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4.4 Conclusion In this chapter, the functionality of the constructed multivariate analysis pipeline was once more extended to incorporate data integration techniques. Various approaches for the fusion of data from the analytical instruments have been evaluated in order to determine whether different instruments provide complementary information, which when brought together in an integrated analysis can provide a more reliable method for spoilage than single instruments. Generalised Procrustes Analysis (GPA) was the first data fusion technique to be investigated. The algorithm attempts to minimise the dissimilarities of the heterogeneous data by applying geometric transformations and simultaneous shape superimposition towards building a single consensus configuration. The alternative technique of consensus PCA (CPCA) was also implemented within the pipeline. The algorithm generates as an output a consensus scores matrix on the “super level”. Prior to permutation testing, no optimal classification method could be determined since the classification results of all different types of classifiers appeared to be equally good. However, in addition to verifying the statistical significance of the obtained results, the outcome of permutation testing clearly established SVMs as more powerful and robust techniques than PLS-DA since they consistently produced higher generalisation accuracies. The results obtained by GPA and CPCA were found to be greatly similar to each other, with the latter taking precedence in the weak cases presented by Procrustes. The values obtained by the fused models were compared to the analysis results of the standalone datasets as presented in Chapter 2. For case study 1, HPLC as a standalone technique produced the best overall , equal to 80%; in this instance, the results of both data integration techniques did not accomplish any improvement in the overall classification accuracy since they did not exceed the accuracy of standalone HPLC. However, these findings may only hold true for this particular case study, and thus the pipeline will be further applied on new real-world case studies as a means of establishing its generalisability. 111
5 Application of the multivariate analysis pipeline on new case studies 5.1 Introduction Thus far, a novel suite of chemometric tools for the integration and analysis of highly heterogeneous analytical datasets has been designed, implemented and tested upon a single case study (“Shelf life beef fillets stored in air at 0, 5, 10, 15 and 20°C”). This chapter aims to verify the applicability of the constructed multivariate analysis pipeline on several independent case studies, and thus go some way to establishing the generic applicability of the developed tool suite. By reproducing the analyses and making the findings available through comprehensive comparison, we ensure that the implemented tool is representative of real-world application, and that it may be further employed by other scientists to studies and areas of inquiry far wider than the present study. 5.2 Materials and Methods Thorough information about the experimental protocols of the new case studies can be found in Argyri (2010), Argyri et al. (2010), Argyri et al. (2011), Argyri et al. (2013) and Papadopoulou et al. (2011). The analytical techniques used in all case studies are the same as the ones of case study 1; besides Raman spectroscopy, the instruments’ technical specifications can be found in Section 2.2.1. In addition, sensory evaluation of the meat samples was performed according to Gill and Jeremiah (1991) as described in Section 2.2.2. Each designated class represents a distinct status of spoilage (fresh, semi-fresh and spoiled samples). The standalone and fused datasets of each case study under investigation were inserted in the implemented analysis pipeline according to Section 4.2.5. 112
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CRANFIELD UNIVERSITY Eleni Anthippi
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ABSTRACT Muscle foods such as meat,
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TABLE OF CONTENTS ABSTRACT ........
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6.2.4 The iWebPlots package .......
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Figure 3-12 Speedup produced by the
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Figure 6-9 Sweave example for the d
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TABLE OF EQUATIONS Equation 1 Mean-
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RMSE RMSECV SSE SVD SVMs SYMBIOSIS-
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Figure 1-1 Evolution from molecular
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1.1.2.1 Fourier Transform Infrared
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1.1.3 Microbial Spoilage in Meat Sy
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The multivariate techniques applied
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1.4 Multivariate Analysis: Unsuperv
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1.4.2 Cluster Analysis Cluster anal
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1.5 Multivariate Analysis: Supervis
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In any linearly separable binary da
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Where ( ) are the Lagrange multipli
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Every kernel is characterised by a
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The “one-against-all” approach
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Furthermore, metrics such as the bi
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1.6.3 Leave-One-Out Cross-Validatio
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In such cases, the model becomes qu
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1.8 Aims and objectives The overall
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2 Development of the multivariate a
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Sensory panel scores were of the hi
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DF (Hz) 2.2.1.5 Electronic Nose (e-
