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

An Evaluation of Popular Copy-Move Forgery Detection Approaches

A copy-move forgery is created by copying and pasting content within the same image, and potentially post-processing it. In recent years, the detection of copy-move forgeries has become one of the most actively researched topics in blind image forensics. A considerable number of different algorithms have been proposed focusing on different types of postprocessed copies. In this paper, we aim to answer which copy-move forgery detection algorithms and processing steps (e.g., matching, filtering, outlier detection, affine transformation estimation) perform best in various postprocessing scenarios. The focus of our analysis is to evaluate the performance of previously proposed feature sets. We achieve this by casting existing algorithms in a common pipeline. In this paper, we examined the 15 most prominent feature sets. We analyzed the detection performance on a per-image basis and on a per-pixel basis. We created a challenging real-world copy-move dataset, and a software framework for systematic image manipulation. Experiments show, that the keypoint-based features SIFT and SURF, as well as the block-based DCT, DWT, KPCA, PCA and Zernike features perform very well. These feature sets exhibit the best robustness against various noise sources and downsampling, while reliably identifying the copied regions.Comment: Main paper: 14 pages, supplemental material: 12 pages, main paper appeared in IEEE Transaction on Information Forensics and Securit

Zernike velocity moments for sequence-based description of moving features

The increasing interest in processing sequences of images motivates development of techniques for sequence-based object analysis and description. Accordingly, new velocity moments have been developed to allow a statistical description of both shape and associated motion through an image sequence. Through a generic framework motion information is determined using the established centralised moments, enabling statistical moments to be applied to motion based time series analysis. The translation invariant Cartesian velocity moments suffer from highly correlated descriptions due to their non-orthogonality. The new Zernike velocity moments overcome this by using orthogonal spatial descriptions through the proven orthogonal Zernike basis. Further, they are translation and scale invariant. To illustrate their benefits and application the Zernike velocity moments have been applied to gait recognition—an emergent biometric. Good recognition results have been achieved on multiple datasets using relatively few spatial and/or motion features and basic feature selection and classification techniques. The prime aim of this new technique is to allow the generation of statistical features which encode shape and motion information, with generic application capability. Applied performance analyses illustrate the properties of the Zernike velocity moments which exploit temporal correlation to improve a shape's description. It is demonstrated how the temporal correlation improves the performance of the descriptor under more generalised application scenarios, including reduced resolution imagery and occlusion