Local Geometric Similarity Research Articles

Revealing Free Energy Landscape From MD Data via Conditional Angle Partition Tree.

Deciphering the free energy landscape of biomolecular structure space is crucial for understanding many complex molecular processes, such as protein-protein interaction, RNA folding, and protein folding. A major source of current dynamic structure data is Molecular Dynamics (MD) simulations. Several methods have been proposed to investigate the free energy landscape from MD data, but all of them rely on the assumption that kinetic similarity is associated with global geometric similarity, which may lead to unsatisfactory results. In this paper, we proposed a new method called Conditional Angle Partition Tree to reveal the hierarchical free energy landscape by correlating local geometric similarity with kinetic similarity. Its application on the benchmark alanine dipeptide MD data showed a much better performance than existing methods in exploring and understanding the free energy landscape. We also applied it to the MD data of Villin HP35. Our results are more reasonable on various aspects than those from other methods and very informative on the hierarchical structure of its energy landscape.

Generalized Incomplete Multiview Clustering With Flexible Locality Structure Diffusion.

An important underlying assumption that guides the success of the existing multiview learning algorithms is the full observation of the multiview data. However, such rigorous precondition clearly violates the common-sense knowledge in practical applications, where in most cases, only incomplete fractions of the multiview data are given. The presence of the incomplete settings generally disables the conventional multiview clustering methods. In this article, we propose a simple but effective incomplete multiview clustering (IMC) framework, which simultaneously considers the local geometric information and the unbalanced discriminating powers of these incomplete multiview observations. Specifically, a novel graph-regularized matrix factorization model, on the one hand, is developed to preserve the local geometric similarities of the learned common representations from different views. On the other hand, the semantic consistency constraint is introduced to stimulate these view-specific representations toward a unified discriminative representation. Moreover, the importance of different views is adaptively determined to reduce the negative influence of the unbalanced incomplete views. Furthermore, an efficient learning algorithm is proposed to solve the resulting optimization problem. Extensive experimental results performed on several incomplete multiview datasets demonstrate that the proposed method can achieve superior clustering performance in comparison with some state-of-the-art multiview learning methods.

Detecting Matching Blunders of Multi-Source Remote Sensing Images via Graph Theory.

Large radiometric and geometric distortion in multi-source images leads to fewer matching points with high matching blunder ratios, and global geometric relationship models between multi-sensor images are inexplicit. Thus, traditional matching blunder detection methods cannot work effectively. To address this problem, we propose two matching blunder detection methods based on graph theory. The proposed methods can build statistically significant clusters in the case of few matching points with high matching blunder ratios, and use local geometric similarity constraints to detect matching blunders when the global geometric relationship is not explicit. The first method (named the complete graph-based method) uses clusters constructed by matched triangles in complete graphs to encode the local geometric similarity of images, and it can detect matching blunders effectively without considering the global geometric relationship. The second method uses the triangular irregular network (TIN) graph to approximate a complete graph to reduce to computational complexity of the first method. We name this the TIN graph-based method. Experiments show that the two graph-based methods outperform the classical random sample consensus (RANSAC)-based method in recognition rate, false rate, number of remaining matching point pairs, dispersion, positional accuracy in simulated and real data (image pairs from Gaofen1, near infrared ray of Gaofen1, Gaofen2, panchromatic Landsat, Ziyuan3, Jilin1and unmanned aerial vehicle). Notably, in most cases, the mean false rates of RANSAC, the complete graph-based method and the TIN graph-based method in simulated data experiments are 0.50, 0.26 and 0.14, respectively. In addition, the mean positional accuracy (RMSE measured in units of pixels) of the three methods is 2.6, 1.4 and 1.5 in real data experiments, respectively. Furthermore, when matching blunder ratio is no higher than 50%, the computation time of the TIN graph-based method is nearly equal to that of the RANSAC-based method, and roughly 2 to 40 times less than that of the complete graph-based method.

A Voxel Graph-Based Resampling Approach for the Aerial Laser Scanning of Urban Buildings

This letter presents a resampling algorithm for the refinement of the aerial laser scanning of urban buildings. We aim at resolving the problems of noise, variable density, and vacancies in the 3-D laser scanning. The assumption is that the points are locally sampled from piecewise building surfaces, so we can generate a new point cloud to present a plausible approximation of the surface based on the local smooth trait. First, we introduce an oversegmentation approach to generate super voxels by analyzing local geometric similarities. Then, each voxel is treated as a node composing a graph. Based on the combination method of the graph-constrained filtering and the interpolation, the resampling approach is designed to reproject the points to their optimized positions. This approach could ensure that the resampling points are faithful to the initial data and maintain a global even density. Furthermore, we evaluated the effectiveness and efficiency of the proposed method on the applications of geometry primitive extraction and surface modeling. The experiments demonstrate that the approach is suitable for improving the quality of aerial scanning data in different aspects.

