Feature selection strategies for identification of Staphylococcus aureus recovered in blood cultures using FT-IR spectroscopy successive projections algorithm for variable selection: A case study

Marques, Aline de Sousa; Melo, Maria Celeste Nunes de; Cidral, Thiago André; Lima, Kássio M. G.

doi:10.1016/j.mimet.2013.12.015

Cited by 29 publications

(12 citation statements)

References 20 publications

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“…Thus, alongside LDA are applied: genetic algorithm (GA-LDA), successive projection algorithm (SPA-LDA), PCA–DA, and partial least squares (PLS-DA). 6 , 8 , 10 − 14 , 16 − 18 …”

Section: Introductionmentioning

confidence: 99%

“…Proteins exhibit higher signal contributions around amide I at ∼1650 cm −1 (80% CO stretching, 10% C−N stretching, and 10% C−N bending) and amide II at ∼1550 cm −1 (60% N−H bending, and 40% C−N stretching); and a lower contribution of amide III at ∼1260 cm −1 (C−N stretching). 6,8,10−12 Studies have reported the use of MIR spectroscopy to detect dengue virus in blood samples, 13 identification of Staphylococcus aureus bacteria in blood samples, 14 and stability studies of blood composition from healthy people. 15 However, one of the difficulties in the use of MIR spectroscopy in virology studies is related to the variability of viruses affecting human organisms.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Studies have reported the use of MIR spectroscopy to detect dengue virus in blood samples, identification of Staphylococcus aureus bacteria in blood samples, and stability studies of blood composition from healthy people . However, one of the difficulties in the use of MIR spectroscopy in virology studies is related to the variability of viruses affecting human organisms.…”

Section: Introductionmentioning

confidence: 99%

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Noninvasive Diagnostic for COVID-19 from Saliva Biofluid via FTIR Spectroscopy and Multivariate Analysis

et al. 2022

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the worst global health crisis in living memory. The reverse transcription polymerase chain reaction (RT-qPCR) is considered the gold standard diagnostic method, but it exhibits limitations in the face of enormous demands. We evaluated a mid-infrared (MIR) data set of 237 saliva samples obtained from symptomatic patients (138 COVID-19 infections diagnosed via RT-qPCR). MIR spectra were evaluated via unsupervised random forest (URF) and classification models. Linear discriminant analysis (LDA) was applied following the genetic algorithm (GA-LDA), successive projection algorithm (SPA-LDA), partial least squares (PLS-DA), and a combination of dimension reduction and variable selection methods by particle swarm optimization (PSO-PLS-DA). Additionally, a consensus class was used. URF models can identify structures even in highly complex data. Individual models performed well, but the consensus class improved the validation performance to 85% accuracy, 93% sensitivity, 83% specificity, and a Matthew’s correlation coefficient value of 0.69, with information at different spectral regions. Therefore, through this unsupervised and supervised framework methodology, it is possible to better highlight the spectral regions associated with positive samples, including lipid (∼1700 cm –1 ), protein (∼1400 cm –1 ), and nucleic acid (∼1200–950 cm –1 ) regions. This methodology presents an important tool for a fast, noninvasive diagnostic technique, reducing costs and allowing for risk reduction strategies.

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“…Thus, alongside LDA are applied: genetic algorithm (GA-LDA), successive projection algorithm (SPA-LDA), PCA–DA, and partial least squares (PLS-DA). 6 , 8 , 10 − 14 , 16 − 18 …”

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Noninvasive Diagnostic for COVID-19 from Saliva Biofluid via FTIR Spectroscopy and Multivariate Analysis

et al. 2022

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“…Basically, SPA-LDA and GA-LDA employ a cost function associated with the average risk of misclassification in a validation set and can also reduce the generalisation problems often associated with collinearity and avoid over-fitting. 3…”

Section: Data Handling Approachesmentioning

confidence: 99%

Near Infrared Spectroscopy as an Emerging Tool for Forensic Entomotoxicology

et al. 2014

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“…In biological samples, the range between 1800 to 900 cm −1 is known as the biofingerprint region because it has a high density of information regarding important biomolecules. The field of study where spectroscopic tools are used to analyze biological samples has become known as biospectroscopy [4,17], and has been widely used in chemometric approaches involving the identification of bacteria [22,23], viruses [42,43], cancer diagnosis [56], forensic entomology [2], among others.…”

Section: Introductionmentioning

confidence: 99%

ATR-FTIR spectroscopy for virus identification: A powerful alternative

Santos

Morais

Lima

2021

BSI

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In pandemic times, like the one we are witnessing for COVID-19, the discussion about new efficient and rapid techniques for diagnosis of diseases is more evident. In this mini-review, we present to the virological scientific community the potential of attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy as a diagnosis technique. Herein, we explain the operation of this technique, as well as its advantages over standard methods. In addition, we also present the multivariate analysis tools that can be used to extract useful information from the data towards classification purposes. Tools such as Principal Component Analysis (PCA), Successive Projections Algorithm (SPA), Genetic Algorithm (GA) and Linear and Quadratic Discriminant Analysis (LDA and QDA) are covered, including examples of published studies. Finally, the advantages and disadvantages of ATR-FTIR spectroscopy are emphasized, as well as future prospects in this field of study that is only growing. One of the main aims of this paper is to encourage the scientific community to explore the potential of this spectroscopic tool to detect changes in biological samples such as those caused by the presence of viruses.

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Feature selection strategies for identification of Staphylococcus aureus recovered in blood cultures using FT-IR spectroscopy successive projections algorithm for variable selection: A case study

Cited by 29 publications

References 20 publications

Noninvasive Diagnostic for COVID-19 from Saliva Biofluid via FTIR Spectroscopy and Multivariate Analysis

Noninvasive Diagnostic for COVID-19 from Saliva Biofluid via FTIR Spectroscopy and Multivariate Analysis

Near Infrared Spectroscopy as an Emerging Tool for Forensic Entomotoxicology

ATR-FTIR spectroscopy for virus identification: A powerful alternative

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