We will discuss about "Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19", Cheng, Jinyu, et al., Briefings in bioinformatics 22.2 (2021): 988-1005. Abstract: Inferring how gene expression in a cell is influenced by cellular microenvironment is of great importance yet challenging. In this study, we …

We will discuss about "Model Reduction for the Chemical Master Equation: an Information-Theoretic Approach", Öcal, Kaan, Guido Sanguinetti, and Ramon Grima., arXiv preprint arXiv:2210.05329 (2022). Abstract: The complexity of mathematical models in biology has rendered model reduction an essential tool in the quantitative biologist's toolkit. For stochastic reaction networks described using the Chemical Master Equation, commonly …

We will discuss about “PI-VAE: Physics-Informed Variational Auto-Encoder for stochastic differential equations”, Zhong, Weiheng, and Hadi Meidani, Computer Methods in Applied Mechanics and Engineering 403 (2023): 115664. Abstract We propose a new class of physics-informed neural networks, called the Physics-Informed Variational Auto-Encoder (PI-VAE), to solve stochastic differential equations (SDEs) or inverse problems involving SDEs. In …

We will discuss about “Detecting critical state before phase transition of complex biological systems by hidden Markov model”, Chen, Pei, et al. Bioinformatics 32.14 (2016): 2143-2150.   Abstract Motivation: Identifying the critical state or pre-transition state just before the occurrence of a phase transition is a challenging task, because the state of the system may …

We will discuss about “Multiparameter persistent homology landscapes identify immune cell spatial patterns in tumors”, Vipond, Oliver, et al, Proceedings of the National Academy of Sciences 118.41 (2021): e2102166118. Abstract Highly resolved spatial data of complex systems encode rich and nonlinear information. Quantification of heterogeneous and noisy data—often with outliers, artifacts, and mislabeled points—such as …