Evaluation of Multi-Objective Optimization Algorithms for NMR Chemical Shift Assignment

An automated NMR chemical shift assignment algorithm was developed using multi-objective optimization techniques. The problem is modeled as a combinatorial optimization problem and its objective parameters are defined separately in different score functions. Some of the heuristic approaches of evolutionary optimization are employed in this problem model. Both, a conventional genetic algorithm and multi-objective methods, i.e., the non-dominated sorting genetic algorithms II and III (NSGA2 and NSGA3), are applied to the problem. The multi-objective approaches consider each objective parameter separately, whereas the genetic algorithm followed a conventional way, where all objectives are combined in one score function. Several improvement steps and repetitions on these algorithms are performed and their combinations are also created as a hyper-heuristic approach to the problem. Additionally, a hill-climbing algorithm is also applied after the evolutionary algorithm steps. The algorithms are tested on several different datasets with a set of 11 commonly used spectra. The test results showed that our algorithm could assign both sidechain and backbone atoms fully automatically without any manual interactions. Our approaches could provide around a 65 success rate and could assign some of the atoms that could not be assigned by other methods.

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Eser Adı
(dc.title)
Evaluation of Multi-Objective Optimization Algorithms for NMR Chemical Shift Assignment
Yazar
(dc.contributor.author)
Sima Etaner Uyar
Yayın Yılı
(dc.date.issued)
2021
Tür
(dc.type)
Makale
Özet
(dc.description.abstract)
An automated NMR chemical shift assignment algorithm was developed using multi-objective optimization techniques. The problem is modeled as a combinatorial optimization problem and its objective parameters are defined separately in different score functions. Some of the heuristic approaches of evolutionary optimization are employed in this problem model. Both, a conventional genetic algorithm and multi-objective methods, i.e., the non-dominated sorting genetic algorithms II and III (NSGA2 and NSGA3), are applied to the problem. The multi-objective approaches consider each objective parameter separately, whereas the genetic algorithm followed a conventional way, where all objectives are combined in one score function. Several improvement steps and repetitions on these algorithms are performed and their combinations are also created as a hyper-heuristic approach to the problem. Additionally, a hill-climbing algorithm is also applied after the evolutionary algorithm steps. The algorithms are tested on several different datasets with a set of 11 commonly used spectra. The test results showed that our algorithm could assign both sidechain and backbone atoms fully automatically without any manual interactions. Our approaches could provide around a 65 success rate and could assign some of the atoms that could not be assigned by other methods.
Açık Erişim Tarihi
(dc.date.available)
2024-03-14
Yayıncı
(dc.publisher)
MDPI
Dil
(dc.language.iso)
En
Konu Başlıkları
(dc.subject)
NMR
Konu Başlıkları
(dc.subject)
Chemical shift assignment
Konu Başlıkları
(dc.subject)
Automated assignment
Konu Başlıkları
(dc.subject)
Multi-objective optimization
Tek Biçim Adres
(dc.identifier.uri)
https://hdl.handle.net/20.500.14081/1329
Dergi
(dc.relation.journal)
Molecules
Dergi Sayısı
(dc.identifier.issue)
12
Esere Katkı Sağlayan
(dc.contributor.other)
Etaner-Uyar, Sima
Esere Katkı Sağlayan
(dc.contributor.other)
Guntert, Peter
Esere Katkı Sağlayan
(dc.contributor.other)
Maden Yilmaz, Emel
DOI
(dc.identifier.doi)
10.3390/molecules26123699
Orcid
(dc.identifier.orcid)
0000-0003-1440-3831
Dergi Cilt
(dc.identifier.volume)
26
wosquality
(dc.identifier.wosquality)
Q2
wosauthorid
(dc.contributor.wosauthorid)
C-7702-2009
Department
(dc.contributor.department)
Bilgisayar Mühendisliği
Wos No
(dc.identifier.wos)
WOS:000666046000001
Veritabanları
(dc.source.platform)
Wos
Veritabanları
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Scopus
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PubMed
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