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- Martyna, Agnieszka, et al.
(författare)
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Likelihood ratio-based probabilistic classifier
- 2023
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Ingår i: Chemometrics and Intelligent Laboratory Systems. - : ELSEVIER. - 0169-7439 .- 1873-3239. ; 240
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Tidskriftsartikel (refereegranskat)abstract
- Modern classification methods are likely to misclassify samples with rare but class-specific data that are more similar (less distant) to the data of another than the original class. This is because they tend to focus on the majority of data, leaving the information provided by the rare data practically ignored. Nevertheless, it is an invaluable source of information that should support classification of samples with such data, despite their low frequency. Current solutions considering the rarity information involve likelihood ratio models (LR). We intend to modify the existing LR models to establish the class membership for the analysed samples by comparing them with the samples of known class label. If two compared samples show similarities of rare but class-specific features it makes the analysed sample much more likely to be a member of this class than any other class, even when its features are less distant to the features of most samples from other classes. The fundamental advantage of the developed methodology is inclusion of information about rare, class-specific features, which is neglected by ordinary classifiers. Converting LR values into probabilities with which a sample belongs to the classes under consideration, generates a powerful tool within the concept of probabilistic classification.
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| 2. |
- Rotari, Marta, et al.
(författare)
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An extension of PARAFAC to analyze multi-group three-way data
- 2024
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Ingår i: Chemometrics and Intelligent Laboratory Systems. - : Elsevier. - 0169-7439 .- 1873-3239. ; 246
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Tidskriftsartikel (refereegranskat)abstract
- This paper introduces a novel methodology for analyzing three-way array data with a multi-group structure. Three-way arrays are commonly observed in various domains, including image analysis, chemometrics, and real-world applications. In this paper, we use a practical case study of process modeling in additive manufacturing, where batches are structured according to multiple groups. Vast volumes of data for multiple variables and process stages are recorded by sensors installed on the production line for each batch. For these three-way arrays, the link between the final product and the observations creates a grouping structure in the observations. This grouping may hamper gaining insight into the process if only some of the groups dominate the controlled variability of the products. In this study, we develop an extension of the PARAFAC model that takes into account the grouping structure of three-way data sets. With this extension, it is possible to estimate a model that is representative of all the groups simultaneously by finding their common structure. The proposed model has been applied to three simulation data sets and a real manufacturing case study. The capability to find the common structure of the groups is compared to PARAFAC and the insights into the importance of variables delivered by the models are discussed.
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| 3. |
- Skantze, Viktor, 1992, et al.
(författare)
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Identification of metabotypes in complex biological data using tensor decomposition
- 2023
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Ingår i: Chemometrics and Intelligent Laboratory Systems. - : Elsevier BV. - 0169-7439 .- 1873-3239. ; 233
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Tidskriftsartikel (refereegranskat)abstract
- Differences in the physiological response to treatment, such as dietary intervention, has led to the development of precision approaches in nutrition and medicine to tailor treatment for improved benefits to the individual. One such approach is to identify metabotypes, i.e., groups of individuals with similar metabolic profiles and/or regulation. Metabotyping has previously been performed using e.g., principal component analysis (PCA) on matrix data. However, metabotyping methods suitable for more complex experimental designs such as repeated measures or cross-over studies are needed. We have developed a metabotyping method for tensor data, based on CANDECOMP/PARAFAC (CP) tensor decomposition. Metabotypes are inferred from CP scores using k-means clustering, and robustness is evaluated using bootstrapping of metabolites. As a proof-of-concept, we identified metabotypes from metabolomics data where 79 metabolites were analyzed in 8 time points postprandially in 17 overweight men that underwent a three-arm dietary crossover intervention. Two metabotypes were found, characterized by differences in amino acid metabolite concentration, that were differentially associated with baseline plasma creatinine (p = 0.007) and with the baseline metabolome (p = 0.004). These results suggest that CP decomposition provides a viable approach for metabotype identification directly from complex, high-dimensional data with improved biological interpretation compared to the more simplistic PCA approach. A simulation study together with results from measured data concluded that several preprocessing methods should be taken into consideration for CP-based metabotyping on complex tensor data.
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