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Representing seismic data effectively for facies categorization poses a challenge. In order to account for all information presented in prestack seismic data for this task, a machine learning model based on Deep Convolutional Autoencoders (DCAE) combined with a K-means clustering to identify seismic facies in a Brazilian pre-Salt layer is utilized. The DCAE reduces the dimensionality of the prestack seismic data by non-linear means, and the resulting latent features are used for K-means clustering. To incorporate geological interpretation, the thickness of the layer of interest was considered when defining the input window for each gather based on the interpreted top and bottom horizons. The results demonstrate through principal component analysis in the latent features that the layer thickness information drives the main behavior of the samples in the study area. Moreover, it is pointed out that considering the layer thickness leads to vertical stretching and squeezing in the input features, influencing the pattern recognition by the DCAE. Nevertheless, the embedding of geological interpretation through layer boundaries generated helpful facies distribution results for assembling the geological model of the reservoir.