scholarly journals RetSynth: Solving all optimal retrosynthesis solutions using dynamically constrained integer linear programming

2017 ◽  
Author(s):  
Leanne S. Whitmore ◽  
Ali Pinar ◽  
Anthe George ◽  
Corey M. Hudson
Keyword(s):  
Linear Programming ◽  
Integer Programming ◽  
Metabolic Network ◽  
Integer Linear Programming ◽  
Software Package ◽  
Singular Solution ◽  
Linear Integer Programming ◽  
Pathway Search ◽  
Large Corpus

AbstractMotivationNaive determination of all the optimal pathways to production of a target chemical on an arbitrarily defined chassis organism is computationally intractable. Methods like linear integer programming can provide a singular solution to this problem, but fail to provide all optimal pathways.ResultsHere we present RetSynth, an algorithm for determining all optimal biological retrosynthesis solutions, given a starting biological chassis and target chemical. By dynamically scaling constraints, additional pathway search scales relative to the number of fully independent branches in the optimal pathways, and not relative to the number of reactions in the database or size of the metabolic network. This feature allows all optimal pathways to be determined for a very large number of chemicals and for a large corpus of potential chassis organisms.AvailabilityThis algorithm is distributed as part of the RetSynth software package, under a BSD 2-clause license at https://www.github.com/sandialabs/RetSynth/

The determination of the most suitable inertia weight strategy for particle swarm optimization via the minimax mixed-integer linear programming model

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Volkan Soner Özsoy
Keyword(s):  
Linear Programming ◽  
Integer Linear Programming ◽  
Mixed Integer Linear Programming ◽  
Pso Algorithm ◽  
Complex Problem ◽  
Mixed Integer ◽  
Swarm Optimization ◽  
Content Type ◽  
Inertia Weight

Purpose This paper aims to consider each strategy of the particle swarm optimization (PSO) as a unit in data envelopment analysis (DEA) and uses the minimax mixed-integer linear programming DEA approach to find the most suitable inertia weight strategy. A total of 15 inertia weight strategies were empirically examined in a suite of 42 benchmark problems in the view of DEA. Design/methodology/approach PSO is very sensitive to inertia weight strategies, and therefore, an important amount of research attempts has been concentrated on these strategies. There is no research into the determination of the most suitable inertia weight strategy; however, there are a large number of comparisons related to the inertia weight strategies. DEA is one of the performance evaluation methods, and its models classify the set of strategies into two distinct sets as efficient and inefficient. However, only one of the strategies should be used in the PSO algorithm. Some effective models were proposed to find the most efficient strategy. Findings The experimental studies demonstrate that an approach is a useful tool in the determination of the most suitable strategy. Besides, if the author encounters a new complex problem whose properties are known, it will help the author to choose the best strategy. Practical implications A heavy oil thermal cracking three lumps model for the simplification of the reaction system was used because it is an important complicated chemical process. In addition, the soil water retention curve (SWRC) plays an important role in diverse facets of agricultural engineering. As the SWRC can be regarded as a nonlinear function between the water content and the soil water potential, Van Genuchten model is proposed to describe this function. To determinate these model parameters, an optimization problem is formulated, which minimizes the difference between the measured and modeled data. Originality/value In this paper, the PSO algorithm is integrated with minimax mixed-integer linear programming to find the most suitable inertia weight strategy. In this way, the best strategy could be chosen for a new more complex problem.

scholarly journals MASALAH GROUND-HOLDING DENGAN DUA TERMINAL DALAM PENGENDALIAN LALU LINTAS UDARA

2014 ◽  
Vol 13 (1) ◽  
pp. 61
Author(s):  
W. PRASETYO ◽  
F. HANUM ◽  
P. T. SUPRIYO
Keyword(s):  
Linear Programming ◽  
Integer Programming ◽  
Integer Linear Programming

Setiap maskapai penerbangan memiliki strategi untuk meminimumkan biaya penundaan antara lain kebijakan ground-holding. Kebijakan ini mampu membuat maskapai untuk menahan pesawatnya di terminal keberangkatan meskipun sudah dijadwalkan untuk lepas landas sehingga setelah sampai di kota tujuan dapat langsung mendarat tanpa harus menunggu di udara. Dalam karya ilmiah ini dibahas tentang penentuan waktu keberangkatan dan kedatangan dari setiap penerbangan yang dapat meminimumkan biaya penundaan. Masalah ground-holding dengan dua terminal dalam pengendalian lalu lintas udara dapat diformulasikan menjadi masalah Pure 0-1 integer linear programming. Dalam penelitian ini dibahas dua kasus dari kebijakan ground-holding. Kasus pertama: seluruh penerbangan dapat menahan pesawatnya di terminal keberangkatan dan dapat tertahan di udara. Kasus kedua: seluruh penerbangan hanya menahan pesawatnya di terminal keberangkatan sehingga pada saat sampai di kota tujuan tidak tertahan di udara. Diberikan simulasi dengan mengasumsikan terdapat 26 penerbangan dan jadwal waktu keberangkatan serta waktu kedatangan dari setiap penerbangan. Jika penerbangan terjadi dari terminal keberangkatan kota awal menuju terminal kedatangan kota tujuan, dengan integer programming tersebut akan diperoleh waktu keberangkatan dan waktu kedatangan yang meminimumkan biaya penundaan.

scholarly journals Penggunaan Metode Branch and Bound dan Gomory Cut dalam Menentukan Solusi Integer Linear Programming

