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Article ; Online: Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs.

Zhou, Zhecheng / Zhuo, Linlin / Fu, Xiangzheng / Zou, Quan

2024 Volume 25, Issue 1

Abstract: Exploring microbial stress responses to drugs is crucial for the advancement of new therapeutic methods. While current artificial intelligence methodologies have expedited our understanding of potential microbial responses to drugs, the models are ... ...

Abstract	Exploring microbial stress responses to drugs is crucial for the advancement of new therapeutic methods. While current artificial intelligence methodologies have expedited our understanding of potential microbial responses to drugs, the models are constrained by the imprecise representation of microbes and drugs. To this end, we combine deep autoencoder and subgraph augmentation technology for the first time to propose a model called JDASA-MRD, which can identify the potential indistinguishable responses of microbes to drugs. In the JDASA-MRD model, we begin by feeding the established similarity matrices of microbe and drug into the deep autoencoder, enabling to extract robust initial features of both microbes and drugs. Subsequently, we employ the MinHash and HyperLogLog algorithms to account intersections and cardinality data between microbe and drug subgraphs, thus deeply extracting the multi-hop neighborhood information of nodes. Finally, by integrating the initial node features with subgraph topological information, we leverage graph neural network technology to predict the microbes' responses to drugs, offering a more effective solution to the 'over-smoothing' challenge. Comparative analyses on multiple public datasets confirm that the JDASA-MRD model's performance surpasses that of current state-of-the-art models. This research aims to offer a more profound insight into the adaptability of microbes to drugs and to furnish pivotal guidance for drug treatment strategies. Our data and code are publicly available at: https://github.com/ZZCrazy00/JDASA-MRD.
MeSH term(s)	Artificial Intelligence ; Algorithms ; Neural Networks, Computer
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbad483
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Revisiting Drug-Protein Interaction Prediction: A Novel Global-Local Perspective.

Zhou, Zhecheng / Liao, Qingquan / Wei, Jinhang / Zhuo, Linlin / Wu, Xiaonan / Fu, Xiangzheng / Zou, Quan

Bioinformatics (Oxford, England)

2024

Abstract: Motivation: Accurate inference of potential Drug-protein interactions (DPIs) aids in understanding drug mechanisms and developing novel treatments. Existing deep learning models, however, struggle with accurate node representation in DPI prediction, ... ...

Abstract	Motivation: Accurate inference of potential Drug-protein interactions (DPIs) aids in understanding drug mechanisms and developing novel treatments. Existing deep learning models, however, struggle with accurate node representation in DPI prediction, limiting their performance. Results: We propose a new computational framework that integrates global and local features of nodes in the drug-protein bipartite graph for efficient DPI inference. Initially, we employ pre-trained models to acquire fundamental knowledge of drugs and proteins and to determine their initial features. Subsequently, the MinHash and HyperLogLog algorithms are utilized to estimate the similarity and set cardinality between drug and protein subgraphs, serving as their local features. Then, an energy-constrained diffusion mechanism is integrated into the transformer architecture, capturing interdependencies between nodes in the drug-protein bipartite graph and extracting their global features. Finally, we fuse the local and global features of nodes and employ multi-layer perceptrons (MLPs) to predict the likelihood of potential DPIs. A comprehensive and precise node representation guarantees efficient prediction of unknown DPIs by the model. Various experiments validate the accuracy and reliability of our model, with molecular docking results revealing its capability to identify potential DPIs not present in existing databases. This approach are expected to offer valuable insights for furthering drug repurposing and personalized medicine research. Availability and implementation: Our code and data are accessible at: https://github.com/ZZCrazy00/DPI. Supplementary information: Supplementary data are available at Bioinformatics online.
Language	English
Publishing date	2024-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btae271
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 2374: Show issues

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Article ; Online: GAM-MDR: probing miRNA-drug resistance using a graph autoencoder based on random path masking.

Zhou, Zhecheng / Du, Zhenya / Jiang, Xin / Zhuo, Linlin / Xu, Yixin / Fu, Xiangzheng / Liu, Mingzhe / Zou, Quan

Briefings in functional genomics

2024

Abstract: MicroRNAs (miRNAs) are found ubiquitously in biological cells and play a pivotal role in regulating the expression of numerous target genes. Therapies centered around miRNAs are emerging as a promising strategy for disease treatment, aiming to intervene ... ...

