Related papers: Perfect Sampling of the Master Equation for Gene R…
In this paper, we introduce a slight variation of the Dominated Coupling From the Past algorithm (DCFTP) of Kendall, for bounded Markov chains. It is based on the control of a (typically non-monotonic) stochastic recursion by a (typically…
We present a highly efficient and accurate hybrid stochastic simulation algorithm (HSSA) for the purpose of simulating a subset of biochemical reactions of large gene regulatory networks (GRN). The algorithm relies on the separability of a…
Single-cell data reveal the presence of biological stochasticity between cells of identical genome and environment, in particular highlighting the transcriptional bursting phenomenon. To account for this property, gene expression may be…
Gene regulatory networks (GRNs) are increasingly used for explaining biological processes with complex transcriptional regulation. A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one…
The recent advancements in graph neural networks (GNNs) have led to state-of-the-art performances in various applications, including chemo-informatics, question-answering systems, and recommender systems. However, scaling up these methods…
At the cellular scale, biochemical processes are governed by random interactions between reactant molecules with small copy counts, leading to behavior that is inherently stochastic. Such systems are often modeled as continuous-time Markov…
We introduce a novel training principle for probabilistic models that is an alternative to maximum likelihood. The proposed Generative Stochastic Networks (GSN) framework is based on learning the transition operator of a Markov chain whose…
We present a new algorithm for the exact uniform sampling of proper \(k\)-colorings of a graph on \(n\) vertices with maximum degree~\(\Delta\). The algorithm is based on partial rejection sampling (PRS) and introduces a soft relaxation of…
We give a Markov chain based perfect sampler for uniform sampling solutions of constraint satisfaction problems (CSP). Under some mild Lov\'asz local lemma conditions where each constraint of the CSP has a small number of forbidden local…
Tensor network states are powerful variational ans\"atze for many-body ground states of quantum lattice models. The use of Monte Carlo sampling techniques in tensor network approaches significantly reduces the cost of tensor contractions,…
Unraveling the complexities of Gene Regulatory Networks (GRNs) is crucial for understanding cellular processes and disease mechanisms. Traditional computational methods often struggle with the dynamic nature of these networks. This study…
We show that efficient approximate sampling algorithms, combined with a slow exponential time oracle for computing its output distribution, can be combined into constructing efficient perfect samplers, which sample exactly from a target…
We give a Markov chain based algorithm for sampling almost uniform solutions of constraint satisfaction problems (CSPs). Assuming a canonical setting for the Lov\'asz local lemma, where each constraint is violated by a small number of…
In this paper we propose a perfect simulation algorithm for the Exponential Random Graph Model, based on the Coupling From The Past method of Propp & Wilson (1996). We use a Glauber dynamics to construct the Markov Chain and we prove the…
We introduce a novel training principle for probabilistic models that is an alternative to maximum likelihood. The proposed Generative Stochastic Networks (GSN) framework is based on learning the transition operator of a Markov chain whose…
The configuration model is a standard tool for uniformly generating random graphs with a specified degree sequence, and is often used as a null model to evaluate how much of an observed network's structure can be explained by its degree…
We present the first class of perfect sampling (also known as exact simulation) algorithms for the steady-state distribution of non-Markovian loss networks. We use a variation of Dominated Coupling From The Past for which we simulate a…
Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating…
We propose a unified framework for adaptive connection sampling in graph neural networks (GNNs) that generalizes existing stochastic regularization methods for training GNNs. The proposed framework not only alleviates over-smoothing and…
Markov State Models (MSMs) are a powerful framework to reproduce the long-time conformational dynamics of biomolecules using a set of short Molecular Dynamics (MD) simulations. However, precise kinetics predictions of MSMs heavily rely on…