Related papers: Inferring Gene Regulatory Network Using An Evoluti…
Gene regulatory networks (GRNs) play a crucial role in the control of cellular functions. Numerous methods have been developed to infer GRNs from gene expression data, including mechanism-based approaches, information-based approaches, and…
Gene regulatory network (GRN) modeling is a well-established theoretical framework for the study of cell-fate specification during developmental processes. Recently, dynamical models of GRNs have been taken as a basis for formalizing the…
Understanding the complex and stochastic nature of Gene Regulatory Networks (GRNs) remains a central challenge in systems biology. Existing modeling paradigms often struggle to effectively capture the intricate, multi-factor regulatory…
In the postgenome era many efforts have been dedicated to systematically elucidate the complex web of interacting genes and proteins. These efforts include experimental and computational methods. Microarray technology offers an opportunity…
Inferring the structure of gene regulatory networks (GRN) from gene expression data has many applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously…
Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…
Accurately reconstructing Gene Regulatory Networks (GRNs) is crucial for understanding gene functions and disease mechanisms. Single-cell RNA sequencing (scRNA-seq) technology provides vast data for computational GRN reconstruction. Since…
In this work, we present GAROM, a new approach for reduced order modelling (ROM) based on generative adversarial networks (GANs). GANs have the potential to learn data distribution and generate more realistic data. While widely applied in…
Statistical inference of genetic regulatory networks is essential for understanding temporal interactions of regulatory elements inside the cells. For inferences of large networks, identification of network structure is typical achieved…
ODE-based models for gene regulatory networks (GRNs) can often be formulated as smooth singular perturbation problems with multiple small parameters, some of which are related to time-scale separation, whereas others are related to…
Reconstructing the causal network in a complex dynamical system plays a crucial role in many applications, from sub-cellular biology to economic systems. Here we focus on inferring gene regulation networks (GRNs) from perturbation or gene…
The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives…
Gene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single cell RNA sequencing (scRNA-seq) data. In…
Bayesian inference for exponential family random graph models (ERGMs) is a doubly-intractable problem because of the intractability of both the likelihood and posterior normalizing factor. Auxiliary variable based Markov Chain Monte Carlo…
Modern data analysis increasingly requires flexible conditional inference P(X_B | X_A) where (X_A, X_B) is an arbitrary partition of observed variable X. Existing approaches are either restricted to a fixed conditioning structure or depend…
Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model…
Living cells are the product of gene expression programs that involve the regulated transcription of thousands of genes. The elucidation of transcriptional regulatory networks in thus needed to understand the cell's working mechanism, and…
Inferring a graphical model or network from observational data from a large number of variables is a well studied problem in machine learning and computational statistics. In this paper we consider a version of this problem that is relevant…
In this article, we propose a new method named fused mixed graphical model (FMGM), which can infer network structures for dichotomous phenotypes. We assumed that the interplay of different omics markers is associated with disease status and…
In this work, we present a quantum circuit model for inferring gene regulatory networks (GRNs). The model is based on the idea of using qubit-qubit entanglement to simulate interactions between genes. We provide preliminary results that…