The association between drugs and side effects encompasses information about approved medications and their documented adverse drug reactions. Traditional experimental approaches for studying this association tend to be time-consuming and expensive. To represent all drug-side effect associations, a bipartite network framework is employed. Consequently, numerous computational methods have been devised to tackle this problem, focusing on predicting new potential associations. However, a significant gap lies in the neglect of the Multi-View Learning (MVL) algorithm, which has the ability to integrate diverse information sources and enhance prediction accuracy. In our study, we have developed a novel predictor named Multi-View Semi-Supervised Sparse Model (Mv3SM) to address the drug side effect prediction problem. Our approach aims to explore the distinctive characteristics of various view features obtained from fully paired multi-view data and mitigate the influence of noisy data. To test the performance of Mv3SM and other computational approaches, we conducted experiments using three benchmark datasets. The obtained results clearly demonstrate that our proposed method achieves superior predictive performance compared to alternative approaches. © IEEE

The identification of DNA N4-methylcytosine (4mC) sites is an important field of bioinformatics. Statistical learning methods and deep learning have been applied in this direction. The previous methods focused on feature representation and feature selection, and did not take into account the deviation of noise samples for recognition. Moreover, these models were not established from the perspective of prediction error distribution. To solve the problem of complex error distribution, we propose a maximum multi-correntropy criterion based kernelized higher-order fuzzy inference system (MMC-KHFIS), which is constructed with multi-correntropy fusion. There are 6 4mC and 8 UCI data sets are employed to evaluate our model. The MMC-KHFIS achieves better performance in the experiment. © 2023

DNA N4-methylcytosine (4mC) site identification is a crucial field in bioinformatics, where machine learning methods have been effectively utilized. Due to the presence of noise, the existing deep learning methods for detecting 4mC have consistently low recognition rates in positive samples. With fuzzy rules and membership functions, fuzzy systems can achieve good results in processing noisy signals. In contrast to traditional fuzzy systems that lack deep feature representation and sample measurement, we introduce novel techniques to enhance generalization and feature representation. By incorporating the neural tangent kernel (NTK) and kernel learning algorithm into the fuzzy system, we propose the fuzzy neural tangent kernel (FNTK) model and the radius-based FNTK (R-FNTK) model to predict DNA 4mC sites. To achieve better generalization performance than traditional kernel functions, we first train the NTK for feature representation learning and sample measurement. Based on the membership function and NTK matrix, different fuzzy kernel matrices are constructed for each fuzzy subset of the fuzzy system. Finally, we utilize two types of iterative kernel optimization algorithms to effectively fuse multiple NTK-based fuzzy kernels and obtain the final prediction model. Rigorous testing using 6 benchmark datasets demonstrates the superiority of our approach, yielding significant improvements in the experiment's performance. © IEEE

The detection of therapeutic peptides is usually a biochemical experimental method, which is time-consuming and labor-intensive. Lots of computational biology methods had been proposed to solve the problem of therapeutic peptide prediction. However, the existing methods did not consider the processing of noisy samples. We propose a kernel risk-sensitive mean p-power error-based echo state network with sparse learning (KRP-ESN-SL). An efficient iterative optimization algorithm is used to train the model. The KRP-ESN-SL has better performance than other methods. © 2022 IEEE.

Detection of therapeutic peptide is a major research direction in the current biopharmaceutical field. However, traditional biochemical experimental detection methods take a lot of time. As supplementary methods for biochemical experiments, the computational methods can improve the efficiency of therapeutic peptide detection. Currently, most machine learning-based therapeutic peptide identification algorithms do not consider the processing of noisy samples. We propose a therapeutic peptide classifier, called weighted echo state networks based on subspace projection (WESN-SP), which reduces the bias caused by high-dimensional noisy features and noisy samples. WESN-SP is trained by sparse Bayesian learning algorithm (SBL) and introduces a weight coefficient for each sample by kernel dependence maximization-based subspace projection. The experimental results show that WESN-SP has better performance than other existing methods. © 2023 The Author(s). Published by Elsevier B.V.

