PRFFECT: a versatile tool for spectroscopists

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Abstract

PRFFECT is a computer program to aid with spectral preprocessing and the development of classification models. Via a simple text interface, PRFFECT allows users to select wavenumber ranges, perform spectral preprocessing, carry out data partitioning (into training and testing datasets), run a Random Forest classification, compute statistical results, and identify important descriptors for the classification. The preprocessing options provided fall into four categories: binning, smoothing, normalisation, and baseline correction. The program outputs a wide-variety of useful data, including classification metrics and graphs showing the importance of individual wavenumbers to the classification models. As proof-of-concept, PRFFECT has been benchmarked on preprocessing and classification of four food analysis datasets. Sensitivities and specificities above 0.92 were obtained in all cases. The results show that different preprocessing procedures are optimal for different datasets. The PRFFECT software is available freely to the community via GitHub. Link: https://github.com/Palmer- Lab/PRFFECT.
LanguageEnglish
Number of pages36
JournalChemometrics and intelligent laboratory systems
Early online date11 Nov 2017
DOIs
Publication statusPublished - 15 Jan 2018

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Keywords

  • spectroscopy
  • FTIR
  • machine learning
  • spectral preprocessing

Cite this

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title = "PRFFECT: a versatile tool for spectroscopists",
abstract = "PRFFECT is a computer program to aid with spectral preprocessing and the development of classification models. Via a simple text interface, PRFFECT allows users to select wavenumber ranges, perform spectral preprocessing, carry out data partitioning (into training and testing datasets), run a Random Forest classification, compute statistical results, and identify important descriptors for the classification. The preprocessing options provided fall into four categories: binning, smoothing, normalisation, and baseline correction. The program outputs a wide-variety of useful data, including classification metrics and graphs showing the importance of individual wavenumbers to the classification models. As proof-of-concept, PRFFECT has been benchmarked on preprocessing and classification of four food analysis datasets. Sensitivities and specificities above 0.92 were obtained in all cases. The results show that different preprocessing procedures are optimal for different datasets. The PRFFECT software is available freely to the community via GitHub. Link: https://github.com/Palmer- Lab/PRFFECT.",
keywords = "spectroscopy, FTIR, machine learning, spectral preprocessing",
author = "Smith, {Benjamin R.} and Baker, {Matthew J.} and Palmer, {David S.}",
year = "2018",
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doi = "10.1016/j.chemolab.2017.10.024",
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issn = "0169-7439",

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T1 - PRFFECT

T2 - Chemometrics and intelligent laboratory systems

AU - Smith, Benjamin R.

AU - Baker, Matthew J.

AU - Palmer, David S.

PY - 2018/1/15

Y1 - 2018/1/15

N2 - PRFFECT is a computer program to aid with spectral preprocessing and the development of classification models. Via a simple text interface, PRFFECT allows users to select wavenumber ranges, perform spectral preprocessing, carry out data partitioning (into training and testing datasets), run a Random Forest classification, compute statistical results, and identify important descriptors for the classification. The preprocessing options provided fall into four categories: binning, smoothing, normalisation, and baseline correction. The program outputs a wide-variety of useful data, including classification metrics and graphs showing the importance of individual wavenumbers to the classification models. As proof-of-concept, PRFFECT has been benchmarked on preprocessing and classification of four food analysis datasets. Sensitivities and specificities above 0.92 were obtained in all cases. The results show that different preprocessing procedures are optimal for different datasets. The PRFFECT software is available freely to the community via GitHub. Link: https://github.com/Palmer- Lab/PRFFECT.

AB - PRFFECT is a computer program to aid with spectral preprocessing and the development of classification models. Via a simple text interface, PRFFECT allows users to select wavenumber ranges, perform spectral preprocessing, carry out data partitioning (into training and testing datasets), run a Random Forest classification, compute statistical results, and identify important descriptors for the classification. The preprocessing options provided fall into four categories: binning, smoothing, normalisation, and baseline correction. The program outputs a wide-variety of useful data, including classification metrics and graphs showing the importance of individual wavenumbers to the classification models. As proof-of-concept, PRFFECT has been benchmarked on preprocessing and classification of four food analysis datasets. Sensitivities and specificities above 0.92 were obtained in all cases. The results show that different preprocessing procedures are optimal for different datasets. The PRFFECT software is available freely to the community via GitHub. Link: https://github.com/Palmer- Lab/PRFFECT.

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KW - FTIR

KW - machine learning

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