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Gillespie direct method with horizon and budget statuses
Definition
Inputs. A finite state set , a finite-channel reaction propensity system from Finite-channel reaction propensity systems and their generator, an initial state , a horizon , and an optional event budget , defaulting to , where . The random source is a sequence with and uniform on , all coordinates mutually independent. The countable product construction for these input laws uses Countable Choice and Dependent Choice by Assuming countable and dependent choice, countable products of arbitrary probability spaces; the exponential law uses Countable Choice by Exponential and Weibull survival specifications define probability laws. For the uniform law, Assuming countable choice, is a sigma-algebra containing every elementary set and is a complete measure extending elementary volume makes the set function in Lebesgue measurable sets, the family , and the restricted set function a measure, and A box in with parameters is Lebesgue measurable of measure , whichever of its faces are included gives its restriction to mass one and interval probabilities equal to interval lengths.
Procedure. Set , , , and record the initial state. While :
- Compute . If , keep the state equal to through and return status absorbed.
- If , return the path prefix through with status budget-exhausted; this status does not assert that the horizon was reached.
- Set . If , keep the state equal to through and return status horizon.
- Set to the least index with . If the null event occurs, use the largest index with . This rule never selects a zero-rate channel.
- Set , , append the marked event , and set .
If the loop reaches , return the path through with status horizon. Each event uses a linear scan of the propensities and a linear cumulative channel search; no update-tree acceleration is part of this procedure. If and the budget expires before , the returned prefix is incomplete.
The procedure assumes an ideal independent random source with the displayed laws. It makes no claim that a finite-state pseudorandom generator supplies independent exact exponential or uniform variables.
Depends on
- The Axiom of Countable Choice ($\mathrm{AC}_\omega$)
- The axiom of dependent choice: a relation in which every element is related to something admits an $\mathbb{N}$-indexed chain
- Independent random elements
- Law or distribution of a random element
- Lebesgue measurable sets, the family $\mathcal{L}(\mathbb{R}^n)$, and the restricted set function $\lambda_n$
- Random elements and real random variables
- Finite-channel reaction propensity systems and their generator
- Assuming countable and dependent choice, countable products of arbitrary probability spaces
- Exponential and Weibull survival specifications define probability laws
- Assuming countable choice, $\mathcal{L}(\mathbb{R}^n)$ is a sigma-algebra containing every elementary set and $\lambda_n$ is a complete measure extending elementary volume
- A box in $\mathbb{R}^n$ with parameters $a_i\le b_i$ is Lebesgue measurable of measure $\prod_{i<n}(b_i-a_i)$, whichever of its faces are included
Used by
Dependency tree · two levels
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Sources
- Daniel T. Gillespie, Exact Stochastic Simulation of Coupled Chemical Reactions (standard reference, not scraped)
- David F. Anderson, Introduction to Stochastic Processes with Applications to Biology, Chapters 6–7 (standard reference, not scraped)