Qian Jiang

Protein secondary structure prediction: A survey of the state of the art

Protein secondary structure prediction (PSSP) is a fundamental task in protein science and computational biology, and it can be used to understand protein 3-dimensional (3-D) structures, further, to learn their biological functions. In the past decade, a large number of methods have been proposed for PSSP. In order to learn the latest progress of PSSP, this paper provides a survey on the development of this field. It first introduces the background and related knowledge of PSSP, including basic concepts, data sets, input data features and prediction accuracy assessment. Then, it reviews the recent algorithmic developments of PSSP, which mainly focus on the latest decade. Finally, it summarizes the corresponding tendencies and challenges in this field. This survey concludes that although various PSSP methods have been proposed, there still exist several further improvements or potential research directions. We hope that the presented guidelines will help nonspecialists and specialists to learn the critical progress in PSSP in recent years.

Multi-focus image fusion method using S-PCNN optimized by particle swarm optimization

This paper proposed a novel image fusion method based on simplified pulse-coupled neural network (S-PCNN), particle swarm optimization (PSO) and block image processing method. In general, the parameters of S-PCNN are set manually, which is complex and time-consuming and usually causes inconsistence. In this paper, the parameters of S-PCNN are set by PSO algorithm to overcome these shortcomings and improve fusion performance. Firstly, source images are divided into several equidimension sub-blocks, and then, spatial frequency is calculated as the characteristic factor of the sub-block to get the whole source image’s characterization factor matrix (CFM), and by this way the operand can be effectively reduced. Secondly, S-PCNN is used for the analysis of the CFM to get its oscillation frequency graph (OFG). Thirdly, the fused CFM will be got according to the OFG. Finally, the fused image will be reconstructed according to the fused CFM and block rule. In this process, the parameters of S-PCNN are set by PSO algorithm to get the best fusion effect. By CFM and block method, the operand of the proposed method will be effectively reduced. The experiments indicate that the multi-focus image fusion algorithm is more efficient than other traditional image fusion algorithms, and it proves that the automatically parameters setting method is effective as well.

A new similarity/distance measure between intuitionistic fuzzy sets based on the transformed isosceles triangles and its applications to pattern recognition

Abstract Intuitionistic fuzzy set (IFS) is a representative model of fuzzy theory, and it is widely used to deal with fuzzy and uncertain problems in many practical applications. In IFS theory, the calculation of the distance and similarity between IFSs are significant techniques that are effective measurement methods for distinguishing the similarity degree between IFSs, and the two measures can be used in pattern recognition, decision-making and so on. In this paper, a novel similarity/distance measure between IFSs is proposed according to the intersections of the transformed isosceles triangles from IFSs, and the isosceles triangles are placed in a square area; furthermore, the properties of the proposed measure are also analyzed to prove whether the measure satisfies the definition of the similarity/distance measure for IFSs or not. The numerical experiments are implemented to test the validity of the proposed measure; in addition, several pattern recognition and clustering problems are also employed to further demonstrate its effectiveness. The experimental results show that the proposed measure is an accurate and superior measure that can avoid the shortcomings of most existing measures. Finally, the directions for future research of this work are also represented in the conclusion.

Multimodal sensor medical image fusion based on nonsubsampled shearlet transform and S-PCNNs in HSV space

Abstract Computational imaging plays an important role in medical treatment for providing more comprehensive medical images. This work proposes a new scheme to fuse computed tomography (CT), magnetic resonance (MRI), and positron emission tomography (PET) images into a single image. A novel two-stage medical image fusion scheme, which is based on non-subsampled shearlet transform (NSST) and simplified pulse coupled neural networks (S-PCNNs), is proposed in the hue-saturation-value (HSV) color space. Firstly, CT and MRI images are decomposed into a set of low and high frequency coefficients by NSST, PET images are transformed into the HSV color space, and then the V component of PET image in the HSV color space. Secondly, intersecting cortical models (ICMs) are utilized to extract the edges and outlines in a larger area from the high frequency coefficients, and S-PCNNs are employed to describe the subtly detailed information in a smaller area. Thirdly, different fusion rules are designed to fuse the corresponding low and high frequency coefficients. At last, the fused medical image is obtained by the inverse HSV and NSST transformation, successively. The experimental results show that the proposed scheme is effective, and it can fuse more information into the final images than conventional methods.

