Understanding disease progression at the molecular pathway level usually requires capturing both structural dependencies between pathways and the temporal dynamics of disease evolution. In this work, we solve the former challenge by developing a biologically informed graph-forming method to efficiently construct pathway graphs for subjects from our newly curated JR5558 mouse transcriptomics dataset. We then develop Graph-level Pseudotime Analysis (GPA) to infer graph-level trajectories that reveal how disease progresses at the population level, rather than in individual subjects. Based on the trajectories estimated by GPA, we identify the most sensitive pathways that drive disease stage transitions. In addition, we measure changes in pathway features using neural stochastic differential equations (SDEs), which enables us to formally define and compute pathway stability and disease bifurcation points (points of no return), two fundamental problems in disease progression research. We further extend our theory to the case when pathways can interact with each other, enabling a more comprehensive and multi-faceted characterization of disease phenotypes. The comprehensive experimental results demonstrate the effectiveness of our framework in reconstructing the dynamics of the pathway, identifying critical transitions, and providing novel insights into the mechanistic understanding of disease evolution.

Artificial intelligence methods have been increasingly turning into a potentially powerful tool in the diagnosis and management of diseases. In this study, we utilized logistic regression (LR), decision tree (DT), gradient boosted decision tree (GBDT), support vector machine (SVM), and multilayer perceptron (MLP) as machine learning models to rapidly diagnose the mycoplasma pneumoniae pneumonia (MPP) in children patients. The classification task was carried out after applying the preprocessing procedure to the MPP dataset. The most efficient results are obtained by GBDT. It provides the best performance with an accuracy of 93.7%. In contrast to standard raw feature weighting, the feature importance takes the underlying correlation structure of the features into account. The most crucial feature of GBDT is the "pulmonary infiltrates range" with a score of 0.5925, followed by "cough" (0.0953) and "pleural effusion" (0.0492). We publicly share our full implementation with the dataset and trained models at https://github.com/zhenguonie/2021_AI4MPP.