The detection of therapeutic peptides is a topic of immense interest in the biomedical field. Conventional biochemical experiment-based detection techniques are tedious and time-consuming. Computational biology has become a useful tool for improving the detection efficiency of therapeutic peptides. Most computational methods do not consider the deviation caused by noise. To improve the generalization performance of therapeutic peptide prediction methods, this work presents a sequence homology score-based deep fuzzy echo-state network with maximizing mixture correntropy (SHS-DFESN-MMC) model. Our method is compared with the existing methods on eight types of therapeutic peptide datasets. The model parameters are determined by 10 fold cross-validation on their training sets and verified by independent test sets. Across the 8 datasets, the average area under the receiver operating characteristic curve (AUC) values of SHS-DFESN-MMC are the highest on both the training (0.926) and independent sets (0.923). © 2024 The Authors

Identification of new indications for existing drugs is crucial through the various stages of drug discovery. Computational methods are valuable in establishing meaningful associations between drugs and diseases. However, most methods predict the drug–disease associations based solely on similarity data, neglecting valuable biological and chemical information. These methods often use basic concatenation to integrate information from different modalities, limiting their ability to capture features from a comprehensive and in-depth perspective. Therefore, a novel multimodal framework called AMDGT was proposed to predict new drug associations based on dual-graph transformer modules. By combining similarity data and complex biochemical information, AMDGT understands the multimodal feature fusion of drugs and diseases effectively and comprehensively with an attention-aware modality interaction architecture. Extensive experimental results indicate that AMDGT surpasses state-of-the-art methods in real-world datasets. Moreover, case and molecular docking studies demonstrated that AMDGT is an effective tool for drug repositioning. Our code is available at GitHub: https://github.com/JK-Liu7/AMDGT. © 2023 The Author(s)

Drug repositioning (DR) is a promising approach for identifying novel indications of existing drugs. Computational methods for drug repositioning have been recognised as effective ways to discover the associations between drugs and diseases. However, most computational DR methods ignore the significance of heterogeneous graph augmentation when conducting contrastive learning, which plays a critical role in improving the generalisation and robustness. The high-order similarity information from multiple data sources is still under-explored. Furthermore, only a limited number of computational DR methods can effectively screen for the most informative negative samples for model training. To address these limitations, we propose a novel DR method called DRMAHGC that employs multi-aspect graph contrastive learning to predict drug-disease associations (DDAs). First, high-order features were generated from the similarity network using a graph-masked autoencoder. Then, heterogeneous graph contrastive learning with structure- and metapath-level augmentation was employed to enhance semantic comprehension and learn expressive representations. Subsequently, the positive-fusion negative sampling strategy was exploited to synthesise informative negative sample embeddings to train the classifier for predicting novel DDAs. Extensive results on three benchmark datasets indicate that DRMAHGC significantly and consistently outperformed the state-of-the-art methods in the DR task. Moreover, the case study of two common diseases further demonstrates its effectiveness and provides novel insights into DRMAHGC in identifying novel DDAs. © 2024 The Author(s)

The accurate prediction of drug-target affinity (DTA) is a crucial step in drug discovery and design. Traditional experiments are very expensive and time-consuming. Recently, deep learning methods have achieved notable performance improvements in DTA prediction. However, one challenge for deep learning-based models is appropriate and accurate representations of drugs and targets, especially the lack of effective exploration of target representations. Another challenge is how to comprehensively capture the interaction information between different instances, which is also important for predicting DTA. In this study, we propose AttentionMGT-DTA, a multi-modal attention-based model for DTA prediction. AttentionMGT-DTA represents drugs and targets by a molecular graph and binding pocket graph, respectively. Two attention mechanisms are adopted to integrate and interact information between different protein modalities and drug-target pairs. The experimental results showed that our proposed model outperformed state-of-the-art baselines on two benchmark datasets. In addition, AttentionMGT-DTA also had high interpretability by modeling the interaction strength between drug atoms and protein residues. Our code is available at https://github.com/JK-Liu7/AttentionMGT-DTA. © 2023 The Author(s)