A lightweight scheme for multi-focus image fusion

The aim of multi-focus image fusion is to fuse the images taken from the same scene with different focuses so that we can obtain a resultant image with all objects in focus. However, the most existing techniques in many cases cannot gain good fusion performance and acceptable complexity simultaneously. In order to improve image fusion efficiency and performance, we propose a lightweight multi-focus image fusion scheme based on Laplacian pyramid transform (LPT) and adaptive pulse coupled neural networks-local spatial frequency (PCNN-LSF), and it only needs to deal with fewer sub-images than common methods. The proposed scheme employs LPT to decompose a source image into the corresponding constituent sub-images. Spatial frequency (SF) is calculated to adjust the linking strength β of PCNN according to the gradient features of the sub-images. Then oscillation frequency graph (OFG) of the sub-images is generated by PCNN model. Local spatial frequency (LSF) of the OFG is calculated as the key step to fuse the sub-images. Incorporating LSF of the OFG into the fusion scheme (LSF of the OFG represents the information of its regional features); it can effectively describe the detailed information of the sub-images. LSF can enhance the features of OFG and makes it easy to extract high quality coefficient of the sub-image. The experiments indicate that the proposed scheme achieves good fusion effect and is more efficient than other commonly used image fusion algorithms.

Multi-Sensor Image Fusion Based on Interval Type-2 Fuzzy Sets and Regional Features in Nonsubsampled Shearlet Transform Domain

Multi-scale geometric analysis, one of the most often-used multi-sensor image fusion (MSIF) techniques, can offer outstanding performance during extracting the features of source image. Interval type-2 fuzzy sets (Type-2 FS) have a good prospect in image fusion field, because it can effectively address the uncertain and fuzzy problem in image fusion for selecting the high-quality pixels or coefficients of source images. We try to extend the application fields of Type-2 FS and improve the performance of MSIF; therefore, this paper presents a hybrid method by combining the local spatial frequency (LSF) with interval Type-2 FS in nonsubsampled shearlet transform (NSST) domain. NSST is used to decompose source images, and interval Type-2 FS and LSF is employed to extract the regional features of source images; so it can extract and fuse the detailed features of different source images accurately. First, NSST is performed to decompose the source images into low frequency and high frequency sub-images. Second, LSF-based fusion rule is applied to fuse low frequency sub-images. Thirdly, a novel fusion process based on interval Type-2 FS is designed to fuse high frequency sub-images. At last, inverse NSST2 (INSST) is implemented to reconstruct the fused images. The experimental and contrastive results of different image sets show that the proposed method is an effective MSIF scheme, which can achieve better fusion effect than the existing representative methods.

Similarity/dissimilarity calculation methods of DNA sequences: A survey

DNA sequence similarity/dissimilarity analysis is a fundamental task in computational biology, which is used to analyze the similarity of different DNA sequences for learning their evolutionary relationships. In past decades, a large number of similarity analysis methods for DNA sequence have been proposed due to the ever-growing demands. In order to learn the advances of DNA sequence similarity analysis, we make a survey and try to promote the development of this field. In this paper, we first introduce the related knowledge of DNA similarities analysis, including the data sets, similarities distance and output data. Then, we review recent algorithmic developments for DNA similarity analysis to represent a survey of the art in this field. At last, we summarize the corresponding tendencies and challenges in this research field. This survey concludes that although various DNA similarity analysis methods have been proposed, there still exist several further improvements or potential research directions in this field.