SAINTIFIK ◽  
2017 ◽  
Vol 2 (1) ◽  
pp. 9-15
Author(s):  
Wahyudin Nur ◽  
Nurul Mukhlisah Abdal
Keyword(s):  
Linear Programming ◽  
Integer Programming ◽  
Branch And Bound ◽  
Integer Linear Programming ◽  
Gomory Cut

Integer Linear Programming adalah sebuah model matematis yang memungkinkan hasil penyelesaian kasus pada Pemrograman Linier berupa bilangan bulat. . Masalah integer linear programming termasuk salah satu bagian riset operasi yang sangat penting karena dalam kehidupan sehari-hari, ada banyak permasalah pemrograman linear yang mengharuskan solusinya integer. Ada beberapa metode untuk menyelesaikan persoalan Integer Programming, tapi yang akan dibahas pada penelitian ini adalah Metode Branch and Bound dan Metode Gomory Cut. Tujuan dari penelitian ini adalah untuk menentukan solusi masalah Integer Linear Programming dan membandingkan hasil yang diperoleh dari Metode Branch and Bound dengan Metode Gomory Cut. Penelitian ini adalah penelitian kepustakaan yang menggunakan berbagai literatur-literatur yang berkaitan dengan topik yang akan diteliti. Hasil penelitian ini menunjukkan solusi yang diperoleh dari metode Branch and Bound samadengan metode Gomory Cut. Dalam pemecahannya metode Branch and Bound memerlukan banyak iterasi simpleks dibanding metode Gomory Cut.Kata kunci: Integer Linear Programming, Metode Branch Bound, Metode Gomory Cut

scholarly journals Maximum likelihood pedigree reconstruction using integer programming

10.29007/sghd ◽  
2018 ◽  
Author(s):  
James Cussens
Keyword(s):  
Linear Programming ◽  
Integer Programming ◽  
Maximum Likelihood ◽  
Programming Problem ◽  
Allele Frequency ◽  
Integer Linear Programming ◽  
Linear Programming Problem ◽  
Pedigree Reconstruction ◽  
Integer Linear Programming Problem ◽  
Family Trees

Pedigrees are `family trees' relating groups of individuals which can usefully be seen as Bayesian networks. The problem of finding a maximum likelihood pedigree from genotypic data is encoded as an integer linear programming problem. Two methods of ensuring that pedigrees are acyclic are considered. Results on obtaining maximum likelihood pedigrees relating 20, 46 and 59 individuals are presented. Running times for larger pedigrees depend strongly on the data used but generally compare well with those in the literature. Solving is particularly fast when allele frequency is uniform.

scholarly journals An Insight into the Characteristic Equation for an Integer Program

2021 ◽  
Vol 6 (2) ◽  
pp. 611-620
Author(s):  
Santosh Kumar ◽  
Elias Munapo ◽  
Philimon Nyamugure
Keyword(s):  
Linear Programming ◽  
Integer Programming ◽  
Characteristic Equation ◽  
Programming Model ◽  
Integer Program ◽  
Optimal Solutions ◽  
Integer Programs ◽  
Linear Integer Programming ◽  
Enhanced Properties ◽  
Insight Into

This article enhances properties and applications associated with the characteristic equation (CE) developed to find an optimal and other ranked-optimal solutions of linear integer programming model. These enhanced properties have applications in the analysis of the multi-objective linear integer programs. The paper also identifies why the CE approach is not possible for some special linear programming (LP) models and creates a challenge for further investigation.

Linear Integer Programming Techniques for Portfolio Design Problem

2020 ◽  
pp. 80-102
Keyword(s):  
Linear Programming ◽  
Integer Programming ◽  
Design Problem ◽  
Linear Models ◽  
Linear Constraint ◽  
Quadratic Model ◽  
Linear Integer Programming ◽  
Constraint Systems ◽  
Programming Techniques ◽  
Portfolio Design

This chapter introduces Integer Linear Programming (ILP) approaches for solving efficiently a ðnancial portfolio design problem. The authors proposed a matricial model in Chapter 3, which is a mathematical quadratic model. A linearization step is considered necessary to apply linear programming techniques. The corresponding matricial model shows clearly that the problem is strongly symmetrical. The row and column symmetries are easily handled by adding a negligible number of new constraints. The authors propose two linear models, which are given in detail and proven. These models represent the problem as linear constraint systems with 0-1 variables, which will be implemented in ILP solver. Experimental results in non-trivial instances of portfolio design problem are given.

scholarly journals An integer programming model for gate assignment problem at airline terminals

2015 ◽  
Vol 11 (2) ◽  
Author(s):  
Chong Kok Chun ◽  
Syarifah Zyurina Nordin
Keyword(s):  
Linear Programming ◽  
Integer Programming ◽  
Integer Linear Programming ◽  
Assignment Problem ◽  
Computational Experiment ◽  
Programming Model ◽  
Computational Experiments ◽  
Walking Distance ◽  
Total Distance ◽  
Gate Assignment

In this paper, we concentrate on a gate assignment problem (GAP) at the airlines terminal. Our problem is to assign an arrival plane to a suitable gate. There are two considerations needed to take. One of its is passenger walking distance from arrival gate to departure gate while another consideration is the transport baggage distance from one gate to another. Our objective is to minimize the total distance between the gates that related to assign the arrival plane to the suitable gates. An integer linear programming (ILP) model is proposed to solve this gate assignment problem. We also conduct a computational experiment using CPLEX 12.1 solver in AIMMS 3.10 software to analyze the performance of the model. Results of the computational experiments are presented. The efficiency of flights assignment is depends on the ratio of the weight for both total passenger traveling distances and total baggage transport distances.

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