Dataset Information

Latent disease similarities and therapeutic repurposing possibilities uncovered by multi-modal generative topic modeling of human diseases

ABSTRACT: Abstract

Motivation

Human diseases are characterized by multiple features such as their pathophysiological, molecular and genetic changes. The rapid expansion of such multi-modal disease-omics space provides an opportunity to re-classify diverse human diseases and to uncover their latent molecular similarities, which could be exploited to repurpose a therapeutic-target for one disease to another.

Results

Herein, we probe this underexplored space by soft-clustering 6955 human diseases by multi-modal generative topic modeling. Focusing on chronic kidney disease and myocardial infarction, two most life-threatening diseases, unveiled are their previously underrecognized molecular similarities to neoplasia and mental/neurological-disorders, and 69 repurposable therapeutic-targets for these diseases. Using an edit-distance-based pathway-classifier, we also find molecular pathways by which these targets could elicit their clinical effects. Importantly, for the 17 targets, the evidence for their therapeutic usefulness is retrospectively found in the pre-clinical and clinical space, illustrating the effectiveness of the method, and suggesting its broader applications across diverse human diseases.

Availability and implementation

The code reported in this article is available at: https://github.com/skozawa170301ktx/MultiModalDiseaseModeling

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

SUBMITTER:

PROVIDER: S-EPMC10133403 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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Project description:BackgroundIn most industrialized societies, regulations, inspections, insurance, and legal options are established to support workers who suffer injury, disease, or death in relation to their work; in practice, these resources are imperfect or even unavailable due to workplace or employer obstruction. Thus, limitations exist to identify unmet needs in occupational safety and health information.ObjectiveThe aim of this study was to explore hidden issues related to occupational accidents by examining social network services (SNS) data using topic modeling.MethodsBased on the results of a Google search for the phrases occupational accident, industrial accident and occupational diseases, a total of 145 websites were selected. From among these websites, we collected 15,244 documents on queries related to occupational accidents between 2002 and 2018. To transform unstructured text into structure data, natural language processing of the Korean language was conducted. We performed the latent Dirichlet allocation (LDA) as a topic model using a Python library. A time-series linear regression analysis was also conducted to identify yearly trends for the given documents.ResultsThe results of the LDA model showed 14 topics with 3 themes: workers' compensation benefits (Theme 1), illicit agreements with the employer (Theme 2), and fatal and non-fatal injuries and vulnerable workers (Theme 3). Theme 1 represented the largest cluster (52.2%) of the collected documents and included keywords related to workers' compensation (ie, company, occupational injury, insurance, accident, approval, and compensation) and keywords describing specific compensation benefits such as medical expense benefits, temporary incapacity benefits, and disability benefits. In the yearly trend, Theme 1 gradually decreased; however, other themes showed an overall increasing pattern. Certain queries (ie, musculoskeletal system, critical care, and foreign workers) showed no significant variation in the number of queries.ConclusionsWe conducted LDA analysis of SNS data of occupational accident-related queries and discovered that the primary concerns of workers posting about occupational injuries and diseases were workers' compensation benefits, fatal and non-fatal injuries, vulnerable workers, and illicit agreements with employers. While traditional systems focus mainly on quantitative monitoring of occupational accidents, qualitative aspects formulated by topic modeling from unstructured SNS queries may be valuable to address inequalities and improve occupational health and safety.