Background Mechanical ventilation (MV) is a lifesaving therapy used for patients with respiratory failure. Nevertheless, MV is associated with numerous complications and increased mortality. The aim of this study is to define the effects of MV on gene expression of direct and peripheral human tissues. Methods Classification models were applied to Genotype-Tissue Expression Project (GTEx) gene expression data of six representative tissues–liver, adipose, skin, nerve-tibial, muscle and lung, for performance comparison and feature analysis. We utilized 18 prediction models using the Random Forest (RF), XGBoost (eXtreme Gradient Boosting) decision tree and ANN (Artificial Neural Network) methods to classify ventilation and non-ventilation samples and to compare their prediction performance for the six tissues. In the model comparison, the AUC (area under receiver operating curve), accuracy, precision, recall, and F1 score were used to evaluate the predictive performance of each model. We then conducted feature analysis per each tissue to detect MV marker genes followed by pathway enrichment analysis for these genes. Results XGBoost outperformed the other methods and predicted samples had undergone MV with an average accuracy for the six tissues of 0.951 and average AUC of 0.945. The feature analysis detected a combination of MV marker genes per each tested tissue, some common across several tissues. MV marker genes were mainly related to inflammation and fibrosis as well as cell development and movement regulation. The MV marker genes were significantly enriched in inflammatory and viral pathways. Conclusion The XGBoost method demonstrated clear enhanced performance and feature analysis compared to the other models. XGBoost was helpful in detecting the tissue-specific marker genes for identifying transcriptomic changes related to MV. Our results show that MV is associated with reduced development and movement in the tissues and higher inflammation and injury not only in direct tissues such as the lungs but also in peripheral tissues and thus should be carefully considered before being implemented.
Background: Mechanical ventilation (MV) is a lifesaving therapy used for patients with respiratory failure. Nevertheless, MV is associated with numerous complications and increased mortality. The aim of this study is to define the effects of MV on gene expression of direct and peripheral human tissues. Methods: Classification models were applied to Genotype-Tissue Expression Project (GTEx) gene expression data of six representative tissues - liver, adipose, skin, nerve-tibial, muscle and lung, for performance comparison and feature analysis. We utilized 18 prediction models using the Random Forest (RF), XGBoost (eXtreme Gradient Boosting) decision tree and ANN (Artificial Neural Network) methods to classify ventilation and non-ventilation samples and to compare their prediction performance for the six tissues. In the model comparison, the AUC (area under receiver operating curve), accuracy, precision, recall, and F1 score were used to evaluate the predictive performance of each model. We then conducted feature analysis per each tissue to detect MV marker genes followed by pathway enrichment analysis for these genes. Results: XGBoost outperformed the other methods and predicted samples had undergone MV with an average accuracy for the six tissues of 0.951 and an average AUC of 0.945. The feature analysis detected a combination of MV marker genes per each tested tissue, some common across several tissues. MV marker genes were mainly related to inflammation and fibrosis as well as cell development and movement regulation. The MV marker genes were significantly enriched in inflammatory and viral pathways. Conclusion: The XGBoost method demonstrated clear enhanced performance and feature analysis compared to the other models. XGBoost was helpful in detecting the tissue-specific marker genes for identifying transcriptomic changes related to MV. Our results show that MV is associated with reduced development and movement in the tissues and higher inflammation and injury not only in direct tissues such as the lungs but also in peripheral tissues and thus should be carefully considered before being implemented.
This paper introduces SocialVec, a general framework for eliciting social world knowledge from social networks, and applies this framework to Twitter. SocialVec learns lowdimensional embeddings of popular accounts, which represent entities of general interest, based on their co-occurrences patterns within the accounts followed by individual users, thus modeling entity similarity in socio-demographic terms. Similar to word embeddings, which facilitate tasks that involve text processing, we expect social entity embeddings to benefit tasks of social flavor. We have learned social embeddings for roughly 200,000 popular accounts from a sample of the Twitter network that includes more than 1.3 million users and the accounts that they follow, and evaluate the resulting embeddings on two different tasks. The first task involves the automatic inference of personal traits of users from their social media profiles. In another study, we exploit SocialVec embeddings for gauging the political bias of news sources in Twitter. In both cases, we prove SocialVec embeddings to be advantageous compared with existing entity embedding schemes. We will make the SocialVec entity embeddings publicly available to support further exploration of social world knowledge as reflected in Twitter.
Social world knowledge is a key ingredient in effective communication and information processing by humans and machines alike. As of today, there exist many knowledge bases that represent factual world knowledge. Yet, there is no resource that is designed to capture social aspects of world knowledge. We believe that this work makes an important step towards the formulation and construction of such a resource. We introduce SocialVec, a general framework for eliciting low-dimensional entity embeddings from the social contexts in which they occur in social networks. In this framework, entities correspond to highly popular accounts which invoke general interest. We assume that entities that individual users tend to co-follow are socially related, and use this definition of social context to learn the entity embeddings. Similar to word embeddings which facilitate tasks that involve text semantics, we expect the learned social entity embeddings to benefit multiple tasks of social flavor. In this work, we elicited the social embeddings of roughly 200K entities from a sample of 1.3M Twitter users and the accounts that they follow. We employ and gauge the resulting embeddings on two tasks of social importance. First, we assess the political bias of news sources in terms of entity similarity in the social embedding space. Second, we predict the personal traits of individual Twitter users based on the social embeddings of entities that they follow. In both cases, we show advantageous or competitive performance using our approach compared with task-specific baselines. We further show that existing entity embedding schemes, which are fact-based, fail to capture social aspects of knowledge. We make the learned social entity embeddings available to the research community to support further exploration of social world knowledge and its applications.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.