Local convolutional features and metric learning for SAR image registration

The conventional synthetic aperture radar (SAR) image registration focuses on designing diverse hand-crafted features and distance metrics. It is still challenging to obtain accurate feature correspondence when influenced by speckle noise and geometric distortion. This paper proposes local convolutional neural network (CNN) features based method to solve the keypoint matching problem, whose contributions are threefold. (1) a feature descriptor based on local convolutional features of image patches (LCFs-P) is deployed to extract more discriminative features than the conventional CNNs. (2) A new feature correspondence scheme based on metric learning is proposed to boost the feature matching performance. (3) A local geometric similarity method is employed to remove the mismatches of the tentative matches. The experimental results on the real SAR dataset and Middlebury dataset demonstrate that the proposed model outperforms the existing state-of-the-art methods in terms of matching accuracy and efficiency.

Example Based Light Sources Generation Method for 3D Scenes

Lighting design is very important to improve rendering quality for some 3D scenes that are used in the VR applications with night simulation. Determining the properties of the light sources requires a large amount of artwork, especially when the number of lights is large. Most virtual scenes always have some geometric objects with similar structures and shapes. Based on this observation, this paper proposes an example based light source generation method by using local geometric similarity. An example model decorated with light source and a target model are input to this method. First this paper segments both model into parts with SDF segmentation algorithm, and find matched parts between the example model to the target. Then two methods are applied to transfer the light sources decorated on the parts of the example model to the corresponding parts of the target model. Minimum spanning tree based light transfer method is used to generated light sources for target parts with the same pattern as lights layout on its corresponding parts from the example model. While texture synthesis based method tiles the light texture generated from the example parts on the surface of the target parts. At last, the position and colors of the light sources are refined. The results demonstrated that this method can quickly and effectively edit light sources for large-scale scenes, reduce the amount of art work and achieve good visual effects.

Slope-Restricted Multi-Scale Feature Matching for Geostationary Satellite Remote Sensing Images

For geostationary meteorological satellite (GSMS) remote sensing image registration, high computational cost and matching error are the two main challenging problems. To address these issues, this paper proposes a novel algorithm named slope-restricted multi-scale feature matching. In multi-scale feature matching, images are subsampled to different scales. From a small scale to a large scale, the offsets between the matched pairs are used to narrow the searching area of feature matching for the next larger scale. Thus, the feature matching is accomplished from coarse to fine, which will make the matching process more accurate and reduce errors. To enhance the matching performance, the outliers in the matched pairs are rectified by using slope-restricted rectification, which is based on local geometric similarity. Compared with other algorithms, the experimental results show that our proposed method is more accurate and efficient.

Image Interpolation Based on Non-local Geometric Similarities and Directional Gradients

Image interpolation offers an efficient way to compose a high-resolution (HR) image from the observed low-resolution (LR) image. Advanced interpolation techniques design the interpolation weighting coefficients by solving a minimum mean-square-error (MMSE) problem in which the local geometric similarity is often considered. However, using local geometric similarities cannot usually make the MMSE-based interpolation as reliable as expected. To solve this problem, we propose a robust interpolation scheme by using the nonlocal geometric similarities to construct the HR image. In our proposed method, the MMSE-based interpolation weighting coefficients are generated by solving a regularized least squares problem that is built upon a number of dual-reference patches drawn from the given LR image and regularized by the directional gradients of these patches. Experimental results demonstrate that our proposed method offers a remarkable quality improvement as compared to some state-of-the-art methods, both objectively and subjectively.

Semisupervised Dual-Geometric Subspace Projection for Dimensionality Reduction of Hyperspectral Image Data

Exploring the geometric prior in the dimensionality reduction (DR) of hyperspectral image data (HID) is an important issue because it can overcome the possible overclassification of spectrally homogeneous areas in the HID classification. In this paper, the local geometric similarity of hyperspectral vectors is explored in both the manifold domain and image domain, and a semisupervised dual-geometric subspace projection (DGSP) approach is proposed for the DR of HID, by utilizing both labeled and unlabeled samples. First, the geometric information in the manifold domain is captured by a sparse coding-based geometric graph, and then, a local-consistency-constrained geometric matrix is defined to reveal the geometric structure in the image domain. Second, unlabeled samples are used to refine the geometric structure by defining a pairwise similarity matrix. Third, three scatter matrices are then derived from these similarity matrices to find the optimal subspace projection that captures the most important properties of the subspaces with respect to classification. Some experiments are taken on the airborne visible infrared imaging spectrometer (AVIRIS) HID to prove the efficiency of the proposed method.

