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

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.

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

Bioinformatics ◽

10.1093/bioinformatics/btaa275 ◽

2020 ◽

Vol 36 (13) ◽

pp. 3982-3987 ◽

Cited By ~ 2

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.

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

Bioinformatics ◽

10.1093/bioinformatics/btaa160 ◽

2020 ◽

Vol 36 (11) ◽

pp. 3350-3356 ◽

Cited By ~ 27

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.

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Semantic Relationships Guided Representation Learning for Facial Action Unit Recognition

Proceedings of the AAAI Conference on Artificial Intelligence ◽

10.1609/aaai.v33i01.33018594 ◽

2019 ◽

Vol 33 ◽

pp. 8594-8601 ◽

Cited By ~ 5

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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Predicting Cross-Species Infection of Swine Influenza Virus with Representation Learning of Amino Acid Features

Computational and Mathematical Methods in Medicine ◽

10.1155/2021/6985008 ◽

2021 ◽

Vol 2021 ◽

pp. 1-12

Author(s):

Zheng Kou ◽

Junjie Li ◽

Xinyue Fan ◽

Saeed Kosari ◽

Xiaoli Qiang

Keyword(s):

Amino Acid ◽

High Performance ◽

Swine Influenza Virus ◽

Swine Influenza ◽

Representation Learning ◽

Influenza Viruses ◽

Feature Representation ◽

Specific Information ◽

Feature Representations ◽

Probabilistic Information

Swine influenza viruses (SIVs) can unforeseeably cross the species barriers and directly infect humans, which pose huge challenges for public health and trigger pandemic risk at irregular intervals. Computational tools are needed to predict infection phenotype and early pandemic risk of SIVs. For this purpose, we propose a feature representation algorithm to predict cross-species infection of SIVs. We built a high-quality dataset of 1902 viruses. A feature representation learning scheme was applied to learn feature representations from 64 well-trained random forest models with multiple feature descriptors of mutant amino acid in the viral proteins, including compositional information, position-specific information, and physicochemical properties. Class and probabilistic information were integrated into the feature representations, and redundant features were removed by feature space optimization. High performance was achieved using 20 informative features and 22 probabilistic information. The proposed method will facilitate SIV characterization of transmission phenotype.

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

Bioinformatics ◽

10.1093/bioinformatics/btaa1074 ◽

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.

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Wasserstein Distance Learns Domain Invariant Feature Representations for Drift Compensation of E-Nose

Sensors ◽

10.3390/s19173703 ◽

2019 ◽

Vol 19 (17) ◽

pp. 3703 ◽

Cited By ~ 3

Author(s):

Yang Tao ◽

Chunyan Li ◽

Zhifang Liang ◽

Haocheng Yang ◽

Juan Xu

Keyword(s):

Feature Space ◽

Representation Learning ◽

Wasserstein Distance ◽

Recognition Algorithm ◽

Feature Representation ◽

Target Domain ◽

Feature Representations ◽

Invariant Feature ◽

Sensor Drift ◽

Drift Compensation

Electronic nose (E-nose), a kind of instrument which combines with the gas sensor and the corresponding pattern recognition algorithm, is used to detect the type and concentration of gases. However, the sensor drift will occur in realistic application scenario of E-nose, which makes a variation of data distribution in feature space and causes a decrease in prediction accuracy. Therefore, studies on the drift compensation algorithms are receiving increasing attention in the field of the E-nose. In this paper, a novel method, namely Wasserstein Distance Learned Feature Representations (WDLFR), is put forward for drift compensation, which is based on the domain invariant feature representation learning. It regards a neural network as a domain discriminator to measure the empirical Wasserstein distance between the source domain (data without drift) and target domain (drift data). The WDLFR minimizes Wasserstein distance by optimizing the feature extractor in an adversarial manner. The Wasserstein distance for domain adaption has good gradient and generalization bound. Finally, the experiments are conducted on a real dataset of E-nose from the University of California, San Diego (UCSD). The experimental results demonstrate that the effectiveness of the proposed method outperforms all compared drift compensation methods, and the WDLFR succeeds in significantly reducing the sensor drift.

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Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction

Bioinformatics ◽

10.1093/bioinformatics/btz965 ◽

2020 ◽

Vol 36 (8) ◽

pp. 2538-2546 ◽

Cited By ~ 9

Author(s):

Jin Li ◽

Sai Zhang ◽

Tao Liu ◽

Chenxi Ning ◽

Zhuoxuan Zhang ◽

...

Keyword(s):

Characteristic Curve ◽

Matrix Completion ◽

Disease Association ◽

Supplementary Information ◽

Convolutional Network ◽

Convolutional Networks ◽

Feature Representations ◽

Disease Similarity ◽

Disease Associations ◽

Association Data

Abstract Motivation Predicting the association between microRNAs (miRNAs) and diseases plays an import role in identifying human disease-related miRNAs. As identification of miRNA-disease associations via biological experiments is time-consuming and expensive, computational methods are currently used as effective complements to determine the potential associations between disease and miRNA. Results We present a novel method of neural inductive matrix completion with graph convolutional network (NIMCGCN) for predicting miRNA-disease association. NIMCGCN first uses graph convolutional networks to learn miRNA and disease latent feature representations from the miRNA and disease similarity networks. Then, learned features were input into a novel neural inductive matrix completion (NIMC) model to generate an association matrix completion. The parameters of NIMCGCN were learned based on the known miRNA-disease association data in a supervised end-to-end way. We compared the proposed method with other state-of-the-art methods. The area under the receiver operating characteristic curve results showed that our method is significantly superior to existing methods. Furthermore, 50, 47 and 48 of the top 50 predicted miRNAs for three high-risk human diseases, namely, colon cancer, lymphoma and kidney cancer, were verified using experimental literature. Finally, 100% prediction accuracy was achieved when breast cancer was used as a case study to evaluate the ability of NIMCGCN for predicting a new disease without any known related miRNAs. Availability and implementation https://github.com/ljatynu/NIMCGCN/ Supplementary information Supplementary data are available at Bioinformatics online.

