Weak Markovian Bisimulation Congruences and Exact CTMC-Level Aggregations for Concurrent Processes

We have recently defined a weak Markovian bisimulation equivalence in an integrated-time setting, which reduces sequences of exponentially timed internal actions to individual exponentially timed internal actions having the same average duration and execution probability as the corresponding sequences. This weak Markovian bisimulation equivalence is a congruence for sequential processes with abstraction and turns out to induce an exact CTMC-level aggregation at steady state for all the considered processes. However, it is not a congruence with respect to parallel composition. In this paper, we show how to generalize the equivalence in a way that a reasonable tradeoff among abstraction, compositionality, and exactness is achieved for concurrent processes. We will see that, by enhancing the abstraction capability in the presence of concurrent computations, it is possible to retrieve the congruence property with respect to parallel composition, with the resulting CTMC-level aggregation being exact at steady state only for a certain subset of the considered processes.Comment: In Proceedings QAPL 2012, arXiv:1207.055

Stochastic kinetics of viral capsid assembly based on detailed protein structures

We present a generic computational framework for the simulation of viral capsid assembly which is quantitative and specific. Starting from PDB files containing atomic coordinates, the algorithm builds a coarse grained description of protein oligomers based on graph rigidity. These reduced protein descriptions are used in an extended Gillespie algorithm to investigate the stochastic kinetics of the assembly process. The association rates are obtained from a diffusive Smoluchowski equation for rapid coagulation, modified to account for water shielding and protein structure. The dissociation rates are derived by interpreting the splitting of oligomers as a process of graph partitioning akin to the escape from a multidimensional well. This modular framework is quantitative yet computationally tractable, with a small number of physically motivated parameters. The methodology is illustrated using two different viruses which are shown to follow quantitatively different assembly pathways. We also show how in this model the quasi-stationary kinetics of assembly can be described as a Markovian cascading process in which only a few intermediates and a small proportion of pathways are present. The observed pathways and intermediates can be related a posteriori to structural and energetic properties of the capsid oligomers

Bayesian Learning and Predictability in a Stochastic Nonlinear Dynamical Model

Bayesian inference methods are applied within a Bayesian hierarchical modelling framework to the problems of joint state and parameter estimation, and of state forecasting. We explore and demonstrate the ideas in the context of a simple nonlinear marine biogeochemical model. A novel approach is proposed to the formulation of the stochastic process model, in which ecophysiological properties of plankton communities are represented by autoregressive stochastic processes. This approach captures the effects of changes in plankton communities over time, and it allows the incorporation of literature metadata on individual species into prior distributions for process model parameters. The approach is applied to a case study at Ocean Station Papa, using Particle Markov chain Monte Carlo computational techniques. The results suggest that, by drawing on objective prior information, it is possible to extract useful information about model state and a subset of parameters, and even to make useful long-term forecasts, based on sparse and noisy observations

Copulas in finance and insurance

Copulas provide a potential useful modeling tool to represent the dependence structure among variables and to generate joint distributions by combining given marginal distributions. Simulations play a relevant role in finance and insurance. They are used to replicate efficient frontiers or extremal values, to price options, to estimate joint risks, and so on. Using copulas, it is easy to construct and simulate from multivariate distributions based on almost any choice of marginals and any type of dependence structure. In this paper we outline recent contributions of statistical modeling using copulas in finance and insurance. We review issues related to the notion of copulas, copula families, copula-based dynamic and static dependence structure, copulas and latent factor models and simulation of copulas. Finally, we outline hot topics in copulas with a special focus on model selection and goodness-of-fit testing

Geographic Gossip: Efficient Averaging for Sensor Networks

Gossip algorithms for distributed computation are attractive due to their simplicity, distributed nature, and robustness in noisy and uncertain environments. However, using standard gossip algorithms can lead to a significant waste in energy by repeatedly recirculating redundant information. For realistic sensor network model topologies like grids and random geometric graphs, the inefficiency of gossip schemes is related to the slow mixing times of random walks on the communication graph. We propose and analyze an alternative gossiping scheme that exploits geographic information. By utilizing geographic routing combined with a simple resampling method, we demonstrate substantial gains over previously proposed gossip protocols. For regular graphs such as the ring or grid, our algorithm improves standard gossip by factors of $n$ and $\sqrt{n}$ respectively. For the more challenging case of random geometric graphs, our algorithm computes the true average to accuracy $\epsilon$ using $O(\frac{n^{1.5}}{\sqrt{\log n}} \log \epsilon^{-1})$ radio transmissions, which yields a $\sqrt{\frac{n}{\log n}}$ factor improvement over standard gossip algorithms. We illustrate these theoretical results with experimental comparisons between our algorithm and standard methods as applied to various classes of random fields.Comment: To appear, IEEE Transactions on Signal Processin

Towards a Collision-Free WLAN: Dynamic Parameter Adjustment in CSMA/E2CA

Carrier Sense Multiple Access with Enhanced Collision Avoidance (CSMA/ECA) is a distributed MAC protocol that allows collision-free access to the medium in WLAN. The only difference between CSMA/ECA and the well-known CSMA/CA is that the former uses a deterministic backoff after successful transmissions. Collision-free operation is reached after a transient state during which some collisions may occur. This article shows that the duration of the transient state can be shortened by appropriately setting the contention parameters. Standard absorbing Markov Chain theory can be used to describe the behaviour of the system in the transient state and to predict the expected number of slots to reach the collision-free operation. The article also introduces CSMA/E2CA, in which a deterministic backoff is used two consecutive times after a successful transmission. CSMA/E2CA converges quicker to collision-free operation and delivers higher performance than CSMA/CA in harsh wireless scenarios with high frame error rates. To achieve collision-free operations when the number of contenders is large, it may be necessary to dynamically adjust the contention parameter. The last part of the article suggests an approach for such parameter adjustment which is validated by simulation results

FrogWild! -- Fast PageRank Approximations on Graph Engines

We propose FrogWild, a novel algorithm for fast approximation of high PageRank vertices, geared towards reducing network costs of running traditional PageRank algorithms. Our algorithm can be seen as a quantized version of power iteration that performs multiple parallel random walks over a directed graph. One important innovation is that we introduce a modification to the GraphLab framework that only partially synchronizes mirror vertices. This partial synchronization vastly reduces the network traffic generated by traditional PageRank algorithms, thus greatly reducing the per-iteration cost of PageRank. On the other hand, this partial synchronization also creates dependencies between the random walks used to estimate PageRank. Our main theoretical innovation is the analysis of the correlations introduced by this partial synchronization process and a bound establishing that our approximation is close to the true PageRank vector. We implement our algorithm in GraphLab and compare it against the default PageRank implementation. We show that our algorithm is very fast, performing each iteration in less than one second on the Twitter graph and can be up to 7x faster compared to the standard GraphLab PageRank implementation