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The stochastic dynamics of biochemical reaction networks can be accurately described by discrete-state Markov processes where each chemical reaction corresponds to a state transition of the process. Due to the largeness problem of the state space, analysis techniques based on an exploration of the state space are often not feasible and the integration of the moments of the underlying probability distribution has become a very popular alternative. In this paper the focus is on a comparison of reconstructed distributions from their moments obtained by two different moment-based analysis methods, the method of moments (MM) and the method of conditional moments (MCM). We use the maximum entropy principle to derive a distribution that fits best to a given sequence of (conditional) moments. For the two gene regulatory networks that we consider we find that the MCM approach is more suitable to describe multimodal distributions and that the reconstruction is more accurate if conditional distributions are considered.
This is a short review of two common approximations in stochastic chemical and biochemical kinetics. It will appear as Chapter 6 in the book Quantitative Biology: Theory, Computational Methods and Examples of Models edited by Brian Munsky, Lev Tsimri
The classical problem of moments is addressed by the maximum entropy approach for one-dimensional discrete distributions. The numerical technique of adaptive support approximation is proposed to reconstruct the distributions in the region where the main part of probability mass is located.
In this paper, we present a systematic stability analysis of the quadrature-based moment method (QBMM) for the one-dimensional Boltzmann equation with BGK or Shakhov models. As reported in recent literature, the method has revealed its potential for
We present the PyHST2 code which is in service at ESRF for phase-contrast and absorption tomography. This code has been engineered to sustain the high data flow typical of the third generation synchrotron facilities (10 terabytes per experiment) by a
Recent results have demonstrated that samplers constructed with flow-based generative models are a promising new approach for configuration generation in lattice field theory. In this paper, we present a set of methods to construct flow models for ta