Dirichlet process mixture models for single-cell RNA-seq clustering

Hot Topic Recognition of Health Rumors Based on Anti-Rumor Articles on the WeChat Official Account Platform: Topic Modeling

BACKGROUND

Social networks have become one of the main channels for obtaining health information. However, they have also become a source of health-related misinformation, which seriously threatens the public's physical and mental health. Governance of health-related misinformation can be implemented through topic identification of rumors on social networks. However, little attention has been paid to studying the types and routes of dissemination of health rumors on the internet, especially rumors regarding health-related information in Chinese social media.

OBJECTIVE

This study aims to explore the types of health-related misinformation favored by WeChat public platform users and their prevalence trends and to analyze the modeling results of the text by using the Latent Dirichlet Allocation model.

METHODS

We used a web crawler tool to capture health rumor-dispelling articles on WeChat rumor-dispelling public accounts. We collected information from health-debunking articles posted between January 1, 2016, and August 31, 2022. Following word segmentation of the collected text, a document topic generation model called Latent Dirichlet Allocation was used to identify and generalize the most common topics. The proportion distribution of the themes was calculated, and the negative impact of various health rumors in different periods was analyzed. Additionally, the prevalence of health rumors was analyzed by the number of health rumors generated at each time point.

RESULTS

We collected 9366 rumor-refuting articles from January 1, 2016, to August 31, 2022, from WeChat official accounts. Through topic modeling, we divided the health rumors into 8 topics, that is, rumors on prevention and treatment of infectious diseases (1284/9366, 13.71%), disease therapy and its effects (1037/9366, 11.07%), food safety (1243/9366, 13.27%), cancer and its causes (946/9366, 10.10%), regimen and disease (1540/9366, 16.44%), transmission (914/9366, 9.76%), healthy diet (1068/9366, 11.40%), and nutrition and health (1334/9366, 14.24%). Furthermore, we summarized the 8 topics under 4 themes, that is, public health, disease, diet and health, and spread of rumors.

CONCLUSIONS

Our study shows that topic modeling can provide analysis and insights into health rumor governance. The rumor development trends showed that most rumors were on public health, disease, and diet and health problems. Governments still need to implement relevant and comprehensive rumor management strategies based on the rumors prevalent in their countries and formulate appropriate policies. Apart from regulating the content disseminated on social media platforms, the national quality of health education should also be improved. Governance of social networks should be clearly implemented, as these rapidly developed platforms come with privacy issues. Both disseminators and receivers of information should ensure a realistic attitude and disseminate health information correctly. In addition, we recommend that sentiment analysis-related studies be conducted to verify the impact of health rumor-related topics.

An interpretable single-cell RNA sequencing data clustering method based on latent Dirichlet allocation

Single-cell RNA sequencing (scRNA-seq) detects whole transcriptome signals for large amounts of individual cells and is powerful for determining cell-to-cell differences and investigating the functional characteristics of various cell types. scRNA-seq datasets are usually sparse and highly noisy. Many steps in the scRNA-seq analysis workflow, including reasonable gene selection, cell clustering and annotation, as well as discovering the underlying biological mechanisms from such datasets, are difficult. In this study, we proposed an scRNA-seq analysis method based on the latent Dirichlet allocation (LDA) model. The LDA model estimates a series of latent variables, i.e. putative functions (PFs), from the input raw cell-gene data. Thus, we incorporated the 'cell-function-gene' three-layer framework into scRNA-seq analysis, as this framework is capable of discovering latent and complex gene expression patterns via a built-in model approach and obtaining biologically meaningful results through a data-driven functional interpretation process. We compared our method with four classic methods on seven benchmark scRNA-seq datasets. The LDA-based method performed best in the cell clustering test in terms of both accuracy and purity. By analysing three complex public datasets, we demonstrated that our method could distinguish cell types with multiple levels of functional specialization, and precisely reconstruct cell development trajectories. Moreover, the LDA-based method accurately identified the representative PFs and the representative genes for the cell types/cell stages, enabling data-driven cell cluster annotation and functional interpretation. According to the literature, most of the previously reported marker/functionally relevant genes were recognized.

Sprod for de-noising spatially resolved transcriptomics data based on position and image information

Spatially resolved transcriptomics (SRT) provide gene expression close to, or even superior to, single-cell resolution while retaining the physical locations of sequencing and often also providing matched pathology images. However, SRT expression data suffer from high noise levels, due to the shallow coverage in each sequencing unit and the extra experimental steps required to preserve the locations of sequencing. Fortunately, such noise can be removed by leveraging information from the physical locations of sequencing, and the tissue organization reflected in corresponding pathology images. In this work, we developed Sprod, based on latent graph learning of matched location and imaging data, to impute accurate SRT gene expression. We validated Sprod comprehensively and demonstrated its advantages over previous methods for removing drop-outs in single-cell RNA-sequencing data. We showed that, after imputation by Sprod, differential expression analyses, pathway enrichment and cell-to-cell interaction inferences are more accurate. Overall, we envision de-noising by Sprod to become a key first step towards empowering SRT technologies for biomedical discoveries.