Prediction and experimental validation of enzyme substrate specificity in protein structures

Structural Genomics aims to elucidate protein structures to identify their functions. Unfortunately, the variation of just a few residues can be enough to alter activity or binding specificity and limit the functional resolution of annotations based on sequence and structure; in enzymes, substrates are especially difficult to predict. Here, large-scale controls and direct experiments show that the local similarity of five or six residues selected because they are evolutionarily important and on the protein surface can suffice to identify an enzyme activity and substrate. A motif of five residues predicted that a previously uncharacterized Silicibacter sp. protein was a carboxylesterase for short fatty acyl chains, similar to hormone-sensitive-lipase-like proteins that share less than 20% sequence identity. Assays and directed mutations confirmed this activity and showed that the motif was essential for catalysis and substrate specificity. We conclude that evolutionary and structural information may be combined on a Structural Genomics scale to create motifs of mixed catalytic and noncatalytic residues that identify enzyme activity and substrate specificity.

IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code) combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dataset using a cognate-similarity threshold. Local structural similarities are detected using the IsoCleft software and ranked according to two criteria (number of atoms in common and Tanimoto score of local structural similarity) and the associated Z-score and p-value measures of statistical significance. The results, including predicted ligands, target proteins, similarity scores, number of atoms in common, etc., are shown in a powerful interactive graphical interface. This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities. Similarities between top scoring ligands serve as an additional tool to judge the quality of the results obtained. We present several examples where IsoCleft Finder provides useful functional information. IsoCleft Finder results are complementary to existing approaches for the prediction of protein function from structure, rational drug design and x-ray crystallography. IsoCleft Finder can be found at: http://bcb.med.usherbrooke.ca/isocleftfinder.

IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities

IsoCleft Finder is a web-based tool for the detection of local geometric and chemical similarities between potential small-molecule binding cavities and a non-redundant dataset of ligand-bound known small-molecule binding-sites. The non-redundant dataset developed as part of this study is composed of 7339 entries representing unique Pfam/PDB-ligand (hetero group code) combinations with known levels of cognate ligand similarity. The query cavity can be uploaded by the user or detected automatically by the system using existing PDB entries as well as user-provided structures in PDB format. In all cases, the user can refine the definition of the cavity interactively via a browser-based Jmol 3D molecular visualization interface. Furthermore, users can restrict the search to a subset of the dataset using a cognate-similarity threshold. Local structural similarities are detected using the IsoCleft software and ranked according to two criteria (number of atoms in common and Tanimoto score of local structural similarity) and the associated Z-score and p-value measures of statistical significance. The results, including predicted ligands, target proteins, similarity scores, number of atoms in common, etc., are shown in a powerful interactive graphical interface. This interface permits the visualization of target ligands superimposed on the query cavity and additionally provides a table of pairwise ligand topological similarities. Similarities between top scoring ligands serve as an additional tool to judge the quality of the results obtained. We present several examples where IsoCleft Finder provides useful functional information. IsoCleft Finder results are complementary to existing approaches for the prediction of protein function from structure, rational drug design and x-ray crystallography. IsoCleft Finder can be found at: http://bcb.med.usherbrooke.ca/isocleftfinder.

Learning-Based Medical Image Magnification Algorithm by Local Geometric Similarity

Image magnification is an important technology in medical image processing.High detail areas in medical images most often have a definite geometric structure or pattern,such as in the case of edges.This paper proposes a learning-based method.Geometric features extracted from the available neighboring pixels in the Low-resolution(LR) image form the training set.Assuming the training set is locally corresponding to geometric features from the High-resolution(HR) image patch to be reconstructed.Local geometric similarity is described as the correspondence.The task of image magnification is formulated as an optimization problem,where the optimization coefficients can adaptively tune its value to effectively propagating the features from the training set to the target HR image patch.The advantages are the ability to produce a magnified image by any factor,and not require any outlier supporters.A Weighted Least Square(WLS) method is provided to offer a convenient way of finding the regularized optimal solution,where the weight function is determined by the non-local means.Simulation and comparison results show that the proposed method is independent,adaptive and can produce sharp edges with rare ringing or jaggy artifacts.

Local quality assessment in homology models using statistical potentials and support vector machines

In this study, we address the problem of local quality assessment in homology models. As a prerequisite for the evaluation of methods for predicting local model quality, we first examine the problem of measuring local structural similarities between a model and the corresponding native structure. Several local geometric similarity measures are evaluated. Two methods based on structural superposition are found to best reproduce local model quality assessments by human experts. We then examine the performance of state-of-the-art statistical potentials in predicting local model quality on three qualitatively distinct data sets. The best statistical potential, DFIRE, is shown to perform on par with the best current structure-based method in the literature, ProQres. A combination of different statistical potentials and structural features using support vector machines is shown to provide somewhat improved performance over published methods.