scholarly journals PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning

2020 ◽  
Vol 36 (13) ◽  
pp. 3982-3987 ◽  
Author(s):  
Yu P Zhang ◽  
Quan Zou
Keyword(s):  
Physicochemical Property ◽  
Prediction Method ◽  
Peptide Identification ◽  
Representation Learning ◽  
Feature Representation ◽  
Supplementary Information ◽  
Therapeutic Peptide ◽  
Therapeutic Peptides ◽  
Peptide Prediction ◽  
Massive Data Processing

Abstract Motivation Peptide is a promising candidate for therapeutic and diagnostic development due to its great physiological versatility and structural simplicity. Thus, identifying therapeutic peptides and investigating their properties are fundamentally important. As an inexpensive and fast approach, machine learning-based predictors have shown their strength in therapeutic peptide identification due to excellences in massive data processing. To date, no reported therapeutic peptide predictor can perform high-quality generic prediction and informative physicochemical properties (IPPs) identification simultaneously. Results In this work, Physicochemical Property-based Therapeutic Peptide Predictor (PPTPP), a Random Forest-based prediction method was presented to address this issue. A novel feature encoding and learning scheme were initiated to produce and rank physicochemical property-related features. Besides being capable of predicting multiple therapeutics peptides with high comparability to established predictors, the presented method is also able to identify peptides’ informative IPP. Results presented in this work not only illustrated the soundness of its working capacity but also demonstrated its potential for investigating other therapeutic peptides. Availability and implementation https://github.com/YPZ858/PPTPP. Supplementary information Supplementary data are available at Bioinformatics online.

ITP-Pred: an interpretable method for predicting, therapeutic peptides with fused features low-dimension representation

2020 ◽  
Author(s):  
Lijun Cai ◽  
Li Wang ◽  
Xiangzheng Fu ◽  
Chenxing Xia ◽  
Xiangxiang Zeng ◽  
...  
Keyword(s):  
Short Term Memory ◽  
Feature Fusion ◽  
Chemical Properties ◽  
Feature Representation ◽  
Therapeutic Peptide ◽  
Independent Verification ◽  
Therapeutic Peptides ◽  
Pharmaceutical Industries ◽  
Peptide Prediction ◽  
Physical And Chemical

Abstract The peptide therapeutics market is providing new opportunities for the biotechnology and pharmaceutical industries. Therefore, identifying therapeutic peptides and exploring their properties are important. Although several studies have proposed different machine learning methods to predict peptides as being therapeutic peptides, most do not explain the decision factors of model in detail. In this work, an Interpretable Therapeutic Peptide Prediction (ITP-Pred) model based on efficient feature fusion was developed. First, we proposed three kinds of feature descriptors based on sequence and physicochemical property encoded, namely amino acid composition (AAC), group AAC and coding autocorrelation, and concatenated them to obtain the feature representation of therapeutic peptide. Then, we input it into the CNN-Bi-directional Long Short-Term Memory (BiLSTM) model to automatically learn recognition of therapeutic peptides. The cross-validation and independent verification experiments results indicated that ITP-Pred has a higher prediction performance on the benchmark dataset than other comparison methods. Finally, we analyzed the output of the model from two aspects: sequence order and physical and chemical properties, mining important features as guidance for the design of better models that can complement existing methods.

PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning

2019 ◽  
Vol 35 (21) ◽  
pp. 4272-4280 ◽  
Author(s):  
Leyi Wei ◽  
Chen Zhou ◽  
Ran Su ◽  
Quan Zou
Keyword(s):  
Characteristic Curve ◽  
Representation Learning ◽  
Feature Representation ◽  
Supplementary Information ◽  
Optimization Strategy ◽  
Feature Representations ◽  
Random Forest Models ◽  
Therapeutic Peptides ◽  
Functional Peptides ◽  
Robust Prediction

