A Dominated Coupling From The Past algorithm for the stochastic simulation of networks of biochemical reactions

<p>Abstract</p> <p>Background</p> <p>In recent years, stochastic descriptions of biochemical reactions based on the Master Equation (ME) have become widespread. These are especially relevant for models involving gene regulation. Gillespie’s Stochastic Simulation Algorithm (SSA) is the most widely used method for the numerical evaluation of these models. The SSA produces exact samples from the distribution of the ME for finite times. However, if the stationary distribution is of interest, the SSA provides no information about convergence or how long the algorithm needs to be run to sample from the stationary distribution with given accuracy. </p> <p>Results</p> <p>We present a proof and numerical characterization of a Perfect Sampling algorithm for the ME of networks of biochemical reactions prevalent in gene regulation and enzymatic catalysis. Our algorithm combines the SSA with Dominated Coupling From The Past (DCFTP) techniques to provide guaranteed sampling from the stationary distribution. The resulting DCFTP-SSA is applicable to networks of reactions with uni-molecular stoichiometries and sub-linear, (anti-) monotone propensity functions. We showcase its applicability studying steady-state properties of stochastic regulatory networks of relevance in synthetic and systems biology.</p> <p>Conclusion</p> <p>The DCFTP-SSA provides an extension to Gillespie’s SSA with guaranteed sampling from the stationary solution of the ME for a broad class of stochastic biochemical networks.</p

Randomized stopping times and provably secure pseudorandom permutation generators

Conventionally, key-scheduling algorithm (KSA) of a cryptographic scheme runs for predefined number of steps. We suggest a different approach by utilization of randomized stopping rules to generate permutations which are indistinguishable from uniform ones. We explain that if the stopping time of such a shuffle is a Strong Stationary Time and bits of the secret key are not reused then these algorithms are immune against timing attacks. We also revisit the well known paper of Mironov~\cite{Mironov2002} which analyses a card shuffle which models KSA of RC4. Mironov states that expected time till reaching uniform distribution is $2n H_n - n$ while we prove that $n H_n+ n$ steps are enough (by finding a new strong stationary time for the shuffle). Nevertheless, both cases require $O(n \log^2 n)$ bits of randomness while one can replace the shuffle used in RC4 (and in Spritz) with a better shuffle which is optimal and needs only $O(n \log n)$ bits

Bayesian Computation with Intractable Likelihoods

This article surveys computational methods for posterior inference with intractable likelihoods, that is where the likelihood function is unavailable in closed form, or where evaluation of the likelihood is infeasible. We review recent developments in pseudo-marginal methods, approximate Bayesian computation (ABC), the exchange algorithm, thermodynamic integration, and composite likelihood, paying particular attention to advancements in scalability for large datasets. We also mention R and MATLAB source code for implementations of these algorithms, where they are available.Comment: arXiv admin note: text overlap with arXiv:1503.0806

Efficiency of simulation in monotone hyper-stable queueing networks

We consider Jackson queueing networks with finite buffer constraints (JQN) and analyze the efficiency of sampling from their stationary distribution. In the context of exact sampling, the monotonicity structure of JQNs ensures that such efficiency is of the order of the coupling time (or meeting time) of two extremal sample paths. In the context of approximate sampling, it is given by the mixing time. Under a condition on the drift of the stochastic process underlying a JQN, which we call hyper-stability, in our main result we show that the coupling time is polynomial in both the number of queues and buffer sizes. Then, we use this result to show that the mixing time of JQNs behaves similarly up to a given precision threshold. Our proof relies on a recursive formula relating the coupling times of trajectories that start from network states having 'distance one', and it can be used to analyze the coupling and mixing times of other Markovian networks, provided that they are monotone. An illustrative example is shown in the context of JQNs with blocking mechanisms

Perfect sampling for multiclass closed queueing networks

International audienceIn this paper we present an exact sampling method for multiclass closed queuing networks. We consider networks for which stationary distribution does not necessarily have a product form. The proposed method uses a compact representation of sets of states, that is used to derive a bounding chain with significantly lower complexity of one-step transition in the coupling from the past scheme. The coupling time of this bounding chain can be larger than the coupling time of the exact chain, but it is finite in expectation. Numerical experiments show that coupling time is close to that of the exact chain. Moreover, the running time of the proposed algorithm outperforms the classical algorithm