FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites.

Glutarylation is a post-translational modification which plays an irreplaceable role in various functions of the cell. Therefore, it is very important to accurately identify the glutarylation substrates and its corresponding glutarylation sites. In recent years, many computational methods of glutarylation sites have emerged one after another, but there are still many limitations, among which noisy data and the class imbalance problem caused by the uncertainty of non-glutarylation sites are great challenges. In this study, we propose a new semi-supervised learning algorithm, named FCCCSR, to identify reliable non-glutarylation lysine sites from unlabeled samples as negative samples. FCCCSR first finds core objects from positive samples according to reverse nearest neighbor information, and then clusters core objects based on natural neighbor structure. Finally, reliable negative samples are selected according to clustering result. With FCCCSR algorithm, we propose a new method named FCCCSR_Glu for glutarylation sites identification. In this study, multi-view features are extracted and fused to describe peptides, including amino acid composition, BLOSUM62, amino acid factors and composition of k-spaced amino acid pairs. Then, reliable negative samples selected by FCCCSR and positive samples are combined to establish models and XGBoost optimized by differential evolution algorithm is used as the classifier. On the independent testing dataset, FCCCSR_Glu achieves 85.18%, 98.36%, 94.31% and 0.8651 in sensitivity, specificity, accuracy and Matthew's Correlation Coefficient, respectively, which is superior to state-of-the-art methods in predicting glutarylation sites. Therefore, FCCCSR_Glu can be a useful tool for glutarylation sites prediction and FCCCSR algorithm can effectively select reliable negative samples from unlabeled samples. The data and code are available on https://github.com/xbbxhbc/FCCCSR_Glu.git.

Quaternion fast and accurate polar harmonic Fourier moments for color image analysis and object recognition.

Image moments, as a kind of global feature descriptor of images, have become a valuable tool for pattern recognition and image analysis. However, traditional methods are mainly used to deal with grayscale images. In this paper, we apply quaternions to fast and accurate polar harmonic Fourier moments, proposing a kind of quaternion fast and accurate polar harmonic Fourier moment (QFAPHFM) capable of handling color images. Furthermore, this paper provides a detailed analysis of the invariance of QFAPHFMs under rotation, scaling, and translation transformations. The experimental results show that QFAPHFMs exhibit excellent performance in both image reconstruction and object recognition tasks. QFAPHFMs achieve accurate image reconstruction under noiseless and noisy conditions, and demonstrate excellent recognition performance in the color-based object recognition tasks.

Fast and accurate computation of polar harmonic Fourier moments for image description.

Continuous orthogonal moments are widely used in various image techniques due to their simplicity and good rotational invariance and stability. In recent years, numerous excellent continuous orthogonal moments have been developed, among which polar harmonic Fourier moments (PHFMs) exhibit strong image description capabilities. However, the numerical integration error is large in the calculation, which seriously affects the calculation accuracy, especially in higher-order calculation. In this paper, a continuous orthogonal moments-fast and accurate PHFM (FAPHFM) is proposed. It utilizes the polar pixel tiling technique to reduce numerical errors in the computation; this method particularly improves the accuracy of higher-order moments of traditional PHFMs. However, as accuracy increases, calculation complexity also increases. To address this issue, an eight-way symmetric/anti-symmetric calculation of the angular and radial functions was performed using the symmetry and anti-symmetry of traditional PHFMs, and clustering of pixels was performed as a way to improve the computational speed. The experimental results show that FAPHFMs perform better in image reconstruction (including noise), with higher computational accuracy, lower time complexity, and better image description ability.

pQLyCar: Peptide-based dynamic query-driven sample rescaling strategy for identifying carboxylation sites combined with KNN and SVM.

Lysine carboxylation is one of the most crucial type of post-translation modification, which plays a significant role in catalytic mechanisms. Therefore, it is essential to study lysine carboxylation and explore its biological mechanism. Compared with traditional experimental methods that are labor-intensive and time-consuming, computational methods are much more convenience and faster. Therefore, it is urgent to establish an accurate carboxylation identification model. Herein we proposed a method, named pQLyCar for identification of lysine carboxylation using SVM as classifier. In pQLyCar, a peptide-based dynamic query-driven sample rescaling strategy (pDQD-SR) is proposed to address the class imbalance of training data, which builds a specific prediction model for each query sample. KNN algorithm calculates distance between samples according to original sequences instead of feature vectors. Information entropy is applied to select optimal size of sliding window and various types of sequence- and position-based features are incorporated for construction of feature space, including residues composition (RC), K-space and position-special amino acid propensity (PSAAP). Finally, the performance of pQLyCar is measured with a specificity of 96.49% and a sensibility of 99.59% using jackknife test method, which indicated that pQLyCar method can be a useful tool for prediction of lysine carboxylation sites.