID-19 from Athens, Greece (N=71) using NanoString nCounter. Finally, we developed a proof-of-concept rapid, isothermal qRT-LAMP assay for the 5-mRNA host signature using the QuantStudio 6 qPCR platform. Results In 71 patients with COVID-19, the 5 mRNA classifier had an AUROC of 0.88 (95% CI 0.80-0.97) for identifying patients with severe respiratory failure and/or 30-day mortality (Figure 1). Applying a preset cutoff based on training data, the 5-mRNA classifier had 100% sensitivity and 46% specificity for identifying mortality, and 88% sensitivity and 68% specificity for identifying severe respiratory failure. Finally, our proof-of-concept qRT-LAMP assay showed high correlation with the reference NanoString 5-mRNA classifier (r=0.95). Figure 1. Validation of the 5-mRNA classifier in the COVID-19 cohort. (A) Expression of the 5 genes used in the logistic regression model in patients with (red) and without (blue) mortality. (B) The 5-mRNA classifier accurately distinguishes non-severe and severe patients with COVID-19 as well as those at risk of death. Conclusion Our 5-mRNA classifier demonstrated very high accuracy for the prediction of COVID-19 severity and could assist in the rapid, point-of-impact assessment of patients with confirmed COVID-19 to determine level of care thereby improving patient management and healthcare burden. Disclosures ljubomir Buturovic, PhD, Inflammatix Inc. (Employee, Shareholder) Purvesh Khatri, PhD, Inflammatix Inc. (Shareholder) Oliver Liesenfeld, MD, Inflammatix Inc. (Employee, Shareholder) James Wacker, n/a, Inflammatix Inc. (Employee, Shareholder) Uros Midic, PhD, Inflammatix Inc. (Employee, Shareholder) Roland Luethy, PhD, Inflammatix Inc. (Employee, Shareholder) David C. Rawling, PhD, Inflammatix Inc. (Employee, Shareholder) Timothy Sweeney, MD, Inflammatix, Inc. (Employee)

An Efficient Chaotic Salp Swarm Optimization Approach Based on Ensemble Algorithm for Solving Class Imbalance Problem

2021 ◽  
Author(s):  
Rekha G ◽  
Krishna Reddy V ◽  
chandrashekar jatoth ◽  
Ugo Fiore
Keyword(s):  
Feature Selection ◽  
Optimization Algorithm ◽  
Optimization Problems ◽  
Fitness Function ◽  
Class Imbalance ◽  
Optimization Approach ◽  
Class Imbalance Problem ◽  
Swarm Optimization ◽  
Adaboost Algorithm ◽  
Wide Range

Abstract Class imbalance problems have attracted the research community but a few works have focused on feature selection with imbalanced datasets. To handle class imbalance problems, we developed a novel fitness function for feature selection using the chaotic salp swarm optimization algorithm, an efficient meta-heuristic optimization algorithm that has been successfully used in a wide range of optimization problems. This paper proposes an Adaboost algorithm with chaotic salp swarm optimization. The most discriminating features are selected using salp swarm optimization and Adaboost classifiers are thereafter trained on the features selected. Experiments show the ability of the proposed technique to find the optimal features with performance maximization of Adaboost.

Application of the C4.5 Algorithm to Predict the Types of Disease in Pigs Based on Android

2021 ◽  
Vol 10 (1) ◽  
pp. 105
Author(s):  
I Gusti Ayu Purnami Indryaswari ◽  
Ida Bagus Made Mahendra
Keyword(s):  
Programming Language ◽  
Test Data ◽  
Training Data ◽  
Data Sets ◽  
Android Application ◽  
C4.5 Algorithm ◽  
Sqlite Database

Many Indonesian people, especially in Bali, make pigs as livestock. Pig livestock are susceptible to various types of diseases and there have been many cases of pig deaths due to diseases that cause losses to breeders. Therefore, the author wants to create an Android-based application that can predict the type of disease in pigs by applying the C4.5 Algorithm. The C4.5 algorithm is an algorithm for classifying data in order to obtain a rule that is used to predict something. In this study, 50 training data sets were used with 8 types of diseases in pigs and 31 symptoms of disease. which is then inputted into the system so that the data is processed so that the system in the form of an Android application can predict the type of disease in pigs. In the testing process, it was carried out by testing 15 test data sets and producing an accuracy value that is 86.7%. In testing the application features built using the Kotlin programming language and the SQLite database, it has been running as expected.

Benchmarking and Field-Testing of the Distributed Quasi-Newton Derivative-Free Optimization Method for Field Development Optimization

2021 ◽  
Author(s):  
Faruk Alpak ◽  
Yixuan Wang ◽  
Guohua Gao ◽  
Vivek Jain
Keyword(s):  
Optimization Problems ◽  
Field Testing ◽  
Optimization Method ◽  
Training Data ◽  
Local Optima ◽  
Field Development ◽  
Derivative Free Optimization ◽  
Derivative Free ◽  
Data Points ◽  
Quasi Newton

