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MVNMDA:一种用于预测 miRNA-疾病关联的多视图网络融合语义和全局特征的方法。

MVNMDA: A Multi-View Network Combing Semantic and Global Features for Predicting miRNA-Disease Association.

机构信息

School of Electronic Infomation, Xijing University, Xi'an 710123, China.

出版信息

Molecules. 2023 Dec 31;29(1):230. doi: 10.3390/molecules29010230.


DOI:10.3390/molecules29010230
PMID:38202814
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10780172/
Abstract

A growing body of experimental evidence suggests that microRNAs (miRNAs) are closely associated with specific human diseases and play critical roles in their development and progression. Therefore, identifying miRNA related to specific diseases is of great significance for disease screening and treatment. In the early stages, the identification of associations between miRNAs and diseases demanded laborious and time-consuming biological experiments that often carried a substantial risk of failure. With the exponential growth in the number of potential miRNA-disease association combinations, traditional biological experimental methods face difficulties in processing massive amounts of data. Hence, developing more efficient computational methods to predict possible miRNA-disease associations and prioritize them is particularly necessary. In recent years, numerous deep learning-based computational methods have been developed and have demonstrated excellent performance. However, most of these methods rely on external databases or tools to compute various auxiliary information. Unfortunately, these external databases or tools often cover only a limited portion of miRNAs and diseases, resulting in many miRNAs and diseases being unable to match with these computational methods. Therefore, there are certain limitations associated with the practical application of these methods. To overcome the above limitations, this study proposes a multi-view computational model called MVNMDA, which predicts potential miRNA-disease associations by integrating features of miRNA and diseases from local views, global views, and semantic views. Specifically, MVNMDA utilizes known association information to construct node initial features. Then, multiple networks are constructed based on known association to extract low-dimensional feature embedding of all nodes. Finally, a cascaded attention classifier is proposed to fuse features from coarse to fine, suppressing noise within the features and making precise predictions. To validate the effectiveness of the proposed method, extensive experiments were conducted on the HMDD v2.0 and HMDD v3.2 datasets. The experimental results demonstrate that MVNMDA achieves better performance compared to other computational methods. Additionally, the case study results further demonstrate the reliable predictive performance of MVNMDA.

摘要

越来越多的实验证据表明,microRNAs(miRNAs)与特定的人类疾病密切相关,并在其发展和进展中发挥关键作用。因此,鉴定与特定疾病相关的 miRNA 对于疾病筛查和治疗具有重要意义。在早期,miRNA 与疾病之间的关联鉴定需要费力且耗时的生物学实验,这些实验往往存在很大的失败风险。随着潜在 miRNA-疾病关联组合数量的指数级增长,传统的生物学实验方法在处理大量数据方面遇到了困难。因此,开发更有效的计算方法来预测可能的 miRNA-疾病关联并对其进行优先级排序尤为必要。近年来,已经开发了许多基于深度学习的计算方法,并表现出优异的性能。然而,这些方法大多依赖于外部数据库或工具来计算各种辅助信息。不幸的是,这些外部数据库或工具通常只覆盖了有限的 miRNA 和疾病部分,导致许多 miRNA 和疾病无法与这些计算方法匹配。因此,这些方法的实际应用存在一定的局限性。为了克服上述限制,本研究提出了一种名为 MVNMDA 的多视图计算模型,通过整合局部视图、全局视图和语义视图中 miRNA 和疾病的特征来预测潜在的 miRNA-疾病关联。具体来说,MVNMDA 利用已知的关联信息来构建节点初始特征。然后,基于已知的关联构建多个网络,以提取所有节点的低维特征嵌入。最后,提出了一个级联注意力分类器,用于从粗到细融合特征,抑制特征内的噪声并进行精确预测。为了验证所提出方法的有效性,在 HMDD v2.0 和 HMDD v3.2 数据集上进行了广泛的实验。实验结果表明,MVNMDA 比其他计算方法具有更好的性能。此外,案例研究结果进一步证明了 MVNMDA 可靠的预测性能。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/ede8fc293aa9/molecules-29-00230-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/114d9307213e/molecules-29-00230-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/d6182a68c49f/molecules-29-00230-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/e4e9eeb14d85/molecules-29-00230-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/0bf17b7252a1/molecules-29-00230-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/69cec5b4ea0a/molecules-29-00230-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/642f8141aa73/molecules-29-00230-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/a4b93e511ca0/molecules-29-00230-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/98a371b7b4f4/molecules-29-00230-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/4e1ab969525c/molecules-29-00230-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/ede8fc293aa9/molecules-29-00230-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/114d9307213e/molecules-29-00230-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/d6182a68c49f/molecules-29-00230-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/e4e9eeb14d85/molecules-29-00230-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/0bf17b7252a1/molecules-29-00230-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/69cec5b4ea0a/molecules-29-00230-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/642f8141aa73/molecules-29-00230-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/a4b93e511ca0/molecules-29-00230-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/98a371b7b4f4/molecules-29-00230-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/4e1ab969525c/molecules-29-00230-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf05/10780172/ede8fc293aa9/molecules-29-00230-g010.jpg

相似文献

[1]
MVNMDA: A Multi-View Network Combing Semantic and Global Features for Predicting miRNA-Disease Association.

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本文引用的文献

[1]
Prediction of miRNA-disease associations by neural network-based deep matrix factorization.

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