Predicting onset of disease progression using temporal disease occurrence networks

Comorbidity progression analysis: patient stratification and comorbidity prediction using temporal comorbidity network

Objective

The study aims to identify distinct population-specific comorbidity progression patterns, timely detect potential comorbidities, and gain better understanding of the progression of comorbid conditions among patients.

Methods

This work presents a comorbidity progression analysis framework that utilizes temporal comorbidity networks (TCN) for patient stratification and comorbidity prediction. We propose a TCN construction approach that utilizes longitudinal, temporal diagnosis data of patients to construct their TCN. Subsequently, we employ the TCN for patient stratification by conducting preliminary analysis, and typical prescription analysis to uncover potential comorbidity progression patterns in different patient groups. Finally, we propose an innovative comorbidity prediction method by utilizing the distance-matched temporal comorbidity network (TCN-DM). This method identifies similar patients with disease prevalence and disease transition patterns and combines their diagnosis information with that of the current patient to predict potential comorbidity at the patient's next visit.

Results

This study validated the capability of the framework using a real-world dataset MIMIC-III, with heart failure (HF) as interested disease to investigate comorbidity progression in HF patients. With TCN, this study can identify four significant distinctive HF subgroups, revealing the progression of comorbidities in patients. Furthermore, compared to other methods, TCN-DM demonstrated better predictive performance with F1-Score values ranging from 0.454 to 0.612, showcasing its superiority.

Conclusions

This study can identify comorbidity patterns for individuals and population, and offer promising prediction for future comorbidity developments in patients.

DAPNet: multi-view graph contrastive network incorporating disease clinical and molecular associations for disease progression prediction

BACKGROUND

Timely and accurate prediction of disease progress is crucial for facilitating early intervention and treatment for various chronic diseases. However, due to the complicated and longitudinal nature of disease progression, the capacity and completeness of clinical data required for training deep learning models remains a significant challenge. This study aims to explore a new method that reduces data dependency and achieves predictive performance comparable to existing research.

METHODS

This study proposed DAPNet, a deep learning-based disease progression prediction model that solely utilizes the comorbidity duration (without relying on multi-modal data or comprehensive medical records) and disease associations from biomedical knowledge graphs to deliver high-performance prediction. DAPNet is the first to apply multi-view graph contrastive learning to disease progression prediction tasks. Compared with other studies on comorbidities, DAPNet innovatively integrates molecular-level disease association information, combines disease co-occurrence and ICD10, and fully explores the associations between diseases; RESULTS: This study validated DAPNet using a de-identified clinical dataset derived from medical claims, which includes 2,714 patients and 10,856 visits. Meanwhile, a kidney dataset (606 patients) based on MIMIC-IV has also been constructed to fully validate its performance. The results showed that DAPNet achieved state-of-the-art performance on the severe pneumonia dataset (F1=0.84, with an improvement of 8.7%), and outperformed the six baseline models on the kidney disease dataset (F1=0.80, with an improvement of 21.3%). Through case analysis, we elucidated the clinical and molecular associations identified by the DAPNet model, which facilitated a better understanding and explanation of potential disease association, thereby providing interpretability for the model.

CONCLUSIONS

The proposed DAPNet, for the first time, utilizes comorbidity duration and disease associations network, enabling more accurate disease progression prediction based on a multi-view graph contrastive learning, which provides valuable insights for early diagnosis and treatment of patients. Based on disease association networks, our research has enhanced the interpretability of disease progression predictions.

Integrated Pleiotropic Gene Set Unveils Comorbidity Insights across Digestive Cancers and Other Diseases

Comorbidities are prevalent in digestive cancers, intensifying patient discomfort and complicating prognosis. Identifying potential comorbidities and investigating their genetic connections in a systemic manner prove to be instrumental in averting additional health challenges during digestive cancer management. Here, we investigated 150 diseases across 18 categories by collecting and integrating various factors related to disease comorbidity, such as disease-associated SNPs or genes from sources like MalaCards, GWAS Catalog and UK Biobank. Through this extensive analysis, we have established an integrated pleiotropic gene set comprising 548 genes in total. Particularly, there enclosed the genes encoding major histocompatibility complex or related to antigen presentation. Additionally, we have unveiled patterns in protein-protein interactions and key hub genes/proteins including TP53, KRAS, CTNNB1 and PIK3CA, which may elucidate the co-occurrence of digestive cancers with certain diseases. These findings provide valuable insights into the molecular origins of comorbidity, offering potential avenues for patient stratification and the development of targeted therapies in clinical trials.

Systematic review and meta-analysis of disease clustering in multimorbidity: a study protocol

INTRODUCTION

Multimorbidity is defined as the presence of two or more chronic diseases. Co-occurring diseases can have synergistic negative effects, and are associated with significant impacts on individual health outcomes and healthcare systems. However, the specific effects of diseases in combination will vary between different diseases. Identifying which diseases are most likely to co-occur in multimorbidity is an important step towards population health assessment and development of policies to prevent and manage multimorbidity more effectively and efficiently. The goal of this project is to conduct a systematic review and meta-analysis of studies of disease clustering in multimorbidity, in order to identify multimorbid disease clusters and test their stability.

METHODS AND ANALYSIS

We will review data from studies of multimorbidity that have used data clustering methodologies to reveal patterns of disease co-occurrence. We propose a network-based meta-analytic approach to perform meta-clustering on a select list of chronic diseases that are identified as priorities for multimorbidity research. We will assess the stability of obtained disease clusters across the research literature to date, in order to evaluate the strength of evidence for specific disease patterns in multimorbidity.

ETHICS AND DISSEMINATION

This study does not require ethics approval as the work is based on published research studies. The study findings will be published in a peer-reviewed journal and disseminated through conference presentations and meetings with knowledge users in health systems and public health spheres.

PROSPERO REGISTRATION NUMBER

CRD42023411249.