Abstract Recently, a novel distributed quasi-Newton (DQN) derivative-free optimization (DFO) method was developed for generic reservoir performance optimization problems including well-location optimization (WLO) and well-control optimization (WCO). DQN is designed to effectively locate multiple local optima of highly nonlinear optimization problems. However, its performance has neither been validated by realistic applications nor compared to other DFO methods. We have integrated DQN into a versatile field-development optimization platform designed specifically for iterative workflows enabled through distributed-parallel flow simulations. DQN is benchmarked against alternative DFO techniques, namely, the Broyden–Fletcher–Goldfarb–Shanno (BFGS) method hybridized with Direct Pattern Search (BFGS-DPS), Mesh Adaptive Direct Search (MADS), Particle Swarm Optimization (PSO), and Genetic Algorithm (GA). DQN is a multi-thread optimization method that distributes an ensemble of optimization tasks among multiple high-performance-computing nodes. Thus, it can locate multiple optima of the objective function in parallel within a single run. Simulation results computed from one DQN optimization thread are shared with others by updating a unified set of training data points composed of responses (implicit variables) of all successful simulation jobs. The sensitivity matrix at the current best solution of each optimization thread is approximated by a linear-interpolation technique using all or a subset of training-data points. The gradient of the objective function is analytically computed using the estimated sensitivities of implicit variables with respect to explicit variables. The Hessian matrix is then updated using the quasi-Newton method. A new search point for each thread is solved from a trust-region subproblem for the next iteration. In contrast, other DFO methods rely on a single-thread optimization paradigm that can only locate a single optimum. To locate multiple optima, one must repeat the same optimization process multiple times starting from different initial guesses for such methods. Moreover, simulation results generated from a single-thread optimization task cannot be shared with other tasks. Benchmarking results are presented for synthetic yet challenging WLO and WCO problems. Finally, DQN method is field-tested on two realistic applications. DQN identifies the global optimum with the least number of simulations and the shortest run time on a synthetic problem with known solution. On other benchmarking problems without a known solution, DQN identified compatible local optima with reasonably smaller numbers of simulations compared to alternative techniques. Field-testing results reinforce the auspicious computational attributes of DQN. Overall, the results indicate that DQN is a novel and effective parallel algorithm for field-scale development optimization problems.

A Comparative Study of Global-Best Harmony Search and Bat Algorithms on Optimization Problems

2013 ◽  
Vol 464 ◽  
pp. 352-357
Author(s):  
Pasura Aungkulanon
Keyword(s):  
Optimization Problems ◽  
Search Algorithm ◽  
Harmony Search ◽  
Computation Time ◽  
Finite Sequence ◽  
Bat Algorithm ◽  
Harmony Search Algorithm ◽  
Response Surfaces ◽  
Sample Mean ◽  
Constrained Problems

The engineering optimization problems are large and complex. Effective methods for solving these problems using a finite sequence of instructions can be categorized into optimization and meta-heuristics algorithms. Meta-heuristics techniques have been proved to solve various real world problems. In this study, a comparison of two meta-heuristic techniques, namely, Global-Best Harmony Search algorithm (GHSA) and Bat algorithm (BATA), for solving constrained optimization problems was carried out. GHSA and BATA are optimization algorithms inspired by the structure of harmony improvisation search process and social behavior of bat echolocation for decision direction. These algorithms were implemented under different natures of three optimization, which are single-peak, multi-peak and curved-ridge response surfaces. Moreover, both algorithms were also applied to constrained engineering problems. The results from non-linear continuous unconstrained functions in the context of response surface methodology and constrained problems can be shown that Bat algorithm seems to be better in terms of the sample mean and variance of design points yields and computation time.

scholarly journals A Distributed Multifactorial Particle Swarm Optimization Approach

2021 ◽  
Author(s):  
Ahlem Aboud ◽  
Nizar Rokbani ◽  
Seyedali Mirjalili ◽  
Abdulrahman M. Qahtani ◽  
Omar Almutiry ◽  
...  
Keyword(s):  
Particle Swarm Optimization ◽  
Optimization Problems ◽  
Beta Function ◽  
Particle Swarm ◽  
Search Space ◽  
Optimization Approach ◽  
Multi Objective Optimization ◽  
Swarm Optimization ◽  
Multi Objective ◽  
New System

<p>Multifactorial Optimization (MFO) and Evolutionary Transfer Optimization (ETO) are new optimization challenging paradigms for which the multi-Objective Particle Swarm Optimization system (MOPSO) may be interesting despite limitations. MOPSO has been widely used in static/dynamic multi-objective optimization problems, while its potentials for multi-task optimization are not completely unveiled. This paper proposes a new Distributed Multifactorial Particle Swarm Optimization algorithm (DMFPSO) for multi-task optimization. This new system has a distributed architecture on a set of sub-swarms that are dynamically constructed based on the number of optimization tasks affected by each particle skill factor. DMFPSO is designed to deal with the issues of handling convergence and diversity concepts separately. DMFPSO uses Beta function to provide two optimized profiles with a dynamic switching behaviour. The first profile, Beta-1, is used for the exploration which aims to explore the search space toward potential solutions, while the second Beta-2 function is used for convergence enhancement. This new system is tested on 36 benchmarks provided by the CEC’2021 Evolutionary Transfer Multi-Objective Optimization Competition. Comparatives with the state-of-the-art methods are done using the Inverted General Distance (IGD) and Mean Inverted General Distance (MIGD) metrics. Based on the MSS metric, this proposal has the best results on most tested problems.</p>

Sign in / Sign up

Export Citation Format

Share Document