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Iterative feature representations improve N4-methylcytosine site prediction

Bioinformatics ◽

10.1093/bioinformatics/btz408 ◽

2019 ◽

Vol 35 (23) ◽

pp. 4930-4937 ◽

Cited By ~ 35

Author(s):

Leyi Wei ◽

Ran Su ◽

Shasha Luan ◽

Zhijun Liao ◽

Balachandran Manavalan ◽

...

Keyword(s):

Feature Space ◽

Feature Representation ◽

Supplementary Information ◽

Accurate Identification ◽

Feature Representations ◽

Genome Wide ◽

A Genome ◽

Benchmark Datasets ◽

Sequential Models ◽

User Friendly

Abstract Motivation Accurate identification of N4-methylcytosine (4mC) modifications in a genome wide can provide insights into their biological functions and mechanisms. Machine learning recently have become effective approaches for computational identification of 4mC sites in genome. Unfortunately, existing methods cannot achieve satisfactory performance, owing to the lack of effective DNA feature representations that are capable to capture the characteristics of 4mC modifications. Results In this work, we developed a new predictor named 4mcPred-IFL, aiming to identify 4mC sites. To represent and capture discriminative features, we proposed an iterative feature representation algorithm that enables to learn informative features from several sequential models in a supervised iterative mode. Our analysis results showed that the feature representations learnt by our algorithm can capture the discriminative distribution characteristics between 4mC sites and non-4mC sites, enlarging the decision margin between the positives and negatives in feature space. Additionally, by evaluating and comparing our predictor with the state-of-the-art predictors on benchmark datasets, we demonstrate that our predictor can identify 4mC sites more accurately. Availability and implementation The user-friendly webserver that implements the proposed 4mcPred-IFL is well established, and is freely accessible at http://server.malab.cn/4mcPred-IFL. Supplementary information Supplementary data are available at Bioinformatics online.

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Meta Learning for Few-Shot One-Class Classification

AI ◽

10.3390/ai2020012 ◽

2021 ◽

Vol 2 (2) ◽

pp. 195-208

Author(s):

Gabriel Dahia ◽

Maurício Pamplona Segundo

Keyword(s):

Feature Representation ◽

Support Vector ◽

Support Vector Data Description ◽

Target Class ◽

Feature Representations ◽

Shot Classification ◽

Training Stage ◽

Comparable Performance ◽

Meta Learning ◽

One Class Classification

We propose a method that can perform one-class classification given only a small number of examples from the target class and none from the others. We formulate the learning of meaningful features for one-class classification as a meta-learning problem in which the meta-training stage repeatedly simulates one-class classification, using the classification loss of the chosen algorithm to learn a feature representation. To learn these representations, we require only multiclass data from similar tasks. We show how the Support Vector Data Description method can be used with our method, and also propose a simpler variant based on Prototypical Networks that obtains comparable performance, indicating that learning feature representations directly from data may be more important than which one-class algorithm we choose. We validate our approach by adapting few-shot classification datasets to the few-shot one-class classification scenario, obtaining similar results to the state-of-the-art of traditional one-class classification, and that improves upon that of one-class classification baselines employed in the few-shot setting.

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A Novel Method to Predict Drug-Target Interactions Based on Large-Scale Graph Representation Learning

Cancers ◽

10.3390/cancers13092111 ◽

2021 ◽

Vol 13 (9) ◽

pp. 2111

Author(s):

Bo-Wei Zhao ◽

Zhu-Hong You ◽

Lun Hu ◽

Zhen-Hao Guo ◽

Lei Wang ◽

...

Keyword(s):

Drug Target ◽

Large Scale ◽

Computational Models ◽

Structural Information ◽

Characteristic Curve ◽

Representation Learning ◽

Graph Representation ◽

Convolutional Network ◽

Novel Method

Identification of drug-target interactions (DTIs) is a significant step in the drug discovery or repositioning process. Compared with the time-consuming and labor-intensive in vivo experimental methods, the computational models can provide high-quality DTI candidates in an instant. In this study, we propose a novel method called LGDTI to predict DTIs based on large-scale graph representation learning. LGDTI can capture the local and global structural information of the graph. Specifically, the first-order neighbor information of nodes can be aggregated by the graph convolutional network (GCN); on the other hand, the high-order neighbor information of nodes can be learned by the graph embedding method called DeepWalk. Finally, the two kinds of feature are fed into the random forest classifier to train and predict potential DTIs. The results show that our method obtained area under the receiver operating characteristic curve (AUROC) of 0.9455 and area under the precision-recall curve (AUPR) of 0.9491 under 5-fold cross-validation. Moreover, we compare the presented method with some existing state-of-the-art methods. These results imply that LGDTI can efficiently and robustly capture undiscovered DTIs. Moreover, the proposed model is expected to bring new inspiration and provide novel perspectives to relevant researchers.

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