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Table 1 Iterative Markov chain Monte Carlo Algorithm

From: Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling

Algorithm 1 Iterative Hybrid Monte Carlo and Metropolis Hastings algorithm

Require: desired distribution p(·), starting value (ω0, λ 0), proposal distribution q λ (·|λ (t)), number of leapfrog steps for HMC L, proposal distribution for stepsize ϵ of leapfrog steps qϵ(·), standard deviation σ ρ for the sampling of the momentum variables ρ, number of Markov chain samples T

1: t ← 0

2: while t <T do

3:   Sample from qϵ(·)

4:   Sample from for all i {1,..., n}

5:   Perform L leapfrog steps with stepsize starting at state (ω(t), ρ (t))

6:   Store resulting candidate state in

7:   Sample u1 from (0, 1)

8:   α1 ← min {1, exp H(ω(t), ρ(t)) - H)}

9:   if u1 <α1 then

10:      ω(t+1)

11:   else

12:      ω(t+1)ω(t)

13:   end if

14:   Sample from q λ (·|λ(t))

15:   Sample u2 from (0, 1)

16:   

17:   if u2 <α2 then

18:      λ(t+1)

19:   else

20:      λ(t+1)λ(t)

21:   end if

22:   Append (ω(t+1), λ(t+1)) to Markov chain

23:   tt + 1

24: end while

25: return Markov chain