TPpred-LE: therapeutic peptide function prediction based on label embedding.

BACKGROUND: Therapeutic peptides play an essential role in human physiology, treatment paradigms and bio-pharmacy. Several computational methods have been developed to identify the functions of therapeutic peptides based on binary classification and multi-label classification. However, these methods fail to explicitly exploit the relationship information among different functions, preventing the further improvement of the prediction performance. Besides, with the development of peptide detection technology, peptide functions will be more comprehensively discovered. Therefore, it is necessary to explore computational methods for detecting therapeutic peptide functions with limited labeled data. RESULTS: In this study, a novel method called TPpred-LE based on Transformer framework was proposed for predicting therapeutic peptide multiple functions, which can explicitly extract the function correlation information by using label embedding methodology and exploit the specificity information based on function-specific classifiers. Besides, we incorporated the multi-label classifier retraining approach (MCRT) into TPpred-LE to detect the new therapeutic functions with limited labeled data. Experimental results demonstrate that TPpred-LE outperforms the other state-of-the-art methods, and TPpred-LE with MCRT is robust for the limited labeled data. CONCLUSIONS: In summary, TPpred-LE is a function-specific classifier for accurate therapeutic peptide function prediction, demonstrating the importance of the relationship information for therapeutic peptide function prediction. MCRT is a simple but effective strategy to detect functions with limited labeled data.

PreTP-Stack: Prediction of Therapeutic Peptides Based on the Stacked Ensemble Learing.

Therapeutic peptide prediction is critical for drug development and therapeutic therapy. Researchers have developed several computational methods to identify different therapeutic peptide types. However, most computational methods focus on identifying the specific type of therapeutic peptides and fail to accurately predict all types of therapeutic peptides. Moreover, it is still challenging to utilize different properties features to predict the therapeutic peptides. In this study, a novel stacking framework PreTP-Stack is proposed for predicting different types of therapeutic peptide. PreTP-Stack is constructed based on ten different features and four predictors (Random Forest, Linear Discriminant Analysis, XGBoost and Support Vector Machine). Then the proposed method constructs an auto-weighted multi-view learning model as a final meta-classifier to enhance the performance of the basic models. Experimental results showed that the proposed method achieved better or highly comparable performance with the state-of-the-art methods for predicting eight types of therapeutic peptides A user-friendly web-server predictor is available at http://bliulab.net/PreTP-Stack.

sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure.

MOTIVATION: Antimicrobial peptides (AMPs) are essential components of therapeutic peptides for innate immunity. Researchers have developed several computational methods to predict the potential AMPs from many candidate peptides. With the development of artificial intelligent techniques, the protein structures can be accurately predicted, which are useful for protein sequence and function analysis. Unfortunately, the predicted peptide structure information has not been applied to the field of AMP prediction so as to improve the predictive performance. RESULTS: In this study, we proposed a computational predictor called sAMPpred-GAT for AMP identification. To the best of our knowledge, sAMPpred-GAT is the first approach based on the predicted peptide structures for AMP prediction. The sAMPpred-GAT predictor constructs the graphs based on the predicted peptide structures, sequence information and evolutionary information. The Graph Attention Network (GAT) is then performed on the graphs to learn the discriminative features. Finally, the full connection networks are utilized as the output module to predict whether the peptides are AMP or not. Experimental results show that sAMPpred-GAT outperforms the other state-of-the-art methods in terms of AUC, and achieves better or highly comparable performance in terms of the other metrics on the eight independent test datasets, demonstrating that the predicted peptide structure information is important for AMP prediction. AVAILABILITY AND IMPLEMENTATION: A user-friendly webserver of sAMPpred-GAT can be accessed at http://bliulab.net/sAMPpred-GAT and the source code is available at https://github.com/HongWuL/sAMPpred-GAT/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AMPpred-EL: An effective antimicrobial peptide prediction model based on ensemble learning.

Antimicrobial peptides (AMPs) are important for the human immune system and are currently applied in clinical trials. AMPs have been received much attention for accurate recognition. Recently, several computational methods for identifying AMPs have been proposed. However, existing methods have difficulty in accurately predicting AMPs. In this paper, we propose a novel AMP prediction method called AMPpred-EL based on an ensemble learning strategy. AMPred-EL is constructed based on ensemble learning combined with LightGBM and logistic regression. Experimental results demonstrate that AMPpred-EL outperforms several state-of-the-art methods on the benchmark datasets and then improves the efficiency performance.

TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model.

