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Propagation Models for Biochemical Reaction Networks

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Conditional probability distribution

In probability theory and statistics, given two jointly distributed random variables and , the conditional probability distribution of given is the probability distribution of when is known to be a particular value; in some cases the conditional probabilities may be expressed as functions containing the unspecified value of as a parameter. When both and are categorical variables, a conditional probability table is typically used to represent the conditional probability.

Discrete Fourier transform

In mathematics, the discrete Fourier transform (DFT) converts a finite sequence of equally-spaced samples of a function into a same-length sequence of equally-spaced samples of the discrete-time Fourier transform (DTFT), which is a complex-valued function of frequency. The interval at which the DTFT is sampled is the reciprocal of the duration of the input sequence. An inverse DFT (IDFT) is a Fourier series, using the DTFT samples as coefficients of complex sinusoids at the corresponding DTFT frequencies.

Joint probability distribution

Given two random variables that are defined on the same probability space, the joint probability distribution is the corresponding probability distribution on all possible pairs of outputs. The joint distribution can just as well be considered for any given number of random variables. The joint distribution encodes the marginal distributions, i.e. the distributions of each of the individual random variables. It also encodes the conditional probability distributions, which deal with how the outputs of one random variable are distributed when given information on the outputs of the other random variable(s).

Krylov subspace

In linear algebra, the order-r Krylov subspace generated by an n-by-n matrix A and a vector b of dimension n is the linear subspace spanned by the of b under the first r powers of A (starting from ), that is, The concept is named after Russian applied mathematician and naval engineer Alexei Krylov, who published a paper about it in 1931. Vectors are linearly independent until , and . Thus, denotes the maximal dimension of a Krylov subspace. The maximal dimension satisfies and . More exactly, , where is the minimal polynomial of .

Iterative method

In computational mathematics, an iterative method is a mathematical procedure that uses an initial value to generate a sequence of improving approximate solutions for a class of problems, in which the n-th approximation is derived from the previous ones. A specific implementation with termination criteria for a given iterative method like gradient descent, hill climbing, Newton's method, or quasi-Newton methods like BFGS, is an algorithm of the iterative method.

Discrete time and continuous time

In mathematical dynamics, discrete time and continuous time are two alternative frameworks within which variables that evolve over time are modeled. Discrete time views values of variables as occurring at distinct, separate "points in time", or equivalently as being unchanged throughout each non-zero region of time ("time period")—that is, time is viewed as a discrete variable. Thus a non-time variable jumps from one value to another as time moves from one time period to the next.

Finite difference method

In numerical analysis, finite-difference methods (FDM) are a class of numerical techniques for solving differential equations by approximating derivatives with finite differences. Both the spatial domain and time interval (if applicable) are discretized, or broken into a finite number of steps, and the value of the solution at these discrete points is approximated by solving algebraic equations containing finite differences and values from nearby points.

Generalized minimal residual method

In mathematics, the generalized minimal residual method (GMRES) is an iterative method for the numerical solution of an indefinite nonsymmetric system of linear equations. The method approximates the solution by the vector in a Krylov subspace with minimal residual. The Arnoldi iteration is used to find this vector. The GMRES method was developed by Yousef Saad and Martin H. Schultz in 1986. It is a generalization and improvement of the MINRES method due to Paige and Saunders in 1975.

Business valuation

Business valuation is a process and a set of procedures used to estimate the economic value of an owner's interest in a business. Here various valuation techniques are used by financial market participants to determine the price they are willing to pay or receive to effect a sale of the business.

Markov chain Monte Carlo

In statistics, Markov chain Monte Carlo (MCMC) methods comprise a class of algorithms for sampling from a probability distribution. By constructing a Markov chain that has the desired distribution as its equilibrium distribution, one can obtain a sample of the desired distribution by recording states from the chain. The more steps that are included, the more closely the distribution of the sample matches the actual desired distribution. Various algorithms exist for constructing chains, including the Metropolis–Hastings algorithm.