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Optimal distribution-preserving downsampling of large biomedical data sets (opdisDownsampling)
(2021)
Motivation: The size of today’s biomedical data sets pushes computer equipment to its limits, even for seemingly standard analysis tasks such as data projection or clustering. Reducing large biomedical data by downsampling is therefore a common early step in data processing, often performed as random uniform class-proportional downsampling. In this report, we hypothesized that this can be optimized to obtain samples that better reflect the entire data set than those obtained using the current standard method. Results: By repeating the random sampling and comparing the distribution of the drawn sample with the distribution of the original data, it was possible to establish a method for obtaining subsets of data that better reflect the entire data set than taking only the first randomly selected subsample, as is the current standard. Experiments on artificial and real biomedical data sets showed that the reconstruction of the remaining data from the original data set from the downsampled data improved significantly. This was observed with both principal component analysis and autoencoding neural networks. The fidelity was dependent on both the number of cases drawn from the original and the number of samples drawn. Conclusions: Optimal distribution-preserving class-proportional downsampling yields data subsets that reflect the structure of the entire data better than those obtained with the standard method. By using distributional similarity as the only selection criterion, the proposed method does not in any way affect the results of a later planned analysis.
The paper focuses on the division of the sensor field into subsets of sensor events and proposes the linear transformation with the smallest achievable error for reproduction: the transform coding approach using the principal component analysis (PCA). For the implementation of the PCA, this paper introduces a new symmetrical, lateral inhibited neural network model, proposes an objective function for it and deduces the corresponding learning rules. The necessary conditions for the learning rate and the inhibition parameter for balancing the crosscorrelations vs. the autocorrelations are computed. The simulation reveals that an increasing inhibition can speed up the convergence process in the beginning slightly. In the remaining paper, the application of the network in picture encoding is discussed. Here, the use of non-completely connected networks for the self-organized formation of templates in cellular neural networks is shown. It turns out that the self-organizing Kohonen map is just the non-linear, first order approximation of a general self-organizing scheme. Hereby, the classical transform picture coding is changed to a parallel, local model of linear transformation by locally changing sets of self-organized eigenvector projections with overlapping input receptive fields. This approach favors an effective, cheap implementation of sensor encoding directly on the sensor chip. Keywords: Transform coding, Principal component analysis, Lateral inhibited network, Cellular neural network, Kohonen map, Self-organized eigenvector jets.