Abstract	MicroRNAs (miRNAs) are found ubiquitously in biological cells and play a pivotal role in regulating the expression of numerous target genes. Therapies centered around miRNAs are emerging as a promising strategy for disease treatment, aiming to intervene in disease progression by modulating abnormal miRNA expressions. The accurate prediction of miRNA-drug resistance (MDR) is crucial for the success of miRNA therapies. Computational models based on deep learning have demonstrated exceptional performance in predicting potential MDRs. However, their effectiveness can be compromised by errors in the data acquisition process, leading to inaccurate node representations. To address this challenge, we introduce the GAM-MDR model, which combines the graph autoencoder (GAE) with random path masking techniques to precisely predict potential MDRs. The reliability and effectiveness of the GAM-MDR model are mainly reflected in two aspects. Firstly, it efficiently extracts the representations of miRNA and drug nodes in the miRNA-drug network. Secondly, our designed random path masking strategy efficiently reconstructs critical paths in the network, thereby reducing the adverse impact of noisy data. To our knowledge, this is the first time that a random path masking strategy has been integrated into a GAE to infer MDRs. Our method was subjected to multiple validations on public datasets and yielded promising results. We are optimistic that our model could offer valuable insights for miRNA therapeutic strategies and deepen the understanding of the regulatory mechanisms of miRNAs. Our data and code are publicly available at GitHub:https://github.com/ZZCrazy00/GAM-MDR.
Language	English
Publishing date	2024-02-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2540916-5
ISSN	2041-2657 ; 2041-2649 ; 2041-2647
ISSN (online)	2041-2657
ISSN	2041-2649 ; 2041-2647
DOI	10.1093/bfgp/elae005
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 6076: Show issues

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Article: Joint masking and self-supervised strategies for inferring small molecule-miRNA associations.

Zhou, Zhecheng / Zhuo, Linlin / Fu, Xiangzheng / Lv, Juan / Zou, Quan / Qi, Ren

Molecular therapy. Nucleic acids

2023 Volume 35, Issue 1, Page(s) 102103

Abstract: Inferring small molecule-miRNA associations (MMAs) is crucial for revealing the intricacies of biological processes and disease mechanisms. Deep learning, renowned for its exceptional speed and accuracy, is extensively used for predicting MMAs. However, ... ...

Abstract	Inferring small molecule-miRNA associations (MMAs) is crucial for revealing the intricacies of biological processes and disease mechanisms. Deep learning, renowned for its exceptional speed and accuracy, is extensively used for predicting MMAs. However, given their heavy reliance on data, inaccuracies during data collection can make these methods susceptible to noise interference. To address this challenge, we introduce the joint masking and self-supervised (JMSS)-MMA model. This model synergizes graph autoencoders with a probability distribution-based masking strategy, effectively countering the impact of noisy data and enabling precise predictions of unknown MMAs. Operating in a self-supervised manner, it deeply encodes the relationship data of small molecules and miRNA through the graph autoencoder, delving into its latent information. Our masking strategy has successfully reduced data noise, enhancing prediction accuracy. To our knowledge, this is the pioneering integration of a masking strategy with graph autoencoders for MMA prediction. Furthermore, the JMSS-MMA model incorporates a node-degree-based decoder, deepening the understanding of the network's structure. Experiments on two mainstream datasets confirm the model's efficiency and precision, and ablation studies further attest to its robustness. We firmly believe that this model will revolutionize drug development, personalized medicine, and biomedical research.
Language	English
Publishing date	2023-12-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2023.102103
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Article ; Online: MHAM-NPI: Predicting ncRNA-protein interactions based on multi-head attention mechanism.

Zhou, Zhecheng / Du, Zhenya / Wei, Jinhang / Zhuo, Linlin / Pan, Shiyao / Fu, Xiangzheng / Lian, Xinze

Computers in biology and medicine

2023 Volume 163, Page(s) 107143

Abstract: Non-coding RNA (ncRNA) is a functional RNA molecule that plays a key role in various fundamental biological processes, such as gene regulation. Therefore, studying the connection between ncRNA and proteins holds significant importance in exploring the ... ...

