A practical guide to pseudo-marginal methods for computational inference in systems biology gan Warne, DJ, Baker, RE, Simpson, MJ

“...For many stochastic models of interest in systems biology, such as those describing biochemical reaction networks, exact quantification of parameter uncertainty through statistical inference is intractable. ...”

Multi-resolution modelling of biomolecules gan Gunaratne, R

“...The parameters for these stochastic models are determined analytically, or inferred from molecular dynamic simulation data via force and velocity correlation statistics for comparison. ...”

Going from microscopic to macroscopic on nonuniform growing domains. gan Yates, C, Baker, R, Erban, R, Maini, P

“...We first demonstrate that an individual-based stochastic model for particle diffusion on such a nonuniform domain partition is equivalent to a PDE model of the same phenomenon on a nongrowing domain, providing the transition rates (which we derive) are chosen correctly and we partition the domain in the correct manner. ...”

Going from microscopic to macroscopic on nonuniform growing domains gan Yates, C, Baker, R, Erban, R, Maini, P

“...We first demonstrate that an individual-based stochastic model for particle diffusion on such a nonuniform domain partition is equivalent to a PDE model of the same phenomenon on a nongrowing domain, providing the transition rates (which we derive) are chosen correctly and we partition the domain in the correct manner. ...”

Going from microscopic to macroscopic on nonuniform growing domains. gan Yates, C, Baker, R, Erban, R, Maini, P

“...We first demonstrate that an individual-based stochastic model for particle diffusion on such a nonuniform domain partition is equivalent to a PDE model of the same phenomenon on a nongrowing domain, providing the transition rates (which we derive) are chosen correctly and we partition the domain in the correct manner. ...”

Scale‐aware space‐time stochastic parameterization of subgrid‐scale velocity enhancement of sea surface fluxes gan Bessac, J, Christensen, HM, Endo, K, Monahan, AH, Weitzel, N

“...We present an approach to develop stochastic models that adapt to resolution in a scale‐aware fashion. ...”

A theoretical investigation of the effect of proliferation and adhesion on monoclonal conversion in the colonic crypt gan Mirams, G, Fletcher, A, Maini, P, Byrne, H

“...By comparing simulation results with those from a simple one-dimensional stochastic model of population dynamics at the base of the crypt, we infer that this sensitivity is due to direct competition between wild-type and mutant cells at the base of the crypt. ...”

Does proximity matter? Distance dependence of adolescent friendships gan Preciado, P, Snijders, T, Burk, W, Stattin, H, Kerr, M

“...The analysis is a three-step process that combines (1) nonparametric logistic regressions to unravel the overall functional form of the dependence of friendship on distance, without assuming it has a particular strength or shape; (2) parametric logistic regressions to construct suitable transformations of distance that can be employed in (3) stochastic models for longitudinal network data, to assess how distance, individual covariates, and network structure shape adolescent friendship dynamics. ...”

A Bayesian approach to the evolution of metabolic networks on a phylogeny gan Mithani, A, Preston, G, Hein, J

“...Using simple (independent loss/gain of reactions) or complex (incorporating dependencies among reactions) stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. ...”

Communication: Distinguishing between short-time non-Fickian diffusion and long-time Fickian diffusion for a random walk on a crowded lattice. gan Ellery, A, Baker, R, Simpson, M

“...A common approach to modeling this kind of hindered transport is to examine the mean squared displacement (MSD) of a motile tracer particle in a lattice-based stochastic random walk in which some lattice sites are occupied by obstacles. Unfortunately, stochastic models can be computationally expensive to analyze because we must average over a large ensemble of identically prepared realizations to obtain meaningful results. ...”

Statistical theory of the continuous double auction gan Smith, E, Farmer, J, Gillemot, L, Krishnamurthy, S

“...On a broader level, this work suggests how stochastic models based on zero-intelligence agents may be useful to probe the structure of market institutions. ...”

Modelling the influence of naturally acquired immunity from subclinical infection on outbreak dynamics and persistence of rabies in domestic dogs gan Gold, S, Donnelly, CA, Woodroffe, R, Nouvellet, P

“...However, empirical studies have detected rabies-specific antibodies in healthy, unvaccinated domestic dogs, potentially due to immunizing, non-lethal exposure. We developed a stochastic model for canine rabies, parameterised for Laikipia County, Kenya, to explore the implications of different scenarios for naturally acquired immunity to rabies in domestic dogs. ...”

Statistical theory of the continuous double auction gan Smith, E, Farmer, J, Gillemot, L, Krishnamurthy, S

“...On a broader level, this work suggests how stochastic models based on zero intelligence agents may be useful to probe the structure of market institutions. ...”

Assessing population differentiation and isolation from single-nucleotide polymorphism data gan Nicholson, G, Smith, A, Jonsson, F, Gustafsson, O, Stefansson, K, Donnelly, P

“...Our model includes the effects of single-nucleotide polymorphism ascertainment and is motivated by population genetics considerations, explicitly in the transient setting after divergence of populations, rather than as the equilibrium of a stochastic model, as is traditionally the case. For the sizes of data set that we consider the method provides good parameter estimates and considerably outperforms estimation methods analogous to those currently used in practice. ...”

Maintaining low prevalence of Schistosoma mansoni: modeling the effect of less frequent treatment gan Ayabina, D, Kura, K, Toor, J, Graham, M, Anderson, RM, Hollingsworth, TD

“...<p><strong>Methods</strong></p> We used 2 independently developed, individual-based stochastic models of schistosomiasis transmission to assess the optimal treatment strategy of a multiyear program to maintain the morbidity control and the EPHP goals. ...”

Parameter estimation of stochastic differential equation gan Haliza Abd. Rahman, Arifah Bahar, Norhayati Rosli, Madihah Md. Salleh

“...The results showed that the Mean Square Errors (MSE) for stochastic model with parameters estimated using optimal knot for 1,000, 5,000 and 10,000 runs of Brownian motions are smaller than the SDE models with estimated parameters using knot selected heuristically. ...”
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Deterministic And Stochastic Simulations Of Infectious Diseases gan Tan, Wai Kiat

“...This deterministic FluSiM is later enhanced into a stochastic model by incorporating stochasticity in disease transmission characteristics. ...”
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Discretized Markov Chain in Damage Assessment Using Rainflow Cycle with Effects of Mean Stress On An Automobile Crankshaft gan Singh, Salvinder, Abdullah, Shahrum, Nik Abdullah, Nik Mohamed

“...We concluded that for the practical application, the proposed stochastic model provides a highly accurate assessment of fatigue damage prediction for improving the safety and controlling the risk factors in terms of structural health monitoring....”
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DER Allocation and Line Repair Scheduling for Storm-induced Failures in Distribution Networks gan Chang, Derek, Shelar, Devendra Anil, Amin, Saurabh, chang, Derek

“...First, we estimate the failure probabilities of DN components (lines) using a stochastic model of line failures which parametrically depends on the location-specific storm wind field. ...”
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The Stochastic Container Relocation Problem gan Galle, Virgile, Manshadi, VH, Borjian Boroujeni, Setareh, Barnhart, Cynthia, Jaillet, Patrick

“...A new multistage stochastic model, called the batch model, is introduced, motivated, and compared with an existing model (the online model). ...”
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