28,263 research outputs found
Inversion using a new low-dimensional representation of complex binary geological media based on a deep neural network
Efficient and high-fidelity prior sampling and inversion for complex
geological media is still a largely unsolved challenge. Here, we use a deep
neural network of the variational autoencoder type to construct a parametric
low-dimensional base model parameterization of complex binary geological media.
For inversion purposes, it has the attractive feature that random draws from an
uncorrelated standard normal distribution yield model realizations with spatial
characteristics that are in agreement with the training set. In comparison with
the most commonly used parametric representations in probabilistic inversion,
we find that our dimensionality reduction (DR) approach outperforms principle
component analysis (PCA), optimization-PCA (OPCA) and discrete cosine transform
(DCT) DR techniques for unconditional geostatistical simulation of a
channelized prior model. For the considered examples, important compression
ratios (200 - 500) are achieved. Given that the construction of our
parameterization requires a training set of several tens of thousands of prior
model realizations, our DR approach is more suited for probabilistic (or
deterministic) inversion than for unconditional (or point-conditioned)
geostatistical simulation. Probabilistic inversions of 2D steady-state and 3D
transient hydraulic tomography data are used to demonstrate the DR-based
inversion. For the 2D case study, the performance is superior compared to
current state-of-the-art multiple-point statistics inversion by sequential
geostatistical resampling (SGR). Inversion results for the 3D application are
also encouraging
Exploring the potential of 3D Zernike descriptors and SVM for protein\u2013protein interface prediction
Abstract Background The correct determination of protein–protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function. The selection of an optimal set of features characterising the protein interface and the development of an effective method to represent and capture the complex protein recognition patterns are of paramount importance for this task. Results In this work we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein–Protein Docking Benchmark 5.0 and compared to other state-of-the-art protein interface predictors (SPPIDER, PrISE and NPS-HomPPI). Conclusions The 3D Zernike descriptors are able to capture the similarity among patterns of physico-chemical and biochemical properties mapped on the protein surface arising from the various spatial arrangements of the underlying residues, and their usage can be easily extended to other sets of amino acid properties. The results suggest that the choice of a proper set of features characterising the protein interface is crucial for the interface prediction task, and that optimality strongly depends on the class of proteins whose interface we want to characterise. We postulate that different protein classes should be treated separately and that it is necessary to identify an optimal set of features for each protein class
Finite Boolean Algebras for Solid Geometry using Julia's Sparse Arrays
The goal of this paper is to introduce a new method in computer-aided
geometry of solid modeling. We put forth a novel algebraic technique to
evaluate any variadic expression between polyhedral d-solids (d = 2, 3) with
regularized operators of union, intersection, and difference, i.e., any CSG
tree. The result is obtained in three steps: first, by computing an independent
set of generators for the d-space partition induced by the input; then, by
reducing the solid expression to an equivalent logical formula between Boolean
terms made by zeros and ones; and, finally, by evaluating this expression using
bitwise operators. This method is implemented in Julia using sparse arrays. The
computational evaluation of every possible solid expression, usually denoted as
CSG (Constructive Solid Geometry), is reduced to an equivalent logical
expression of a finite set algebra over the cells of a space partition, and
solved by native bitwise operators.Comment: revised version submitted to Computer-Aided Geometric Desig
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