Abstract	Non-coding RNA (ncRNA) is a functional RNA molecule that plays a key role in various fundamental biological processes, such as gene regulation. Therefore, studying the connection between ncRNA and proteins holds significant importance in exploring the function of ncRNA. Although many efficient and accurate methods have been developed by modern biological scientists, accurate predictions still pose a major challenge for various issues. In our approach, we utilize a multi-head attention mechanism to merge residual connections, allowing for the automatic learning of ncRNA and protein sequence features. Specifically, the proposed method projects node features into multiple spaces based on multi-head attention mechanism, thereby obtaining different feature interaction patterns in these spaces. By stacking interaction layers, higher-order interaction modes can be derived, while still preserving the initial feature information through the residual connection. This strategy effectively leverages the sequence information of ncRNA and protein, enabling the capture of hidden high-order features. The final experimental results demonstrate the effectiveness of our method, with AUC values of 97.4%, 98.5%, and 94.8% achieved on the NPInter v2.0, RPI807, and RPI488 datasets, respectively. These impressive results solidify our method as a powerful tool for exploring the connection between ncRNAs and proteins. We have uploaded the implementation code on GitHub: https://github.com/ZZCrazy00/MHAM-NPI.
MeSH term(s)	RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; Proteins/metabolism
Chemical Substances	RNA, Untranslated ; Proteins
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2023.107143
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Zs.A 653: Show issues

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Article ; Online: GCFMCL: predicting miRNA-drug sensitivity using graph collaborative filtering and multi-view contrastive learning.

Wei, Jinhang / Zhuo, Linlin / Zhou, Zhecheng / Lian, Xinze / Fu, Xiangzheng / Yao, Xiaojun

Briefings in bioinformatics

2023 Volume 24, Issue 4

Abstract: Studies have shown that the mechanism of action of many drugs is related to miRNA. In-depth research on the relationship between miRNA and drugs can provide theoretical foundations and practical approaches for various areas, such as drug target discovery, ...

Abstract	Studies have shown that the mechanism of action of many drugs is related to miRNA. In-depth research on the relationship between miRNA and drugs can provide theoretical foundations and practical approaches for various areas, such as drug target discovery, drug repositioning and biomarker research. Traditional biological experiments to test miRNA-drug susceptibility are costly and time-consuming. Thus, sequence- or topology-based deep learning methods are recognized in this field for their efficiency and accuracy. However, these methods have limitations in dealing with sparse topologies and higher-order information of miRNA (drug) feature. In this work, we propose GCFMCL, a model for multi-view contrastive learning based on graph collaborative filtering. To the best of our knowledge, this is the first attempt that incorporates contrastive learning strategy into the graph collaborative filtering framework to predict the sensitivity relationships between miRNA and drug. The proposed multi-view contrastive learning method is divided into topological contrastive objective and feature contrastive objective: (1) For the homogeneous neighbors of the topological graph, we propose a novel topological contrastive learning method via constructing the contrastive target through the topological neighborhood information of nodes. (2) The proposed model obtains feature contrastive targets from high-order feature information according to the correlation of node features, and mines potential neighborhood relationships in the feature space. The proposed multi-view comparative learning effectively alleviates the impact of heterogeneous node noise and graph data sparsity in graph collaborative filtering, and significantly enhances the performance of the model. Our study employs a dataset derived from the NoncoRNA and ncDR databases, encompassing 2049 experimentally validated miRNA-drug sensitivity associations. Five-fold cross-validation shows that the Area Under the Curve (AUC), Area Under the Precision-Recall Curve (AUPR) and F1-score (F1) of GCFMCL reach 95.28%, 95.66% and 89.77%, which outperforms the state-of-the-art (SOTA) method by the margin of 2.73%, 3.42% and 4.96%, respectively. Our code and data can be accessed at https://github.com/kkkayle/GCFMCL.
MeSH term(s)	Area Under Curve ; Databases, Factual ; Drug Delivery Systems ; Drug Discovery ; MicroRNAs/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2023-07-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbad247
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SGAE-MDA: Exploring the MiRNA-disease associations in herbal medicines based on semi-supervised graph autoencoder.