MOTIVATION: Therapeutic peptide prediction is important for the discovery of efficient therapeutic peptides and drug development. Researchers have developed several computational methods to identify different therapeutic peptide types. However, these computational methods focus on identifying some specific types of therapeutic peptides, failing to predict the comprehensive types of therapeutic peptides. Moreover, it is still challenging to utilize different properties to predict the therapeutic peptides. RESULTS: In this study, an adaptive multi-view based on the tensor learning framework TPpred-ATMV is proposed for predicting different types of therapeutic peptides. TPpred-ATMV constructs the class and probability information based on various sequence features. We constructed the latent subspace among the multi-view features and constructed an auto-weighted multi-view tensor learning model to utilize the high correlation based on the multi-view features. Experimental results showed that the TPpred-ATMV is better than or highly comparable with the other state-of-the-art methods for predicting eight types of therapeutic peptides. AVAILABILITY AND IMPLEMENTATION: The code of TPpred-ATMV is accessed at: https://github.com/cokeyk/TPpred-ATMV. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Evaluating the Effects of Non-Isomorphic Rotation on 3D Manipulation Tasks in Mixed Reality Simulation.

As a hyper-natural interaction technique in 3D user interfaces, non-isomorphic rotation has been considered an effective approach for rotation tasks, where a static or dynamic control-display gain can be applied to amplify or attenuate a rotation. However, it is not clear whether non-isomorphic rotation can benefit 6-degree-of-freedom (6-DOF) manipulation tasks in AR and VR. In this article, we extended the usability studies of non-isomorphic rotation from rotation-only tasks to 6-DOF manipulation tasks and analyzed the collected data using a 2-component model. Using a mixed reality (MR) simulation approach, we also investigated whether environment (AR or VR) had an impact on 3D manipulation tasks. The results reveal that although both static and dynamic non-isomorphic rotation techniques could save time and effort in ballistic phases, only dynamic non-isomorphic rotation was significantly faster than isomorphic rotation. Interestingly, while environment had no significant impact on overall user performance, we found evidence that it could affect fine-tuning in correction phases. We also found that most participants preferred AR over VR, indicating that environmental visual realism could be helpful to improve user experience.

A Privacy-Preserving Cross-Domain Healthcare Wearables Recommendation Algorithm Based on Domain-Dependent and Domain-Independent Feature Fusion.

Recently, recommender systems are applied to provide personalized recomendation for healthcare wearables. However, due to the sparsity problem, traditional recommendation algorithms are difficult to achieve desired performance. Considering that consumers often buy and rate other types of items on E-commerce platforms, we can leverage significant information in the auxiliary domains to improve the recommendation performance of healthcare wearables, which can be regarded as cross-domain recommendation. However, traditional cross-domain recommendation model cannot fully represent user's characteristics and fail to consider the leaks of original auxiliary domain ratings during the information transfer process. To overcome the two shortcomings, this paper proposes a Privacy-Preserving Cross-Domain Healthcare Wearables Recommendation algorithm (PPCDHWRec). Firstly, user's characteristics are divided into domain-dependent features and domain-independent features, which complement each other and fully depict the user's characteristics. Secondly, inspired by the latent factor model, we factorize the original rating information of each auxiliary domain by Funk-SVD and Orthogonal Nonnegative Matrix Tri-Factorization (ONMTF) model, to obtain user's domain-dependent and domain-independent features, respectively. Finally, the Factorization Machine algorithm is used to fuse the obtained user's features with the target domain information to provide the recommendation results. By hiding the item latent factors obtained in the factorization process, PPCDHWRec ensures that the original information cannot be inferred from the transferred user hidden vector. Hence, PPCDHWRec is a privacy-preserving recommendation model. Experiments on two groups of auxiliary domains, having high and low correlations with target domain, show the effectiveness of PPCDHWRec.

PreTP-EL: prediction of therapeutic peptides based on ensemble learning.

Therapeutic peptides are important for understanding the correlation between peptides and their therapeutic diagnostic potential. The therapeutic peptides can be further divided into different types based on therapeutic function sharing different characteristics. Although some computational approaches have been proposed to predict different types of therapeutic peptides, they failed to accurately predict all types of therapeutic peptides. In this study, a predictor called PreTP-EL has been proposed via employing the ensemble learning approach to fuse the different features and machine learning techniques in order to capture the different characteristics of various therapeutic peptides. Experimental results showed that PreTP-EL outperformed other competing methods. Availability and implementation: A user-friendly web-server of PreTP-EL predictor is available at http://bliulab.net/PreTP-EL.