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Figure 2-3 Data intersection The fi
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3. Validation Techniques In the cas
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Figure 2-4 The process of construct
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2.3 Results and Discussion 2.3.1 Pr
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(b) HPLC data (c) e-nose data Figur
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In the case of FTIR, linear classif
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2.3.2.2 Class Prediction Accuracies
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Figure 2-7 Class prediction rates o
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The topology of the three-dimension
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Figure 2-9 Three-dimensional error
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Furthermore, a thorough comparison
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Page 77 and 78: precision of the classification acc
Page 79 and 80: Figure 3-3 The steps of the Nelder-
Page 81 and 82: 3.3 Results and Discussion 3.3.1 Li
Page 83 and 84: 3.3.2 Nonlinear Models In order to
Page 85 and 86: 9) 10) 11) 12) 13) 14) 15) 16) Figu
Page 87 and 88: As an additional visual aid, these
Page 89 and 90: a) Number of iterations b) Number o
Page 91 and 92: Figure 3-10 Comparison of the execu
Page 93 and 94: Figure 3-12 Speedup produced by the
Page 95 and 96: 4 Integration of Heterogeneous Data
Page 97 and 98: 4.2.2 Procrustes Analysis Procruste
Page 99 and 100: symmetric method since the ordering
Page 101 and 102: Figure 4-3 Steps of CPCA for the da
Page 103 and 104: 4.2.5 Data Integration and Analysis
Page 105 and 106: Figure 4-4 Data integration workflo
Page 107 and 108: a) GPA b) CPCA Figure 4-6 The conse
Page 109 and 110: accuracies as the linear models; po
Page 111 and 112: Figure 4-8 Classification Results f
Page 113 and 114: Similar to FTIR, the PLS-DA ensembl
Page 115 and 116: Figure 4-9 Class prediction rates o
Page 117 and 118: 4.3.3 Permutation Tests Even though
Page 119 and 120: Even though the interpretation of t
Page 121 and 122: Figure 4-12 Distribution plots of t
Page 123 and 124: RBF SVMs Datasets Original %CC Mean
Page 125: Figure 4-14 Boxplots representing t
Page 129 and 130: Figure 5-1 Mean FTIR spectra for ca
Page 131 and 132: 5.2.2.2 Fourier Transform Infrared
Page 133 and 134: 5.2.2.4 Data Overview For each expe
Page 135 and 136: 5.2.3.3 High Throughput Liquid Chro
Page 137 and 138: Figure 5-5 displays the PCA scores
Page 139 and 140: (a) GPA (b) CPCA Figure 5-6 The con
Page 141 and 142: observation confirms that indeed CP
Page 143 and 144: Figure 5-8 Class prediction rates o
Page 145 and 146: (a) RBF SVMs (b) PLS-DA Figure 5-9
Page 149 and 150: Figure 5-12 Execution times of the
Page 151 and 152: (a) FTIR data (b) Raman data Figure
Page 153 and 154: The classification results for the
Page 155 and 156: Figure 5-16 Class prediction rates
Page 157 and 158: (a) RBF SVMs (b) PLS-DA Figure 5-17
Page 161 and 162: Figure 5-20 Execution times of the
Page 163 and 164: (a) FTIR data (b) HPLC data 148
Page 165 and 166: (a) GPA (b) CPCA Figure 5-22 The co
Page 167 and 168: The classification results of the f
Page 169 and 170: Figure 5-24 Classification Results
Page 171 and 172: Figure 5-25 Class prediction rates
Page 173 and 174: The permutation results for the dat
Page 175 and 176: Figure 5-28 Distribution plots of t
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RBF SVMs Datasets Original %CC Mean
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Figure 5-30 Boxplots representing t
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5.4 Comparison of the individual ca
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Figure 5-32 Investigating the commo
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6 Development of improved visualisa
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6.2.2 Generating static graphs As d
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Figure 6-2 Construction process of
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6.2.2.2 Generating dynamic reports
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activity, while simultaneously the
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or disappeared (Wang et al., 2008).
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ectangles, circles and/or irregular
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In addition to the static figures g
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c) graphics package d) ggplot2 pack
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In addition to aesthetics, faceting
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Datasets FTIR HPLC e-nose PLS-DA (L
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Figure 6-10 Interactive dendrogram
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6.4 Conclusion The work reported in
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large number of individual models i
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The generated suite of tools, as pr
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In addition, the difficulty to corr
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REFERENCES Almeida, J. A. S., Barbo
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Processing., Proceedings of the 12t
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Clarke, B., Fokoué, E. and Zhang,
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spectroscopy and machine learning",
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Gower, J. C. (1975), "Generalized p
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Jardon, M. (2006), Systems Biology:
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Nicolaou, N., Xu, Y. and Goodacre,
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Shah, A. A., Barthel, D., Lukasiak,
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Vera, G., Jansen, R. and Suppi, R.
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Xu, Y. and Goodacre, R. (2012), "Mu
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