Xu, Lei / Fu, Xiangzheng / Zhuo, Linlin / Zhou, Zhecheng / Liao, Xuefeng / Tian, Sha / Kang, Ruofei / Chen, Yifan

Methods (San Diego, Calif.)

2023 Volume 221, Page(s) 73–81

Abstract: Research indicates that miRNAs present in herbal medicines are crucial for identifying disease markers, advancing gene therapy, facilitating drug delivery, and so on. These miRNAs maintain stability in the extracellular environment, making them viable ... ...

Abstract	Research indicates that miRNAs present in herbal medicines are crucial for identifying disease markers, advancing gene therapy, facilitating drug delivery, and so on. These miRNAs maintain stability in the extracellular environment, making them viable tools for disease diagnosis. They can withstand the digestive processes in the gastrointestinal tract, positioning them as potential carriers for specific oral drug delivery. By engineering plants to generate effective, non-toxic miRNA interference sequences, it's possible to broaden their applicability, including the treatment of diseases such as hepatitis C. Consequently, delving into the miRNA-disease associations (MDAs) within herbal medicines holds immense promise for diagnosing and addressing miRNA-related diseases. In our research, we propose the SGAE-MDA model, which harnesses the strengths of a graph autoencoder (GAE) combined with a semi-supervised approach to uncover potential MDAs in herbal medicines more effectively. Leveraging the GAE framework, the SGAE-MDA model exactly integrates the inherent feature vectors of miRNAs and disease nodes with the regulatory data in the miRNA-disease network. Additionally, the proposed semi-supervised learning approach randomly hides the partial structure of the miRNA-disease network, subsequently reconstructing them within the GAE framework. This technique effectively minimizes network noise interference. Through comparison against other leading deep learning models, the results consistently highlighted the superior performance of the proposed SGAE-MDA model. Our code and dataset can be available at: https://github.com/22n9n23/SGAE-MDA.
MeSH term(s)	MicroRNAs/genetics ; Algorithms ; Computational Biology/methods ; Supervised Machine Learning ; Plant Extracts
Chemical Substances	MicroRNAs ; Plant Extracts
Language	English
Publishing date	2023-12-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2023.12.002
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 3239: Show issues

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Article ; Online: An Effective Plant Small Secretory Peptide Recognition Model Based on Feature Correction Strategy.

Wang, Rui / Zhou, Zhecheng / Wu, Xiaonan / Jiang, Xin / Zhuo, Linlin / Liu, Mingzhe / Li, Hao / Fu, Xiangzheng / Yao, Xiaojun

Journal of chemical information and modeling

2023 Volume 64, Issue 7, Page(s) 2798–2806

Abstract: Plant small secretory peptides (SSPs) play an important role in the regulation of biological processes in plants. Accurately predicting SSPs enables efficient exploration of their functions. Traditional experimental verification methods are very reliable ...

Abstract	Plant small secretory peptides (SSPs) play an important role in the regulation of biological processes in plants. Accurately predicting SSPs enables efficient exploration of their functions. Traditional experimental verification methods are very reliable and accurate, but they require expensive equipment and a lot of time. The method of machine learning speeds up the prediction process of SSPs, but the instability of feature extraction will also lead to further limitations of this type of method. Therefore, this paper proposes a new feature-correction-based model for SSP recognition in plants, abbreviated as SE-SSP. The model mainly includes the following three advantages: First, the use of transformer encoders can better reveal implicit features. Second, design a feature correction module suitable for sequences, named 2-D SENET, to adaptively adjust the features to obtain a more robust feature representation. Third, stack multiple linear modules to further dig out the deep information on the sample. At the same time, the training based on a contrastive learning strategy can alleviate the problem of sparse samples. We construct experiments on publicly available data sets, and the results verify that our model shows an excellent performance. The proposed model can be used as a convenient and effective SSP prediction tool in the future. Our data and code are publicly available at https://github.com/wrab12/SE-SSP/.
MeSH term(s)	Biological Transport ; Electric Power Supplies ; Machine Learning ; Peptides ; Research Design
Chemical Substances	Peptides
Language	English
Publishing date	2023-08-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c00868
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