Abstract Motivation Prediction of therapeutic peptides is critical for the discovery of novel and efficient peptide-based therapeutics. Computational methods, especially machine learning based methods, have been developed for addressing this need. However, most of existing methods are peptide-specific; currently, there is no generic predictor for multiple peptide types. Moreover, it is still challenging to extract informative feature representations from the perspective of primary sequences. Results In this study, we have developed PEPred-Suite, a bioinformatics tool for the generic prediction of therapeutic peptides. In PEPred-Suite, we introduce an adaptive feature representation strategy that can learn the most representative features for different peptide types. To be specific, we train diverse sequence-based feature descriptors, integrate the learnt class information into our features, and utilize a two-step feature optimization strategy based on the area under receiver operating characteristic curve to extract the most discriminative features. Using the learnt representative features, we trained eight random forest models for eight different types of functional peptides, respectively. Benchmarking results showed that as compared with existing predictors, PEPred-Suite achieves better and robust performance for different peptides. As far as we know, PEPred-Suite is currently the first tool that is capable of predicting so many peptide types simultaneously. In addition, our work demonstrates that the learnt features can reliably predict different peptides. Availability and implementation The user-friendly webserver implementing the proposed PEPred-Suite is freely accessible at http://server.malab.cn/PEPred-Suite. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Identification of Sub-Golgi protein localization by use of deep representation learning features

2020 ◽  
Author(s):  
Zhibin Lv ◽  
Pingping Wang ◽  
Quan Zou ◽  
Qinghua Jiang
Keyword(s):  
Golgi Apparatus ◽  
Protein Identification ◽  
Protein Localization ◽  
Protein Biosynthesis ◽  
Representation Learning ◽  
Eukaryotic Cell ◽  
Feature Representation ◽  
Supplementary Information ◽  
Golgi Localization ◽  
Golgi Protein

Abstract Motivation The Golgi apparatus has a key functional role in protein biosynthesis within the eukaryotic cell with malfunction resulting in various neurodegenerative diseases. For a better understanding of the Golgi apparatus, it is essential to identification of sub-Golgi protein localization. Although some machine learning methods have been used to identify sub-Golgi localization proteins by sequence representation fusion, more accurate sub-Golgi protein identification is still challenging by existing methodology. Results we developed a protein sub-Golgi localization identification protocol using deep representation learning features with 107 dimensions. By this protocol, we demonstrated that instead of multi-type protein sequence feature representation fusion as in previous state-of-the-art sub-Golgi-protein localization classifiers, it is sufficient to exploit only one type of feature representation for more accurately identification of sub-Golgi proteins. Compared with independent testing results for benchmark datasets, our protocol is able to perform generally, reliably, and robustly for sub-Golgi protein localization prediction. Availability A use-friendly webserver is freely accessible at http://isGP-DRLF.aibiochem.net and the prediction code is accessible at https://github.com/zhibinlv/isGP-DRLF. Supplementary information Supplementary data are available at Bioinformatics online.

TP-MV: Therapeutic protein prediction by multi-view learning

2021 ◽  
Vol 17 ◽  
Author(s):  
Ke Yan ◽  
Hongwu Lv ◽  
Yichen Guo ◽  
Jie Wen ◽  
Bin Liu
Keyword(s):  
Drug Development ◽  
The Other ◽  
Challenging Problem ◽  
Peptide Recognition ◽  
Therapeutic Peptide ◽  
Discriminative Feature ◽  
Protein Prediction ◽  
Benchmark Datasets ◽  
Therapeutic Peptides ◽  
Peptide Prediction

Background: Therapeutic peptide prediction is critical for drug development and therapy. Researchers have been studying this essential task, developing several computational methods to identify different therapeutic peptide types. Objective: Most predictors are the specific methods for certain peptides. Currently, developing methods to predict the presence of multiple peptides remains a challenging problem. Moreover, it is still challenging to combine different features to make the therapeutic prediction. Method: In this paper, we proposed a new ensemble method TP-MV for general therapeutic peptide recognition. TP-MV is developed using the stacking framework in conjunction with the KNN, SVM, ET, RF, and XGB. Then TP-MV constructs a multi-view learning model as meta-classifiers to extract the discriminative feature for different peptides. Results: In the experiment, the proposed method outperforms the other existing methods on the benchmark datasets, indicating that the proposed method has the ability to predict multiple therapeutic peptides simultaneously. Conclusion: The TP-MV is a useful tool for predicting therapeutic peptides.

HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation

2020 ◽  
Vol 36 (11) ◽  
pp. 3350-3356 ◽  
Author(s):  
Md Mehedi Hasan ◽  
Nalini Schaduangrat ◽  
Shaherin Basith ◽  
Gwang Lee ◽  
Watshara Shoombuatong ◽  
...  
Keyword(s):  
Hemolytic Activity ◽  
Prediction Models ◽  
Basic Research ◽  
Representation Learning ◽  
Feature Representation ◽  
Supplementary Information ◽  
Sequence Information ◽  
Drug Candidates ◽  
Activity Performance ◽  
Robust Prediction

Abstract Motivation Therapeutic peptides failing at clinical trials could be attributed to their toxicity profiles like hemolytic activity, which hamper further progress of peptides as drug candidates. The accurate prediction of hemolytic peptides (HLPs) and its activity from the given peptides is one of the challenging tasks in immunoinformatics, which is essential for drug development and basic research. Although there are a few computational methods that have been proposed for this aspect, none of them are able to identify HLPs and their activities simultaneously. Results In this study, we proposed a two-layer prediction framework, called HLPpred-Fuse, that can accurately and automatically predict both hemolytic peptides (HLPs or non-HLPs) as well as HLPs activity (high and low). More specifically, feature representation learning scheme was utilized to generate 54 probabilistic features by integrating six different machine learning classifiers and nine different sequence-based encodings. Consequently, the 54 probabilistic features were fused to provide sufficiently converged sequence information which was used as an input to extremely randomized tree for the development of two final prediction models which independently identify HLP and its activity. Performance comparisons over empirical cross-validation analysis, independent test and case study against state-of-the-art methods demonstrate that HLPpred-Fuse consistently outperformed these methods in the identification of hemolytic activity. Availability and implementation For the convenience of experimental scientists, a web-based tool has been established at http://thegleelab.org/HLPpred-Fuse. Contact [email protected] or [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

An Integrated Prediction Method for Identifying Protein-Protein Interactions

2020 ◽  
Vol 17 (4) ◽  
pp. 271-286
Author(s):  
Chang Xu ◽  
Limin Jiang ◽  
Zehua Zhang ◽  
Xuyao Yu ◽  
Renhai Chen ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Feature Vector ◽  
Prediction Method ◽  
Feature Representation ◽  
Protein Interaction Networks ◽  
Learning Approach ◽  
Biological Processes ◽  
Integrated Learning ◽  
Protein Protein Interactions ◽  
Training Process

Background: Protein-Protein Interactions (PPIs) play a key role in various biological processes. Many methods have been developed to predict protein-protein interactions and protein interaction networks. However, many existing applications are limited, because of relying on a large number of homology proteins and interaction marks. Methods: In this paper, we propose a novel integrated learning approach (RF-Ada-DF) with the sequence-based feature representation, for identifying protein-protein interactions. Our method firstly constructs a sequence-based feature vector to represent each pair of proteins, viaMultivariate Mutual Information (MMI) and Normalized Moreau-Broto Autocorrelation (NMBAC). Then, we feed the 638- dimentional features into an integrated learning model for judging interaction pairs and non-interaction pairs. Furthermore, this integrated model embeds Random Forest in AdaBoost framework and turns weak classifiers into a single strong classifier. Meanwhile, we also employ double fault detection in order to suppress over-adaptation during the training process. Results: To evaluate the performance of our method, we conduct several comprehensive tests for PPIs prediction. On the H. pyloridataset, our method achieves 88.16% accuracy and 87.68% sensitivity, the accuracy of our method is increased by 0.57%. On the S. cerevisiaedataset, our method achieves 95.77% accuracy and 93.36% sensitivity, the accuracy of our method is increased by 0.76%. On the Humandataset, our method achieves 98.16% accuracy and 96.80% sensitivity, the accuracy of our method is increased by 0.6%. Experiments show that our method achieves better results than other outstanding methods for sequence-based PPIs prediction. The datasets and codes are available at https://github.com/guofei-tju/RF-Ada-DF.git.

mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation

2018 ◽  
Vol 35 (16) ◽  
pp. 2757-2765 ◽  
Author(s):  
Balachandran Manavalan ◽  
Shaherin Basith ◽  
Tae Hwan Shin ◽  
Leyi Wei ◽  
Gwang Lee
Keyword(s):  
Nearest Neighbor ◽  
Feature Representation ◽  
Superior Performance ◽  
Supplementary Information ◽  
Gradient Boosting ◽  
Support Vector ◽  
Pharmaceutical Drugs ◽  
K Nearest Neighbor ◽  
Feature Descriptors ◽  
Predicted Probability

AbstractMotivationCardiovascular disease is the primary cause of death globally accounting for approximately 17.7 million deaths per year. One of the stakes linked with cardiovascular diseases and other complications is hypertension. Naturally derived bioactive peptides with antihypertensive activities serve as promising alternatives to pharmaceutical drugs. So far, there is no comprehensive analysis, assessment of diverse features and implementation of various machine-learning (ML) algorithms applied for antihypertensive peptide (AHTP) model construction.ResultsIn this study, we utilized six different ML algorithms, namely, Adaboost, extremely randomized tree (ERT), gradient boosting (GB), k-nearest neighbor, random forest (RF) and support vector machine (SVM) using 51 feature descriptors derived from eight different feature encodings for the prediction of AHTPs. While ERT-based trained models performed consistently better than other algorithms regardless of various feature descriptors, we treated them as baseline predictors, whose predicted probability of AHTPs was further used as input features separately for four different ML-algorithms (ERT, GB, RF and SVM) and developed their corresponding meta-predictors using a two-step feature selection protocol. Subsequently, the integration of four meta-predictors through an ensemble learning approach improved the balanced prediction performance and model robustness on the independent dataset. Upon comparison with existing methods, mAHTPred showed superior performance with an overall improvement of approximately 6–7% in both benchmarking and independent datasets.Availability and implementationThe user-friendly online prediction tool, mAHTPred is freely accessible at http://thegleelab.org/mAHTPred.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals Semantic Relationships Guided Representation Learning for Facial Action Unit Recognition

2019 ◽  
Vol 33 ◽  
pp. 8594-8601 ◽  
Author(s):  
Guanbin Li ◽  
Xin Zhu ◽  
Yirui Zeng ◽  
Qing Wang ◽  
Liang Lin
Keyword(s):  
Neural Network ◽  
Facial Expressions ◽  
Mutual Exclusion ◽  
Representation Learning ◽  
Feature Representation ◽  
Semantic Relationship ◽  
Action Unit ◽  
Facial Action ◽  
Feature Representations ◽  
Regional Feature

Facial action unit (AU) recognition is a crucial task for facial expressions analysis and has attracted extensive attention in the field of artificial intelligence and computer vision. Existing works have either focused on designing or learning complex regional feature representations, or delved into various types of AU relationship modeling. Albeit with varying degrees of progress, it is still arduous for existing methods to handle complex situations. In this paper, we investigate how to integrate the semantic relationship propagation between AUs in a deep neural network framework to enhance the feature representation of facial regions, and propose an AU semantic relationship embedded representation learning (SRERL) framework. Specifically, by analyzing the symbiosis and mutual exclusion of AUs in various facial expressions, we organize the facial AUs in the form of structured knowledge-graph and integrate a Gated Graph Neural Network (GGNN) in a multi-scale CNN framework to propagate node information through the graph for generating enhanced AU representation. As the learned feature involves both the appearance characteristics and the AU relationship reasoning, the proposed model is more robust and can cope with more challenging cases, e.g., illumination change and partial occlusion. Extensive experiments on the two public benchmarks demonstrate that our method outperforms the previous work and achieves state of the art performance.

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