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NECo: A node embedding algorithm for multiplex heterogeneous networks.

ABSTRACT: Complex diseases such as hypertension, cancer, and diabetes cause nearly 70% of the deaths in the U.S. and involve multiple genes and their interactions with environmental factors. Therefore, identification of genetic factors to understand and decrease the morbidity and mortality from complex diseases is an important and challenging task. With the generation of an unprecedented amount of multi-omics datasets, network-based methods have become popular to represent the multilayered complex molecular interactions. Particularly node embeddings, the low-dimensional representations of nodes in a network are utilized for gene function prediction. Integrated network analysis of multi-omics data alleviates the issues related to missing data and lack of context-specific datasets. Most of the node embedding methods, however, are unable to integrate multiple types of datasets from genes and phenotypes. To address this limitation, we developed a node embedding algorithm called Node Embeddings of Complex networks (NECo) that can utilize multilayered heterogeneous networks of genes and phenotypes. We evaluated the performance of NECo using genotypic and phenotypic datasets from rat (Rattus norvegicus) disease models to classify hypertension disease-related genes. Our method significantly outperformed the state-of-the-art node embedding methods, with AUC of 94.97% compared 85.98% in the second-best performer, and predicted genes not previously implicated in hypertension.

SUBMITTER: Dursun C

PROVIDER: S-EPMC8466723 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:In the field of deep learning, the processing of large network models on billions or even tens of billions of nodes and numerous edge types is still flawed, and the accuracy of recommendations is greatly compromised when large network embeddings are applied to recommendation systems. To solve the problem of inaccurate recommendations caused by processing deficiencies in large networks, this paper combines the attributed multiplex heterogeneous network with the attention mechanism that introduces the softsign and sigmoid function characteristics and derives a new framework SSN_GATNE-T (S represents the softsign function, SN represents the attention mechanism introduced by the Softsign function, and GATNE-T represents the transductive embeddings learning for attribute multiple heterogeneous networks). The attributed multiplex heterogeneous network can help obtain more user-item information with more attributes. No matter how many nodes and types are included in the model, our model can handle it well, and the improved attention mechanism can help annotations to obtain more useful information via a combination of the two. This can help to mine more potential information to improve the recommendation effect; in addition, the application of the softsign function in the fully connected layer of the model can better reduce the loss of potential user information, which can be used for accurate recommendation by the model. Using the Adam optimizer to optimize the model can not only make our model converge faster, but it is also very helpful for model tuning. The proposed framework SSN_GATNE-T was tested for two different types of datasets, Amazon and YouTube, using three evaluation indices, ROC-AUC (receiver operating characteristic-area under curve), PR-AUC (precision recall-area under curve) and F1 (F1-score), and found that SSN_GATNE-T improved on all three evaluation indices compared to the mainstream recommendation models currently in existence. This not only demonstrates that the framework can deal well with the shortcomings of obtaining accurate interaction information due to the presence of a large number of nodes and edge types of the embedding of large network models, but also demonstrates the effectiveness of addressing the shortcomings of large networks to improve recommendation performance. In addition, the model is also a good solution to the cold start problem.

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NECo: A node embedding algorithm for multiplex heterogeneous networks.

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