Ole-Christian Galbo Engstrøm

Ole-Christian Galbo Engstrøm, Erik Schou Dreier, Birthe Møller Jespersen et al.

Based on previous work, we assess the use of NIR-HSI images for calibrating models on two datasets, focusing on protein content regression and grain variety classification. Limited reference data for protein content is expanded by subsampling and associating it with the bulk sample. However, this method introduces significant biases due to skewed leptokurtic prediction distributions, affecting both PLS-R and deep CNN models. We propose adjustments to mitigate these biases, improving mean protein reference predictions. Additionally, we investigate the impact of grain-to-background ratios on both tasks. Higher ratios yield more accurate predictions, but including lower-ratio images in calibration enhances model robustness for such scenarios.

Ole-Christian Galbo Engstrøm

This thesis investigates the application of near-infrared hyperspectral imaging (NIR-HSI) for food quality analysis. The investigation is conducted through four studies operating with five research hypotheses. For several analyses, the studies compare models based on convolutional neural networks (CNNs) and partial least squares (PLS). Generally, joint spatio-spectral analysis with CNNs outperforms spatial analysis with CNNs and spectral analysis with PLS when modeling parameters where chemical and physical visual information are relevant. When modeling chemical parameters with a 2-dimensional (2D) CNN, augmenting the CNN with an initial layer dedicated to performing spectral convolution enhances its predictive performance by learning a spectral preprocessing similar to that applied by domain experts. Still, PLS-based spectral modeling performs equally well for analysis of the mean content of chemical parameters in samples and is the recommended approach. Modeling the spatial distribution of chemical parameters with NIR-HSI is limited by the ability to obtain spatially resolved reference values. Therefore, a study used bulk mean references for chemical map generation of fat content in pork bellies. A PLS-based approach gave non-smooth chemical maps and pixel-wise predictions outside the range of 0-100\%. Conversely, a 2D CNN augmented with a spectral convolution layer mitigated all issues arising with PLS. The final study attempted to model barley's germinative capacity by analyzing NIR spectra, RGB images, and NIR-HSI images. However, the results were inconclusive due to the dataset's low degree of germination. Additionally, this thesis has led to the development of two open-sourced Python packages. The first facilitates fast PLS-based modeling, while the second facilitates very fast cross-validation of PLS and other classical machine learning models with a new algorithm.

Ole-Christian Galbo Engstrøm, Erik Schou Dreier, Birthe Møller Jespersen et al.

We provide an open-source dataset of RGB and NIR-HSI (near-infrared hyperspectral imaging) images with associated segmentation masks and NIR spectra of 2242 individual malting barley kernels. We imaged every kernel pre-exposure to moisture and every 24 hours after exposure to moisture for five consecutive days. Every barley kernel was labeled as germinated or not germinated during each image acquisition. The barley kernels were imaged with black filter paper as the background, facilitating straight-forward intensity threshold-based segmentation, e.g., by Otsu's method. This dataset facilitates time series analysis of germination time for barley kernels using either RGB image analysis, NIR spectral analysis, NIR-HSI analysis, or a combination hereof.

Ole-Christian Galbo Engstrøm, Michela Albano-Gaglio, Erik Schou Dreier et al.

Current approaches to chemical map generation from hyperspectral images are based on models such as partial least squares (PLS) regression, generating pixel-wise predictions that do not consider spatial context and suffer from a high degree of noise. This study proposes an end-to-end deep learning approach using a modified version of U-Net and a custom loss function to directly obtain chemical maps from hyperspectral images, skipping all intermediate steps required for traditional pixel-wise analysis. This study compares the U-Net with the traditional PLS regression on a real dataset of pork belly samples with associated mean fat reference values. The U-Net obtains a test set root mean squared error that is 7% lower than that of PLS regression on the task of mean fat prediction. At the same time, U-Net generates fine detail chemical maps where 99.91% of the variance is spatially correlated. Conversely, only 2.37% of the variance in the PLS-generated chemical maps is spatially correlated, indicating that each pixel-wise prediction is largely independent of neighboring pixels. Additionally, while the PLS-generated chemical maps contain predictions far beyond the physically possible range of 0-100%, U-Net learns to stay inside this range. Thus, the findings of this study indicate that U-Net is superior to PLS for chemical map generation.

Ole-Christian Galbo Engstrøm, Martin Holm Jensen

We present algorithms that substantially accelerate partition-based cross-validation for machine learning models that require matrix products $\mathbf{X}^\mathbf{T}\mathbf{X}$ and $\mathbf{X}^\mathbf{T}\mathbf{Y}$. Our algorithms have applications in model selection for, for example, principal component analysis (PCA), principal component regression (PCR), ridge regression (RR), ordinary least squares (OLS), and partial least squares (PLS). Our algorithms support all combinations of column-wise centering and scaling of $\mathbf{X}$ and $\mathbf{Y}$, and we demonstrate in our accompanying implementation that this adds only a manageable, practical constant over efficient variants without preprocessing. We prove the correctness of our algorithms under a fold-based partitioning scheme and show that the running time is independent of the number of folds; that is, they have the same time complexity as that of computing $\mathbf{X}^\mathbf{T}\mathbf{X}$ and $\mathbf{X}^\mathbf{T}\mathbf{Y}$ and space complexity equivalent to storing $\mathbf{X}$, $\mathbf{Y}$, $\mathbf{X}^\mathbf{T}\mathbf{X}$, and $\mathbf{X}^\mathbf{T}\mathbf{Y}$. Importantly, unlike alternatives found in the literature, we avoid data leakage due to preprocessing. We achieve these results by eliminating redundant computations in the overlap between training partitions. Concretely, we show how to manipulate $\mathbf{X}^\mathbf{T}\mathbf{X}$ and $\mathbf{X}^\mathbf{T}\mathbf{Y}$ using only samples from the validation partition to obtain the preprocessed training partition-wise $\mathbf{X}^\mathbf{T}\mathbf{X}$ and $\mathbf{X}^\mathbf{T}\mathbf{Y}$. To our knowledge, we are the first to derive correct and efficient cross-validation algorithms for any of the $16$ combinations of column-wise centering and scaling, for which we also prove only $12$ give distinct matrix products.